From 3e06890ce45f573cdd58b6edf5a8ceb20942df48 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Mon, 12 Sep 2016 14:07:58 -0700 Subject: [PATCH 001/560] Fixed incorrect links to the member node profile from search results. --- metacatui/src/main/webapp/js/templates/resultsItem.html | 2 +- .../main/webapp/js/themes/dataone/templates/resultsItem.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/resultsItem.html b/metacatui/src/main/webapp/js/templates/resultsItem.html index 38b1c5240..678491beb 100644 --- a/metacatui/src/main/webapp/js/templates/resultsItem.html +++ b/metacatui/src/main/webapp/js/templates/resultsItem.html @@ -1,5 +1,5 @@ <% if(memberNode && memberNode.logo){ %> - + <% } %>
diff --git a/metacatui/src/main/webapp/js/themes/dataone/templates/resultsItem.html b/metacatui/src/main/webapp/js/themes/dataone/templates/resultsItem.html index d6d8b07fb..3e91be392 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/templates/resultsItem.html +++ b/metacatui/src/main/webapp/js/themes/dataone/templates/resultsItem.html @@ -1,5 +1,5 @@ <% if(memberNode && memberNode.logo){ %> - + <% } %>
From fda90174cce5ca1892a846d3edbc30855cd87b05 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 13 Sep 2016 17:21:09 -0700 Subject: [PATCH 002/560] Multiple improvements to the annotations usability and appearance --- .../src/main/webapp/css/metacatui-common.css | 82 +++++++++++++++++- .../js/templates/annotationPopover.html | 23 +++++ .../js/themes/dataone/css/metacatui.css | 13 ++- .../js/themes/dataone/img/annotator-icons.png | Bin 0 -> 5654 bytes .../src/main/webapp/js/views/AnnotatorView.js | 53 ++++++----- .../src/main/webapp/js/views/MetadataView.js | 2 +- 6 files changed, 144 insertions(+), 29 deletions(-) create mode 100644 metacatui/src/main/webapp/js/templates/annotationPopover.html create mode 100644 metacatui/src/main/webapp/js/themes/dataone/img/annotator-icons.png diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 1a50af47b..5475dddae 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1307,6 +1307,7 @@ img.icon{ } .annotation-target{ height: 0px; + margin-left: 180px; } .annotator-listing > .annotator-checkbox:nth-child(2n), .annotator-listing > .annotator-checkbox:nth-child(3n) { @@ -1326,11 +1327,84 @@ img.icon{ display: none; } .annotation.tag { - padding: .25em .5em; + padding: .35em .75em; margin-right: 5px; - -webkit-border-radius: 2px; - -moz-border-radius: 2px; - border-radius: 2px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + font-style: normal; + font-weight: 400; + text-shadow: none; + box-shadow: none; + text-align: center; + margin-top: 10px; + margin-bottom: 10px; +} +.annotation-viewer-container .annotation.tag{ + margin-left: 5px; +} +.annotator-tags, +.annotator-viewer .annotator-item, +.annotator-viewer div{ + border-top: 0px; +} +.annotator-tags > .annotator-tag, +.annotator-annotation .annotator-tag{ + display: none; +} +.annotator-viewer div:first-of-type{ + padding-top: 0px; + padding-bottom: 0px; +} +.annotator-widget * { + font-style: normal; + color: #333; +} +.annotator-widget .subtle{ + color: #999; +} +.annotator-widget .smaller{ + font-size: .9em; +} +.annotator-widget .tag-date{ + display: block; + padding-left: 0px; +} +.annotator-viewer .container { + padding-top: 10px; + margin-top: 10px; +} +.annotator-viewer .annotator-controls{ + display: none; +} +.annotation-flag.btn { + border-width: 0px; + margin-bottom: 0px; + margin-right: 10px; + margin-left: -7px; + border-top-left-radius: 0px; + border-bottom-left-radius: 0px; + border: 0px; + padding: 0.42em .75em; + font-size: 1em; + line-height: 0em; + margin-top: -3px; +} +.annotation-flag.btn:hover{ + border-width: 0px; +} +.annotator-editor .annotator-controls{ + background-image: none; + background-color: #FFF; + padding-top: 10px; +} +.annotator-editor .annotator-checkbox, +.annotator-editor #annotator-field-4, +.annotator-editor .annotator-item label[for="annotator-field-4"]{ + display: none !important; +} +.ui-autocomplete.annotator{ + z-index: 9999; } /****************************************** * Images, Maps, and Media diff --git a/metacatui/src/main/webapp/js/templates/annotationPopover.html b/metacatui/src/main/webapp/js/templates/annotationPopover.html new file mode 100644 index 000000000..d8095fa41 --- /dev/null +++ b/metacatui/src/main/webapp/js/templates/annotationPopover.html @@ -0,0 +1,23 @@ +
+ <%=concept.label%> +
+

+ Definition: + <%=concept.desc%> +

+
+ +
+

+ Added by <%=user%> + <%=created.toDateString()%> + <% if(updated){ %> + Updated on + <%=updated.toDateString()%> + + <% } %> +

+
+
\ No newline at end of file diff --git a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css index 7c1d3699b..4e5c38fcc 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css @@ -12,7 +12,8 @@ font: 400 14px/20px Helvetica, Arial, "sans serif"; } - a { + a, + .annotator-widget a { color: #1C6E84; font-weight: 600; } @@ -965,7 +966,13 @@ label.control-label{ background-color: #1C6E84; color: #FFF; } - +.btn.annotation-flag{ + background-color: #98d2eb; + color: #FFF; +} +.btn.annotation-flag:hover{ + background-color: #85daff; +} /* Registry CSS -------------------------------------------------- */ @@ -1348,7 +1355,7 @@ label.control-label{ } ul.ui-autocomplete.ui-front{ - z-index: 999; + z-index: 9999; } li.ui-menu-item{ diff --git a/metacatui/src/main/webapp/js/themes/dataone/img/annotator-icons.png b/metacatui/src/main/webapp/js/themes/dataone/img/annotator-icons.png new file mode 100644 index 0000000000000000000000000000000000000000..34c8ac5dfc3d95e8e933e99c8bea8ce0e286d1d8 GIT binary patch literal 5654 zcmV+x7U}7UP)KLZ*U+IBfRsybQWXdwQbLP>6pAqfylh#{fb6;Z(vMMVS~$e@S=j*ftg6;Uhf59&ghTmgWD0l;*T zI709Y^p6lP1rIRMx#05C~cW=H_Aw*bJ-5DT&Z2n+x)QHX^p z00esgV8|mQcmRZ%02D^@S3L16t`O%c004NIvOKvYIYoh62rY33S640`D9%Y2D-rV&neh&#Q1i z007~1e$oCcFS8neI|hJl{-P!B1ZZ9hpmq0)X0i`JwE&>$+E?>%_LC6RbVIkUx0b+_+BaR3cnT7Zv!AJxW zizFb)h!jyGOOZ85F;a?DAXP{m@;!0_IfqH8(HlgRxt7s3}k3K`kFu>>-2Q$QMFfPW!La{h336o>X zu_CMttHv6zR;&ZNiS=X8v3CR#fknUxHUxJ0uoBa_M6WNWeqIg~6QE69c9o#eyhGvpiOA@W-aonk<7r1(?fC{oI5N*U!4 zfg=2N-7=cNnjjOr{yriy6mMFgG#l znCF=fnQv8CDz++o6_Lscl}eQ+l^ZHARH>?_s@|##Rr6KLRFA1%Q+=*RRWnoLsR`7U zt5vFIcfW3@?wFpwUVxrVZ>QdQz32KIeJ}k~{cZZE^+ya? 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", - "

Label: " + concept.label + "

", - "

Definition: " + concept.desc + "

", - "
", - "
", - "

Created: " + created.toDateString() + "

", - "

Updated: " + updated.toDateString() + "

", - "

User: " + user + "

", - "
" - ); + + if(created.valueOf() == updated.valueOf()) updated = null; + + var annotationPopover = view.annotationPopoverTemplate({ + containerId: containerId, + concept: concept, + created: created, + updated: updated, + user: user, + annotation: annotation + }); + $(element).after(annotationPopover); }; appLookupModel.bioportalGetConcepts(conceptUri, renderAnnotation); @@ -313,7 +318,7 @@ define(['jquery', }); }; - var annotatorEl = $(this); + var annotatorEl = (typeof this.$el != "undefined")? this.$el : this; //look up the concept details for each annotation _.each(annotations, function(annotation) { @@ -341,7 +346,7 @@ define(['jquery', return; } - var bubble = $.parseHTML(annotatorEl.data("annotator-view").annotationTemplate({ + var bubble = $.parseHTML($(annotatorEl).data("annotator-view").annotationTemplate({ annotation: annotation, concept: concept, canEdit: canEdit @@ -358,9 +363,15 @@ define(['jquery', $(target).bind("mouseover", hoverAnnotation); $(target).bind("mouseout", hoverAnnotation); - target = $(bubble).find(".annotation-flag").filter("[data-id='" + annotation.id + "']"); + target = $(bubble).filter(".annotation-flag[data-id='" + annotation.id + "']"); $(target).bind("click", flagAnnotation); - target = $(bubble).find(".annotation-delete").filter("[data-id='" + annotation.id + "']"); + + $(target).tooltip({ + trigger: "hover", + title: "Flag this tag as incorrect" + }); + + target = $(bubble).filter(".annotation-delete[data-id='" + annotation.id + "']"); $(target).bind("click", deleteAnnotation); }; diff --git a/metacatui/src/main/webapp/js/views/MetadataView.js b/metacatui/src/main/webapp/js/views/MetadataView.js index bbbaf9cdc..261ff83dc 100644 --- a/metacatui/src/main/webapp/js/views/MetadataView.js +++ b/metacatui/src/main/webapp/js/views/MetadataView.js @@ -1144,7 +1144,7 @@ define(['jquery', } if(matches.length){ - container = matches.parents(".entitydetails").first(); + container = $(matches).parents(".entitydetails").first(); container.attr("data-id", id); return container; } From 46de4a33cc982ee7648e05f275e9ead7bf5abe68 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Wed, 14 Sep 2016 17:59:41 -0700 Subject: [PATCH 003/560] Added an AnnotationModel for easier interaction between AnnotatorJS and Backbone. Create custom popover for annotations instead of using the AnnotatorJS viewer (which was having issues with displaying multiple annotations per annotation-target) --- .../main/webapp/js/models/AnnotationModel.js | 35 ++++ .../main/webapp/js/templates/annotation.html | 2 +- .../js/templates/annotationPopover.html | 6 +- .../js/themes/dataone/models/AppModel.js | 8 +- .../src/main/webapp/js/views/AnnotatorView.js | 160 +++++++++++------- 5 files changed, 143 insertions(+), 68 deletions(-) create mode 100644 metacatui/src/main/webapp/js/models/AnnotationModel.js diff --git a/metacatui/src/main/webapp/js/models/AnnotationModel.js b/metacatui/src/main/webapp/js/models/AnnotationModel.js new file mode 100644 index 000000000..3bb6acc4a --- /dev/null +++ b/metacatui/src/main/webapp/js/models/AnnotationModel.js @@ -0,0 +1,35 @@ +/*global define */ +define(['jquery', 'underscore', 'backbone'], + function($, _, Backbone) { + 'use strict'; + + // Annotation Model + // ------------------ + var Annotation = Backbone.Model.extend({ + defaults: { + + }, + + initialize: function(options){ + + }, + + bioportalGetConcepts: function(uri) { + var model = this; + appLookupModel.bioportalGetConcepts(uri, function(concepts){ + model.set("concept", concepts[0]); + }); + }, + + orcidGetConcepts: function(uri) { + var model = this; + appLookupModel.orcidGetConcepts(uri, function(concepts){ + model.set("concept", concepts[0]); + }); + } + + + }); + + return Annotation; +}); \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index 662541ce5..decaf29e7 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -3,7 +3,7 @@ + title="<%=concept.label %>"> <%=concept.label %> <% diff --git a/metacatui/src/main/webapp/js/templates/annotationPopover.html b/metacatui/src/main/webapp/js/templates/annotationPopover.html index d8095fa41..6b4c3c913 100644 --- a/metacatui/src/main/webapp/js/templates/annotationPopover.html +++ b/metacatui/src/main/webapp/js/templates/annotationPopover.html @@ -1,9 +1,9 @@
- <%=concept.label%> + <%=annotation.concept.label%>

Definition: - <%=concept.desc%> + <%=annotation.concept.desc%>

- Added by <%=user%> + Added by <%=annotation.user%> <%=created.toDateString()%> <% if(updated){ %> Updated on diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index fbbc32b2c..2730b4c72 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -35,11 +35,11 @@ define(['jquery', 'underscore', 'backbone'], maxDownloadSize: 3000000000, metcatVersion: "2.7.2", - baseUrl: window.location.origin || (window.location.protocol + "//" + window.location.host), + baseUrl: "https://cn-sandbox-2.test.dataone.org",//window.location.origin || (window.location.protocol + "//" + window.location.host), // the most likely item to change is the Metacat deployment context context: '', d1Service: "/cn/v2", - d1CNBaseUrl: "https://cn.dataone.org", + d1CNBaseUrl: "https://cn-sandbox-2.test.dataone.org", d1CNService: "/cn/v2", viewServiceUrl: null, packageServiceUrl: null, @@ -57,7 +57,7 @@ define(['jquery', 'underscore', 'backbone'], nodeServiceUrl: null, // NOTE: include your bioportal apikey for suggested classes // see: http://bioportal.bioontology.org/account - //bioportalSearchUrl: "https://data.bioontology.org/search?ontologies=ECSO&apikey=24e4775e-54e0-11e0-9d7b-005056aa3316&pagesize=1000&suggest=true&q=", + bioportalSearchUrl: "https://data.bioontology.org/search?ontologies=ECSO&apikey=24e4775e-54e0-11e0-9d7b-005056aa3316&pagesize=1000&suggest=true&q=", //bioportalSearchUrl: null, // use this to deactivate the annotator view //orcidBaseUrl: "https://sandbox.orcid.org", //orcidSearchUrl: null, @@ -71,7 +71,7 @@ define(['jquery', 'underscore', 'backbone'], //signInUrlLdap: null, tokenUrl: null, checkTokenUrl: null, - //annotatorUrl: null, + annotatorUrl: null, prov: true, useSeriesId: true }, diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index ef36f7e99..7bd845ed4 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -4,6 +4,7 @@ define(['jquery', 'annotator', 'underscore', 'backbone', + 'models/AnnotationModel', 'text!templates/annotation.html', 'text!templates/annotationPopover.html' ], @@ -12,6 +13,7 @@ define(['jquery', Annotator, _, Backbone, + AnnotationModel, AnnotationTemplate, AnnotationPopoverTemplate) { 'use strict'; @@ -28,6 +30,7 @@ define(['jquery', annotationPopoverTemplate: _.template(AnnotationPopoverTemplate), rendered: false, + annotations: [], // Delegated events for creating new items, and clearing completed ones. events: { @@ -54,6 +57,7 @@ define(['jquery', $("body").annotator('destroy'); } + this.annotations = []; }, setUpAnnotator: function() { @@ -193,6 +197,7 @@ define(['jquery', // showing the viewer show the concepts with labels, definitions and audit info this.$el.annotator('subscribe', 'annotationViewerShown', function(viewer, annotations) { console.log("annotationViewerShown: " + viewer); + $(viewer.element).find(".annotator-tag").each(function(index, element) { var conceptUri = $(element).html(); var renderAnnotation = function(concepts) { @@ -253,6 +258,17 @@ define(['jquery', } this.rendered = true; + var view = this; + + //Create a new model for each annotation + _.each(annotations, function(annotation){ + var annModel = new AnnotationModel().set(annotation); + if(Array.isArray(view.annotations)) + view.annotations.push(annModel); + else + view.annotations = [annModel]; + }); + // sort the annotations by xpath annotations = _.sortBy(annotations, function(ann) { return ann.resource; @@ -275,8 +291,7 @@ define(['jquery', // summarize annotation count in citation block $(".citation-container > .controls-well").prepend("" + annotations.length + " annotations"); - - + var flagAnnotation = function(event) { var annotationId = $(event.target).attr("data-id"); console.log("flagging annotation id: " + annotationId); @@ -318,76 +333,28 @@ define(['jquery', }); }; - var annotatorEl = (typeof this.$el != "undefined")? this.$el : this; + var annotatorEl = (typeof this.$el != "undefined")? this.$el : this, + view = $(annotatorEl).data("annotator-view"); //look up the concept details for each annotation - _.each(annotations, function(annotation) { + _.each(this.annotations, function(annotation) { - if (annotation.tags[0]) { - + if (annotation.get("tags")[0]) { // look up concepts where we can - var conceptUri = annotation.tags[0]; - var renderAnnotation = function(concepts) { - - var concept = _.findWhere(concepts, {value: conceptUri}); - - var canEdit = - _.contains(annotation.permissions.admin, appUserModel.get("username")) - || - _.contains(annotation.permissions.update, appUserModel.get("username")) - || - _.contains(annotation.permissions.delete, appUserModel.get("username")); - - // render it in the document - var highlight = $("[data-annotation-id='" + annotation.id + "']"); - var section = $(highlight).closest(".tab-pane").children(".annotation-container"); - if (!section.html()) { - console.log("Highlights not completed yet - cannot render annotation"); - return; - } - - var bubble = $.parseHTML($(annotatorEl).data("annotator-view").annotationTemplate({ - annotation: annotation, - concept: concept, - canEdit: canEdit - }).trim()); - - section.prepend(bubble); - console.log("rendered tag in section: " + section.html()); - - // bind after rendering - var target = $(bubble).filter(".hover-proxy"); - console.log("binding annotation actions for target: " + $(target).size()); - console.log("binding annotation actions for target: " + annotation.id); - - $(target).bind("mouseover", hoverAnnotation); - $(target).bind("mouseout", hoverAnnotation); - - target = $(bubble).filter(".annotation-flag[data-id='" + annotation.id + "']"); - $(target).bind("click", flagAnnotation); - - $(target).tooltip({ - trigger: "hover", - title: "Flag this tag as incorrect" - }); - - target = $(bubble).filter(".annotation-delete[data-id='" + annotation.id + "']"); - $(target).bind("click", deleteAnnotation); - - }; + var conceptUri = annotation.get("tags")[0]; // give time for the highlights to render setTimeout(function() { - // look it up and provide the callback - if (annotation["oa:Motivation"] == "prov:wasAttributedTo") { - appLookupModel.orcidGetConcepts(conceptUri, renderAnnotation); + if (annotation.get("oa:Motivation") == "prov:wasAttributedTo") { + annotation.orcidGetConcepts(conceptUri); } else { - appLookupModel.bioportalGetConcepts(conceptUri, renderAnnotation); + annotation.bioportalGetConcepts(conceptUri); } }, 500); - + + annotation.on("change:concept", view.renderAnnotation, view); } else { // for comments, just render it in the document @@ -404,6 +371,79 @@ define(['jquery', }, + renderAnnotation: function(annotationModel) { + + var canEdit = + _.contains(annotationModel.get("permissions").admin, appUserModel.get("username")) + || + _.contains(annotationModel.get("permissions").update, appUserModel.get("username")) + || + _.contains(annotationModel.get("permissions").delete, appUserModel.get("username")); + + // render it in the document + var highlight = $("[data-annotation-id='" + annotationModel.get("id") + "']"); + var section = $(highlight).closest(".tab-pane").children(".annotation-container"); + if (!section.html()) { + console.log("Highlights not completed yet - cannot render annotation"); + return; + } + + //Render the annotation tag itself + var annotationTag = $.parseHTML(this.annotationTemplate({ + annotation: annotationModel.toJSON(), + concept: annotationModel.get("concept"), + canEdit: canEdit + }).trim()); + section.prepend(annotationTag); + + //Attach the annotation object for later + $(annotationTag).data("annotation", annotationModel); + + var view = this; + + //Create the popover for this element + $(annotationTag).on("mouseover", { view: this }, this.showDetails); + + // bind after rendering + var target = $(annotationTag).filter(".hover-proxy"); + target = $(annotationTag).filter(".annotation-flag[data-id='" + annotation.id + "']"); + $(target).bind("click", flagAnnotation); + + $(target).tooltip({ + trigger: "hover", + title: "Flag this tag as incorrect" + }); + + target = $(annotationTag).filter(".annotation-delete[data-id='" + annotation.id + "']"); + $(target).bind("click", deleteAnnotation); + + }, + + showDetails: function(e){ + var annotation = $(e.target).data("annotation"); + + var created = new Date(annotation.get("created")); + var updated = new Date(annotation.get("updated")); + var containerId = "viewer-" + annotation.get("id"); + + if(created.valueOf() == updated.valueOf()) updated = null; + + var annotationPopover = e.data.view.annotationPopoverTemplate({ + containerId: containerId, + created: created, + updated: updated, + annotation: annotation.toJSON() + }); + $(e.target).popover({ + trigger: "hover", + html: true, + title: "blah",//annotation.get("concept").label, + content: annotationPopover, + placement: "top" + }); + $(e.target).popover("show"); + }, + launchEditor: function(event) { var target = event.target; // select the text to annotate From d16fb5d51530c4b7f761691f7706021b8d59e171 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 16 Sep 2016 10:30:33 -0700 Subject: [PATCH 004/560] More improvements to the annotations, particularly with flagging --- .../src/main/webapp/css/metacatui-common.css | 24 +++++- .../main/webapp/js/models/AnnotationModel.js | 4 +- .../main/webapp/js/templates/annotation.html | 2 +- .../js/templates/annotationPopover.html | 6 +- .../src/main/webapp/js/views/AnnotatorView.js | 77 +++++++++++++------ 5 files changed, 82 insertions(+), 31 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 5475dddae..6907ef1ac 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1341,7 +1341,8 @@ img.icon{ margin-bottom: 10px; } .annotation-viewer-container .annotation.tag{ - margin-left: 5px; + margin-bottom: 10px; + display: inline-block; } .annotator-tags, .annotator-viewer .annotator-item, @@ -1377,7 +1378,8 @@ img.icon{ .annotator-viewer .annotator-controls{ display: none; } -.annotation-flag.btn { +.annotation-flag.btn, +.annotation-delete.btn { border-width: 0px; margin-bottom: 0px; margin-right: 10px; @@ -1390,9 +1392,18 @@ img.icon{ line-height: 0em; margin-top: -3px; } -.annotation-flag.btn:hover{ +.annotation-flag.btn:hover, +.annotation-delete.btn:hover{ border-width: 0px; } +.annotation-delete.btn-warning { + background-image: inherit; + background-color: #b32d2d; + color: white; +} +.annotation-viewer-container p.warning{ + color: #d00000; +} .annotator-editor .annotator-controls{ background-image: none; background-color: #FFF; @@ -1406,6 +1417,13 @@ img.icon{ .ui-autocomplete.annotator{ z-index: 9999; } +.popover-title { + text-transform: capitalize; +} +.annotation.tag.warning { + background-color: #999; + color: #DDD; +} /****************************************** * Images, Maps, and Media ********************************************/ diff --git a/metacatui/src/main/webapp/js/models/AnnotationModel.js b/metacatui/src/main/webapp/js/models/AnnotationModel.js index 3bb6acc4a..854f8af5c 100644 --- a/metacatui/src/main/webapp/js/models/AnnotationModel.js +++ b/metacatui/src/main/webapp/js/models/AnnotationModel.js @@ -10,6 +10,8 @@ define(['jquery', 'underscore', 'backbone'], }, + //url: appModel.get(""), + initialize: function(options){ }, @@ -27,8 +29,6 @@ define(['jquery', 'underscore', 'backbone'], model.set("concept", concepts[0]); }); } - - }); return Annotation; diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index decaf29e7..522280b7f 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -26,7 +26,7 @@ <% } else { diff --git a/metacatui/src/main/webapp/js/templates/annotationPopover.html b/metacatui/src/main/webapp/js/templates/annotationPopover.html index 6b4c3c913..8a8409428 100644 --- a/metacatui/src/main/webapp/js/templates/annotationPopover.html +++ b/metacatui/src/main/webapp/js/templates/annotationPopover.html @@ -1,5 +1,9 @@

- <%=annotation.concept.label%> + <%=annotation.concept.label%> + <% if (annotation.reject) { %> +

This annotation has been flagged as incorrect.

+ <% } + %>

Definition: diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index 7bd845ed4..b9fe87cda 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -34,7 +34,9 @@ define(['jquery', // Delegated events for creating new items, and clearing completed ones. events: { - "click .add-tag" : "launchEditor" + "click .add-tag" : "launchEditor", + "click .annotation-flag" : "flagAnnotation", + "click .annotation-delete" : "deleteAnnotation" }, initialize: function () { @@ -291,24 +293,6 @@ define(['jquery', // summarize annotation count in citation block $(".citation-container > .controls-well").prepend("" + annotations.length + " annotations"); - - var flagAnnotation = function(event) { - var annotationId = $(event.target).attr("data-id"); - console.log("flagging annotation id: " + annotationId); - var annotations = view.$el.data('annotator').plugins.Store.annotations; - var annotation = _.findWhere(annotations, {id: annotationId}); - annotation.reject = !annotation.reject; - view.$el.data('annotator').updateAnnotation(annotation); - - }; - var deleteAnnotation = function(event) { - var annotationId = $(event.target).attr("data-id"); - console.log("deleting annotation id: " + annotationId); - var annotations = view.$el.data('annotator').plugins.Store.annotations; - var annotation = _.findWhere(annotations, {id: annotationId}); - view.$el.data('annotator').deleteAnnotation(annotation); - - }; // define hover action to mimic hovering the highlighted region var hoverAnnotation = function(event) { @@ -406,20 +390,65 @@ define(['jquery', // bind after rendering var target = $(annotationTag).filter(".hover-proxy"); - target = $(annotationTag).filter(".annotation-flag[data-id='" + annotation.id + "']"); - $(target).bind("click", flagAnnotation); + target = $(annotationTag).filter(".annotation-flag[data-id='" + annotationModel.get("id") + "']"); + //$(target).bind("click", this.flagAnnotation); $(target).tooltip({ trigger: "hover", title: "Flag this tag as incorrect" }); - target = $(annotationTag).filter(".annotation-delete[data-id='" + annotation.id + "']"); - $(target).bind("click", deleteAnnotation); + var deleteBtn = $(annotationTag).filter(".annotation-delete"); + $(deleteBtn).tooltip({ + trigger: "hover", + title: "Delete this tag" + }); + + target = $(annotationTag).filter(".annotation-delete[data-id='" + annotationModel.get("id") + "']"); + //$(target).bind("click", this.deleteAnnotation); + + }, + + flagAnnotation : function(e) { + + //Get the flag button + var flagButton = e.target; + if(!$(flagButton).is(".annotation-flag")){ + flagButton = $(flagButton).parents(".annotation-flag"); + } + + //Get the annotation + var annotation = $(flagButton).data("annotation"); + + //If there is no annotation, exit. + if(!annotation) return; + + //Get the annotation object + var anns = this.$el.data("annotator").plugins.Store.annotations; + var annObj = _.findWhere(anns, {id: annotation.get("id")}); + + //Reject it! + annObj.reject = !annObj.reject; + + //Update it + this.$el.data('annotator').updateAnnotation(annObj); + }, + + deleteAnnotation : function(e) { + var annotationId = $(e.target).attr("data-id"); + console.log("deleting annotation id: " + annotationId); + var annotations = view.$el.data('annotator').plugins.Store.annotations; + var annotation = _.findWhere(annotations, {id: annotationId}); + view.$el.data('annotator').deleteAnnotation(annotation); }, showDetails: function(e){ + //Don't show the details for the flag button + if(!$(e.target).is(".annotation.tag")) return; + //Don't execute this code again if we already set up a popover + else if(typeof $(e.target).data("popover") != "undefined") return; + var annotation = $(e.target).data("annotation"); var created = new Date(annotation.get("created")); @@ -437,7 +466,7 @@ define(['jquery', $(e.target).popover({ trigger: "hover", html: true, - title: "blah",//annotation.get("concept").label, + title: annotation.get("concept").label, content: annotationPopover, placement: "top" }); From 9855142f8c194f6b5c96550d16dc57bea9bb178f Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 16 Sep 2016 17:08:09 -0700 Subject: [PATCH 005/560] Multiple improvements to the annotation UI --- .../src/main/webapp/css/metacatui-common.css | 22 ++++- .../src/main/webapp/js/models/LookupModel.js | 35 +------ .../main/webapp/js/templates/annotation.html | 2 +- .../js/templates/annotationPopover.html | 13 ++- .../js/themes/dataone/css/metacatui.css | 7 -- .../src/main/webapp/js/views/AnnotatorView.js | 97 ++++++++++++++++--- 6 files changed, 112 insertions(+), 64 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 6907ef1ac..dc0822151 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1313,7 +1313,8 @@ img.icon{ .annotator-listing > .annotator-checkbox:nth-child(3n) { display: none; } -#annotator-field-0{ +#annotator-field-0, +#annotator-field-5{ display: none; } .annotator-widget span{ @@ -1326,6 +1327,9 @@ img.icon{ .annotator-filter{ display: none; } +.annotator-field p{ + padding: 10px; +} .annotation.tag { padding: .35em .75em; margin-right: 5px; @@ -1387,7 +1391,7 @@ img.icon{ border-top-left-radius: 0px; border-bottom-left-radius: 0px; border: 0px; - padding: 0.42em .75em; + padding: 6px; font-size: 1em; line-height: 0em; margin-top: -3px; @@ -1396,12 +1400,17 @@ img.icon{ .annotation-delete.btn:hover{ border-width: 0px; } -.annotation-delete.btn-warning { +.annotation-delete.btn-warning, +.annotation-flag.btn-warning { background-image: inherit; - background-color: #b32d2d; + background-color: #da4f49; color: white; } -.annotation-viewer-container p.warning{ +.annotation-delete.btn-warning:hover, +.annotation-flag.btn-warning:hover{ + background-color: #f73f3f; +} +.annotation-viewer-container .warning{ color: #d00000; } .annotator-editor .annotator-controls{ @@ -1420,6 +1429,9 @@ img.icon{ .popover-title { text-transform: capitalize; } +.annotation-viewer-container .concept a{ + white-space: pre-wrap; +} .annotation.tag.warning { background-color: #999; color: #DDD; diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 3966b0d8b..b351f7290 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -12,39 +12,8 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], }, initialize: function() { - - // Autocomplete widget extension to provide description tooltips. - $.widget( "app.hoverAutocomplete", $.ui.autocomplete, { - - // Set the content attribute as the "item.desc" value. - // This becomes the tooltip content. - _renderItem: function( ul, item ) { - // if we have a label, use it for the title - var title = item.value; - if (item.label) { - title = item.label; - } - // if we have a description, use it for the content - var content = item.value; - if (item.desc) { - content = item.desc; - if (item.desc != item.value) { - content += " (" + item.value + ")"; - } - } - var element = this._super( ul, item ) - .attr( "data-title", title ) - .attr( "data-content", content ); - element.popover( - { - placement: "right", - trigger: "hover", - container: 'body' - - }); - return element; - } - }); + + }, diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index 522280b7f..7953c3372 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -31,7 +31,7 @@ <% } else { %> -

- Added by <%=annotation.user%> + <% + var creator = annotation.name || annotation.user; + %> + Added by <%=creator%> <%=created.toDateString()%>

diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/Map.js b/metacatui/src/main/webapp/js/themes/arctic/models/Map.js index ea8a11fbb..8fbb59354 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/Map.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/Map.js @@ -15,10 +15,10 @@ define(['jquery', 'underscore', 'backbone', 'gmaps'], //The options for the map using the Google Maps API MapOptions syntax mapOptions: (gmaps)? - { zoom: 3, - minZoom: 3, + { zoom: 2, + minZoom: 2, maxZoom: 16, - center: new google.maps.LatLng(71, -98), + center: new google.maps.LatLng(45, -98), disableDefaultUI: true, zoomControl: true, zoomControlOptions: { diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js index 150b8e900..ada31e121 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js @@ -39,7 +39,7 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], submitter: [], username: [], attribute: [], - //annotation: [], + annotation: [], additionalCriteria: [], dataSource: [], id: [], From ba6dc64695c8e64b295ba27e61b8960e426e34c3 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 09:45:50 -0700 Subject: [PATCH 007/560] Display tooltips for annotation tags --- .../src/main/webapp/css/metacatui-common.css | 7 +++++ .../main/webapp/js/templates/annotation.html | 29 ++++++++++--------- .../src/main/webapp/js/views/AnnotatorView.js | 7 ++--- 3 files changed, 25 insertions(+), 18 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index dc0822151..44ee3071d 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1410,6 +1410,13 @@ img.icon{ .annotation-flag.btn-warning:hover{ background-color: #f73f3f; } +.annotation-flag.btn-success { + background-color: #5bb75b; + color: #FFF; +} +.annotation-flag.btn-success:hover{ + background-color: #66ce66; +} .annotation-viewer-container .warning{ color: #d00000; } diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index 7953c3372..de7c71f39 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -19,26 +19,29 @@ <% } -if (canEdit) { - - if (annotation.reject) { - %> - - <% - } else { - %> - - <% - } -} -%> +<% } %> diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index e9b69e127..a2da2e497 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -451,17 +451,14 @@ define(['jquery', target = $(annotationTag).filter(".annotation-flag[data-id='" + annotationModel.get("id") + "']"); //$(target).bind("click", this.flagAnnotation); - $(target).tooltip({ - trigger: "hover", - title: "Flag as incorrect" - }); - var deleteBtn = $(annotationTag).filter(".annotation-delete"); $(deleteBtn).tooltip({ trigger: "hover", title: "Delete" }); + $(annotationTag).filter(".tooltip-this").tooltip(); + target = $(annotationTag).filter(".annotation-delete[data-id='" + annotationModel.get("id") + "']"); //$(target).bind("click", this.deleteAnnotation); From 66c73cd87e9b22880a6a2dcf68d66b0a2a7ebd5c Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 09:46:55 -0700 Subject: [PATCH 008/560] Add optional test corpus filtering --- .../src/main/webapp/js/themes/dataone/models/Search.js | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js index ada31e121..a9210108d 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js @@ -40,6 +40,7 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], username: [], attribute: [], annotation: [], + //test_corpus_sm: "F", additionalCriteria: [], dataSource: [], id: [], @@ -220,6 +221,8 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], //----All other filters with a basic name:value pair pattern---- var otherFilters = ["attribute", "formatType", "rightsHolder", "submitter"]; + if(this.filterIsAvailable("test_corpus_sm")) otherFilters.push("test_corpus_sm"); + //Start the query string var query = ""; @@ -410,8 +413,11 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], // Does this need to be wrapped in quotes? if(model.needsQuotes(filterValue)) filterValue = "%22" + encodeURIComponent(filterValue) + "%22"; else filterValue = encodeURIComponent(filterValue); + + //Get the field name + var fieldName = model.fieldNameMap[filterName] || filterName; - query += "+" + model.fieldNameMap[filterName] + ":" + filterValue; + query += "+" + fieldName + ":" + filterValue; } } }); From c54eef1c7806a5a7cedf4ee7d703fa78287b6c48 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 27 Sep 2016 12:12:39 -0700 Subject: [PATCH 009/560] add function for expanding free-text search terms using the ontology in bioportal. --- .../src/main/webapp/js/models/LookupModel.js | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index b351f7290..133d86ef0 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -67,6 +67,39 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], }); }, + bioportalExpand: function(term, response) { + + // make sure we have something to lookup + if (!appModel.get('bioportalSearchUrl')) { + response(null); + return; + } + + var terms = []; + + var query = appModel.get('bioportalSearchUrl') + term; + $.get(query, function(data, textStatus, xhr) { + + _.each(data.collection, function(obj) { + // use the preferred label + var prefLabel = obj['prefLabel']; + terms.push(prefLabel); + + // add the synonyms + var synonyms = obj['synonym']; + if (synonyms) { + _.each(synonyms, function(synonym) { + terms.push(synonym); + } + } + + }); + + response(terms); + + }); + }, + bioportalGetConcepts: function(uri, callback) { var concepts = this.get('concepts')[uri]; From 5f2632f887c68df308cb729df47f1755324cd612 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 27 Sep 2016 12:29:37 -0700 Subject: [PATCH 010/560] add synonyms to autocomplete choices so we can display them in the UI. Also add place-holder for retrieving child concepts of our matches (not implemented). --- .../src/main/webapp/js/models/LookupModel.js | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 133d86ef0..f73e0db85 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -32,12 +32,35 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], _.each(data.collection, function(obj) { var choice = {}; choice.label = obj['prefLabel']; + var synonyms = obj['synonym']; + if (synonyms) { + choice.synonyms = []; + _.each(synonyms, function(synonym) { + choice.synonyms.push(synonym); + } + } choice.filterLabel = obj['prefLabel']; choice.value = obj['@id']; if (obj['definition']) { choice.desc = obj['definition'][0]; } + + // TODO: process the children recursively + var childrenUrl = obj['links']['children']; + if (false) { + //if (childrenUrl) { + + $.get(childrenUrl, function(data, textStatus, xhr) { + + _.each(data.collection, function(obj) { + // it is the same response format as above + + }) + }); + + } + // mark items that we know we have matches for if (allValues) { var matchingChoice = _.findWhere(allValues, {value: choice.value}); From cea56f79955f44b0684e91cd0ea184bac3b28578 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 13:05:22 -0700 Subject: [PATCH 011/560] Added 'Add nested dataset' sequence diagram and mockup --- .../editor/use-cases/add-a-nested-dataset.rst | 76 ++++++++++++++++++ .../images/add-nested-dataset-mockup.png | Bin 0 -> 207126 bytes .../add-nested-dataset-sequence-diagram.png | Bin 0 -> 61036 bytes 3 files changed, 76 insertions(+) create mode 100644 metacatui/docs/design/editor/use-cases/images/add-nested-dataset-mockup.png create mode 100644 metacatui/docs/design/editor/use-cases/images/add-nested-dataset-sequence-diagram.png diff --git a/metacatui/docs/design/editor/use-cases/add-a-nested-dataset.rst b/metacatui/docs/design/editor/use-cases/add-a-nested-dataset.rst index 477f997fc..57e59bfaa 100644 --- a/metacatui/docs/design/editor/use-cases/add-a-nested-dataset.rst +++ b/metacatui/docs/design/editor/use-cases/add-a-nested-dataset.rst @@ -5,6 +5,82 @@ Scenario -------- As a scientist, I want to add a nested dataset to an existing dataset folder so I can easily organize related data. + +Mockup Image +------------ + +.. image:: images/add-nested-dataset-mockup.png + +Technical Sequence Diagram +--------------------------- +.. @startuml images/add-nested-dataset-sequence-diagram.png + + !include ../plantuml-styles.txt + skinparam SequenceGroupBorderColor #AAAAAA + skinparam SequenceGroupBorderThickness #AAAAAA + + actor "Scientist" + participant EMLView as EMLView <> + participant DataPackageView as DataPackageView <> + participant DataItemView as DataItemView <> + participant DataPackage as DataPackage <> + participant EML as EML <> + participant Router as Router <> + + EMLView -> DataPackage : on("new-folder", handleNewFolder) + DataPackageView -> DataItemView : listenTo("add-folder", addFolder) + + Scientist -> DataItemView : clicks on "Add a folder" + + DataPackageView -> DataPackageView : addFolder() + activate DataPackageView + DataPackageView -> DataPackage : new() + + activate DataPackage + DataPackage -> EML : new() + activate EML + EML --> DataPackage : newEML + deactivate EML + DataPackage -> DataPackage : add(newEML) + DataPackage --> DataPackageView : newPackage + deactivate DataPackage + + DataPackageView -> DataItemView : new(newPackage) + deactivate DataPackageView + + activate DataItemView + DataItemView -> DataItemView : render() + DataItemView -> DataItemView : on("blur #titleText", handleChange()) + DataItemView --> Scientist: shows new folder row + note right + We highlight and focus the + title for the scientist to change + end note + deactivate DataItemView + + activate Scientist + Scientist -> DataItemView : Enters title + deactivate Scientist + + activate DataItemView + DataItemView -> DataItemView : handleChange() + DataItemView -> EML : set("title", title) + activate EML + DataItemView -> EML : getParent() + EML --> DataItemView : dataPackage + deactivate EML + DataItemView -> DataPackage : trigger("new-folder") + deactivate DataItemView + + DataPackage -> EMLView : handleNewFolder(dataPackage) + activate EMLView + EMLView -> Router : navigate("#view/{pid}", dataPackage) + deactivate EMLView + + @enduml + +.. image:: images/add-nested-dataset-sequence-diagram.png + diff --git a/metacatui/docs/design/editor/use-cases/images/add-nested-dataset-mockup.png b/metacatui/docs/design/editor/use-cases/images/add-nested-dataset-mockup.png new file mode 100644 index 0000000000000000000000000000000000000000..c329026a71cfb2225075943063a3230e93cb2222 GIT binary patch literal 207126 zcmeFZXHb)0_$`WJ!-k@QNK+Azu2kuwA{~^_dq=u-LJ2A=N);h=h}3{IDWO9|q$L#T 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[PATCH 012/560] fix syntax issues --- .../src/main/webapp/js/models/LookupModel.js | 42 +++++++++++++++---- 1 file changed, 35 insertions(+), 7 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index f73e0db85..310cce9ae 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -37,7 +37,7 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], choice.synonyms = []; _.each(synonyms, function(synonym) { choice.synonyms.push(synonym); - } + }); } choice.filterLabel = obj['prefLabel']; choice.value = obj['@id']; @@ -45,16 +45,44 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], choice.desc = obj['definition'][0]; } - - // TODO: process the children recursively + // process the children - just one level var childrenUrl = obj['links']['children']; - if (false) { - //if (childrenUrl) { + if (childrenUrl) { $.get(childrenUrl, function(data, textStatus, xhr) { _.each(data.collection, function(obj) { - // it is the same response format as above + var choice = {}; + choice.label = obj['prefLabel']; + var synonyms = obj['synonym']; + if (synonyms) { + choice.synonyms = []; + _.each(synonyms, function(synonym) { + choice.synonyms.push(synonym); + }); + } + choice.filterLabel = obj['prefLabel']; + choice.value = obj['@id']; + if (obj['definition']) { + choice.desc = obj['definition'][0]; + } + + // mark items that we know we have matches for + if (allValues) { + var matchingChoice = _.findWhere(allValues, {value: choice.value}); + if (matchingChoice) { + choice.label = "*" + choice.label; + + // remove it from the local value - why have two? + if (localValues) { + localValues = _.reject(localValues, function(obj) { + return obj.value == matchingChoice.value; + }); + } + } + } + + availableTags.push(choice); }) }); @@ -113,7 +141,7 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], if (synonyms) { _.each(synonyms, function(synonym) { terms.push(synonym); - } + }); } }); From e024de87e798c2442cef2ca477bd6e58b6f60cc0 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 16:02:37 -0700 Subject: [PATCH 013/560] Add back hoverAutocomplete initialization, but in the AppView --- .../src/main/webapp/js/views/AnnotatorView.js | 8 +-- metacatui/src/main/webapp/js/views/AppView.js | 37 ++++++++++++ .../main/webapp/js/views/DataCatalogView.js | 56 ++++++++++++++++++- 3 files changed, 96 insertions(+), 5 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index a2da2e497..d39bd0ffd 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -123,7 +123,7 @@ define(['jquery', this.$el.annotator().annotator('addPlugin', 'Tags'); // Initialize the autocomplete widget extension to provide description tooltips. - $.widget( "app.hoverAutocomplete", $.ui.autocomplete, { + $.widget( "app.semHoverAutocomplete", $.ui.autocomplete, { // Set the content attribute as the "item.desc" value. // This becomes the tooltip content. @@ -175,7 +175,7 @@ define(['jquery', }); - this.$el.data('annotator').plugins.Tags.input.hoverAutocomplete({ + this.$el.data('annotator').plugins.Tags.input.semHoverAutocomplete({ source: appLookupModel.bioportalSearch, position: { my: "left top", @@ -225,7 +225,7 @@ define(['jquery', // change the autocomplete depending on type of element being annotated var type = $(resourceElem).attr('type'); if (type == "orcid_sm" || type == "party") { - view.$el.data('annotator').plugins.Tags.input.hoverAutocomplete({ + view.$el.data('annotator').plugins.Tags.input.semHoverAutocomplete({ source: appLookupModel.orcidSearch, //focus: focus }); @@ -233,7 +233,7 @@ define(['jquery', $.extend(annotation, {"field": "orcid_sm"}); } else { - view.$el.data('annotator').plugins.Tags.input.hoverAutocomplete({ + view.$el.data('annotator').plugins.Tags.input.semHoverAutocomplete({ source: appLookupModel.bioportalSearch, //focus: focus }); diff --git a/metacatui/src/main/webapp/js/views/AppView.js b/metacatui/src/main/webapp/js/views/AppView.js index cedb4bdc3..6c96fb17a 100644 --- a/metacatui/src/main/webapp/js/views/AppView.js +++ b/metacatui/src/main/webapp/js/views/AppView.js @@ -84,6 +84,8 @@ define(['jquery', this.listenTo(appModel, "change:title", this.changeTitle); this.listenForActivity(); + + this.initializeWidgets(); }, //Changes the web document's title @@ -379,6 +381,41 @@ define(['jquery', }, + initializeWidgets: function(){ + // Autocomplete widget extension to provide description tooltips. + $.widget( "app.hoverAutocomplete", $.ui.autocomplete, { + + // Set the content attribute as the "item.desc" value. + // This becomes the tooltip content. + _renderItem: function( ul, item ) { + // if we have a label, use it for the title + var title = item.value; + if (item.label) { + title = item.label; + } + // if we have a description, use it for the content + var content = item.value; + if (item.desc) { + content = item.desc; + if (item.desc != item.value) { + content += " (" + item.value + ")"; + } + } + var element = this._super( ul, item ) + .attr( "data-title", title ) + .attr( "data-content", content ); + element.popover( + { + placement: "right", + trigger: "hover", + container: 'body' + + }); + return element; + } + }); + }, + /********************** Utilities ********************************/ // Various utility functions to use across the app // /************ Function to add commas to large numbers ************/ diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 73e34e4e0..a234b47ae 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -1433,7 +1433,61 @@ define(['jquery', }); } - $('#annotation_input').hoverAutocomplete({ + + //Set up the hover autocomplete for semantics pick lists + $.widget( "app.semHoverAutocomplete", $.ui.autocomplete, { + + // Set the content attribute as the "item.desc" value. + // This becomes the tooltip content. + _renderItem: function( ul, item ) { + // if we have a label, use it for the title + var title = item.value; + if (item.label) { + title = item.label; + } + + // if we have a description, use it for the content + var content = '

'; + if (item.desc) { + content += '' + item.label + ''; + if (item.desc != item.value) { + content += '

Definition: ' + item.desc + '

'; + content += '

Concept URI: ' + item.value + '

'; + } + } + content += "
" + + //Set up the popover + var element = this._super( ul, item ); + element.popover({ + placement: "right", + trigger: "manual", + container: 'body', + title: title, + html: true, + content: content + }) + .on("mouseenter", function () { + var _this = this; + $(this).popover("show"); + $(".popover").on("mouseleave", function () { + $(_this).popover('hide'); + }); + }) + .on("mouseleave", function () { + var _this = this; + setTimeout(function () { + if (!$(".popover:hover").length) { + $(_this).popover("hide"); + } + }, 300); + }); + return element; + } + }); + + + $('#annotation_input').semHoverAutocomplete({ source: function (request, response) { var term = $.ui.autocomplete.escapeRegex(request.term) From 4d9157f92c65d65c613435929662f5282f6e6e0b Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 16:18:50 -0700 Subject: [PATCH 014/560] Add API key to bioportal search in lookupmodel --- metacatui/src/main/webapp/js/models/LookupModel.js | 2 +- .../src/main/webapp/js/themes/dataone/models/AppModel.js | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 310cce9ae..870a0fab0 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -49,7 +49,7 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], var childrenUrl = obj['links']['children']; if (childrenUrl) { - $.get(childrenUrl, function(data, textStatus, xhr) { + $.get(childrenUrl + "?apikey=" + appModel.get("bioportalAPIKey"), function(data, textStatus, xhr) { _.each(data.collection, function(obj) { var choice = {}; diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index 2730b4c72..f518fe885 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -57,7 +57,8 @@ define(['jquery', 'underscore', 'backbone'], nodeServiceUrl: null, // NOTE: include your bioportal apikey for suggested classes // see: http://bioportal.bioontology.org/account - bioportalSearchUrl: "https://data.bioontology.org/search?ontologies=ECSO&apikey=24e4775e-54e0-11e0-9d7b-005056aa3316&pagesize=1000&suggest=true&q=", + bioportalAPIKey: "24e4775e-54e0-11e0-9d7b-005056aa3316", + bioportalSearchUrl: null, //bioportalSearchUrl: null, // use this to deactivate the annotator view //orcidBaseUrl: "https://sandbox.orcid.org", //orcidSearchUrl: null, @@ -179,6 +180,10 @@ define(['jquery', 'underscore', 'backbone'], if(this.get("d1CNBaseUrl").indexOf("cn.dataone.org") > -1) this.set("googleAnalyticsKey", "UA-15017327-17"); + //Set up the bioportal search URL + if((typeof this.get("bioportalAPIKey") == "string") && this.get("bioportalAPIKey").length) + this.set("bioportalSearchUrl", "https://data.bioontology.org/search?ontologies=ECSO&apikey=" + this.get("bioportalAPIKey") + "&pagesize=1000&suggest=true&q=") + this.on("change:pid", this.changePid); }, From ad56824f84f2fd72a18c7fdc9b8cf633f1b983b5 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Tue, 27 Sep 2016 16:20:51 -0700 Subject: [PATCH 015/560] Remove jquerysidr library which is not in use --- metacatui/src/main/webapp/components/jquery.sidr.min.js | 4 ---- metacatui/src/main/webapp/js/app.js | 5 ----- 2 files changed, 9 deletions(-) delete mode 100644 metacatui/src/main/webapp/components/jquery.sidr.min.js diff --git a/metacatui/src/main/webapp/components/jquery.sidr.min.js b/metacatui/src/main/webapp/components/jquery.sidr.min.js deleted file mode 100644 index c0e3deb49..000000000 --- a/metacatui/src/main/webapp/components/jquery.sidr.min.js +++ /dev/null @@ -1,4 +0,0 @@ -/*! Sidr - v1.2.1 - 2013-11-06 - * https://github.com/artberri/sidr - * Copyright (c) 2013 Alberto Varela; Licensed MIT */ -(function(e){var t=!1,i=!1,n={isUrl:function(e){var t=RegExp("^(https?:\\/\\/)?((([a-z\\d]([a-z\\d-]*[a-z\\d])*)\\.)+[a-z]{2,}|((\\d{1,3}\\.){3}\\d{1,3}))(\\:\\d+)?(\\/[-a-z\\d%_.~+]*)*(\\?[;&a-z\\d%_.~+=-]*)?(\\#[-a-z\\d_]*)?$","i");return t.test(e)?!0:!1},loadContent:function(e,t){e.html(t)},addPrefix:function(e){var t=e.attr("id"),i=e.attr("class");"string"==typeof t&&""!==t&&e.attr("id",t.replace(/([A-Za-z0-9_.\-]+)/g,"sidr-id-$1")),"string"==typeof i&&""!==i&&"sidr-inner"!==i&&e.attr("class",i.replace(/([A-Za-z0-9_.\-]+)/g,"sidr-class-$1")),e.removeAttr("style")},execute:function(n,s,a){"function"==typeof s?(a=s,s="sidr"):s||(s="sidr");var r,d,l,c=e("#"+s),u=e(c.data("body")),f=e("html"),p=c.outerWidth(!0),g=c.data("speed"),h=c.data("side"),m=c.data("displace"),v=c.data("onOpen"),y=c.data("onClose"),x="sidr"===s?"sidr-open":"sidr-open "+s+"-open";if("open"===n||"toggle"===n&&!c.is(":visible")){if(c.is(":visible")||t)return;if(i!==!1)return o.close(i,function(){o.open(s)}),void 0;t=!0,"left"===h?(r={left:p+"px"},d={left:"0px"}):(r={right:p+"px"},d={right:"0px"}),u.is("body")&&(l=f.scrollTop(),f.css("overflow-x","hidden").scrollTop(l)),m?u.addClass("sidr-animating").css({width:u.width(),position:"absolute"}).animate(r,g,function(){e(this).addClass(x)}):setTimeout(function(){e(this).addClass(x)},g),c.css("display","block").animate(d,g,function(){t=!1,i=s,"function"==typeof a&&a(s),u.removeClass("sidr-animating")}),v()}else{if(!c.is(":visible")||t)return;t=!0,"left"===h?(r={left:0},d={left:"-"+p+"px"}):(r={right:0},d={right:"-"+p+"px"}),u.is("body")&&(l=f.scrollTop(),f.removeAttr("style").scrollTop(l)),u.addClass("sidr-animating").animate(r,g).removeClass(x),c.animate(d,g,function(){c.removeAttr("style").hide(),u.removeAttr("style"),e("html").removeAttr("style"),t=!1,i=!1,"function"==typeof a&&a(s),u.removeClass("sidr-animating")}),y()}}},o={open:function(e,t){n.execute("open",e,t)},close:function(e,t){n.execute("close",e,t)},toggle:function(e,t){n.execute("toggle",e,t)},toogle:function(e,t){n.execute("toggle",e,t)}};e.sidr=function(t){return o[t]?o[t].apply(this,Array.prototype.slice.call(arguments,1)):"function"!=typeof t&&"string"!=typeof t&&t?(e.error("Method "+t+" does not exist on jQuery.sidr"),void 0):o.toggle.apply(this,arguments)},e.fn.sidr=function(t){var i=e.extend({name:"sidr",speed:200,side:"left",source:null,renaming:!0,body:"body",displace:!0,onOpen:function(){},onClose:function(){}},t),s=i.name,a=e("#"+s);if(0===a.length&&(a=e("
").attr("id",s).appendTo(e("body"))),a.addClass("sidr").addClass(i.side).data({speed:i.speed,side:i.side,body:i.body,displace:i.displace,onOpen:i.onOpen,onClose:i.onClose}),"function"==typeof i.source){var r=i.source(s);n.loadContent(a,r)}else if("string"==typeof i.source&&n.isUrl(i.source))e.get(i.source,function(e){n.loadContent(a,e)});else if("string"==typeof i.source){var d="",l=i.source.split(",");if(e.each(l,function(t,i){d+='
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"}),i.renaming){var c=e("
").html(d);c.find("*").each(function(t,i){var o=e(i);n.addPrefix(o)}),d=c.html()}n.loadContent(a,d)}else null!==i.source&&e.error("Invalid Sidr Source");return this.each(function(){var t=e(this),i=t.data("sidr");i||(t.data("sidr",s),"ontouchstart"in document.documentElement?(t.bind("touchstart",function(e){e.originalEvent.touches[0],this.touched=e.timeStamp}),t.bind("touchend",function(e){var t=Math.abs(e.timeStamp-this.touched);200>t&&(e.preventDefault(),o.toggle(s))})):t.click(function(e){e.preventDefault(),o.toggle(s)}))})}})(jQuery); \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/app.js b/metacatui/src/main/webapp/js/app.js index f9c96c12b..cffc6e2ef 100644 --- a/metacatui/src/main/webapp/js/app.js +++ b/metacatui/src/main/webapp/js/app.js @@ -31,7 +31,6 @@ require.config({ jquery: '../components/jquery', jqueryui: '../components/jquery-ui-1.10.3.custom.min', jqueryform: '../components/jquery.form', - jquerysidr: '../components/jquery.sidr.min', underscore: '../components/underscore-min', backbone: '../components/backbone-min', bootstrap: '../components/bootstrap.min', @@ -68,10 +67,6 @@ require.config({ annotator: { exports: 'Annotator' }, - jquerysidr: { - deps: ['jquery'], - exports: 'jquerysidr' - }, jws: { exports: 'JWS', deps: ['jsrasign'], From 56e8603a8071f275266ef0dbacc2a1aaaacfdbd7 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 27 Sep 2016 17:36:07 -0700 Subject: [PATCH 016/560] include synonyms when showing concept details in search and annotator views --- metacatui/src/main/webapp/js/models/LookupModel.js | 13 +++++++++++-- .../main/webapp/js/templates/annotationPopover.html | 10 ++++++++++ .../src/main/webapp/js/views/DataCatalogView.js | 9 +++++++++ 3 files changed, 30 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 870a0fab0..8b578a505 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -47,13 +47,14 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], // process the children - just one level var childrenUrl = obj['links']['children']; - if (childrenUrl) { + if (false) { + //if (childrenUrl) { $.get(childrenUrl + "?apikey=" + appModel.get("bioportalAPIKey"), function(data, textStatus, xhr) { _.each(data.collection, function(obj) { var choice = {}; - choice.label = obj['prefLabel']; + choice.label = "--" + obj['prefLabel']; var synonyms = obj['synonym']; if (synonyms) { choice.synonyms = []; @@ -179,6 +180,14 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], if (obj['definition']) { concept.desc = obj['definition'][0]; } + // add the synonyms + var synonyms = obj['synonym']; + if (synonyms) { + concept.synonyms = []; + _.each(synonyms, function(synonym) { + concept.synonyms.push(synonym); + }); + } concepts.push(concept); diff --git a/metacatui/src/main/webapp/js/templates/annotationPopover.html b/metacatui/src/main/webapp/js/templates/annotationPopover.html index 67bb45080..87f4bf8b9 100644 --- a/metacatui/src/main/webapp/js/templates/annotationPopover.html +++ b/metacatui/src/main/webapp/js/templates/annotationPopover.html @@ -5,6 +5,16 @@ <% } %>
+ <% if (annotation.concept.synonyms) { %> +

+ Synonyms: + <% + _.each(annotation.concept.synonyms, function(synonym) { + print(synonym, "
"); + }); + %> +

+ <% } %>

Definition: <%=annotation.concept.desc%> diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index a234b47ae..078f166ca 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -1450,6 +1450,15 @@ define(['jquery', var content = '

'; if (item.desc) { content += '' + item.label + ''; + if (item.synonyms) { + content += '

Synonyms: '; + _.each(item.synonyms, function(synonym) { + content += synonym + "
"; + }); + + content += '

'; + + } if (item.desc != item.value) { content += '

Definition: ' + item.desc + '

'; content += '

Concept URI: ' + item.value + '

'; From 52b2c36ad13cff459d865c72424b7260450e5eda Mon Sep 17 00:00:00 2001 From: leinfelder Date: Thu, 29 Sep 2016 16:19:19 -0700 Subject: [PATCH 017/560] only use the first person from the accounts lookup when showing annotation details. --- metacatui/src/main/webapp/js/models/AnnotationModel.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/AnnotationModel.js b/metacatui/src/main/webapp/js/models/AnnotationModel.js index 6532df0b1..b19b29a44 100644 --- a/metacatui/src/main/webapp/js/models/AnnotationModel.js +++ b/metacatui/src/main/webapp/js/models/AnnotationModel.js @@ -43,8 +43,8 @@ define(['jquery', 'underscore', 'backbone'], url: appModel.get("accountsUrl") + encodeURIComponent(username), type: "GET", success: function(data, textStatus, xhr){ - var lastName = $(data).find("person").find("familyName").text(), - firstName = $(data).find("person").find("givenName").text(); + var lastName = $(data).find("person").first().find("familyName").text(), + firstName = $(data).find("person").first().find("givenName").text(); model.set("name", firstName + " " + lastName); From d2e19e24766fcc0a5421cd049b715e73e39faa8c Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 30 Sep 2016 16:13:41 -0700 Subject: [PATCH 018/560] do not display the annotation adder for arbitrary text selections. https://github.com/DataONEorg/sem-prov-design/issues/212 --- .../src/main/webapp/js/themes/dataone/css/metacatui.css | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css index 232143e2d..5d64683c0 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css @@ -966,6 +966,12 @@ label.control-label{ background-color: #1C6E84; color: #FFF; } + +.annotator-adder { + opacity: 0.0; + pointer-events: none; + +} /* Registry CSS -------------------------------------------------- */ From 31bd5eabc619a5df13591470c4d14d6df5e6dd7f Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 30 Sep 2016 16:39:32 -0700 Subject: [PATCH 019/560] show tag icon next to attributes that have one or more annotations. https://github.com/DataONEorg/sem-prov-design/issues/211 --- metacatui/src/main/webapp/js/views/AnnotatorView.js | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index d39bd0ffd..e3f633c77 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -425,6 +425,15 @@ define(['jquery', // render it in the document var highlight = $("[data-annotation-id='" + annotationModel.get("id") + "']"); var section = $(highlight).closest(".tab-pane").children(".annotation-container"); + var tab = $(highlight).closest(".tab-pane"); + //console.log("tab: " + tab); + var tabControl = $("a[href='#" + $(tab).attr("id") + "'"); + //console.log("tabControl: " + tabControl); + var icons = $(tabControl).find(".icon-tag"); + if ($(icons).size() == 0) { + tabControl.prepend("") + } + if (!section.html()) { console.log("Highlights not completed yet - cannot render annotation"); return; From 0c25bdf9c2a02023cd5bf8a28ce96d8c9629c032 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 4 Oct 2016 19:24:20 -0700 Subject: [PATCH 020/560] use BioPortal batch endpoint for looking up concept details for annotations on a page before rendering. Note: using JSON.stringify() which may not be supported on all browsers. Note2: BP service seems to be limiting batch responses to 10 classes. I've asked them if there is a way to request more in a batch. https://github.com/DataONEorg/sem-prov-design/issues/208 --- .../src/main/webapp/js/models/LookupModel.js | 63 +++++++++++++++++++ .../js/themes/dataone/models/AppModel.js | 1 + .../src/main/webapp/js/views/AnnotatorView.js | 24 ++++++- 3 files changed, 87 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 8b578a505..9a03147c1 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -102,6 +102,7 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], return obj.value == matchingChoice.value; }); } + //availableTags.push(choice); } } @@ -197,6 +198,68 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], callback(concepts); }); }, + + bioportalGetConceptsBatch: function(uris, callback) { + + // make sure we have something to lookup + if (!appModel.get('bioportalBatchUrl')) { + return; + } + // prepare the request JSON + var batchData = {}; + batchData["http://www.w3.org/2002/07/owl#Class"] = {}; + batchData["http://www.w3.org/2002/07/owl#Class"]["display"] = "prefLabel,synonym,definition"; + batchData["http://www.w3.org/2002/07/owl#Class"]["collection"] = []; + _.each(uris, function(uri) { + var item = {}; + item["class"] = uri; + item["ontology"] = "http://data.bioontology.org/ontologies/ECSO"; + batchData["http://www.w3.org/2002/07/owl#Class"]["collection"].push(item); + }); + + var url = appModel.get('bioportalBatchUrl'); + var model = this; + $.ajax(url, + { + method: "POST", + //url: url, + data: JSON.stringify(batchData), + contentType: "application/json", + headers: { + "Authorization": "apikey token="+ appModel.get("bioportalAPIKey") + }, + error: function(e) { + alert(e); + }, + success: function(data, textStatus, xhr) { + + _.each(data["http://www.w3.org/2002/07/owl#Class"], function(obj) { + var concept = {}; + concept.label = obj['prefLabel']; + concept.value = obj['@id']; + if (obj['definition']) { + concept.desc = obj['definition'][0]; + } + // add the synonyms + var synonyms = obj['synonym']; + if (synonyms) { + concept.synonyms = []; + _.each(synonyms, function(synonym) { + concept.synonyms.push(synonym); + }); + } + + var conceptList = []; + conceptList.push(concept); + model.get('concepts')[concept.value] = conceptList; + + }); + + callback.apply(); + } + }); + + }, orcidGetConcepts: function(uri, callback) { diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index f518fe885..f2229d7b3 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -59,6 +59,7 @@ define(['jquery', 'underscore', 'backbone'], // see: http://bioportal.bioontology.org/account bioportalAPIKey: "24e4775e-54e0-11e0-9d7b-005056aa3316", bioportalSearchUrl: null, + bioportalBatchUrl: "https://data.bioontology.org/batch", //bioportalSearchUrl: null, // use this to deactivate the annotator view //orcidBaseUrl: "https://sandbox.orcid.org", //orcidSearchUrl: null, diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index e3f633c77..b083bc136 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -296,11 +296,33 @@ define(['jquery', this.$el.annotator('subscribe', 'annotationCreated', this.reindexPid); this.$el.annotator('subscribe', 'annotationUpdated', this.reindexPid); this.$el.annotator('subscribe', 'annotationDeleted', this.handleDelete); - this.$el.annotator('subscribe', 'annotationsLoaded', this.renderAnnotations); + this.$el.annotator('subscribe', 'annotationsLoaded', this.preRenderAnnotations); }, + preRenderAnnotations : function(annotations) { + + var uris = []; + + //look up the concept details in a batch + _.each(annotations, function(annotation) { + if (annotation.tags[0]) { + // look up concepts where we can + var conceptUri = annotation.tags[0]; + uris.push(conceptUri); + } + }); + + // now look them up and render when finished + var annotatorEl = (typeof this.$el != "undefined")? this.$el : this, + view = $(annotatorEl).data("annotator-view"); + appLookupModel.bioportalGetConceptsBatch( + uris, + function() {view.renderAnnotations(annotations);}); + + }, + renderAnnotations : function(annotations) { // keep from duplicating From 3e2b7ef2494f0d015f27d193c7b38013bfba22dd Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 5 Oct 2016 12:16:55 -0700 Subject: [PATCH 021/560] add all descendants to term expansion. https://github.com/DataONEorg/sem-prov-design/issues/214 --- .../src/main/webapp/js/models/LookupModel.js | 25 ++++++++++++++++--- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 9a03147c1..ef9596e64 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -144,12 +144,29 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], _.each(synonyms, function(synonym) { terms.push(synonym); }); - } - + } + // process the descendants + var descendantsUrl = obj['links']['descendants']; + //if (false) { + if (descendantsUrl) { + + $.get(childrenUrl + "?apikey=" + appModel.get("bioportalAPIKey"), function(data, textStatus, xhr) { + _.each(data.collection, function(obj) { + var prefLabel = obj['prefLabel']; + var synonyms = obj['synonym']; + if (synonyms) { + _.each(synonyms, function(synonym) { + terms.push(synonym); + }); + } + }); + + // callback + response(terms); + }); + } }); - response(terms); - }); }, From 11b380139320364dfc6fca680188d66520a16324 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 5 Oct 2016 16:38:35 -0700 Subject: [PATCH 022/560] put flagging/delete controls in a dropdown. still needs a Lauren polish :). https://github.com/DataONEorg/sem-prov-design/issues/209 --- .../main/webapp/js/templates/annotation.html | 43 +++++++++++++------ 1 file changed, 30 insertions(+), 13 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index de7c71f39..5491dac86 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -1,7 +1,7 @@ <% if (concept) { %> <%=concept.label %> @@ -19,29 +19,46 @@ <% } +%> +
+ + + +
From 64ce9ec682d8722358743413ab4e042b93bd4d59 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Thu, 6 Oct 2016 10:17:17 -0700 Subject: [PATCH 023/560] Merge changes to download button from 1.12 branch --- .../webapp/js/templates/downloadButton.html | 2 +- .../main/webapp/js/views/PackageTableView.js | 27 +++++++------------ 2 files changed, 11 insertions(+), 18 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/downloadButton.html b/metacatui/src/main/webapp/js/templates/downloadButton.html index c2d6f4a79..4391b9af5 100644 --- a/metacatui/src/main/webapp/js/templates/downloadButton.html +++ b/metacatui/src/main/webapp/js/templates/downloadButton.html @@ -14,7 +14,7 @@ if((typeof tooLarge !== "undefined") && tooLarge){ className += " tooltip-this disabled"; - attributes += ' disabled data-title="This file is too large to download. Please contact us about how to access this data." data-position="top" data-trigger="hover"'; + attributes += ' disabled data-title="This dataset is too large to download as a package. Please download the files individually or contact us for alternate data access." data-position="top" data-trigger="hover"'; } %> diff --git a/metacatui/src/main/webapp/js/views/PackageTableView.js b/metacatui/src/main/webapp/js/views/PackageTableView.js index ca32e60dc..b01228cbb 100644 --- a/metacatui/src/main/webapp/js/views/PackageTableView.js +++ b/metacatui/src/main/webapp/js/views/PackageTableView.js @@ -338,23 +338,16 @@ define(['jquery', 'underscore', 'backbone', 'models/PackageModel', 'text!templat //Download button cell var downloadBtnCell = $(document.createElement("td")).addClass("download-btn btn-container"); - if(memberModel.get("size") < appModel.get("maxDownloadSize")){ - var downloadButtonHTML = this.downloadButtonTemplate({ - href: url, - fileName: entityName, - id: memberModel.get("id"), - isPublic: memberModel.get("isPublic"), - }); - var downloadButton = $.parseHTML(downloadButtonHTML.trim()); - - if(appUserModel.get("loggedIn") && !memberModel.get("isPublic")) - $(downloadButton).on("click", null, this, this.download); - } - else{ - var downloadButton = $.parseHTML(this.downloadButtonTemplate({ - tooLarge: true - }).trim()); - } + var downloadButtonHTML = this.downloadButtonTemplate({ + href: url, + fileName: entityName, + id: memberModel.get("id"), + isPublic: memberModel.get("isPublic"), + }); + var downloadButton = $.parseHTML(downloadButtonHTML.trim()); + + if(appUserModel.get("loggedIn") && !memberModel.get("isPublic")) + $(downloadButton).on("click", null, this, this.download); $(downloadBtnCell).append(downloadButton); $(tr).append(downloadBtnCell); From 6e5fdbb81bdc1e37a32abce41fde740a21f7c87c Mon Sep 17 00:00:00 2001 From: leinfelder Date: Thu, 6 Oct 2016 15:27:11 -0700 Subject: [PATCH 024/560] include bioportal tree view component. not yet used. https://github.com/DataONEorg/sem-prov-design/issues/210 --- .../bioportal/jquery.ncbo.tree-2.0.2.js | 421 ++++++++++++++++++ .../bioportal/jquery.ncbo.tree-2.0.2.min.js | 1 + .../components/bioportal/jquery.ncbo.tree.css | 323 ++++++++++++++ .../bioportal/jquery.ncbo.tree.min.css | 1 + metacatui/src/main/webapp/js/app.js | 4 + .../src/main/webapp/js/templates/appHead.html | 1 + .../src/main/webapp/js/views/AnnotatorView.js | 2 + 7 files changed, 753 insertions(+) create mode 100644 metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js create mode 100644 metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.min.js create mode 100644 metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.css create mode 100644 metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.min.css diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js new file mode 100644 index 000000000..6da0c8112 --- /dev/null +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js @@ -0,0 +1,421 @@ +/* +* jQuery SimpleTree Drag&Drop plugin +* Update on 22th May 2008 +* Version 0.3 +* +* Licensed under BSD +* Copyright (c) 2008, Peter Panov , IKEEN Group http://www.ikeen.com +* All rights reserved. +* +* Redistribution and use in source and binary forms, with or without +* modification, are permitted provided that the following conditions are met: +* * Redistributions of source code must retain the above copyright +* notice, this list of conditions and the following disclaimer. +* * Redistributions in binary form must reproduce the above copyright +* notice, this list of conditions and the following disclaimer in the +* documentation and/or other materials provided with the distribution. +* * Neither the name of the Peter Panov, IKEEN Group nor the +* names of its contributors may be used to endorse or promote products +* derived from this software without specific prior written permission. +* +* THIS SOFTWARE IS PROVIDED BY Peter Panov, IKEEN Group ``AS IS'' AND ANY +* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +* DISCLAIMED. IN NO EVENT SHALL Peter Panov, IKEEN Group BE LIABLE FOR ANY +* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND +* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +(function($) { + var NCBOTree = function(element, opt) { + var _this = this; + var OPTIONS; + var ROOT_ID = "roots"; + var mousePressed = false; + var $TREE_CONTAINER; + var TREE; + var ROOT; + var startingRoot; + + OPTIONS = { + autoclose: false, + beforeExpand: false, + afterExpand: false, + afterExpandError: false, + afterSelect: false, + afterJumpToClass: false, + timeout: 999999, + treeClass: "ncboTree", + autocompleteClass: "ncboAutocomplete", + width: 350, + ncboAPIURL: "http://data.bioontology.org", + ncboUIURL: "http://bioportal.bioontology.org", + apikey: null, + ontology: null, + startingClass: null, + startingRoot: ROOT_ID, + defaultRoot: ROOT_ID + }; + + OPTIONS = $.extend(OPTIONS, opt); + + // Required options + if (OPTIONS.apikey == null) + throw new Error("You must provide an API Key for NCBO Tree Widget to operate"); + + if (OPTIONS.ontology == null) + throw new Error("You must provide an ontology id for NCBO Tree Widget to operate"); + + this.options = function() { + return OPTIONS; + } + + this.jumpToClass = function(cls, callback) { + ROOT.html($("").html("Loading...").css("font-size", "smaller")); + $.ajax({ + url: determineHTTPS(OPTIONS.ncboAPIURL) + "/ontologies/" + OPTIONS.ontology + "/classes/" + encodeURIComponent(cls) + "/tree", + data: {apikey: OPTIONS.apikey, display: "prefLabel,hasChildren", no_context: true}, + contentType: 'json', + crossDomain: true, + success: function(roots) { + roots = findRootNode(roots); + ROOT.html(formatNodes(roots)); + setTreeNodes(ROOT, false); + + if (typeof callback == 'function') { + callback(); + } + + _this.selectClass(cls); + if (typeof OPTIONS.afterJumpToClass == 'function') { + OPTIONS.afterJumpToClass(cls); + } + $TREE_CONTAINER.trigger("afterJumpToClass", cls); + } + }); + } + + this.selectClass = function(cls) { + var foundClass = $(TREE.find("a[data-id='" + encodeURIComponent(cls) + "']")); + $(TREE.find("a.active")[0]).removeClass("active"); + foundClass.addClass("active"); + } + + this.selectedClass = function() { + var cls = $(TREE.find("a.active")[0]); + if (cls.length == 0) { + return null; + } else { + return { + id: decodeURIComponent(cls.data("id")), + prefLabel: cls.html(), + URL: cls.attr("href") + }; + } + } + + this.changeOntology = function(ont) { + var newTree = $("
    ").append($("
  • ").addClass("root")); + $TREE_CONTAINER.html(""); + TREE = newTree; + OPTIONS.ontology = ont; + _this.init(); + } + + // format the nodes to match what simpleTree is expecting + var formatNodes = function(nodes) { + var holder = $(""); + var ul = $("
      ") + + // Sort by prefLabel + nodes.sort(function(a, b) { + var aName = a.prefLabel.toLowerCase(); + var bName = b.prefLabel.toLowerCase(); + return ((aName < bName) ? -1 : ((aName > bName) ? 1 : 0)); + }); + + $.each(nodes, function(index, node) { + var li = $("
    • "); + var a = $("").attr("href", determineHTTPS(node.links.self)).html(node.prefLabel); + a.attr("data-id", encodeURIComponent(node["@id"])); + + ul.append(li.append(a)); + + var hasChildrenNotExpanded = typeof node.children !== 'undefined' && node.hasChildren && node.children.length == 0; + if (node.hasChildren && typeof node.children === 'undefined' || hasChildrenNotExpanded) { + var ajax_ul = $("
        ").addClass("ajax"); + var ajax_li = $("
      • "); + var ajax_a = $("").attr("href", node.links.children); + li.append(ajax_ul.append(ajax_li.append(ajax_a))); + } else if (typeof node.children !== 'undefined' && node.children.length > 0) { + var child_ul = formatNodes(node.children); + li.attr("class", "folder-open") + li.append(child_ul); + } + }); + + holder.append(ul) + return holder.html(); + } + + var findRootNode = function(nodes) { + var startingRoot = (OPTIONS.startingRoot == OPTIONS.defaultRoot) ? null : OPTIONS.startingRoot; + if (startingRoot == null) {return nodes;} + + var foundNode = false; + var searchQueue = nodes; + + while (searchQueue.length > 0 || foundNode == false) { + var node = searchQueue.shift(); + if (node["@id"] == startingRoot) { + foundNode = [node]; + } else if (typeof node.children !== 'undefined' && node.children.length > 0) { + searchQueue = searchQueue.concat(node.children); + } + } + + return foundNode; + } + + var closeNearby = function(obj) { + $(obj).siblings().filter('.folder-open, .folder-open-last').each(function() { + var childUl = $('>ul',this); + var className = this.className; + this.className = className.replace('open', 'close'); + childUl.hide(); + }); + }; + + var nodeToggle = function(obj) { + var childUl = $('>ul',obj); + if (childUl.is(':visible')) { + obj.className = obj.className.replace('open','close'); + childUl.hide(); + } else { + obj.className = obj.className.replace('close','open'); + childUl.show(); + if (OPTIONS.autoclose) + closeNearby(obj); + if (childUl.is('.ajax')) + setAjaxNodes(childUl, obj.id); + } + }; + + var setAjaxNodes = function(node, parentId, successCallback, errorCallback) { + if (typeof OPTIONS.beforeExpand == 'function') { + OPTIONS.beforeExpand(node); + } + $TREE_CONTAINER.trigger("beforeExpand", node); + + var url = determineHTTPS($.trim($('a', node).attr("href"))); + if (url) { + $.ajax({ + type: "GET", + url: url, + data: {apikey: OPTIONS.apikey, display: "prefLabel,hasChildren", no_context: true}, + crossDomain: true, + contentType: 'json', + timeout: OPTIONS.timeout, + success: function(response) { + var nodes = formatNodes(response.collection) + node.removeAttr('class'); + node.html(nodes); + $.extend(node, {url:url}); + setTreeNodes(node, true); + if (typeof OPTIONS.afterExpand == 'function') { + OPTIONS.afterExpand(node); + } + $TREE_CONTAINER.trigger("afterExpand", node); + if (typeof successCallback == 'function') { + successCallback(node); + } + }, + error: function(response) { + if (typeof OPTIONS.afterExpandError == 'function') { + OPTIONS.afterExpandError(node); + } + if (typeof errorCallback == 'function') { + errorCallback(node); + } + $TREE_CONTAINER.trigger("afterExpandError", node); + } + }); + } + }; + + var setTreeNodes = function(obj, useParent) { + obj = useParent ? obj.parent() : obj; + $('li>a', obj).addClass('text').bind('selectstart', function() { + return false; + }).click(function() { + var parent = $(this).parent(); + var selectedNode = $(this); + $('.active', TREE).attr('class', 'text'); + if (this.className == 'text') { + this.className = 'active'; + } + if (typeof OPTIONS.afterSelect == 'function') { + OPTIONS.afterSelect(decodeURIComponent(selectedNode.data("id")), selectedNode.text(), selectedNode); + } + $TREE_CONTAINER.trigger("afterSelect", [decodeURIComponent(selectedNode.data("id")), selectedNode.text(), selectedNode]); + return false; + }).bind("contextmenu",function() { + $('.active', TREE).attr('class', 'text'); + if (this.className == 'text') { + this.className = 'active'; + } + if (typeof OPTIONS.afterContextMenu == 'function') { + OPTIONS.afterContextMenu(parent); + } + return false; + }).mousedown(function(event) { + mousePressed = true; + cloneNode = $(this).parent().clone(); + var LI = $(this).parent(); + return false; + }); + + $('li', obj).each(function(i) { + var className = this.className; + var open = false; + var cloneNode=false; + var LI = this; + var childNode = $('>ul',this); + if (childNode.size() > 0) { + var setClassName = 'folder-'; + if (className && className.indexOf('open') >= 0) { + setClassName = setClassName + 'open'; + open = true; + } else { + setClassName = setClassName+'close'; + } + this.className = setClassName + ($(this).is(':last-child') ? '-last' : ''); + + if (!open || className.indexOf('ajax') >= 0) + childNode.hide(); + + setTrigger(this); + } else { + var setClassName = 'doc'; + this.className = setClassName + ($(this).is(':last-child') ? '-last' : ''); + } + }).before('
      •  
        • ') + .filter(':last-child') + .after('
      • '); + }; + + var setTrigger = function(node) { + $('>a',node).before(''); + var trigger = $('>.trigger', node); + trigger.click(function(event) { + nodeToggle(node); + }); + // TODO: $.browser was removed in jQuery 1.9, check IE compatability + // if (!$.browser.msie) { + // trigger.css('float','left'); + // } + }; + + var determineHTTPS = function(url) { + return url.replace("http:", ('https:' == document.location.protocol ? 'https:' : 'http:')); + } + + var initAutocomplete = function() { + // Add the autocomplete + var autocompleteContainer = $("
        ").addClass(OPTIONS.autocompleteClass).addClass("ncboTree"); + var input = $("") + .addClass(OPTIONS.autocompleteClass) + .css("width", OPTIONS.width) + .attr("placeholder", "Search for class..."); + autocompleteContainer.append(input); + input.NCBOAutocomplete({ + url: OPTIONS.ncboAPIURL + "/search", + searchParameter: "q", + resultAttribute: "collection", + property: "prefLabel", + searchTextSuffix: "*", + searchFromRoot: startingRoot, + onSelect: function(item, searchInput) { + _this.jumpToClass(item["@id"]); + searchInput.val(""); + }, + minCharacters: 3, + additionalParameters: { + apikey: OPTIONS.apikey, + no_context: true, + ontologies: OPTIONS.ontology + } + }); + $TREE_CONTAINER.append(autocompleteContainer); + } + + // Populate roots and init tree + this.init = function() { + $TREE_CONTAINER = element; + TREE = $("
          ").append($("
        • ").addClass("root")); + ROOT = $('.root', TREE); + TREE.css("width", OPTIONS.width).addClass(OPTIONS.treeClass); + $TREE_CONTAINER.html(""); + + // Only set starting root when something other than roots is selected + startingRoot = (OPTIONS.startingRoot == OPTIONS.defaultRoot) ? null : OPTIONS.startingRoot; + + initAutocomplete(); + $TREE_CONTAINER.append(TREE); + + if (OPTIONS.startingClass !== null) { + _this.jumpToClass(OPTIONS.startingClass); + OPTIONS.startingClass = null; + } else { + ROOT.html($("").html("Loading...").css("font-size", "smaller")); + $.ajax({ + url: determineHTTPS(OPTIONS.ncboAPIURL) + "/ontologies/" + OPTIONS.ontology + "/classes/" + encodeURIComponent(OPTIONS.startingRoot), + data: {apikey: OPTIONS.apikey, display: "prefLabel,hasChildren", no_context: true}, + contentType: 'json', + crossDomain: true, + success: function(roots) { + // Flatten potentially nested arrays + roots = $.map([roots], function(n) { + return n; + }); + ROOT.html(formatNodes(roots)); + setTreeNodes(ROOT, false); + } + }); + } + }; + } + + // Returns the original object(s) so they can be chained + $.fn.NCBOTree = function(options) { + return this.each(function() { + var $this = $(this); + + // Return early if this element already has a plugin instance + if ($this.data('NCBOTree')) return; + + // pass options to plugin constructor + var ncboTree = new NCBOTree($this, options); + this.NCBOTree = ncboTree; + + // Add the autocomplete code + $.ajax({ + url: ncboTree.options().ncboUIURL.replace("http:", ('https:' == document.location.protocol ? 'https:' : 'http:')) + "/widgets/jquery.ncbo.autocomplete.js", + type: "GET", + crossDomain: true, + dataType: "script", + success: function() { + ncboTree.init(); + + // Store plugin object in this element's data + $this.data('NCBOTree', ncboTree); + } + }); + }); + } + +}(jQuery)); \ No newline at end of file diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.min.js b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.min.js new file mode 100644 index 000000000..7c2a0ad4f --- /dev/null +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.min.js @@ -0,0 +1 @@ +!function(t){var e=function(e,a){var n,o,s,r,i,l=this,c="roots",d=!1;if(n={autoclose:!1,beforeExpand:!1,afterExpand:!1,afterExpandError:!1,afterSelect:!1,afterJumpToClass:!1,timeout:999999,treeClass:"ncboTree",autocompleteClass:"ncboAutocomplete",width:350,ncboAPIURL:"http://data.bioontology.org",ncboUIURL:"http://bioportal.bioontology.org",apikey:null,ontology:null,startingClass:null,startingRoot:c,defaultRoot:c},n=t.extend(n,a),null==n.apikey)throw new Error("You must provide an API Key for NCBO Tree Widget to operate");if(null==n.ontology)throw new Error("You must provide an ontology id for NCBO Tree Widget to operate");this.options=function(){return n},this.jumpToClass=function(e,a){r.html(t("").html("Loading...").css("font-size","smaller")),t.ajax({url:y(n.ncboAPIURL)+"/ontologies/"+n.ontology+"/classes/"+encodeURIComponent(e)+"/tree",data:{apikey:n.apikey,display:"prefLabel,hasChildren",no_context:!0},contentType:"json",crossDomain:!0,success:function(t){t=f(t),r.html(p(t)),C(r,!1),"function"==typeof a&&a(),l.selectClass(e),"function"==typeof n.afterJumpToClass&&n.afterJumpToClass(e),o.trigger("afterJumpToClass",e)}})},this.selectClass=function(e){var a=t(s.find("a[data-id='"+encodeURIComponent(e)+"']"));t(s.find("a.active")[0]).removeClass("active"),a.addClass("active")},this.selectedClass=function(){var e=t(s.find("a.active")[0]);return 0==e.length?null:{id:decodeURIComponent(e.data("id")),prefLabel:e.html(),URL:e.attr("href")}},this.changeOntology=function(e){var a=t("
            ").append(t("
          • ").addClass("root"));o.html(""),s=a,n.ontology=e,l.init()};var p=function(e){var a=t(""),n=t("
              ");return e.sort(function(t,e){var a=t.prefLabel.toLowerCase(),n=e.prefLabel.toLowerCase();return n>a?-1:a>n?1:0}),t.each(e,function(e,a){var o=t("
            • "),s=t("").attr("href",y(a.links.self)).html(a.prefLabel);s.attr("data-id",encodeURIComponent(a["@id"])),n.append(o.append(s));var r="undefined"!=typeof a.children&&a.hasChildren&&0==a.children.length;if(a.hasChildren&&"undefined"==typeof a.children||r){var i=t("
                ").addClass("ajax"),l=t("
              • "),c=t("").attr("href",a.links.children);o.append(i.append(l.append(c)))}else if("undefined"!=typeof a.children&&a.children.length>0){var d=p(a.children);o.attr("class","folder-open"),o.append(d)}}),a.append(n),a.html()},f=function(t){var e=n.startingRoot==n.defaultRoot?null:n.startingRoot;if(null==e)return t;for(var a=!1,o=t;o.length>0||0==a;){var s=o.shift();s["@id"]==e?a=[s]:"undefined"!=typeof s.children&&s.children.length>0&&(o=o.concat(s.children))}return a},u=function(e){t(e).siblings().filter(".folder-open, .folder-open-last").each(function(){var e=t(">ul",this),a=this.className;this.className=a.replace("open","close"),e.hide()})},h=function(e){var a=t(">ul",e);a.is(":visible")?(e.className=e.className.replace("open","close"),a.hide()):(e.className=e.className.replace("close","open"),a.show(),n.autoclose&&u(e),a.is(".ajax")&&m(a,e.id))},m=function(e,a,s,r){"function"==typeof n.beforeExpand&&n.beforeExpand(e),o.trigger("beforeExpand",e);var i=y(t.trim(t("a",e).attr("href")));i&&t.ajax({type:"GET",url:i,data:{apikey:n.apikey,display:"prefLabel,hasChildren",no_context:!0},crossDomain:!0,contentType:"json",timeout:n.timeout,success:function(a){var r=p(a.collection);e.removeAttr("class"),e.html(r),t.extend(e,{url:i}),C(e,!0),"function"==typeof n.afterExpand&&n.afterExpand(e),o.trigger("afterExpand",e),"function"==typeof s&&s(e)},error:function(t){"function"==typeof n.afterExpandError&&n.afterExpandError(e),"function"==typeof r&&r(e),o.trigger("afterExpandError",e)}})},C=function(e,a){e=a?e.parent():e,t("li>a",e).addClass("text").bind("selectstart",function(){return!1}).click(function(){var e=(t(this).parent(),t(this));return t(".active",s).attr("class","text"),"text"==this.className&&(this.className="active"),"function"==typeof n.afterSelect&&n.afterSelect(decodeURIComponent(e.data("id")),e.text(),e),o.trigger("afterSelect",[decodeURIComponent(e.data("id")),e.text(),e]),!1}).bind("contextmenu",function(){return t(".active",s).attr("class","text"),"text"==this.className&&(this.className="active"),"function"==typeof n.afterContextMenu&&n.afterContextMenu(parent),!1}).mousedown(function(e){d=!0,cloneNode=t(this).parent().clone();t(this).parent();return!1}),t("li",e).each(function(e){var a=this.className,n=!1,o=t(">ul",this);if(o.size()>0){var s="folder-";a&&a.indexOf("open")>=0?(s+="open",n=!0):s+="close",this.className=s+(t(this).is(":last-child")?"-last":""),(!n||a.indexOf("ajax")>=0)&&o.hide(),g(this)}else{var s="doc";this.className=s+(t(this).is(":last-child")?"-last":"")}}).before('
              •  
                • ').filter(":last-child").after('
              • ')},g=function(e){t(">a",e).before('');var a=t(">.trigger",e);a.click(function(t){h(e)})},y=function(t){return t.replace("http:","https:"==document.location.protocol?"https:":"http:")},v=function(){var e=t("
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                  ").append(t("
                • ").addClass("root")),r=t(".root",s),s.css("width",n.width).addClass(n.treeClass),o.html(""),i=n.startingRoot==n.defaultRoot?null:n.startingRoot,v(),o.append(s),null!==n.startingClass?(l.jumpToClass(n.startingClass),n.startingClass=null):(r.html(t("").html("Loading...").css("font-size","smaller")),t.ajax({url:y(n.ncboAPIURL)+"/ontologies/"+n.ontology+"/classes/"+encodeURIComponent(n.startingRoot),data:{apikey:n.apikey,display:"prefLabel,hasChildren",no_context:!0},contentType:"json",crossDomain:!0,success:function(e){e=t.map([e],function(t){return t}),r.html(p(e)),C(r,!1)}}))}};t.fn.NCBOTree=function(a){return this.each(function(){var n=t(this);if(!n.data("NCBOTree")){var o=new e(n,a);this.NCBOTree=o,t.ajax({url:o.options().ncboUIURL.replace("http:","https:"==document.location.protocol?"https:":"http:")+"/widgets/jquery.ncbo.autocomplete.js",type:"GET",crossDomain:!0,dataType:"script",success:function(){o.init(),n.data("NCBOTree",o)}})}})}}(jQuery); \ No newline at end of file diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.css b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.css new file mode 100644 index 000000000..d0bfceaea --- /dev/null +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.css @@ -0,0 +1,323 @@ +/******************** +## TREE VIEW +*********************/ +div.tree_error { + background: none repeat scroll 0 0 lightYellow; + font-weight: 600; + padding: 5px 10px; +} +.expansion_error { + color: red; + font-size: x-small; + font-style: oblique; + padding: 0 3px; +} +.ncboTree { + margin:0; + padding:0; + font-family: sans-serif; +} +.ncboTree li { + list-style: none; + margin:0; + padding:0 0 0 22px; + line-height: 14px; +} +.ncboTree li span { + display:inline; + clear: left; + white-space: nowrap; +} +.ncboTree ul { + margin:0; + padding:0; +} +.ncboTree .root ul { + margin:0; +} +.ncboTree .root { + margin-left:-16px !important; +} +.ncboTree .line { + padding:0; + line-height: 3px; + height:3px; + font-size:3px; + background: 0 0 no-repeat transparent url(data:image/gif;base64,R0lGODlhUAAUAIABAICAgP///yH5BAEAAAEALAAAAABQABQAAAI0jI+py+0PG4i02ouz3mryD4bi+HjkiabqYq7uC2NtTNd2MN/6Tub8D5QFh8SKr4hEHpOQAgA7); +} +.ncboTree .line-last { + padding:0; + line-height: 3px; + height:3px; + font-size:3px; + background: 0 0 no-repeat transparent url(data:image/gif;base64,R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==); +} +.ncboTree .line-over { + padding:0; + line-height: 3px; + height:3px; + font-size:3px; + background: 0 0 no-repeat transparent url(data:image/gif;base64,R0lGODlhUAAUAMQfAICAgEVFRUZHRoKBgUlISKKionl6enJycmRkY2tra/Ly81JSUpGRkaqqq8rLyrOzstnZ2cLDwk1NTfv8+/f39+zt7Lq7u+fn5lhYV////15eXuDg4NLS0omKipqamf///yH5BAEAAB8ALAAAAABQABQAAAV44CeOH0CSQXCubOu+cAwHAvFJ3/Jhn/Yhn8Tn8DF8Bp/Oh/HxfAqfxufxsXwiH8eH84F8Np/Lp/JRfCifyScjM7FSsrh8Tq/b73Q3fs/v+/9zeoCDhIWGMIKHiouMeImNkJGSJI+TlpeFlZibnHeanaChL5+ipZshADs=); +} +.ncboTree .line-over-last { + padding:0; + line-height: 3px; + height:3px; + font-size:3px; + background: 0 0 no-repeat transparent url(data:image/gif;base64,R0lGODlhUAAUAMQeAEVFRWtra+fn5k1NTWRkY3l6enJycklISMrLyvLy8////5qamV5eXvf397q7u1hYV8LDwkZHRoKBgbOzspGRkVJSUtnZ2eDg4Ozt7Pv8+6qqq9LS0omKiqKiov///wAAACH5BAEAAB4ALAAAAABQABQAAAVooCeOZOkBgKmubOu+8AhEhzd4lfd4jEd4AY/BU/BIPBwPxbPwdDwaz8Tj8EA8CM/GY/FcPAIPxpPwNDwZjyK2QrHf8Lh8Tq/b7/i8fs/v+/+AgYKDhIWGh4iJiouMjY6PkJGSk5SViSEAOw==); +} +.ncboTree .folder-open { + background: 0 -2px no-repeat #fff 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+} +.ncboTree .doc { + background: 0 -1px no-repeat #fff 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+} +.ncboTree .doc-last { + background: 0 -1px no-repeat #fff url(data:image/gif;base64,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); +} +.ncboTree .doc a.active { + padding-left: 4px; + margin-left: -4px; +} +.ncboTree .ajax { + background: no-repeat 0 0 #ffffff url(data:image/gif;base64,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); + height: 16px; + display:none; +} +.ncboTree .ajax li { + display:none; + margin:0; + padding:0; +} +.ncboTree .trigger { + display:inline; + margin-left:-28px; + width: 28px; + height: 11px; + cursor:pointer; +} +.ncboTree .text { + cursor: default; +} +.ncboTree .active { + cursor: default; + background-color: #B9D5E4; + font-weight: bold; + padding-top: 1px; + padding-right: 4px; + padding-bottom: 1px; + padding-left: 0px; + line-height: 16px; +} +.ncboTree a, .ncboTree a:hover { + text-decoration: none; + color: black; + font-size: 11pt; +} +.ncboTree a:hover { + cursor: pointer; +} + +/* + * jQuery UI CSS Framework 1.8.7 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + */ + +/* Layout helpers +----------------------------------*/ +.ncboAutocomplete .ui-front { z-index: 100; } +.ncboAutocomplete .ui-helper-hidden { display: none; } +.ncboAutocomplete .ui-helper-hidden-accessible { position: absolute !important; clip: rect(1px 1px 1px 1px); clip: rect(1px,1px,1px,1px); } +.ncboAutocomplete .ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; } +.ncboAutocomplete .ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; } +.ncboAutocomplete .ui-helper-clearfix { display: inline-block; } +/* required comment for clearfix to work in Opera \*/ +* html .ncboAutocomplete .ui-helper-clearfix { height:1%; } +.ncboAutocomplete .ui-helper-clearfix { display:block; } +/* end clearfix */ +.ncboAutocomplete .ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); } + + +/* Interaction Cues +----------------------------------*/ +.ncboAutocomplete .ui-state-disabled { cursor: default !important; } + + +/* Icons +----------------------------------*/ + +/* states and images */ +.ncboAutocomplete .ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; } + + +/* Misc visuals +----------------------------------*/ + +/* Overlays */ +.ncboAutocomplete .ui-widget-overlay { position: fixed; top: 0; left: 0; width: 100%; height: 100%; } + +.jsonSuggest a { + font-size: .8em; +} + +.jsonSuggest a:hover { + cursor: pointer; + font-size: .8em; +} + +/* + * jQuery UI CSS Framework 1.8.7 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + * + * To view and modify this theme, visit http://jqueryui.com/themeroller/?ctl=themeroller + */ + + +/* Component containers +----------------------------------*/ +.ncboAutocomplete .ui-widget { font-family: Arial,sans-serif; font-size: 1em; } +.ncboAutocomplete .ui-widget .ui-widget { font-size: 1em; } +.ncboAutocomplete .ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Arial,sans-serif; font-size: 1em; } +.ncboAutocomplete .ui-widget-content { border: 1px solid #B6B6B6; background: #ffffff; color: #4F4F4F; } +.ncboAutocomplete .ui-widget-content a { color: #4F4F4F; } +.ncboAutocomplete .ui-widget-header { border: 1px solid #B6B6B6; color: #4F4F4F; font-weight: bold; } +.ncboAutocomplete .ui-widget-header { + background: #ededed 0 0 repeat-x; /* Old browsers */ + background: -moz-linear-gradient(top, #ededed 0%, #c4c4c4 100%); /* FF3.6+ */ + background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,#ededed), color-stop(100%,#c4c4c4)); /* Chrome,Safari4+ */ + background: -webkit-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* Chrome10+,Safari5.1+ */ + background: -o-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* Opera11.10+ */ + background: -ms-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* IE10+ */ + background: linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* W3C */ +} +.ncboAutocomplete .ui-widget-header a { color: #4F4F4F; } + +/* Interaction states +----------------------------------*/ +.ncboAutocomplete .ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #B6B6B6; font-weight: normal; color: #4F4F4F; } +.ncboAutocomplete .ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { + background: #ededed 0 0 repeat-x; /* Old browsers */ + background: -moz-linear-gradient(top, #ededed 0%, #c4c4c4 100%); /* FF3.6+ */ + background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,#ededed), color-stop(100%,#c4c4c4)); /* Chrome,Safari4+ */ + background: -webkit-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* Chrome10+,Safari5.1+ */ + background: -o-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* Opera11.10+ */ + background: -ms-linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* IE10+ */ + background: linear-gradient(top, #ededed 0%,#c4c4c4 100%); /* W3C */ + -webkit-box-shadow: 0 1px 0 rgba(255,255,255,0.6) inset; + -moz-box-shadow: 0 1px 0 rgba(255,255,255,0.6) inset; + box-shadow: 0 1px 0 rgba(255,255,255,0.6) inset; +} +.ncboAutocomplete .ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #4F4F4F; text-decoration: none; } +.ncboAutocomplete .ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #9D9D9D; font-weight: normal; color: #313131; } +.ncboAutocomplete .ui-state-hover a, .ui-state-hover a:hover { color: #313131; text-decoration: none; } +.ncboAutocomplete .ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { + outline: none; + color: #1c4257; border: 1px solid #7096ab; + background: #ededed 0 -50px repeat-x; /* Old browsers */ + background: -moz-linear-gradient(top, #b9e0f5 0%, #92bdd6 100%); /* FF3.6+ */ + background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,#b9e0f5), color-stop(100%,#92bdd6)); /* Chrome,Safari4+ */ + background: -webkit-linear-gradient(top, #b9e0f5 0%,#92bdd6 100%); /* Chrome10+,Safari5.1+ */ + background: -o-linear-gradient(top, #b9e0f5 0%,#92bdd6 100%); /* Opera11.10+ */ + background: -ms-linear-gradient(top, #b9e0f5 0%,#92bdd6 100%); /* IE10+ */ + background: linear-gradient(top, #b9e0f5 0%,#92bdd6 100%); /* W3C */ + -webkit-box-shadow: none; + -moz-box-shadow: none; + box-shadow: none; +} +.ncboAutocomplete .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #313131; text-decoration: none; } +.ncboAutocomplete .ui-widget :active { outline: none; } + +/* Icons +----------------------------------*/ + +/* Misc visuals +----------------------------------*/ + +/* + * jQuery UI Autocomplete 1.8.7 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Autocomplete#theming + */ +.ncboAutocomplete .ui-autocomplete { + position: absolute; cursor: default; z-index: 3; + -moz-border-radius: 0; + -webkit-border-radius: 0; + border-radius: 0; + -moz-box-shadow: 0 1px 5px rgba(0,0,0,0.3); + -webkit-box-shadow: 0 1px 5px rgba(0,0,0,0.3); + box-shadow: 0 1px 5px rgba(0,0,0,0.3); +} + +/* workarounds */ +* html .ncboAutocomplete .ui-autocomplete { width:1px; } /* without this, the menu expands to 100% in IE6 */ + +/* + * jQuery UI Menu 1.8.7 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Menu#theming + */ +.ncboAutocomplete .ui-menu { + list-style:none; + padding: 2px; + margin: 0; + display:block; + float: left; +} +.ncboAutocomplete .ui-menu .ui-menu { + margin-top: -3px; +} +.ncboAutocomplete .ui-menu .ui-menu-item { + margin:0; + padding: 0; + zoom: 1; + float: left; + clear: left; + width: 100%; +} +.ncboAutocomplete .ui-menu .ui-menu-item a { + text-decoration:none; + display:block; + padding:.2em .4em; + line-height:1.5; + zoom:1; +} +.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-focus, +.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-hover, +.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-active { + font-weight: normal; + margin: -1px; + background: #5f83b9; + color: #FFFFFF; + text-shadow: 0px 1px 1px #234386; + border-color: #466086; + -moz-border-radius: 0; + -webkit-border-radius: 0; + border-radius: 0; +} diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.min.css b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.min.css new file mode 100644 index 000000000..7323dddfa --- /dev/null +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree.min.css @@ -0,0 +1 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bottom,color-stop(0,#ededed),color-stop(100%,#c4c4c4));background:-webkit-linear-gradient(top,#ededed 0,#c4c4c4 100%);background:-o-linear-gradient(top,#ededed 0,#c4c4c4 100%);background:-ms-linear-gradient(top,#ededed 0,#c4c4c4 100%);background:linear-gradient(top,#ededed 0,#c4c4c4 100%);-webkit-box-shadow:0 1px 0 rgba(255,255,255,0.6) inset;-moz-box-shadow:0 1px 0 rgba(255,255,255,0.6) inset;box-shadow:0 1px 0 rgba(255,255,255,0.6) inset}.ncboAutocomplete .ui-state-default a,.ui-state-default a:link,.ui-state-default a:visited{color:#4f4f4f;text-decoration:none}.ncboAutocomplete .ui-state-hover,.ui-widget-content .ui-state-hover,.ui-widget-header .ui-state-hover,.ui-state-focus,.ui-widget-content .ui-state-focus,.ui-widget-header .ui-state-focus{border:1px solid #9d9d9d;font-weight:normal;color:#313131}.ncboAutocomplete .ui-state-hover a,.ui-state-hover a:hover{color:#313131;text-decoration:none}.ncboAutocomplete .ui-state-active,.ui-widget-content .ui-state-active,.ui-widget-header .ui-state-active{outline:0;color:#1c4257;border:1px solid #7096ab;background:#ededed 0 -50px repeat-x;background:-moz-linear-gradient(top,#b9e0f5 0,#92bdd6 100%);background:-webkit-gradient(linear,left top,left bottom,color-stop(0,#b9e0f5),color-stop(100%,#92bdd6));background:-webkit-linear-gradient(top,#b9e0f5 0,#92bdd6 100%);background:-o-linear-gradient(top,#b9e0f5 0,#92bdd6 100%);background:-ms-linear-gradient(top,#b9e0f5 0,#92bdd6 100%);background:linear-gradient(top,#b9e0f5 0,#92bdd6 100%);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none}.ncboAutocomplete .ui-state-active a,.ui-state-active a:link,.ui-state-active a:visited{color:#313131;text-decoration:none}.ncboAutocomplete .ui-widget :active{outline:0}.ncboAutocomplete .ui-autocomplete{position:absolute;cursor:default;z-index:3;-moz-border-radius:0;-webkit-border-radius:0;border-radius:0;-moz-box-shadow:0 1px 5px rgba(0,0,0,0.3);-webkit-box-shadow:0 1px 5px rgba(0,0,0,0.3);box-shadow:0 1px 5px rgba(0,0,0,0.3)}* html .ncboAutocomplete .ui-autocomplete{width:1px}.ncboAutocomplete .ui-menu{list-style:none;padding:2px;margin:0;display:block;float:left}.ncboAutocomplete .ui-menu .ui-menu{margin-top:-3px}.ncboAutocomplete .ui-menu .ui-menu-item{margin:0;padding:0;zoom:1;float:left;clear:left;width:100%}.ncboAutocomplete .ui-menu .ui-menu-item a{text-decoration:none;display:block;padding:.2em .4em;line-height:1.5;zoom:1}.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-focus,.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-hover,.ncboAutocomplete .ui-menu .ui-menu-item a.ui-state-active{font-weight:normal;margin:-1px;background:#5f83b9;color:#fff;text-shadow:0 1px 1px #234386;border-color:#466086;-moz-border-radius:0;-webkit-border-radius:0;border-radius:0} \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/app.js b/metacatui/src/main/webapp/js/app.js index cffc6e2ef..0c44f205e 100644 --- a/metacatui/src/main/webapp/js/app.js +++ b/metacatui/src/main/webapp/js/app.js @@ -44,6 +44,7 @@ require.config({ nGeohash: '../components/geohash/main', fancybox: '../components/fancybox/jquery.fancybox.pack', //v. 2.1.5 annotator: '../components/annotator/v1.2.10/annotator-full', + bioportal: '../components/bioportal/jquery.ncbo.tree-2.0.2.min', clipboard: '../components/clipboard.min', //Have a null fallback for our d3 components for browsers that don't support SVG d3: d3URL, @@ -67,6 +68,9 @@ require.config({ annotator: { exports: 'Annotator' }, + bioportal: { + exports: 'Bioportal' + }, jws: { exports: 'JWS', deps: ['jsrasign'], diff --git a/metacatui/src/main/webapp/js/templates/appHead.html b/metacatui/src/main/webapp/js/templates/appHead.html index 155cd00d5..5e2d507eb 100644 --- a/metacatui/src/main/webapp/js/templates/appHead.html +++ b/metacatui/src/main/webapp/js/templates/appHead.html @@ -9,6 +9,7 @@ + diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index b083bc136..cde9df9e1 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -2,6 +2,7 @@ define(['jquery', 'jqueryui', 'annotator', + 'bioportal', 'underscore', 'backbone', 'models/AnnotationModel', @@ -11,6 +12,7 @@ define(['jquery', function($, $ui, Annotator, + Bioportal, _, Backbone, AnnotationModel, From 500f953e31bc6d3ef010caa9dab197d707b5c8c1 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Thu, 6 Oct 2016 15:30:04 -0700 Subject: [PATCH 025/560] remove child handling block - too many requests when uncommented. --- .../src/main/webapp/js/models/LookupModel.js | 45 ------------------- 1 file changed, 45 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index ef9596e64..0af329252 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -45,51 +45,6 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], choice.desc = obj['definition'][0]; } - // process the children - just one level - var childrenUrl = obj['links']['children']; - if (false) { - //if (childrenUrl) { - - $.get(childrenUrl + "?apikey=" + appModel.get("bioportalAPIKey"), function(data, textStatus, xhr) { - - _.each(data.collection, function(obj) { - var choice = {}; - choice.label = "--" + obj['prefLabel']; - var synonyms = obj['synonym']; - if (synonyms) { - choice.synonyms = []; - _.each(synonyms, function(synonym) { - choice.synonyms.push(synonym); - }); - } - choice.filterLabel = obj['prefLabel']; - choice.value = obj['@id']; - if (obj['definition']) { - choice.desc = obj['definition'][0]; - } - - // mark items that we know we have matches for - if (allValues) { - var matchingChoice = _.findWhere(allValues, {value: choice.value}); - if (matchingChoice) { - choice.label = "*" + choice.label; - - // remove it from the local value - why have two? - if (localValues) { - localValues = _.reject(localValues, function(obj) { - return obj.value == matchingChoice.value; - }); - } - } - } - - availableTags.push(choice); - - }) - }); - - } - // mark items that we know we have matches for if (allValues) { var matchingChoice = _.findWhere(allValues, {value: choice.value}); From f442ab8a9a3c19f6b2c96a7e6ab714beb229a90d Mon Sep 17 00:00:00 2001 From: leinfelder Date: Thu, 6 Oct 2016 15:59:26 -0700 Subject: [PATCH 026/560] use emphasis instead of asterisk to indicate matched concept. https://github.com/DataONEorg/sem-prov-design/issues/217 --- metacatui/src/main/webapp/css/metacatui-common.css | 3 +++ metacatui/src/main/webapp/js/models/LookupModel.js | 3 ++- metacatui/src/main/webapp/js/views/DataCatalogView.js | 3 +++ 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 44ee3071d..4ad223893 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -25,6 +25,9 @@ .strong{ font-weight: bold; } +.emphasis{ + font-style: italic; +} .large{ font-size: 1.5em; padding: 1em; diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 0af329252..54b603e93 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -49,7 +49,8 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], if (allValues) { var matchingChoice = _.findWhere(allValues, {value: choice.value}); if (matchingChoice) { - choice.label = "*" + choice.label; + //choice.label = "*" + choice.label; + choice.match = true; // remove it from the local value - why have two? if (localValues) { diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 078f166ca..593ce9f9f 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -1468,6 +1468,9 @@ define(['jquery', //Set up the popover var element = this._super( ul, item ); + if (item.match) { + element.addClass("emphasis"); + } element.popover({ placement: "right", trigger: "manual", From fbbd8e0bc3670a5b3b0ade2e743c5e5dff47fd8b Mon Sep 17 00:00:00 2001 From: leinfelder Date: Thu, 6 Oct 2016 16:39:45 -0700 Subject: [PATCH 027/560] rework CSS for the dropdown button for flagging an annotation. https://github.com/DataONEorg/sem-prov-design/issues/209 --- .../src/main/webapp/css/metacatui-common.css | 8 ++------ .../main/webapp/js/templates/annotation.html | 10 +++++++--- .../src/main/webapp/js/views/AnnotatorView.js | 17 ++++++++++------- 3 files changed, 19 insertions(+), 16 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 4ad223893..c3d9ce480 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1301,8 +1301,9 @@ img.icon{ margin-left: 180px; } .annotation-container .add-tag{ + margin-left: 10px; margin-top: 10px; - margin-bottom: 10px; + margin-bottom: 20px; text-shadow: none; } .annotation-attribute-name{ @@ -1334,8 +1335,6 @@ img.icon{ padding: 10px; } .annotation.tag { - padding: .35em .75em; - margin-right: 5px; -webkit-border-radius: 4px; -moz-border-radius: 4px; border-radius: 4px; @@ -1344,11 +1343,8 @@ img.icon{ text-shadow: none; box-shadow: none; text-align: center; - margin-top: 10px; - margin-bottom: 10px; } .annotation-viewer-container .annotation.tag{ - margin-bottom: 10px; display: inline-block; } .annotator-tags, diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index 5491dac86..d5adfd116 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -1,11 +1,13 @@ +
                  + <% if (concept) { %> - <%=concept.label %> - + <% } else if (annotation.tags[0]) { %> @@ -20,12 +22,13 @@ <% } %> -
                  +
                  diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index cde9df9e1..d443e2070 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -471,28 +471,30 @@ define(['jquery', }).trim()); section.prepend(annotationTag); + // this is what we really want to attach to + var target = $(annotationTag).find(".hover-proxy"); + //Attach the annotation object for later - $(annotationTag).data("annotation", annotationModel); + $(target).data("annotation", annotationModel); var view = this; //Create the popover for this element - $(annotationTag).on("mouseover", { view: this }, this.showDetails); + $(target).on("mouseover", { view: this }, this.showDetails); // bind after rendering - var target = $(annotationTag).filter(".hover-proxy"); - target = $(annotationTag).filter(".annotation-flag[data-id='" + annotationModel.get("id") + "']"); + //target = $(annotationTag).find(".annotation-flag[data-id='" + annotationModel.get("id") + "']"); //$(target).bind("click", this.flagAnnotation); - var deleteBtn = $(annotationTag).filter(".annotation-delete"); + var deleteBtn = $(annotationTag).find(".annotation-delete"); $(deleteBtn).tooltip({ trigger: "hover", title: "Delete" }); - $(annotationTag).filter(".tooltip-this").tooltip(); + $(annotationTag).find(".tooltip-this").tooltip(); - target = $(annotationTag).filter(".annotation-delete[data-id='" + annotationModel.get("id") + "']"); + //target = $(annotationTag).find(".annotation-delete[data-id='" + annotationModel.get("id") + "']"); //$(target).bind("click", this.deleteAnnotation); }, @@ -556,6 +558,7 @@ define(['jquery', html: true, title: annotation.get("concept").label, content: annotationPopover, + container: 'body', placement: "top" }).on("mouseenter", function () { var _this = this; From 7fe1aa6a78a84f5b79b91cd4c23b2fff17827eda Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 7 Oct 2016 13:49:48 -0700 Subject: [PATCH 028/560] merge MDQ view into master --- .../src/main/webapp/css/metacatui-common.css | 88 ++++ .../src/main/webapp/js/routers/router.js | 18 + .../src/main/webapp/js/templates/mdqRun.html | 390 ++++++++++++++++++ .../main/webapp/js/templates/mdqSuites.html | 12 + .../js/themes/default/css/metacatui.css | 1 - .../main/webapp/js/views/DonutChartView.js | 55 ++- .../src/main/webapp/js/views/MdqRunView.js | 293 +++++++++++++ 7 files changed, 853 insertions(+), 4 deletions(-) create mode 100644 metacatui/src/main/webapp/js/templates/mdqRun.html create mode 100644 metacatui/src/main/webapp/js/templates/mdqSuites.html create mode 100644 metacatui/src/main/webapp/js/views/MdqRunView.js diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index c3d9ce480..5aa39c74b 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -784,6 +784,94 @@ img.icon{ width: calc(100% - 214px); } +/* MDQ */ + +#mdqResult .alert [data-toggle="collapse"]:after +{ + /*content: "\e072"; "play" icon */ + content: "-"; + float: right; + color: #b0c5d8; + font-size: 18px; + line-height: 22px; +} +#mdqResult .alert [data-toggle="collapse"].collapsed:after +{ + content: "+"; +} + +.mdq .popover { + max-width: 50%; +} + +#mdqResult .progress { + margin-bottom: 10px; + margin-top: 0px; +} + +#mdqResult .progress-bar-success { + opacity: 0.50; +} + +#mdqTypeSummary { + float: right; + width: 75%; +} + +#mdqResult #data-chart { + height: 220px; + width: 250px; + margin:0px; +} + +#mdqResult .panel-heading { + overflow: auto; +} + +/* different colors for each pie slice */ +#mdqResult .donut.data > g:nth-child(1) .donut-arc { + fill: #dff0d8; +} +#mdqResult .donut.data > g:nth-child(1) .donut-arc-label, +#mdqResult .donut.data > g:nth-child(1) .donut-arc.active { + fill: #468847; +} + +#mdqResult .donut.data > g:nth-child(2) .donut-arc { + fill: #fcf8e3; +} +#mdqResult .donut.data > g:nth-child(2) .donut-arc-label, +#mdqResult .donut.data > g:nth-child(2) .donut-arc.active { + fill: #c09853; +} + +#mdqResult .donut.data > g:nth-child(3) .donut-arc { + fill: #f2dede; +} +#mdqResult .donut.data > g:nth-child(3) .donut-arc-label, +#mdqResult .donut.data > g:nth-child(3) .donut-arc.active { + fill: #b94a48; +} + +#mdqResult .donut.data > g:nth-child(4) .donut-arc { + fill: #d9edf7; +} +#mdqResult .donut.data > g:nth-child(4) .donut-arc-label, +#mdqResult .donut.data > g:nth-child(4) .donut-arc.active { + fill: #3a87ad; +} + +#mdqResult .donut-labels{ + opacity: 0.0; +} + +#mdqResult .donut-arc.active + .donut-labels, +#mdqResult .donut-arc.active + .donut-labels .donut-arc-count.rotated{ + opacity: 1; + font-weight: bold; +} + + /* Prov chart popovers */ .prov-chart .popover{ min-width: 300px; diff --git a/metacatui/src/main/webapp/js/routers/router.js b/metacatui/src/main/webapp/js/routers/router.js index 63b594d41..93f8df59b 100644 --- a/metacatui/src/main/webapp/js/routers/router.js +++ b/metacatui/src/main/webapp/js/routers/router.js @@ -25,6 +25,7 @@ function ($, _, Backbone) { 'signup' : 'renderLdap', // use ldapweb for registration 'account(/:stage)' : 'renderLdap', // use ldapweb for different stages 'share(/:stage/*pid)' : 'renderRegistry', // registry page + 'mdq(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'api(/:anchorId)' : 'renderAPI' // API page }, @@ -131,6 +132,23 @@ function ($, _, Backbone) { this.renderText(options); }, + renderMdqRun: function (suiteId, pid) { + this.routeHistory.push("mdq"); + + if (!appView.mdqRunView) { + require(["views/MdqRunView"], function(MdqRunView) { + appView.mdqRunView = new MdqRunView(); + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + }); + } else { + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + } + }, + renderTools: function (anchorId) { this.routeHistory.push("tools"); appModel.set('anchorId', anchorId); diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html new file mode 100644 index 000000000..ac4d82501 --- /dev/null +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -0,0 +1,390 @@ +<% if (typeof objectIdentifier === 'undefined') { %> + +
                  +
                  +

                  Upload Metadata document for QC

                  +
                  +
                  +
                  + + +
                  +
                  +
                  + +<% } %> + +
                  + +<% if (typeof result !== 'undefined') { %> + +
                  +
                  + +
                  +

                  Metadata Quality report for <%= objectIdentifier %>

                  + + +

                  + After running your metadata package against our standard set of metadata, data, and congruency checks, + we have found the following potential issues. + Please assist us in improving the discoverability and reusability of your research data by addressing the issues below. +

                  +
                  + +
                  + +
                  + +
                  + + <% + var types = _.keys(groupedByType); + _.each(types, function(type) { + var results = groupedByType[type]; + var total = results.length; + var success = 0; + _.each(results, function(result) { + if (result.status == "SUCCESS") { + success++; + } + }); + var width = (success/total) * 100; + width = width.toFixed(0); + + %> + <%=type%>: <%=width%>% complete +
                  +
                  + +
                  +
                  + <% + + }); + + %> + +
                  + +
                  +
                  + <% + + var total = result.length; + if (groupedResults.BLUE) { + total = total - groupedResults.BLUE.length; + } + + %> + + <% if (groupedResults.GREEN) { %> + + + +
                  +
                    + + <% + _.each(groupedResults.GREEN, function(result) { + %> + +
                  • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> +
                    + + <%= result.check.name %> + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> +
                    + <%= result.check.description %> + + + + + + + + + + + +
                    • + <% + }); + %> + +
                  +
                  + + <% } %> + + + + <% if (groupedResults.ORANGE) { %> + + + +
                  +
                    + + <% + _.each(groupedResults.ORANGE, function(result) { + %> + +
                  • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> +
                    + + <%= result.check.name %> + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> +
                    + <%= result.check.description %> + + + + + + + + + + + +
                    • + <% + }); + %> + +
                  +
                  + + <% } %> + + <% if (groupedResults.RED) { %> + + + +
                  +
                    + + <% + _.each(groupedResults.RED, function(result) { + %> + +
                  • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> +
                    + + <%= result.check.name %> + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> +
                    + <%= result.check.description %> + + + + + + + + + + + +
                    • + <% + }); + %> + +
                  +
                  + + <% } %> + + <% if (groupedResults.BLUE) { %> + + +
                  +
                    + + + <% + _.each(groupedResults.BLUE, function(result) { + %> +
                  • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> +
                    + + <%= result.check.name %> + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> +
                    + <%= result.check.description %> + + + + + + + + + +
                    • + <% + }); + %> + +
                  +
                  + + <% } %> + + +
                  + +
                  + +<% } %> +
                  \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/templates/mdqSuites.html b/metacatui/src/main/webapp/js/templates/mdqSuites.html new file mode 100644 index 000000000..80aeddffc --- /dev/null +++ b/metacatui/src/main/webapp/js/templates/mdqSuites.html @@ -0,0 +1,12 @@ +

                  +Suite: + +

                  \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css index 4c7c45fcd..f4b0166fe 100644 --- a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css @@ -1800,7 +1800,6 @@ svg .default{ width: 100%; } - .donut-title-count{ font-size: 24px; } diff --git a/metacatui/src/main/webapp/js/views/DonutChartView.js b/metacatui/src/main/webapp/js/views/DonutChartView.js index 061f47fe8..217549685 100644 --- a/metacatui/src/main/webapp/js/views/DonutChartView.js +++ b/metacatui/src/main/webapp/js/views/DonutChartView.js @@ -34,6 +34,7 @@ define(['jquery', 'underscore', 'backbone', 'd3'], this.total = options.total || 0; this.formatLabel=options.formatLabel || function(d){ return d } this.data = this.formatDonutData(options.data, options.total) || [{label: "", count: 0, perc: 0}]; + this.keepOrder = options.keepOrder || false; this.drawLabels = (this.data) }, @@ -86,10 +87,22 @@ define(['jquery', 'underscore', 'backbone', 'd3'], * Draw the arcs * ======================================================================== */ - + + // sort or not + var theData = donut.value( + function(d) { + return d.perc + }); + if (this.keepOrder) { + theData = donut.value( + function(d) { + return d.perc + }).sort(null); + } //Set up a group for each arc we will create - var arcs = vis.selectAll("g.arc") - .data(donut.value(function(d) { return d.perc })) //connect data to this group + var arcs = + vis.selectAll("g.arc") + .data(theData) //connect data to this group .enter().append("svg:g") .attr("class", "donut-arc-group") .attr("transform", @@ -339,6 +352,42 @@ define(['jquery', 'underscore', 'backbone', 'd3'], return counts; } + //Check if the data is preformatted + if((typeof counts[0] == "object") && (typeof counts[0].label != "undefined") && (typeof counts[0].count != "undefined")){ + //If there are no percentages in the formatted data, find the total and set the percentage of each arc + if(typeof counts[0].perc == "undefined"){ + var countNums = _.pluck(counts, "count"); + var sum = 0; + _.each(counts, function(c){ + sum += c.count; + }); + + _.each(counts, function(thisCount){ + thisCount.perc = thisCount.count/sum; + }); + } + + return counts; + } + + //Check if the data is preformatted + if((typeof counts[0] == "object") && (typeof counts[0].label != "undefined") && (typeof counts[0].count != "undefined")){ + //If there are no percentages in the formatted data, find the total and set the percentage of each arc + if(typeof counts[0].perc == "undefined"){ + var countNums = _.pluck(counts, "count"); + var sum = 0; + _.each(counts, function(c){ + sum += c.count; + }); + + _.each(counts, function(thisCount){ + thisCount.perc = thisCount.count/sum; + }); + } + + return counts; + } + var newArray = []; var otherPercent = 0; var otherCount = 0; diff --git a/metacatui/src/main/webapp/js/views/MdqRunView.js b/metacatui/src/main/webapp/js/views/MdqRunView.js new file mode 100644 index 000000000..f6f9d0c53 --- /dev/null +++ b/metacatui/src/main/webapp/js/views/MdqRunView.js @@ -0,0 +1,293 @@ +/*global define */ +define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/mdqRun.html', 'text!templates/mdqSuites.html', 'text!templates/loading.html'], + function($, _, Backbone, d3, DonutChart, MdqRunTemplate, SuitesTemplate, LoadingTemplate) { + 'use strict'; + + // Build the Footer view of the application + var MdqRunView = Backbone.View.extend({ + + el: '#Content', + + events: { + "click input[type='submit']" : "submitForm", + "change #suiteId" : "switchSuite" + }, + + suitesUrl: "/mdq-webapp/webapi/suites/", + + url: null, + + pid: null, + + suiteId: null, + + loadingTemplate: _.template(LoadingTemplate), + + template: _.template(MdqRunTemplate), + + suitesTemplate: _.template(SuitesTemplate), + + + initialize: function () { + + }, + + switchSuite: function(event) { + console.log("Switching Suite"); + + var select = $(event.target); + + var suiteId = $(select).val(); + + uiRouter.navigate("mdq/s=" + suiteId + "/" + this.pid, {trigger: true}); + + return false; + }, + + render: function () { + + // use the requested suite if provided + if (!this.suiteId) { + this.suiteId = "arctic.data.center.suite.1"; + } + this.url = this.suitesUrl + this.suiteId + "/run"; + + var viewRef = this; + + if (this.pid) { + + this.showLoading(); + + // fetch the metadata contents by the pid + var xhr = new XMLHttpRequest(); + xhr.onreadystatechange = function(){ + if (this.readyState == 4 && this.status == 200){ + //this.response is what you're looking for + //handler(this.response); + console.log(this.response, typeof this.response); + var documentBlob = this.response; + // send to MDQ as blob + var formData = new FormData(); + formData.append('document', documentBlob); + console.log("Submitting Blob to MDQ"); + viewRef.showResults(formData); + } + } + var url = appModel.get("objectServiceUrl") + this.pid; + xhr.open('GET', url); + xhr.responseType = 'blob'; + xhr.withCredentials = true; + xhr.setRequestHeader("Authorization", "Bearer " + appUserModel.get("token")); + xhr.send(); + + } else { + this.$el.html(this.template({})); + } + + }, + + showLoading: function() { + this.$el.html(this.loadingTemplate()); + }, + + show: function() { + var view = this; + this.$el.hide(); + this.$el.fadeIn({duration: "slow"}); + }, + + // lookup the suites we can run + showAvailableSuites: function() { + var viewRef = this; + + try { + var args = { + url: this.suitesUrl, + type: 'GET', + success: function(data, textStatus, xhr) { + viewRef.$el.find('#suites').append( + viewRef.suitesTemplate( + { + suiteId: viewRef.suiteId, + suiteIds: data + })); + //Initialize all popover elements + //$('.popover-this').popover(); + } + }; + $.ajax(args); + } catch (error) { + console.log(error.stack); + } + }, + + submitForm: function(event) { + console.log("Submitting form to MDQ"); + + var form = $(event.target).parents("form"); + + var formData = new FormData($(form)[0]); + + this.showResults(formData); + + return false; + + }, + + // do the work of sending the data and rendering the results + showResults: function(formData) { + var viewRef = this; + + try { + var args = { + url: this.url, + cache: false, + data: formData, + contentType: false, //"multipart/form-data", + processData: false, + type: 'POST', + success: function(data, textStatus, xhr) { + var groupedResults = viewRef.groupResults(data.result); + var groupedByType = viewRef.groupByType(data.result); + + data = _.extend(data, + { + objectIdentifier: viewRef.pid, + suiteId: viewRef.suiteId, + groupedResults: groupedResults, + groupedByType: groupedByType + }); + + viewRef.$el.html(viewRef.template(data)); + viewRef.drawScoreChart(data.result, groupedResults); + viewRef.showAvailableSuites(); + viewRef.show(); + //Initialize all popover elements + $('.popover-this').popover(); + } + }; + $.ajax(args); + } catch (error) { + console.log(error.stack); + } + }, + + groupResults: function(results) { + var groupedResults = _.groupBy(results, function(result) { + var color; + + // simple cases + // always blue for info and skip + if (result.check.level == 'INFO') { + color = 'BLUE'; + return color; + } + if (result.status == 'SKIP') { + color = 'BLUE'; + return color; + } + // always green for success + if (result.status == 'SUCCESS') { + color = 'GREEN'; + return color; + } + + // handle failures and warnings + if (result.status == 'FAILURE') { + color = 'RED'; + if (result.check.level == 'OPTIONAL') { + color = 'ORANGE'; + } + } + if (result.status == 'ERROR') { + color = 'ORANGE'; + if (result.check.level == 'REQUIRED') { + color = 'RED'; + } + } + //console.log("result color:" + color); + return color; + + }); + + // make sure we have everything, even if empty + if (!groupedResults.BLUE) { + groupedResults.BLUE = []; + } + if (!groupedResults.GREEN) { + groupedResults.GREEN = []; + } + if (!groupedResults.ORANGE) { + groupedResults.ORANGE = []; + } + if (!groupedResults.RED) { + groupedResults.RED = []; + } + + var total = results.length; + if (groupedResults.BLUE) { + total = total - groupedResults.BLUE.length; + } + + return groupedResults; + }, + + groupByType: function(results) { + var groupedResults = _.groupBy(results, function(result) { + return result.check.type || "uncategorized"; + }); + + return groupedResults; + }, + + drawScoreChart: function(results, groupedResults){ + + var dataCount = results.length; + + + var data = [ + {label: "Pass", count: groupedResults.GREEN.length, perc: groupedResults.GREEN.length/results.length }, + {label: "Warn", count: groupedResults.ORANGE.length, perc: groupedResults.ORANGE.length/results.length}, + {label: "Fail", count: groupedResults.RED.length, perc: groupedResults.RED.length/results.length}, + {label: "Info", count: groupedResults.BLUE.length, perc: groupedResults.BLUE.length/results.length}, + ]; + /* + var data = [ + "Pass", groupedResults.GREEN.length, + "Warning", groupedResults.ORANGE.length, + "Fail", groupedResults.RED.length, + "Info", groupedResults.BLUE.length, + ]; + */ + + var svgClass = "data"; + + //If d3 isn't supported in this browser or didn't load correctly, insert a text title instead + if(!d3){ + this.$('.format-charts-data').html("

                  " + appView.commaSeparateNumber(dataCount) + " data files

                  "); + + return; + } + + //Draw a donut chart + var donut = new DonutChart({ + id: "data-chart", + data: data, + total: dataCount, + titleText: "checks", + titleCount: dataCount, + svgClass: svgClass, + countClass: "data", + height: 250, + width: 250, + keepOrder: true, + formatLabel: function(name) { + return name; + } + }); + this.$('.format-charts-data').html(donut.render().el); + } + + }); + return MdqRunView; +}); From a4a8e140a965ec9888481b7a53b040fd23039b25 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 7 Oct 2016 14:06:37 -0700 Subject: [PATCH 029/560] add MDQ link from main metadata view --- .../src/main/webapp/js/templates/metadataControls.html | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/metadataControls.html b/metacatui/src/main/webapp/js/templates/metadataControls.html index f4a491fbb..568f907ef 100644 --- a/metacatui/src/main/webapp/js/templates/metadataControls.html +++ b/metacatui/src/main/webapp/js/templates/metadataControls.html @@ -1,6 +1,9 @@
                  - Copy Citation - + + Copy Citation + + + Quality report <% if(!model.isPublic){ %>
                  From 196692edfeb5aa52d9b0927acdc770769ed3c403 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Mon, 10 Oct 2016 11:55:19 -0700 Subject: [PATCH 030/560] Search for data-pid, not data-id, when searching for an entity details container element. --- metacatui/src/main/webapp/js/views/MetadataView.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/views/MetadataView.js b/metacatui/src/main/webapp/js/views/MetadataView.js index 261ff83dc..fd0ef927a 100644 --- a/metacatui/src/main/webapp/js/views/MetadataView.js +++ b/metacatui/src/main/webapp/js/views/MetadataView.js @@ -1078,7 +1078,7 @@ define(['jquery', } //Metacat 2.4.2 and up will have the Online Distribution Link marked - var link = this.$(".entitydetails a[data-id='" + id + "']"); + var link = this.$(".entitydetails a[data-pid='" + id + "']"); //Otherwise, try looking for an anchor with the id matching this object's id if(!link.length) From b98b86180030753bac854536f82f8fd002d051f9 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Mon, 10 Oct 2016 14:54:42 -0700 Subject: [PATCH 031/560] use synchronous call to expand given term. https://github.com/DataONEorg/sem-prov-design/issues/214 --- .../src/main/webapp/js/models/LookupModel.js | 30 +++++++++++++------ 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/LookupModel.js b/metacatui/src/main/webapp/js/models/LookupModel.js index 54b603e93..e9ec6265b 100644 --- a/metacatui/src/main/webapp/js/models/LookupModel.js +++ b/metacatui/src/main/webapp/js/models/LookupModel.js @@ -76,7 +76,7 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], }); }, - bioportalExpand: function(term, response) { + bioportalExpand: function(term) { // make sure we have something to lookup if (!appModel.get('bioportalSearchUrl')) { @@ -85,9 +85,15 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], } var terms = []; + var countdown = 0; var query = appModel.get('bioportalSearchUrl') + term; - $.get(query, function(data, textStatus, xhr) { + $.ajax( + { + url: query, + method: "GET", + async: false, // we want to wait for the response! + success: function(data, textStatus, xhr) { _.each(data.collection, function(obj) { // use the preferred label @@ -104,9 +110,16 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], // process the descendants var descendantsUrl = obj['links']['descendants']; //if (false) { - if (descendantsUrl) { + if (descendantsUrl && countdown > 0) { + + countdown--; - $.get(childrenUrl + "?apikey=" + appModel.get("bioportalAPIKey"), function(data, textStatus, xhr) { + $.ajax( + { + url: descendantsUrl + "?apikey=" + appModel.get("bioportalAPIKey"), + method: "GET", + async: false, + success: function(data, textStatus, xhr) { _.each(data.collection, function(obj) { var prefLabel = obj['prefLabel']; var synonyms = obj['synonym']; @@ -116,14 +129,13 @@ define(['jquery', 'jqueryui', 'underscore', 'backbone'], }); } }); - - // callback - response(terms); - }); + } + }); } }); - + } }); + return terms; }, bioportalGetConcepts: function(uri, callback) { From b82fbaeb9b22ffad17e9ba1c2181784ae638f271 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Mon, 10 Oct 2016 14:56:02 -0700 Subject: [PATCH 032/560] expand attribute text term using synonyms and close matches from bioportal. https://github.com/DataONEorg/sem-prov-design/issues/214 --- .../main/webapp/js/themes/dataone/models/Search.js | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js index a9210108d..3a20a407f 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/Search.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/Search.js @@ -219,7 +219,7 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], getQuery: function(filter){ //----All other filters with a basic name:value pair pattern---- - var otherFilters = ["attribute", "formatType", "rightsHolder", "submitter"]; + var otherFilters = ["formatType", "rightsHolder", "submitter"]; if(this.filterIsAvailable("test_corpus_sm")) otherFilters.push("test_corpus_sm"); @@ -261,6 +261,15 @@ define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], }); } + //---expand attribute using ontology --- + if(this.filterIsAvailable("attribute") && ((filter == "attribute") || getAll) && this.get("attribute").length){ + var attribute = this.get('attribute'); + if (attribute) { + var expandedAttributes = appLookupModel.bioportalExpand(attribute[0].value); + query += "+" + this.getGroupedQuery(this.fieldNameMap["attribute"], expandedAttributes, {operator: "OR"}); + } + } + //---Identifier--- if(this.filterIsAvailable("id") && ((filter == "id") || getAll) && this.get("id").length){ var identifiers = this.get('id'); From 2c8f1a286ef2833840646d9c6e44e26820ca8054 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 11 Oct 2016 12:12:13 -0700 Subject: [PATCH 033/560] enable search link to see results for the same measurement concept. https://github.com/DataONEorg/sem-prov-design/issues/215 --- .../main/webapp/js/templates/annotation.html | 11 +++++- .../src/main/webapp/js/views/AnnotatorView.js | 35 +++++++++++++++++++ 2 files changed, 45 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index d5adfd116..3e90db6cb 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -27,7 +27,16 @@
                    -
                  • Find similar packages
                    • +
                  • + Find similar packages +
                    • <% if (canEdit && !annotation.reject) { diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index d443e2070..2793425f4 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -38,6 +38,7 @@ define(['jquery', events: { "click .add-tag" : "launchEditor", "click .annotation-flag" : "flagAnnotation", + "click .annotation-similar" : "similarAnnotation", "click .annotation-delete" : "deleteAnnotation" }, @@ -499,6 +500,40 @@ define(['jquery', }, + similarAnnotation : function(e) { + + //Get the button + var btn = e.target; + if(!$(btn).is(".annotation-similar")){ + btn = $(btn).parents(".annotation-similar"); + } + + //Get the annotation id + var uri = $(btn).attr("data-concept-uri"); + var label = $(btn).attr("data-concept-label"); + var description = $(btn).attr("data-concept-description"); + + // Clear the search and map model to start a fresh search + appSearchModel.clear(); + appSearchModel.set(appSearchModel.defaults); + mapModel.clear(); + mapModel.set(mapModel.defaults); + + // construct the filter + var filter = { + value: uri, + filterLabel: label, + label: label, + description: description + }; + + // set the search model + appSearchModel.set("annotation", [filter]); + + // navigate to search results + uiRouter.navigate('data', {trigger: true}); + }, + flagAnnotation : function(e) { //Get the flag button From abc7c6273359fb261e10e2a85b47f38a7273da96 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 11 Oct 2016 15:27:33 -0700 Subject: [PATCH 034/560] enable tree-based drill down. https://github.com/DataONEorg/sem-prov-design/issues/216 --- .../src/main/webapp/css/metacatui-common.css | 15 ++++ .../main/webapp/js/templates/annotation.html | 18 ++++- .../src/main/webapp/js/views/AnnotatorView.js | 79 ++++++++++++++++++- 3 files changed, 107 insertions(+), 5 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 5aa39c74b..63b959770 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1530,6 +1530,21 @@ img.icon{ background-color: #999; color: #DDD; } + +/** Hide the search when in the dropdown menu **/ +.dropdown-menu .ncboAutocomplete { + display: none; +} + +/** hide the tree until we have it where we want it **/ +#bioportal-tree { + display: none; +} +.dropdown-menu #bioportal-tree { + display: block; +} + + /****************************************** * Images, Maps, and Media ********************************************/ diff --git a/metacatui/src/main/webapp/js/templates/annotation.html b/metacatui/src/main/webapp/js/templates/annotation.html index 3e90db6cb..7c87b15b7 100644 --- a/metacatui/src/main/webapp/js/templates/annotation.html +++ b/metacatui/src/main/webapp/js/templates/annotation.html @@ -1,4 +1,4 @@ -
                    +
                    <% if (concept) { %> @@ -23,7 +23,7 @@ } %> -
                    +
                    +
                    +
                    diff --git a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css index ba69c51fc..939387e23 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css @@ -445,10 +445,10 @@ i.glyphicons-icon.white { .icon-circle-badge{ background-color: #1C6E84; } -.annotator-widget::after, +/*.annotator-widget::after, .annotator-widget a::after{ background-image: url('../img/annotator-icons.png'); -} +}*/ /* TABLES diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index 3a2b5138e..eb03cbffb 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -381,7 +381,7 @@ define(['jquery', $(view.$el.data('annotator').plugins.Tags.input).val(classId); // make it pretty - $("#bioportal-tree-label").html("" + prefLabel + ""); + $("#bioportal-tree-label").html("" + prefLabel + ""); // prevent default action return false; diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index f7f90a9ed..a37551e22 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -268,6 +268,14 @@ define(['jquery', startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType" }); + $("[data-category='annotation'] .expand-collapse-control").popover({ + html: true, + placement: "bottom", + trigger:"click", + content: tree, + container: "#bioportal-popover" + }); + // set up the listener to jump to search results tree.on("afterSelect", this.selectConcept); tree.on("afterJumpToClass", this.afterJumpToClass); From 4a5f59c6b3dda47a2f68830478fad91cb272a776 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 14 Oct 2016 14:05:19 -0700 Subject: [PATCH 051/560] add data-category attribute to tree popover container so event correctly triggers search --- metacatui/src/main/webapp/js/templates/search.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/templates/search.html b/metacatui/src/main/webapp/js/templates/search.html index 5169d2167..4e41123fa 100644 --- a/metacatui/src/main/webapp/js/templates/search.html +++ b/metacatui/src/main/webapp/js/templates/search.html @@ -214,7 +214,7 @@
                    Filter by:
                    -
                    +
                    From 15de61ff3d11dda6625a9f1b3a1ce29829f44b49 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 14 Oct 2016 14:06:03 -0700 Subject: [PATCH 052/560] triggger mouseout so as not to have residual tooltip hover --- metacatui/src/main/webapp/js/views/DataCatalogView.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index a37551e22..56a108468 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -303,6 +303,9 @@ define(['jquery', var view = $("#Content").data("data-catalog-view"); view.updateTextFilters(event, item); + // hide the hover + $(selectedNode).trigger("mouseout"); + // reset the tree for next search var tree = $("#bioportal-tree").data("NCBOTree"); var options = tree.options(); From 171ab41453c507361f800e2ee0d42ee25d41b976 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Mon, 17 Oct 2016 14:17:01 -0700 Subject: [PATCH 053/560] only show MDQ button when the appModel is configured for it. --- metacatui/src/main/webapp/js/models/AppModel.js | 4 +++- metacatui/src/main/webapp/js/templates/metadataControls.html | 4 +++- metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js | 4 +++- .../src/main/webapp/js/themes/dataone/models/AppModel.js | 4 +++- metacatui/src/main/webapp/js/views/MdqRunView.js | 2 +- metacatui/src/main/webapp/js/views/MetadataView.js | 1 + 6 files changed, 14 insertions(+), 5 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/AppModel.js b/metacatui/src/main/webapp/js/models/AppModel.js index 0dc158cbe..e9c162c17 100644 --- a/metacatui/src/main/webapp/js/models/AppModel.js +++ b/metacatui/src/main/webapp/js/models/AppModel.js @@ -66,7 +66,9 @@ define(['jquery', 'underscore', 'backbone'], //accountsMapsUrl: null, groupsUrl: null, prov: true, - useSeriesId: true + useSeriesId: true, + mdqUrl: null //"/mdq-webapp/webapi/" + }, defaultView: "data", diff --git a/metacatui/src/main/webapp/js/templates/metadataControls.html b/metacatui/src/main/webapp/js/templates/metadataControls.html index 568f907ef..da70d72e9 100644 --- a/metacatui/src/main/webapp/js/templates/metadataControls.html +++ b/metacatui/src/main/webapp/js/templates/metadataControls.html @@ -3,7 +3,9 @@ Copy Citation - Quality report + <% if (mdqUrl){ %> + Quality report + <% } %> <% if(!model.isPublic){ %>
                    diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js index 7bca02520..9af2d1fb6 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js @@ -71,7 +71,9 @@ define(['jquery', 'underscore', 'backbone'], tokenUrl: null, checkTokenUrl: null, prov: true, - useSeriesId: true + useSeriesId: true, + mdqUrl: "/mdq-webapp/webapi/" + }, defaultView: "data", diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index f2229d7b3..18703404d 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -75,7 +75,9 @@ define(['jquery', 'underscore', 'backbone'], checkTokenUrl: null, annotatorUrl: null, prov: true, - useSeriesId: true + useSeriesId: true, + mdqUrl: "/mdq-webapp/webapi/" + }, defaultView: "data", diff --git a/metacatui/src/main/webapp/js/views/MdqRunView.js b/metacatui/src/main/webapp/js/views/MdqRunView.js index f6f9d0c53..c595b7078 100644 --- a/metacatui/src/main/webapp/js/views/MdqRunView.js +++ b/metacatui/src/main/webapp/js/views/MdqRunView.js @@ -13,7 +13,7 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/ "change #suiteId" : "switchSuite" }, - suitesUrl: "/mdq-webapp/webapi/suites/", + suitesUrl: appModel.get("mdqUrl") + "suites/", url: null, diff --git a/metacatui/src/main/webapp/js/views/MetadataView.js b/metacatui/src/main/webapp/js/views/MetadataView.js index 61fc0eed1..d9a006a83 100644 --- a/metacatui/src/main/webapp/js/views/MetadataView.js +++ b/metacatui/src/main/webapp/js/views/MetadataView.js @@ -784,6 +784,7 @@ define(['jquery', var controlsContainer = this.controlsTemplate({ citation: $(this.citationContainer).text(), url: window.location, + mdqUrl: appModel.get("mdqUrl"), model: this.model.toJSON() }); From 2ac55a639103f2752c3634a86cfdd5030aa58b31 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Mon, 17 Oct 2016 16:40:29 -0700 Subject: [PATCH 054/560] Added annotation data-category attribute in search template --- metacatui/src/main/webapp/js/templates/search.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/templates/search.html b/metacatui/src/main/webapp/js/templates/search.html index 5169d2167..4e41123fa 100644 --- a/metacatui/src/main/webapp/js/templates/search.html +++ b/metacatui/src/main/webapp/js/templates/search.html @@ -214,7 +214,7 @@
                    Filter by:
                    -
                    +
                    From 8d745cb3114022428bc643c706c9dc6ffa230466 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 18 Oct 2016 11:53:11 -0700 Subject: [PATCH 055/560] include MDQ in arcic router theme --- .../webapp/js/themes/arctic/routers/router.js | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js index 17f63f345..a34885f4f 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js @@ -18,6 +18,7 @@ function ($, _, Backbone) { 'signin' : 'renderTokenSignIn', "signinsuccess" : "renderSignInSuccess", 'share(/:stage/*pid)' : 'renderRegistry', // registry page + 'mdq(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'api(/:anchorId)' : 'renderAPI' // API page }, @@ -249,6 +250,23 @@ function ($, _, Backbone) { } }, + renderMdqRun: function (suiteId, pid) { + this.routeHistory.push("mdq"); + + if (!appView.mdqRunView) { + require(["views/MdqRunView"], function(MdqRunView) { + appView.mdqRunView = new MdqRunView(); + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + }); + } else { + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + } + }, + logout: function (param) { //Clear our browsing history when we log out this.routeHistory.length = 0; From f90ca15af1ecf084d592a5eb460eda0cb260a41a Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 18 Oct 2016 12:02:45 -0700 Subject: [PATCH 056/560] default arctic theme to use MDQ engine on mn-demo-8 for now --- metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js index 9af2d1fb6..311b69db7 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js @@ -72,7 +72,7 @@ define(['jquery', 'underscore', 'backbone'], checkTokenUrl: null, prov: true, useSeriesId: true, - mdqUrl: "/mdq-webapp/webapi/" + mdqUrl: "https://mn-demo-8.test.dataone.org/mdq-webapp/webapi/" }, From 835c1b6f823ea11125e371bd9ed67bdc2c118191 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Tue, 18 Oct 2016 12:04:27 -0700 Subject: [PATCH 057/560] slighty reduce width of mdq summary to better fit in arctic theme --- metacatui/src/main/webapp/css/metacatui-common.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 96936193b..5544f5b5d 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -815,7 +815,7 @@ img.icon{ #mdqTypeSummary { float: right; - width: 75%; + width: 70%; } #mdqResult #data-chart { From 17b2efcb9dce6fa8e85f9c71ecdd3c870ef33d9c Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 12:40:02 -0700 Subject: [PATCH 058/560] scroll to concept in tree after "jumping" to it from the look-ahead --- .../src/main/webapp/js/views/AnnotatorView.js | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index eb03cbffb..632933b15 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -312,7 +312,9 @@ define(['jquery', startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType" }); - tree.on("afterSelect", view.selectConcept); + tree.on("afterSelect", view.selectConcept); + tree.on("afterJumpToClass", view.jumpToClass); + //alert('Augmented annotation with additional properties, annotation: ' + annotation); } @@ -388,6 +390,18 @@ define(['jquery', }, + jumpToClass : function(event, classId) { + + // set in the editor + // scroll to selected part + var node = $("#bioportal-tree-annotator").find("a[data-id='" + encodeURIComponent(classId) + "']"); + var position = $(node).position().top - 200; + + // scroll to selected part + $("#bioportal-tree-annotator").scrollTop(position) + + }, + preRenderAnnotations : function(annotations) { var uris = []; From 25542da4e6bf7aa18cb3b8a1993337824d5879d7 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 13:33:56 -0700 Subject: [PATCH 059/560] show placeholder tooltip in cases where we do not get a definition from BP - this is helpful for debugging whether it is BP tree or our tooltip-this not being initialized correctly. --- .../components/bioportal/jquery.ncbo.tree-2.0.2.js | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js index 6eed0e2f9..69ec7b4cd 100644 --- a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js @@ -142,13 +142,15 @@ var li = $("
                  • "); var a = $("").attr("href", determineHTTPS(node.links.self)).html(node.prefLabel); a.attr("data-id", encodeURIComponent(node["@id"])); + var def = "No definition provided."; if (node["definition"]) { - a.attr("data-title", node["definition"][0]); - a.attr("data-placement", "right"); - a.attr("data-trigger", "hover"); - a.attr("data-container", "body"); - a.addClass("tooltip-this"); + def = node["definition"][0]; } + a.attr("data-title", def); + a.attr("data-placement", "right"); + a.attr("data-trigger", "hover"); + a.attr("data-container", "body"); + a.addClass("tooltip-this"); ul.append(li.append(a)); From e8403bf33b161b95f35160591fdd17358dd55f22 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 13:38:06 -0700 Subject: [PATCH 060/560] re-root the tree after selecting a concept from the look-ahead. also reset the tree to Measurement Type after canceling the "add annotation" dialog so we can get back to all MT concepts. --- .../src/main/webapp/js/views/AnnotatorView.js | 42 +++++++++++++++---- 1 file changed, 34 insertions(+), 8 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index 632933b15..883fc9da6 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -275,6 +275,21 @@ define(['jquery', var view = this; + this.$el.annotator('subscribe', 'annotationEditorShown', function() { + // reroot tree at starting class + var tree = $("#bioportal-tree-annotator").data("NCBOTree"); + if (tree) { + var options = tree.options(); + $.extend(options, {startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType"}); + tree.init(); + } + // clear any values that are lingering + var view = $('#metadata-container').data("annotator-view"); + $(view.$el.data('annotator').plugins.Tags.input).val(""); + $("#bioportal-tree-label").html(""); + + }); + // subscribe to annotation events, to get the exact resource being annotated this.$el.annotator('subscribe', 'beforeAnnotationCreated', function(annotation, arg0, arg1) { var annotator = view.$el.data('annotator'); @@ -313,7 +328,9 @@ define(['jquery', }); tree.on("afterSelect", view.selectConcept); - tree.on("afterJumpToClass", view.jumpToClass); + tree.on("afterJumpToClass", view.jumpToClass); + tree.on("afterExpand", view.afterExpand); // for the tool tips + //alert('Augmented annotation with additional properties, annotation: ' + annotation); @@ -392,14 +409,23 @@ define(['jquery', jumpToClass : function(event, classId) { - // set in the editor - // scroll to selected part - var node = $("#bioportal-tree-annotator").find("a[data-id='" + encodeURIComponent(classId) + "']"); - var position = $(node).position().top - 200; + var reroot = true; // for easier changing of our minds :) + if (reroot) { + // reroot tree at new class + var tree = $("#bioportal-tree-annotator").data("NCBOTree"); + var options = tree.options(); + $.extend(options, {startingRoot: classId}); + tree.init(); + + // ensure tooltips are activated + $(".tooltip-this").tooltip(); + } else { + // scroll to selected part + var node = $("#bioportal-tree-annotator").find("a[data-id='" + encodeURIComponent(classId) + "']"); + var position = $(node).position().top - 200; + $("#bioportal-tree-annotator").scrollTop(position) + } - // scroll to selected part - $("#bioportal-tree-annotator").scrollTop(position) - }, preRenderAnnotations : function(annotations) { From be4190aed8a86ae4f61dbe295c6d5ada372fbb32 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 13:59:42 -0700 Subject: [PATCH 061/560] hide the annotation popover when triggering a search --- metacatui/src/main/webapp/js/views/DataCatalogView.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 56a108468..9994b3492 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -306,6 +306,9 @@ define(['jquery', // hide the hover $(selectedNode).trigger("mouseout"); + // hide the popover + $("[data-category='annotation'] .expand-collapse-control").trigger("click"); + // reset the tree for next search var tree = $("#bioportal-tree").data("NCBOTree"); var options = tree.options(); From d5179cf457742187ec948bec4f62e013d4b28438 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 16:43:24 -0700 Subject: [PATCH 062/560] split check.selector.xpath by | when rendering in view. --- metacatui/src/main/webapp/js/templates/mdqRun.html | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index ac4d82501..44c49cd54 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -143,7 +143,13 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    data-trigger="focus" data-html="true" data-title="Selectors" - data-content="
                    <% _.each(result.check.selector, function(selector) { print('
                    ', selector.name, '
                    '); print('
                    ', selector.xpath, '
                    '); }); %>
                    "> + data-content="
                    <% + _.each(result.check.selector, function(selector) { + print('
                    ', selector.name, '
                    '); + _.each(selector.xpath.split('|'), function(path) { + print('
                    ', path, '
                    '); + }); + }); %>
                    ">                     From 9a315a1e29b98265e9bcd688b3fe12cc582de7d4 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Wed, 19 Oct 2016 16:44:28 -0700 Subject: [PATCH 063/560] include mdq in dataone theme - defaulting to mn-demo-8 mdq deployment for now --- .../js/themes/dataone/models/AppModel.js | 3 ++- .../webapp/js/themes/dataone/routers/router.js | 18 ++++++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index 18703404d..ab7c71ef2 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -76,7 +76,7 @@ define(['jquery', 'underscore', 'backbone'], annotatorUrl: null, prov: true, useSeriesId: true, - mdqUrl: "/mdq-webapp/webapi/" + mdqUrl: "https://mn-demo-8.test.dataone.org/mdq-webapp/webapi/" }, @@ -94,6 +94,7 @@ define(['jquery', 'underscore', 'backbone'], this.set('authServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/isAuthorized/'); this.set('queryServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/query/solr/'); this.set('metaServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/meta/'); + this.set('objectServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/object/'); this.set('resolveServiceUrl', this.get('d1CNBaseUrl') + this.get('d1Service') + '/resolve/'); this.set('nodeServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/node'); diff --git a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js index 111de0f6f..eeac93848 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js @@ -17,6 +17,7 @@ function ($, _, Backbone) { 'profile(/*username)(/s=:section)(/s=:subsection)' : 'renderProfile', 'my-account' : 'renderUserSettings', 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI + 'mdq(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'logout' : 'logout', // logout the user 'signout' : 'logout', // logout the user 'signin' : 'renderTokenSignIn', @@ -64,6 +65,23 @@ function ($, _, Backbone) { this.navigate(_.last(this.hashHistory), {replace: true}); }, + renderMdqRun: function (suiteId, pid) { + this.routeHistory.push("mdq"); + + if (!appView.mdqRunView) { + require(["views/MdqRunView"], function(MdqRunView) { + appView.mdqRunView = new MdqRunView(); + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + }); + } else { + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + } + }, + renderText: function(options){ if(!appView.textView){ require(['views/TextView'], function(TextView){ From 045aa0bbd7127390e019be462b15a6e61d7b7e64 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Thu, 20 Oct 2016 15:36:03 -0700 Subject: [PATCH 064/560] Fix bug where ontology tree was not bound to events after closing the popover. --- .../main/webapp/js/views/DataCatalogView.js | 21 +++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 56a108468..d7874a08d 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -267,13 +267,30 @@ define(['jquery', ontology: "ECSO", startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType" }); - + $("[data-category='annotation'] .expand-collapse-control").popover({ html: true, placement: "bottom", - trigger:"click", + trigger:"manual", content: tree, container: "#bioportal-popover" + }).on("click", function(){ + if($($(this).data().popover.options.content).is(":visible")){ + //Detach the tree from the popover so it doesn't get removed by Bootstrap + $(this).data().popover.options.content.detach(); + //Hide the popover + $(this).popover("hide"); + } + else{ + //Get the popover content + var content = $(this).data().popoverContent || $(this).data().popover.options.content.detach(); + //Cache it + $(this).data({ popoverContent: content }); + //Show the popover + $(this).popover("show"); + //Insert the tree into the popover content + $(this).data().popover.options.content = content; + } }); // set up the listener to jump to search results From a6b57b404c711dbe758f26f51518ba82739fa3fc Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Thu, 20 Oct 2016 15:42:38 -0700 Subject: [PATCH 065/560] Merge --- .../bioportal/jquery.ncbo.tree-2.0.2.js | 12 +++--- .../src/main/webapp/css/metacatui-common.css | 2 +- .../src/main/webapp/js/templates/mdqRun.html | 8 +++- .../js/themes/arctic/models/AppModel.js | 2 +- .../webapp/js/themes/arctic/routers/router.js | 18 ++++++++ .../js/themes/dataone/models/AppModel.js | 3 +- .../js/themes/dataone/routers/router.js | 18 ++++++++ .../src/main/webapp/js/views/AnnotatorView.js | 42 ++++++++++++++++++- .../main/webapp/js/views/DataCatalogView.js | 5 ++- 9 files changed, 99 insertions(+), 11 deletions(-) diff --git a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js index 6eed0e2f9..69ec7b4cd 100644 --- a/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js +++ b/metacatui/src/main/webapp/components/bioportal/jquery.ncbo.tree-2.0.2.js @@ -142,13 +142,15 @@ var li = $("
                  • "); var a = $("").attr("href", determineHTTPS(node.links.self)).html(node.prefLabel); a.attr("data-id", encodeURIComponent(node["@id"])); + var def = "No definition provided."; if (node["definition"]) { - a.attr("data-title", node["definition"][0]); - a.attr("data-placement", "right"); - a.attr("data-trigger", "hover"); - a.attr("data-container", "body"); - a.addClass("tooltip-this"); + def = node["definition"][0]; } + a.attr("data-title", def); + a.attr("data-placement", "right"); + a.attr("data-trigger", "hover"); + a.attr("data-container", "body"); + a.addClass("tooltip-this"); ul.append(li.append(a)); diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 96936193b..5544f5b5d 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -815,7 +815,7 @@ img.icon{ #mdqTypeSummary { float: right; - width: 75%; + width: 70%; } #mdqResult #data-chart { diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index ac4d82501..44c49cd54 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -143,7 +143,13 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    data-trigger="focus" data-html="true" data-title="Selectors" - data-content="
                    <% _.each(result.check.selector, function(selector) { print('
                    ', selector.name, '
                    '); print('
                    ', selector.xpath, '
                    '); }); %>
                    "> + data-content="
                    <% + _.each(result.check.selector, function(selector) { + print('
                    ', selector.name, '
                    '); + _.each(selector.xpath.split('|'), function(path) { + print('
                    ', path, '
                    '); + }); + }); %>
                    ">                     diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js index 9af2d1fb6..311b69db7 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js @@ -72,7 +72,7 @@ define(['jquery', 'underscore', 'backbone'], checkTokenUrl: null, prov: true, useSeriesId: true, - mdqUrl: "/mdq-webapp/webapi/" + mdqUrl: "https://mn-demo-8.test.dataone.org/mdq-webapp/webapi/" }, diff --git a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js index 17f63f345..a34885f4f 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js @@ -18,6 +18,7 @@ function ($, _, Backbone) { 'signin' : 'renderTokenSignIn', "signinsuccess" : "renderSignInSuccess", 'share(/:stage/*pid)' : 'renderRegistry', // registry page + 'mdq(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'api(/:anchorId)' : 'renderAPI' // API page }, @@ -249,6 +250,23 @@ function ($, _, Backbone) { } }, + renderMdqRun: function (suiteId, pid) { + this.routeHistory.push("mdq"); + + if (!appView.mdqRunView) { + require(["views/MdqRunView"], function(MdqRunView) { + appView.mdqRunView = new MdqRunView(); + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + }); + } else { + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + } + }, + logout: function (param) { //Clear our browsing history when we log out this.routeHistory.length = 0; diff --git a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js index 18703404d..ab7c71ef2 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/dataone/models/AppModel.js @@ -76,7 +76,7 @@ define(['jquery', 'underscore', 'backbone'], annotatorUrl: null, prov: true, useSeriesId: true, - mdqUrl: "/mdq-webapp/webapi/" + mdqUrl: "https://mn-demo-8.test.dataone.org/mdq-webapp/webapi/" }, @@ -94,6 +94,7 @@ define(['jquery', 'underscore', 'backbone'], this.set('authServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/isAuthorized/'); this.set('queryServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/query/solr/'); this.set('metaServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/meta/'); + this.set('objectServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/object/'); this.set('resolveServiceUrl', this.get('d1CNBaseUrl') + this.get('d1Service') + '/resolve/'); this.set('nodeServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/node'); diff --git a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js index 111de0f6f..eeac93848 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js @@ -17,6 +17,7 @@ function ($, _, Backbone) { 'profile(/*username)(/s=:section)(/s=:subsection)' : 'renderProfile', 'my-account' : 'renderUserSettings', 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI + 'mdq(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'logout' : 'logout', // logout the user 'signout' : 'logout', // logout the user 'signin' : 'renderTokenSignIn', @@ -64,6 +65,23 @@ function ($, _, Backbone) { this.navigate(_.last(this.hashHistory), {replace: true}); }, + renderMdqRun: function (suiteId, pid) { + this.routeHistory.push("mdq"); + + if (!appView.mdqRunView) { + require(["views/MdqRunView"], function(MdqRunView) { + appView.mdqRunView = new MdqRunView(); + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + }); + } else { + appView.mdqRunView.suiteId = suiteId; + appView.mdqRunView.pid = pid; + appView.showView(appView.mdqRunView); + } + }, + renderText: function(options){ if(!appView.textView){ require(['views/TextView'], function(TextView){ diff --git a/metacatui/src/main/webapp/js/views/AnnotatorView.js b/metacatui/src/main/webapp/js/views/AnnotatorView.js index eb03cbffb..883fc9da6 100644 --- a/metacatui/src/main/webapp/js/views/AnnotatorView.js +++ b/metacatui/src/main/webapp/js/views/AnnotatorView.js @@ -275,6 +275,21 @@ define(['jquery', var view = this; + this.$el.annotator('subscribe', 'annotationEditorShown', function() { + // reroot tree at starting class + var tree = $("#bioportal-tree-annotator").data("NCBOTree"); + if (tree) { + var options = tree.options(); + $.extend(options, {startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType"}); + tree.init(); + } + // clear any values that are lingering + var view = $('#metadata-container').data("annotator-view"); + $(view.$el.data('annotator').plugins.Tags.input).val(""); + $("#bioportal-tree-label").html(""); + + }); + // subscribe to annotation events, to get the exact resource being annotated this.$el.annotator('subscribe', 'beforeAnnotationCreated', function(annotation, arg0, arg1) { var annotator = view.$el.data('annotator'); @@ -312,7 +327,11 @@ define(['jquery', startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType" }); - tree.on("afterSelect", view.selectConcept); + tree.on("afterSelect", view.selectConcept); + tree.on("afterJumpToClass", view.jumpToClass); + tree.on("afterExpand", view.afterExpand); // for the tool tips + + //alert('Augmented annotation with additional properties, annotation: ' + annotation); } @@ -388,6 +407,27 @@ define(['jquery', }, + jumpToClass : function(event, classId) { + + var reroot = true; // for easier changing of our minds :) + if (reroot) { + // reroot tree at new class + var tree = $("#bioportal-tree-annotator").data("NCBOTree"); + var options = tree.options(); + $.extend(options, {startingRoot: classId}); + tree.init(); + + // ensure tooltips are activated + $(".tooltip-this").tooltip(); + } else { + // scroll to selected part + var node = $("#bioportal-tree-annotator").find("a[data-id='" + encodeURIComponent(classId) + "']"); + var position = $(node).position().top - 200; + $("#bioportal-tree-annotator").scrollTop(position) + } + + }, + preRenderAnnotations : function(annotations) { var uris = []; diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index d7874a08d..6a167ec0a 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -267,7 +267,7 @@ define(['jquery', ontology: "ECSO", startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType" }); - + $("[data-category='annotation'] .expand-collapse-control").popover({ html: true, placement: "bottom", @@ -323,6 +323,9 @@ define(['jquery', // hide the hover $(selectedNode).trigger("mouseout"); + // hide the popover + $("[data-category='annotation'] .expand-collapse-control").trigger("click"); + // reset the tree for next search var tree = $("#bioportal-tree").data("NCBOTree"); var options = tree.options(); From 201fb35b81ebbc06b042acee2d1f03b4c79172ab Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Thu, 20 Oct 2016 16:32:51 -0700 Subject: [PATCH 066/560] Use obsoletes instead of obsoletedBy in the Stats view (#profile) for the Uploads chart --- metacatui/src/main/webapp/js/models/Stats.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/Stats.js b/metacatui/src/main/webapp/js/models/Stats.js index 863504bd3..fb74b4315 100644 --- a/metacatui/src/main/webapp/js/models/Stats.js +++ b/metacatui/src/main/webapp/js/models/Stats.js @@ -329,7 +329,7 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], var query = "q=" + this.get('query') + "+formatType:(METADATA OR DATA)" + //Weeds out resource maps and annotations "+dateUploaded:[" + this.firstPossibleUpload + "%20TO%20NOW]" + //Weeds out badly formatted dates - "+-obsoletedBy:*"+ //Only count one version of a revision chain + "+-obsoletes:*"+ //Only count one version of a revision chain "&fl=dateUploaded" + "&rows=1" + "&sort=dateUploaded+asc" + @@ -359,10 +359,10 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], model.set('totalUploads', data.response.numFound); var dataQuery = "q=" + model.get('query') + - "+-obsoletedBy:*+formatType:DATA"; + "+-obsoletes:*+formatType:DATA"; var metadataQuery = "q=" + model.get('query') + - "+-obsoletedBy:*+formatType:METADATA"; + "+-obsoletes:*+formatType:METADATA"; var facets = "&rows=0" + "&facet=true" + From 61a6b36c61c7df4bdeb6f8fc848f71c07083ab6f Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 21 Oct 2016 09:06:01 -0700 Subject: [PATCH 067/560] Fix bug in bioportal tree widget where annotation filter could not be applied (related to last commit about the tree popover) --- metacatui/src/main/webapp/js/views/DataCatalogView.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 6a167ec0a..3e3d0c91d 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -324,10 +324,11 @@ define(['jquery', $(selectedNode).trigger("mouseout"); // hide the popover - $("[data-category='annotation'] .expand-collapse-control").trigger("click"); + var annotationFilterEl = $("[data-category='annotation'] .expand-collapse-control"); + annotationFilterEl.trigger("click"); // reset the tree for next search - var tree = $("#bioportal-tree").data("NCBOTree"); + var tree = annotationFilterEl.data().popoverContent.data("NCBOTree"); var options = tree.options(); $.extend(options, {startingRoot: "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType"}); tree.changeOntology("ECSO"); @@ -345,7 +346,7 @@ define(['jquery', afterJumpToClass : function(event, classId) { // re-root the tree at this concept - var tree = $("#bioportal-tree").data("NCBOTree"); + var tree = $("[data-category='annotation'] .expand-collapse-control").data().popoverContent.data("NCBOTree"); var options = tree.options(); $.extend(options, {startingRoot: classId}); From 62a7e45ba193605ba4788a7fec29b10919feee76 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 21 Oct 2016 12:09:12 -0700 Subject: [PATCH 068/560] Display the citation as a header Clean up some of the styling in mdq page --- .../src/main/webapp/css/metacatui-common.css | 12 ++- .../src/main/webapp/js/models/SolrResult.js | 10 +- .../src/main/webapp/js/templates/mdqRun.html | 98 +++++++++---------- .../webapp/js/themes/arctic/css/metacatui.css | 24 +++-- .../src/main/webapp/js/views/CitationView.js | 28 ++++-- .../src/main/webapp/js/views/MdqRunView.js | 16 ++- 6 files changed, 112 insertions(+), 76 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 5544f5b5d..013fb1ee5 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -165,6 +165,10 @@ footer{ h3{ font-size: 1.5em; } +header .citation { + margin-bottom: 20px; + display: block; +} /****************************************** ** Buttons *** @@ -830,7 +834,7 @@ img.icon{ /* different colors for each pie slice */ #mdqResult .donut.data > g:nth-child(1) .donut-arc { - fill: #dff0d8; + fill: #b3e69f; } #mdqResult .donut.data > g:nth-child(1) .donut-arc-label, #mdqResult .donut.data > g:nth-child(1) .donut-arc.active { @@ -838,7 +842,7 @@ img.icon{ } #mdqResult .donut.data > g:nth-child(2) .donut-arc { - fill: #fcf8e3; + fill: #fff0a1; } #mdqResult .donut.data > g:nth-child(2) .donut-arc-label, #mdqResult .donut.data > g:nth-child(2) .donut-arc.active { @@ -846,7 +850,7 @@ img.icon{ } #mdqResult .donut.data > g:nth-child(3) .donut-arc { - fill: #f2dede; + fill: #fbb0b0; } #mdqResult .donut.data > g:nth-child(3) .donut-arc-label, #mdqResult .donut.data > g:nth-child(3) .donut-arc.active { @@ -854,7 +858,7 @@ img.icon{ } #mdqResult .donut.data > g:nth-child(4) .donut-arc { - fill: #d9edf7; + fill: #91d7fb; } #mdqResult .donut.data > g:nth-child(4) .donut-arc-label, #mdqResult .donut.data > g:nth-child(4) .donut-arc.active { diff --git a/metacatui/src/main/webapp/js/models/SolrResult.js b/metacatui/src/main/webapp/js/models/SolrResult.js index 86eb6dea1..250923ab9 100644 --- a/metacatui/src/main/webapp/js/models/SolrResult.js +++ b/metacatui/src/main/webapp/js/models/SolrResult.js @@ -246,11 +246,11 @@ define(['jquery', 'underscore', 'backbone'], xhr.send(); }, - getInfo: function(){ + getInfo: function(fields){ var model = this; -// var fields = "id,seriesId,fileName,resourceMap,formatType,formatId,obsoletedBy,isDocumentedBy,documents,title,origin,pubDate,dateUploaded,datasource,isAuthorized,isPublic,size,read_count_i,isService,serviceTitle,serviceEndpoint,serviceOutput,serviceDescription" - var fields = "id,seriesId,fileName,resourceMap,formatType,formatId,obsoletedBy,isDocumentedBy,documents,title,origin,pubDate,dateUploaded,datasource,isAuthorized,isPublic,size,read_count_i"; + if(!fields) + var fields = "id,seriesId,fileName,resourceMap,formatType,formatId,obsoletedBy,isDocumentedBy,documents,title,origin,pubDate,dateUploaded,datasource,isAuthorized,isPublic,size,read_count_i"; var query = "q="; //Do not search for seriesId when it is not configured in this model/app @@ -297,6 +297,10 @@ define(['jquery', 'underscore', 'backbone'], $.ajax(_.extend(requestSettings, appUserModel.createAjaxSettings())); }, + getCitationInfo: function(){ + this.getInfo("id,seriesId,origin,pubDate,dateUploaded,title,datasource"); + }, + notFound: function(){ this.set({"notFound": true}, {silent: true}); this.trigger("404"); diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index 44c49cd54..6f9c75f9f 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -18,61 +18,57 @@

                    Upload Metadata document for QC

                    <% if (typeof result !== 'undefined') { %> -
                    -
                    - -
                    -

                    Metadata Quality report for <%= objectIdentifier %>

                    - - -

                    - After running your metadata package against our standard set of metadata, data, and congruency checks, - we have found the following potential issues. - Please assist us in improving the discoverability and reusability of your research data by addressing the issues below. -

                    -
                    - -
                    +
                    +

                    Metadata Quality Report

                    + +
                    + +
                    +
                    + + +

                    + After running your metadata against our standard set of metadata, data, and congruency checks, + we have found the following potential issues. + Please assist us in improving the discoverability and reusability of your research data by addressing the issues below. +

                    +
                    + +
                    + +
                    +
                    -
                    - -
                    + <% + var types = _.keys(groupedByType); + _.each(types, function(type) { + var results = groupedByType[type]; + var total = results.length; + var success = 0; + _.each(results, function(result) { + if (result.status == "SUCCESS") { + success++; + } + }); + var width = (success/total) * 100; + width = width.toFixed(0); - <% - var types = _.keys(groupedByType); - _.each(types, function(type) { - var results = groupedByType[type]; - var total = results.length; - var success = 0; - _.each(results, function(result) { - if (result.status == "SUCCESS") { - success++; - } - }); - var width = (success/total) * 100; - width = width.toFixed(0); + %> + <%=type%>: <%=width%>% complete +
                    +
                    - %> - <%=type%>: <%=width%>% complete -
                    -
                    - -
                    -
                    - <% - - }); +
                    +
                    + <% }); %> +
                    +
                    - %> - -
                    - -
                    -
                    +
                    <% var total = result.length; diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index 1c274904e..7b5ec48ba 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -129,8 +129,8 @@ } h1{ - font-weight: normal; - font-family: "Aller"; + font-weight: bold; + } .bold-header{ @@ -1322,13 +1322,21 @@ svg .no-activity, margin-bottom: 20px; } - /**----------------------------------------**/ +/* MDQ CSS +-------------------------------------------------- */ + +#mdqTypeSummary #suites{ + display: none; +} + +/* Metadata Index CSS +-------------------------------------------------- */ + +.metadata-index { + padding: 2%; + width: 96%; +} - .metadata-index { - padding: 2%; - width: 96%; - } - /* Registry CSS -------------------------------------------------- */ diff --git a/metacatui/src/main/webapp/js/views/CitationView.js b/metacatui/src/main/webapp/js/views/CitationView.js index 38d55dba1..2f3474b1a 100644 --- a/metacatui/src/main/webapp/js/views/CitationView.js +++ b/metacatui/src/main/webapp/js/views/CitationView.js @@ -1,5 +1,5 @@ -define(['jquery', 'underscore', 'backbone'], - function($, _, Backbone) { +define(['jquery', 'underscore', 'backbone', 'models/SolrResult'], + function($, _, Backbone, SolrResult) { 'use strict'; @@ -8,21 +8,24 @@ define(['jquery', 'underscore', 'backbone'], initialize: function(options){ if((options === undefined) || (!options)) var options = {}; - this.id = options.id || null; + this.pid = options.pid || null; this.attributes = options.attributes || null; this.className += options.className || ""; this.model = options.model || null; this.metadata = options.metadata || null; this.createLink = (options.createLink == false) ? false : true; + //If no model was passed, continue on + if(!this.model && !this.metadata) + return; //If a metadata doc was passed but no data or package model, then save the metadata as our model, too - if(!this.model && this.metadata) this.model = this.metadata; + else if(!this.model && this.metadata) this.model = this.metadata; //If the model is a Package, then get the metadata doc in this package else if(this.model.type == "Package") this.metadata = this.model.getMetadata(); //If the model is a metadata doc and there was no other metadata specified, then use the model else if((this.model.get("formatType") == "METADATA") && !this.metadata) - this.metadata = this.model; + this.metadata = this.model; }, tagName : "cite", @@ -30,7 +33,6 @@ define(['jquery', 'underscore', 'backbone'], className : "citation", events: { - //"click .route-to-metadata" : "routeToMetadata" }, /* @@ -38,8 +40,18 @@ define(['jquery', 'underscore', 'backbone'], */ render: function(){ - if(!this.model && !this.metadata) return this; - + //If there is no model provided but there is a pid + if(!this.model && !this.metadata && this.pid){ + //Create a model + this.metadata = new SolrResult({id: this.pid}); + this.model = this.metadata; + + //Retrieve the citation info for this model and render once we have it + var view = this; + this.model.on("change", function(){ view.render.call(view); }); + this.model.getCitationInfo(); + return; + } //Create the citation from the metadata doc if we have one else if(this.metadata){ var authors = this.metadata.get("origin"), diff --git a/metacatui/src/main/webapp/js/views/MdqRunView.js b/metacatui/src/main/webapp/js/views/MdqRunView.js index c595b7078..7391bbd04 100644 --- a/metacatui/src/main/webapp/js/views/MdqRunView.js +++ b/metacatui/src/main/webapp/js/views/MdqRunView.js @@ -1,6 +1,6 @@ /*global define */ -define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/mdqRun.html', 'text!templates/mdqSuites.html', 'text!templates/loading.html'], - function($, _, Backbone, d3, DonutChart, MdqRunTemplate, SuitesTemplate, LoadingTemplate) { +define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'views/CitationView', 'text!templates/mdqRun.html', 'text!templates/mdqSuites.html', 'text!templates/loading.html'], + function($, _, Backbone, d3, DonutChart, CitationView, MdqRunTemplate, SuitesTemplate, LoadingTemplate) { 'use strict'; // Build the Footer view of the application @@ -80,6 +80,11 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/ xhr.setRequestHeader("Authorization", "Bearer " + appUserModel.get("token")); xhr.send(); + //Render a Citation View for the page header + var citationView = new CitationView({ pid: this.pid }); + citationView.render(); + this.citationView = citationView; + } else { this.$el.html(this.template({})); } @@ -90,6 +95,12 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/ this.$el.html(this.loadingTemplate()); }, + showCitation: function(){ + if(!this.citationView) return false; + + this.$("#mdqCitation").prepend(this.citationView.el); + }, + show: function() { var view = this; this.$el.hide(); @@ -161,6 +172,7 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'DonutChart', 'text!templates/ viewRef.$el.html(viewRef.template(data)); viewRef.drawScoreChart(data.result, groupedResults); viewRef.showAvailableSuites(); + viewRef.showCitation(); viewRef.show(); //Initialize all popover elements $('.popover-this').popover(); From ada530ce73f6be639cb9bc8992e72ba26a1608e3 Mon Sep 17 00:00:00 2001 From: leinfelder Date: Fri, 21 Oct 2016 13:23:14 -0700 Subject: [PATCH 069/560] put check details in a popover. render multiple outputs more clearly. refs #53 --- .../src/main/webapp/js/templates/mdqRun.html | 85 ++++++++++++------- 1 file changed, 54 insertions(+), 31 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index 44c49cd54..9421b60d3 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -99,9 +99,7 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    _.each(groupedResults.GREEN, function(result) { %> -
                  • - - +
                  • <% _.each(result.output, function(output) { %> @@ -109,19 +107,27 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    <% } else { %> - <%- output.value %> +
                    <%- output.value %>
                    <% } %> <% }); %> -
                    - <%= result.check.name %> <%= result.status %> <%= result.check.level %> <%= result.check.type %> -
                    - <%= result.check.description %> + + + + + Metadata Quality report for <%= objectIdentifier %> _.each(groupedResults.ORANGE, function(result) { %> -
                  • - - +
                  • <% _.each(result.output, function(output) { %> @@ -192,20 +196,27 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    <% } else { %> - <%- output.value %> +
                    <%- output.value %>
                    <% } %> <% }); %> -
                    - <%= result.check.name %> <%= result.status %> <%= result.check.level %> <%= result.check.type %> -
                    - <%= result.check.description %> - + + +                     + + Metadata Quality report for <%= objectIdentifier %> _.each(groupedResults.RED, function(result) { %> -
                  • - - +
                  • <% _.each(result.output, function(output) { %> @@ -267,20 +276,27 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    <% } else { %> - <%- output.value %> +
                    <%- output.value %>
                    <% } %> <% }); %> -
                    - <%= result.check.name %> <%= result.status %> <%= result.check.level %> <%= result.check.type %> -
                    - <%= result.check.description %> + +                     + + Metadata Quality report for <%= objectIdentifier %> _.each(groupedResults.BLUE, function(result) { %>
                  • - <% _.each(result.output, function(output) { @@ -341,19 +356,27 @@

                    Metadata Quality report for <%= objectIdentifier %>

                    <% } else { %> - <%- output.value %> +
                    <%- output.value %>
                    <% } %> <% }); %> -
                    - <%= result.check.name %> <%= result.status %> <%= result.check.level %> <%= result.check.type %> -
                    - <%= result.check.description %> + + +                     + + Date: Fri, 21 Oct 2016 16:05:54 -0700 Subject: [PATCH 070/560] do not show suite selector in arctic view. --- .../src/main/webapp/js/themes/arctic/css/metacatui.css | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index 1c274904e..1fe6bf57d 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -1197,6 +1197,13 @@ svg .no-activity, color: #1f254f; } +/** +MDQ items +**/ +#suites { + display: none; +} + /* Metadata rendering CSS -------------------------------------------------- */ #Metadata { From fc5326b34c7fdb54d1c9e91fff6ff9ba1fcfac30 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 21 Oct 2016 19:08:16 -0700 Subject: [PATCH 071/560] Merge --- .../src/main/webapp/css/metacatui-common.css | 48 +- .../src/main/webapp/js/templates/mdqRun.html | 467 +++++++----------- 2 files changed, 221 insertions(+), 294 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 013fb1ee5..350298639 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -18,6 +18,8 @@ .badge{ margin-left: 10px; margin-right: 10px; + text-shadow: none; + font-weight: normal; } .danger{ color: #960303; @@ -39,6 +41,20 @@ .success{ color: green; } +.list-group-item.success { + background-color: #dff0d8; +} +.list-group-item.warning{ + background-color: #fcf8e3; + color: #c09853; +} +.list-group-item.danger { + background-color: #f2dede; +} +.list-group-item.info{ + background-color: #d9edf7; + color: #3a87ad; +} .tooltip{ font-size: 12px; } @@ -248,7 +264,8 @@ header .citation { border-color: #DDD; color: #333; } -.notification.success{ +.notification.success, +.icon.success{ color: #008000; } .notification.error{ @@ -817,6 +834,32 @@ img.icon{ opacity: 0.50; } +.list-group-item.success .icon-caret-right, +.list-group-item.success .icon-caret-down, +.list-group-item.warning .icon-caret-right, +.list-group-item.warning .icon-caret-down, +.list-group-item.info .icon-caret-right, +.list-group-item.info .icon-caret-down, +.list-group-item.danger .icon-caret-down, +.list-group-item.danger .icon-caret-down{ + color: #333; +} +.list-group-item.collapse { + padding: 0px; +} +.list-group-item.collapse.in{ + padding: 10px 15px; +} +.list-group-item.fail .icon{ + color: #960303; +} +.list-group-item.fail .icon-remove{ + font-size: 1em; + color: #FFF; +} +.list-group-item.fail .icon-sign-blank{ + font-size: 1.3em; +} #mdqTypeSummary { float: right; width: 70%; @@ -828,9 +871,6 @@ img.icon{ margin:0px; } -#mdqResult .panel-heading { - overflow: auto; -} /* different colors for each pie slice */ #mdqResult .donut.data > g:nth-child(1) .donut-arc { diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index 6f9c75f9f..e007bf5c5 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -68,7 +68,6 @@

                    Metadata Quality Report

                    • -
                    <% var total = result.length; @@ -77,313 +76,201 @@

                    Metadata Quality Report

                    } %> - - <% if (groupedResults.GREEN) { %> - -                     +
                      + <% if (groupedResults.GREEN) { %> -
                      -
                        - - <% - _.each(groupedResults.GREEN, function(result) { - %> - -
                      • - - - <% - _.each(result.output, function(output) { - %> - <% if (output.type && output.type.includes('image')) { %> - - - <% } else { %> - <%- output.value %> - <% } %> - <% - }); - %> -
                        - - <%= result.check.name %> - <%= result.status %> - <%= result.check.level %> - <%= result.check.type %> -
                        - <%= result.check.description %> - - - - - +
                      • +

                        + + Passed <%=groupedResults.GREEN.length%> checks out of <%= total %>. Good job! +

                        +
                        • - - - - - - - <% - }); - %> - -
                      -
                      - - <% } %> - - + - <% if (groupedResults.ORANGE) { %> - - + <% + _.each(groupedResults.GREEN, function(result) { + %> -
                      -
                        - - <% - _.each(groupedResults.ORANGE, function(result) { - %> - -
                      • - - - <% - _.each(result.output, function(output) { - %> - <% if (output.type && output.type.includes('image')) { %> - - - <% } else { %> - <%- output.value %> - <% } %> - <% - }); - %> -
                        - - <%= result.check.name %> - <%= result.status %> - <%= result.check.level %> - <%= result.check.type %> -
                        - <%= result.check.description %> - - - - - - - - - - - -
                        • - <% - }); - %> +
                      • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> + + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> + + + + + + +
                        • + <% }); %> + <% } %> -
                      -
                      + <% if (groupedResults.ORANGE) { %> +
                    • +

                      + + Warning for <%=groupedResults.ORANGE.length%> checks. Please review these warnings. +

                      +
                      • + <% + _.each(groupedResults.ORANGE, function(result) { + %> +
                    • + + + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> + + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> + + + + + +
                      • + <% }); %> <% } %> <% if (groupedResults.RED) { %> +
                    • +

                      + + Failed <%=groupedResults.RED.length%> checks. Please correct these issues. +

                      +
                      • - - -
                      -
                        - - <% - _.each(groupedResults.RED, function(result) { - %> - -
                      • - - - <% - _.each(result.output, function(output) { - %> - <% if (output.type && output.type.includes('image')) { %> - - - <% } else { %> - <%- output.value %> - <% } %> - <% - }); - %> -
                        - - <%= result.check.name %> - <%= result.status %> - <%= result.check.level %> - <%= result.check.type %> -
                        - <%= result.check.description %> - - - - - - - - - - - -
                        • - <% - }); - %> - -
                      -
                      + <% + _.each(groupedResults.RED, function(result) { + %> +
                    • + + + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> + + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> + + + + + +
                      • + <% }); %> <% } %> <% if (groupedResults.BLUE) { %> - - -
                      -
                        +
                      • +

                        + + <%=groupedResults.BLUE.length%> informational checks. These may include skips, errors and failures. +

                        +
                        • - <% - _.each(groupedResults.BLUE, function(result) { - %> -
                      • - - - <% - _.each(result.output, function(output) { - %> - <% if (output.type && output.type.includes('image')) { %> - - - <% } else { %> - <%- output.value %> - <% } %> - <% - }); - %> -
                        - - <%= result.check.name %> - <%= result.status %> - <%= result.check.level %> - <%= result.check.type %> -
                        - <%= result.check.description %> - - - - - - - - - -
                        • - <% - }); - %> + <% + _.each(groupedResults.BLUE, function(result) { + %> +
                      • + + + <% + _.each(result.output, function(output) { + %> + <% if (output.type && output.type.includes('image')) { %> + + + <% } else { %> + <%- output.value %> + <% } %> + <% + }); + %> + + <%= result.status %> + <%= result.check.level %> + <%= result.check.type %> -
                      -
                      - + + + + + + + <% }); %> <% } %> - - +
                    From 62b8028b38a1dbe0a105f1cf9050631b0015bd80 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 21 Oct 2016 19:26:35 -0700 Subject: [PATCH 072/560] Fixed issues from last Git merge Fix some styling issues with MDQ view --- .../src/main/webapp/css/metacatui-common.css | 4 + .../src/main/webapp/js/templates/mdqRun.html | 259 +----------------- 2 files changed, 6 insertions(+), 257 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 350298639..a5962a6dd 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -846,9 +846,13 @@ img.icon{ } .list-group-item.collapse { padding: 0px; + border: 0px; + margin-bottom: 0px; } .list-group-item.collapse.in{ padding: 10px 15px; + border: 1px solid #DDD; + margin-bottom: -1px; } .list-group-item.fail .icon{ color: #960303; diff --git a/metacatui/src/main/webapp/js/templates/mdqRun.html b/metacatui/src/main/webapp/js/templates/mdqRun.html index c34df1944..5fde04681 100644 --- a/metacatui/src/main/webapp/js/templates/mdqRun.html +++ b/metacatui/src/main/webapp/js/templates/mdqRun.html @@ -79,51 +79,12 @@

                    Metadata Quality Report

                    diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/resultsItem.html b/metacatui/src/main/webapp/js/themes/arctic/templates/resultsItem.html index d6190c7d1..60106768f 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/resultsItem.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/resultsItem.html @@ -25,7 +25,7 @@ } else{ var URLid = resourceMap || id; - print(''); + print(''); } %>
                    From 2c819f7123ff75892e65000fe374c1a4153a9621 Mon Sep 17 00:00:00 2001 From: lauren-palmer Date: Fri, 4 Nov 2016 14:48:50 -0400 Subject: [PATCH 082/560] Merge changes from the 1.12 branch --- metacatui/src/main/webapp/index.html | 2 +- .../src/main/webapp/js/models/AppModel.js | 2 +- metacatui/src/main/webapp/js/models/Search.js | 13 +- .../src/main/webapp/js/templates/search.html | 40 +- .../main/webapp/js/themes/arctic/config.js | 1 + .../js/themes/arctic/models/AppModel.js | 2 +- .../webapp/js/themes/arctic/models/Search.js | 696 ++++++++++++++++++ .../js/themes/dataone/models/AppModel.js | 6 +- .../webapp/js/themes/dataone/models/Search.js | 22 +- .../js/themes/goa/templates/search.html | 29 +- metacatui/src/main/webapp/loader.js | 2 +- 11 files changed, 769 insertions(+), 46 deletions(-) create mode 100644 metacatui/src/main/webapp/js/themes/arctic/models/Search.js diff --git a/metacatui/src/main/webapp/index.html b/metacatui/src/main/webapp/index.html index 02586310c..3993f5a1a 100644 --- a/metacatui/src/main/webapp/index.html +++ b/metacatui/src/main/webapp/index.html @@ -11,7 +11,7 @@ - + + diff --git a/metacatui/test/js/chai-backbone.js b/metacatui/test/js/chai-backbone.js new file mode 100644 index 000000000..564b880cc --- /dev/null +++ b/metacatui/test/js/chai-backbone.js @@ -0,0 +1,110 @@ +// Generated by CoffeeScript 1.7.1 +(function() { + (function(chaiBackbone) { + if (typeof require === "function" && typeof exports === "object" && typeof module === "object") { + return module.exports = chaiBackbone; + } else if (typeof define === "function" && define.amd) { + return define(function() { + return chaiBackbone; + }); + } else { + return chai.use(chaiBackbone); + } + })(function(chai, utils) { + var flag, inspect, routeTo; + inspect = utils.inspect; + flag = utils.flag; + chai.Assertion.addMethod('trigger', function(trigger, options) { + var definedActions; + if (options == null) { + options = {}; + } + definedActions = flag(this, 'whenActions') || []; + definedActions.push({ + negate: flag(this, 'negate'), + before: function(context) { + this.callback = sinon.spy(); + return flag(context, 'object').on(trigger, this.callback); + }, + after: function(context) { + var negate, _ref; + negate = flag(context, 'negate'); + flag(context, 'negate', this.negate); + context.assert(this.callback.called, "expected to trigger " + trigger, "expected not to trigger " + trigger); + if (options["with"] != null) { + context.assert((_ref = this.callback).calledWith.apply(_ref, options["with"]), "expected trigger to be called with " + (inspect(options["with"])) + ", but was called with " + (inspect(this.callback.args[0])) + ".", "expected trigger not to be called with " + (inspect(options["with"])) + ", but was"); + } + return flag(context, 'negate', negate); + } + }); + return flag(this, 'whenActions', definedActions); + }); + chai.Assertion.addProperty('route', function() { + return flag(this, 'routing', true); + }); + routeTo = function(router, methodName, options) { + var consideredRouter, current_history, route, stub, _i, _len, _ref; + if (options == null) { + options = {}; + } + if (!((typeof router === 'object') && (router instanceof Backbone.Router))) { + throw new TypeError('provided router is not a Backbone.Router'); + } + current_history = Backbone.history; + Backbone.history = new Backbone.History; + stub = sinon.stub(router, methodName); + router._bindRoutes(); + if (options.considering != null) { + _ref = options.considering; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + consideredRouter = _ref[_i]; + consideredRouter._bindRoutes(); + } + } + Backbone.history.root = '/'; + route = flag(this, 'object'); + Backbone.history.location = { + pathname: '/' + }; + Backbone.history.loadUrl(route); + Backbone.history = current_history; + router[methodName].restore(); + this.assert(stub.calledOnce, "expected `" + route + "` to route to " + methodName, "expected `" + route + "` not to route to " + methodName); + if (options["arguments"] != null) { + return this.assert(stub.calledWith.apply(stub, options["arguments"]), "expected `" + methodName + "` to be called with " + (inspect(options["arguments"])) + ", but was called with " + (inspect(stub.args[0])) + " instead", "expected `" + methodName + "` not to be called with " + (inspect(options["arguments"])) + ", but was"); + } + }; + chai.Assertion.overwriteProperty('to', function(_super) { + return function() { + if (flag(this, 'routing')) { + return routeTo; + } else { + return _super.apply(this, arguments); + } + }; + }); + return chai.Assertion.addMethod('call', function(methodName) { + var definedActions, object; + object = flag(this, 'object'); + definedActions = flag(this, 'whenActions') || []; + definedActions.push({ + negate: flag(this, 'negate'), + before: function(context) { + this.originalMethod = object[methodName]; + this.spy = sinon.spy(); + object[methodName] = this.spy; + return typeof object.delegateEvents === "function" ? object.delegateEvents() : void 0; + }, + after: function(context) { + object[methodName] = this.originalMethod; + if (typeof object.delegateEvents === "function") { + object.delegateEvents(); + } + return context.assert(this.spy.callCount > 0, this.spy.printf("expected %n to have been called at least once"), this.spy.printf("expected %n to not have been called")); + } + }); + return flag(this, 'whenActions', definedActions); + }); + }); + +}).call(this); diff --git a/metacatui/test/js/chai-jquery.js b/metacatui/test/js/chai-jquery.js new file mode 100644 index 000000000..819a27d66 --- /dev/null +++ b/metacatui/test/js/chai-jquery.js @@ -0,0 +1,231 @@ +(function (chaiJquery) { + // Module systems magic dance. + if (typeof require === "function" && typeof exports === "object" && typeof module === "object") { + // NodeJS + module.exports = chaiJquery; + } else if (typeof define === "function" && define.amd) { + // AMD + define(['jquery'], function ($) { + return function (chai, utils) { + return chaiJquery(chai, utils, $); + }; + }); + } else { + // Other environment (usually diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js index e35adce58..10f1ae7e0 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js @@ -18,7 +18,7 @@ define(["jquery", "underscore", "backbone", "models/metadata/eml211/EMLEntity"], /* Attributes from EML */ caseSensitive: null, // The case sensitivity of the table records - numberOfrecords: null, // the number of records in the table + numberOfRecords: null, // the number of records in the table /* Attributes not from EML */ nodeOrder: [ // The order of the top level XML element nodes From 1c7a0923fbb46e6cedbbae104706461695dda218 Mon Sep 17 00:00:00 2001 From: Christopher Jones Date: Sun, 10 Sep 2017 22:07:29 -0600 Subject: [PATCH 408/560] Include dataTables in existing entities Look for both otherEntity and dataTables when determining if we have existing entities during serialization. This keeps us from inserting new dataTables rather than updating the existing dataTables in the DOM. refs #180 --- .../src/main/webapp/js/models/metadata/eml211/EML211.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js index 841132094..1a8f01610 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js @@ -694,17 +694,17 @@ define(['jquery', 'underscore', 'backbone', 'uuid', this.getEMLPosition(eml, "project").after(this.get("project").updateDOM()); //Get the existing taxon coverage nodes from the EML - var existingEntities = datasetNode.find("otherEntity"); + var existingEntities = datasetNode.find("otherEntity, dataTable"); //Serialize the entities - _.each(this.get("entities"), function(entity, position){ + _.each(this.get("entities"), function(entity, position) { //Update the existing node if it exists - if(existingEntities.length-1 >= position){ + if(existingEntities.length - 1 >= position) { $(existingEntities[position]).replaceWith(entity.updateDOM()); } //Or, append new nodes - else{ + else { this.getEMLPosition(eml, "otherentity").after(entity.updateDOM()); } From d556837ac9b2a68c5721d6700eb98f1248c1d6c3 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Tue, 12 Sep 2017 17:34:21 -0400 Subject: [PATCH 409/560] Changed the remove and edit buttons to a dropdown button in the DataItemView --- .../src/main/webapp/css/metacatui-common.css | 45 ++++++++++--------- .../main/webapp/js/templates/dataItem.html | 12 ++++- .../webapp/js/themes/arctic/css/metacatui.css | 22 ++++++--- .../src/main/webapp/js/views/DataItemView.js | 6 +-- 4 files changed, 52 insertions(+), 33 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 9879c6df1..05058cf6e 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3343,14 +3343,30 @@ ul.side-nav-items { margin-right: 10px; width: 1.4em; } -.data-package-item.loading .edit.icon, -.data-package-item.loading .edit.icon:hover{ - cursor: default; - color: #999; +.data-package-item .btn.edit{ + width: 85px; + color: #19B36A; +} +.data-package-item .btn-group .btn{ + background-color: white; +} +.data-package-item .dropdown-menu{ + border-color: #CCC; + border-width: 1px; + border-style: solid; + margin-top: 6px; } .data-package-item.error-saving .disable-layer{ width: 70px; } +.data-package-item .btn-group .dropdown-toggle { + border-bottom-left-radius: 0px; + border-top-left-radius: 0px; + width: 25px; +} +.data-package-item button{ + border-color: #CCC; +} /* Editor package table status column */ .data-package-item .status{ @@ -3391,29 +3407,14 @@ ul.side-nav-items { opacity: .6; } -.Editor #data-package-table ul li a span { - margin-left: .3em; - margin-right: .3em; - text-align: right; -} - -.Editor #data-package-table ul li i { - margin-left: .3em; - margin-right: .3em; -} - /* Editor package table button dropdown */ .Editor #data-package-table td:last-of-type ul { - margin-right: 20px; - background-color: #1F254F; border-radius: 4px; + left: 0px; + width: 107px; + min-width: 85px; } -/* Editor package table button dropdown list items */ -.Editor #data-package-table td:last-of-type ul li { - margin-right: 20px; - background-color: #1F254F; -} #data-package-container + .ui-resizable-handle{ border: 1px solid #D5D5D5; diff --git a/metacatui/src/main/webapp/js/templates/dataItem.html b/metacatui/src/main/webapp/js/templates/dataItem.html index ae0e304aa..df9230c39 100644 --- a/metacatui/src/main/webapp/js/templates/dataItem.html +++ b/metacatui/src/main/webapp/js/templates/dataItem.html @@ -72,7 +72,15 @@ <% } else { %> - - + +
                    + + + +
                    <% } %> diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index a681976ec..d7395e121 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -567,14 +567,24 @@ footer .logos a:hover, a:focus{ } .Editor .dropdown-menu li a:hover { - background-color: #19B36A; + color: #19B36A; } - -.data-package-item .edit{ - color: #19B36A; +.data-package-item .btn.edit:hover, +.data-package-item .btn.edit:focus{ + background-color: white; + border-color: #CCC; +} +.data-package-item .btn-group .dropdown-toggle:hover{ + background-color: white; } -.data-package-item .edit:hover{ - color: #22ea8b; +#data-package-table td:last-of-type ul li{ + background-color: #FFF; +} +.data-package-item .dropdown-menu li a { + background-color: #FFF; + color: #19B36A; + font-family: "Helvetica Neue",Helvetica,Arial,sans-serif; + font-weight: normal; } .data-package-item .bar{ background-color: #1E254F; diff --git a/metacatui/src/main/webapp/js/views/DataItemView.js b/metacatui/src/main/webapp/js/views/DataItemView.js index 9783d1dc4..4c9eb5414 100644 --- a/metacatui/src/main/webapp/js/views/DataItemView.js +++ b/metacatui/src/main/webapp/js/views/DataItemView.js @@ -36,9 +36,9 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', "drop" : "addFiles", // Drag & drop, adds the files into the collection "click .removeFiles" : "handleRemove", // Edit dropdown, remove sci{data,meta} from collection "click .cancel" : "handleCancel", // Cancel a file load - "change: percentLoaded": "updateLoadProgress", // Update the file read progress bar - "mouseover .remove" : "previewRemove", - "mouseout .remove" : "previewRemove" + "change: percentLoaded": "updateLoadProgress" // Update the file read progress bar + // "mouseover .remove" : "previewRemove", + // "mouseout .remove" : "previewRemove" }, /* Initialize the object - post constructor */ From 8b33539091c4396eebb22b77ef7825326f623645 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Tue, 12 Sep 2017 18:22:58 -0400 Subject: [PATCH 410/560] Merge changes --- metacatui/src/main/webapp/index.html | 4 ++-- .../src/main/webapp/js/models/metadata/eml211/EML211.js | 8 ++++---- .../main/webapp/js/models/metadata/eml211/EMLDataTable.js | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/metacatui/src/main/webapp/index.html b/metacatui/src/main/webapp/index.html index 33cbdcfd6..b109db57a 100644 --- a/metacatui/src/main/webapp/index.html +++ b/metacatui/src/main/webapp/index.html @@ -12,9 +12,9 @@ diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js index 841132094..1a8f01610 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js @@ -694,17 +694,17 @@ define(['jquery', 'underscore', 'backbone', 'uuid', this.getEMLPosition(eml, "project").after(this.get("project").updateDOM()); //Get the existing taxon coverage nodes from the EML - var existingEntities = datasetNode.find("otherEntity"); + var existingEntities = datasetNode.find("otherEntity, dataTable"); //Serialize the entities - _.each(this.get("entities"), function(entity, position){ + _.each(this.get("entities"), function(entity, position) { //Update the existing node if it exists - if(existingEntities.length-1 >= position){ + if(existingEntities.length - 1 >= position) { $(existingEntities[position]).replaceWith(entity.updateDOM()); } //Or, append new nodes - else{ + else { this.getEMLPosition(eml, "otherentity").after(entity.updateDOM()); } diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js index e35adce58..10f1ae7e0 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLDataTable.js @@ -18,7 +18,7 @@ define(["jquery", "underscore", "backbone", "models/metadata/eml211/EMLEntity"], /* Attributes from EML */ caseSensitive: null, // The case sensitivity of the table records - numberOfrecords: null, // the number of records in the table + numberOfRecords: null, // the number of records in the table /* Attributes not from EML */ nodeOrder: [ // The order of the top level XML element nodes From e3ab1d011144a106de870b01bc25e647add296b8 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Tue, 12 Sep 2017 18:28:01 -0400 Subject: [PATCH 411/560] Fix CSS glitch in ProfileViews --- metacatui/src/main/webapp/js/themes/knb/css/metacatui.css | 3 +++ 1 file changed, 3 insertions(+) diff --git a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css index 95a354f39..7bcbaa684 100644 --- a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css @@ -1140,6 +1140,9 @@ img[src*="gstatic.com/"], img[src*="googleapis.com/"] { margin-left: 20px; margin-top: 30px; } +.member-list .group { + min-width: 100px; +} /* The universal color for data */ svg .data, From 337765df7084b593a4eb002853a2a29ff814ef66 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 14 Sep 2017 13:15:53 -0400 Subject: [PATCH 412/560] Show a yellow circle in the DataItemView when an object is successfully uploaded but has not attribute metadata. --- .../src/main/webapp/css/metacatui-common.css | 16 +++++++-- .../main/webapp/js/templates/dataItem.html | 24 ++++++++----- .../webapp/js/themes/arctic/css/metacatui.css | 10 +++--- .../src/main/webapp/js/views/DataItemView.js | 36 +++++++++++++++---- 4 files changed, 66 insertions(+), 20 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 05058cf6e..9fc00b6c9 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3350,6 +3350,10 @@ ul.side-nav-items { .data-package-item .btn-group .btn{ background-color: white; } +.data-package-item .btn.warning { + background-color: #FFF; + color: #ffbc00; +} .data-package-item .dropdown-menu{ border-color: #CCC; border-width: 1px; @@ -3367,7 +3371,16 @@ ul.side-nav-items { .data-package-item button{ border-color: #CCC; } - +.data-package-item.remove-preview { + opacity: 1; +} +.data-package-item.remove-preview .name, +.data-package-item.remove-preview .status, +.data-package-item.remove-preview .size, +.data-package-item.remove-preview .type, +.data-package-item.remove-preview .type-icon{ + opacity: .3; +} /* Editor package table status column */ .data-package-item .status{ width: 60px; @@ -3776,7 +3789,6 @@ textarea.xlarge{ } /* ---- Remove icons in the Editor ---- */ -.data-package-item .remove, .metadata-container .remove{ color: #cecece; } diff --git a/metacatui/src/main/webapp/js/templates/dataItem.html b/metacatui/src/main/webapp/js/templates/dataItem.html index df9230c39..1919ecfac 100644 --- a/metacatui/src/main/webapp/js/templates/dataItem.html +++ b/metacatui/src/main/webapp/js/templates/dataItem.html @@ -1,13 +1,13 @@  <% if ( typeof type !== "undefined" && type !== null && type == "Metadata" ) { %> <% var indentFolder = nodeLevel * 40; %> - + <% } else { %> <% var indentFile = (nodeLevel + 1) * 40; %> - + <% } %> @@ -33,17 +33,17 @@ <% if ( typeof sizeStr != "undefined" && sizeStr ) { %> - <%= sizeStr %> + <%= sizeStr %> <% } else {%> - <%= size %> + <%= size %> <% } %> <% if (type && type != "Metadata") { %> - <%= type %> + <%= type %> <% } else { %> - + <% } %> @@ -52,12 +52,16 @@
                    + <% } else if( (!uploadStatus || uploadStatus == "c") && type != "Metadata" && numAttributes == 0 ) { %> + <% } else if( uploadStatus == "c" ) { %> <% } else if( uploadStatus == "e" ) { %> <% } else if( uploadStatus == "q" && type != "Metadata"){ %> - +
                    +
                    +
                    <% } else if( uploadStatus == "l" && type != "Metadata"){ %> <% } %> @@ -74,7 +78,11 @@ <% } else { %>
                    - + <% if( (!uploadStatus || uploadStatus == "c") && type != "Metadata" && numAttributes == 0 ){ %> + + <% } else { %> + + <% } %> diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index d7395e121..88e99a4b5 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -565,17 +565,19 @@ footer .logos a:hover, a:focus{ box-sizing: border-box; text-align: center; } - -.Editor .dropdown-menu li a:hover { - color: #19B36A; -} .data-package-item .btn.edit:hover, .data-package-item .btn.edit:focus{ background-color: white; border-color: #CCC; } +.data-package-item .btn-group .btn:hover, .data-package-item .btn-group .dropdown-toggle:hover{ background-color: white; + border-color: #CCC; + color: #146660; +} +.data-package-item .dropdown-menu a{ + color: #146660; } #data-package-table td:last-of-type ul li{ background-color: #FFF; diff --git a/metacatui/src/main/webapp/js/views/DataItemView.js b/metacatui/src/main/webapp/js/views/DataItemView.js index 4c9eb5414..7cad606d3 100644 --- a/metacatui/src/main/webapp/js/views/DataItemView.js +++ b/metacatui/src/main/webapp/js/views/DataItemView.js @@ -36,9 +36,9 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', "drop" : "addFiles", // Drag & drop, adds the files into the collection "click .removeFiles" : "handleRemove", // Edit dropdown, remove sci{data,meta} from collection "click .cancel" : "handleCancel", // Cancel a file load - "change: percentLoaded": "updateLoadProgress" // Update the file read progress bar - // "mouseover .remove" : "previewRemove", - // "mouseout .remove" : "previewRemove" + "change: percentLoaded": "updateLoadProgress", // Update the file read progress bar + "mouseover .remove" : "previewRemove", + "mouseout .remove" : "previewRemove" }, /* Initialize the object - post constructor */ @@ -64,6 +64,17 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', if(Array.isArray(attributes.title)) attributes.title = attributes.title[0]; + //Get the number of attributes for this item + attributes.numAttributes = 0; + var parentEML = MetacatUI.rootDataPackage.where({ + id: this.model.get("isDocumentedBy")[0] + }); + if(parentEML.type == "EML"){ + var entity = parentEML.getEntity(this.model); + if(entity) + attributes.numAttributes = entity.get("attributeList").length; + } + this.$el.html( this.template(attributes) ); this.$el.find(".dropdown-toggle").dropdown(); @@ -93,23 +104,25 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', this.$el.removeClass("loading"); } else if(this.model.get("uploadStatus") == "q"){ - this.$(".status .icon").tooltip({ + this.$(".status .progress").tooltip({ placement: "top", trigger: "hover", html: true, - title: "
                    Ready to Submit
                    ", + title: "
                    Starting Upload
                    ", container: "body" }); this.$el.removeClass("loading"); } else if(this.model.get("uploadStatus") == "c"){ - this.$(".status .icon").tooltip({ + + this.$(".status .icon").tooltip({ placement: "top", trigger: "hover", html: true, title: "
                    Upload complete
                    ", container: "body" }); + this.$el.removeClass("loading"); } else if(this.model.get("uploadStatus") == "l"){ @@ -149,6 +162,17 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', this.$el.addClass("loading"); } + else if (( !this.model.get("uploadStatus") || this.model.get("uploadStatus") == "c" ) && attributes.numAttributes == 0){ + this.$(".status .icon").tooltip({ + placement: "top", + trigger: "hover", + html: true, + title: "
                    This file needs to be described - Click 'Describe'
                    ", + container: "body" + }); + + this.$el.removeClass("loading"); + } else{ this.$el.removeClass("loading"); } From 6b6b501f8098c1cca4316f9cb451f60ea98887eb Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 14 Sep 2017 13:22:32 -0400 Subject: [PATCH 413/560] Fix bug related to last commit Closes #261 --- .../src/main/webapp/js/views/DataItemView.js | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/DataItemView.js b/metacatui/src/main/webapp/js/views/DataItemView.js index 7cad606d3..6be2979d4 100644 --- a/metacatui/src/main/webapp/js/views/DataItemView.js +++ b/metacatui/src/main/webapp/js/views/DataItemView.js @@ -113,6 +113,17 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', }); this.$el.removeClass("loading"); } + else if (( !this.model.get("uploadStatus") || this.model.get("uploadStatus") == "c" ) && attributes.numAttributes == 0){ + this.$(".status .icon").tooltip({ + placement: "top", + trigger: "hover", + html: true, + title: "
                    This file needs to be described - Click 'Describe'
                    ", + container: "body" + }); + + this.$el.removeClass("loading"); + } else if(this.model.get("uploadStatus") == "c"){ this.$(".status .icon").tooltip({ @@ -162,17 +173,6 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', this.$el.addClass("loading"); } - else if (( !this.model.get("uploadStatus") || this.model.get("uploadStatus") == "c" ) && attributes.numAttributes == 0){ - this.$(".status .icon").tooltip({ - placement: "top", - trigger: "hover", - html: true, - title: "
                    This file needs to be described - Click 'Describe'
                    ", - container: "body" - }); - - this.$el.removeClass("loading"); - } else{ this.$el.removeClass("loading"); } From 3eed483f1a5110e33a30b81fc3be3d24de68dc3b Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 14 Sep 2017 17:51:01 -0400 Subject: [PATCH 414/560] Listen to changes to the attribute lists for each EMLEntity and update the status icon when attributes are added. --- .../main/webapp/js/collections/DataPackage.js | 14 ++++ .../js/models/metadata/eml211/EML211.js | 3 +- .../js/models/metadata/eml211/EMLEntity.js | 3 + .../main/webapp/js/templates/dataItem.html | 6 +- .../src/main/webapp/js/views/DataItemView.js | 65 ++++++++++++++++--- 5 files changed, 80 insertions(+), 11 deletions(-) diff --git a/metacatui/src/main/webapp/js/collections/DataPackage.js b/metacatui/src/main/webapp/js/collections/DataPackage.js index a74e52da9..5aa56b705 100644 --- a/metacatui/src/main/webapp/js/collections/DataPackage.js +++ b/metacatui/src/main/webapp/js/collections/DataPackage.js @@ -393,12 +393,16 @@ define(['jquery', 'underscore', 'backbone', 'rdflib', "uuid", "md5", // Get the isDocumentedBy relationships documentsStatements = this.dataPackageGraph.statementsMatching( undefined, CITO("documents"), undefined, undefined); + + var sciMetaPids = []; _.each(documentsStatements, function(documentsStatement) { // Extract and URI-decode the metadata pid scimetaID = decodeURIComponent( _.last(documentsStatement.subject.value.split("/"))); + + sciMetaPids.push(scimetaID); // Extract and URI-decode the data pid scidataID = decodeURIComponent( @@ -426,6 +430,10 @@ define(['jquery', 'underscore', 'backbone', 'rdflib', "uuid", "md5", dataObj.set("isDocumentedBy", isDocBy); } }, this); + + //Put the science metadata pids first + memberPIDs = _.difference(memberPIDs, sciMetaPids); + _.each(_.uniq(sciMetaPids), function(id){ memberPIDs.unshift(id); }); //Retrieve the model for each member _.each(memberPIDs, function(pid){ @@ -452,11 +460,17 @@ define(['jquery', 'underscore', 'backbone', 'rdflib', "uuid", "md5", //Trigger a replace event so other parts of the app know when a model has been replaced with a different type oldModel.trigger("replace", newModel); + + if(newModel.type == "EML") + collection.trigger("add:EML"); }); } else{ newModel.set("synced", true); collection.add(newModel, { replace: true }); + + if(newModel.type == "EML") + collection.trigger("add:EML"); } }); diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js index 1a8f01610..38e59c026 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js @@ -58,7 +58,8 @@ define(['jquery', 'underscore', 'backbone', 'uuid', entities: [], //An array of EMLEntities pubplace: null, methods: null, // An EMLMethods objects - project: null // An EMLProject object + project: null, // An EMLProject object + units: [] }); }, diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLEntity.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLEntity.js index dbc27f63e..e0699a26e 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLEntity.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLEntity.js @@ -187,6 +187,9 @@ define(["jquery", "underscore", "backbone", "models/DataONEObject", } else { this.get("attributeList").splice(index, attribute); } + + console.log("change:attributeList for " + this.cid + " " + this.get("entityName")); + this.trigger("change:attributeList"); }, /* diff --git a/metacatui/src/main/webapp/js/templates/dataItem.html b/metacatui/src/main/webapp/js/templates/dataItem.html index 1919ecfac..5c3975b5c 100644 --- a/metacatui/src/main/webapp/js/templates/dataItem.html +++ b/metacatui/src/main/webapp/js/templates/dataItem.html @@ -54,6 +54,10 @@
                    <% } else if( (!uploadStatus || uploadStatus == "c") && type != "Metadata" && numAttributes == 0 ) { %> + <% } else if( type != "Metadata" && numAttributes > 0 && hasAttributeChanges && entityIsValid ) { %> + + <% } else if( type != "Metadata" && !entityIsValid ) { %> + <% } else if( uploadStatus == "c" ) { %> <% } else if( uploadStatus == "e" ) { %> @@ -81,7 +85,7 @@ <% if( (!uploadStatus || uploadStatus == "c") && type != "Metadata" && numAttributes == 0 ){ %> <% } else { %> - + <% } %>
                    -

                    Have a look at the +

                    Have a look at the NASA Global Change Master Directory (GCMD) (particularly under EARTH SCIENCE > Biosphere) and see if you can find keywords that appropriately describe your data set. If not, use your own keywords.

                    From 3ee8cdb038c1332a73165e62a8a94f9426492cff Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Mon, 18 Sep 2017 14:27:33 -0400 Subject: [PATCH 422/560] Fixed a bug where a new keywordSet was created for each keyword row, rather than grouping by thesaurus. Closes #268 --- .../webapp/js/views/metadata/EML211View.js | 125 ++++++++---------- 1 file changed, 56 insertions(+), 69 deletions(-) diff --git a/metacatui/src/main/webapp/js/views/metadata/EML211View.js b/metacatui/src/main/webapp/js/views/metadata/EML211View.js index 1480eba1c..601d45266 100644 --- a/metacatui/src/main/webapp/js/views/metadata/EML211View.js +++ b/metacatui/src/main/webapp/js/views/metadata/EML211View.js @@ -211,13 +211,13 @@ define(['underscore', 'jquery', 'backbone', //Iterate over each keyword and add a text input for the keyword value and a dropdown menu for the thesaurus _.each(this.model.get("keywordSets"), function(keywordSetModel){ _.each(keywordSetModel.get("keywords"), function(keyword){ - this.addKeyword(keyword, keywordSetModel); + this.addKeyword(keyword, keywordSetModel.get("thesaurus")); }, this); }, this); - //Add an empty row for adding a new keyword - this.addKeyword(); - + //Add a new keyword row + this.addKeyword(); + //Alternate Ids var altIdsEls = this.createBasicTextFields("alternateIdentifier", "Add a new alternate identifier"); $(overviewEl).find(".altids").append(altIdsEls); @@ -794,7 +794,7 @@ define(['underscore', 'jquery', 'backbone', $(e.target).parents(".funding-row").toggleClass("remove-preview"); }, - addKeyword: function(keyword, model){ + addKeyword: function(keyword, thesaurus){ if(typeof keyword != "string" || !keyword){ var keyword = ""; @@ -804,33 +804,33 @@ define(['underscore', 'jquery', 'backbone', else if(this.$(".keyword.new").length > 1) return; } - - if(!model) var model = new EMLKeywordSet({ parentModel: this.model }); - - var thesaurus = model.get("thesaurus"), - row = $(document.createElement("div")).addClass("row-fluid keyword-row").data({ model: model }), - keywordInput = $(document.createElement("input")).attr("type", "text").addClass("keyword span10").val(keyword), + + //Create the keyword row HTML + var row = $(document.createElement("div")).addClass("row-fluid keyword-row"), + keywordInput = $(document.createElement("input")).attr("type", "text").addClass("keyword span10").attr("placeholder", "Add one new keyword"), thesInput = $(document.createElement("select")).addClass("thesaurus span2").append( $(document.createElement("option")).val("None").text("None")).append( $(document.createElement("option")).val("GCMD").text("GCMD")), removeButton; - if(thesaurus && thesaurus.indexOf("GCMD") > -1) - thesInput.val("GCMD"); + // Piece together the inputs + row.append(keywordInput, thesInput); + + //Select GCMD in the select menu + if(thesaurus && thesaurus.indexOf("GCMD") > -1) + thesInput.val("GCMD"); - if(!keyword) { + if(!keyword) row.addClass("new"); - keywordInput.attr("placeholder", "Add one new keyword"); - } - - // Start adding children to the row - row.append(keywordInput, thesInput); - - // Add a remove button unless this is the .new keyword - if(keyword) { + else{ + + //Set the keyword value on the text input + keywordInput.val(keyword); + + // Add a remove button unless this is the .new keyword row.append(this.createRemoveButton(null, 'keywordSets', 'div.keyword-row', 'div.keywords')); - } - + } + this.$(".keywords").append(row); }, @@ -894,59 +894,46 @@ define(['underscore', 'jquery', 'backbone', //TODO: Comma and semi-colon seperate keywords updateKeywords: function(e){ - if(!e) return; - var row = $(e.target).parent(".keyword-row"), - keyword = row.find("input").val(), - thesaurus = row.find("select").val(), - model = row.data("model"), - allKeywords = []; + var keywordSets = this.model.get("keywordSets"), + newKeywordSets = []; - if(keyword.length == 0 && thesaurus === 'None') return; - - //If the thesaurus has changed or if there is no model - if(!model || (thesaurus != model.get("thesaurus") && model.get("keywords").length > 2)){ + //Get all the keywords in the view + _.each(this.$(".keyword-row"), function(thisRow){ + var thesaurus = $(thisRow).find("select").val(), + keyword = $(thisRow).find("input").val(); - //Remove the keyword from the model that has a changed thesaurus - if(model) - model.set("keywords", _.without(model.get("keywords"), keyword)); + if(!keyword) return; - //Create a new EMLKeywordSet model - model = new EMLKeywordSet({ parentModel: this.model }); + var keywordSet = _.find(newKeywordSets, function(keywordSet){ + return keywordSet.get("thesaurus") == thesaurus; + }); - //This is the only keyword in the new model - allKeywords = [keyword]; + if(typeof keywordSet != "undefined"){ + keywordSet.get("keywords").push(keyword); + } + else{ + newKeywordSets.push(new EMLKeywordSet({ + parentModel: this.model, + keywords: [keyword], + thesaurus: thesaurus + })); + } - //Update the keywordSets array in the EML211 model - this.model.get("keywordSets").push(model); - - //Update the model attached to the DOM - row.data({ model: model }); - - } - //If the thesaurus hasn't changed, then find all the keywords that belong in this model - else{ - //Get all the keywords in the model - _.each(this.$(".keyword-row"), function(thisRow){ - if($(thisRow).data("model") == model){ - allKeywords.push($(thisRow).find("input").val()); - } - }, this); - - //Make sure this model is set on the EML211 model - if(!_.contains(this.model.get("keywordSets"), model)) - this.model.get("keywordSets").push(model); - } + }, this); - //Update the model with the new keywords and thesaurus - model.set("keywords", allKeywords); - model.set("thesaurus", thesaurus); + //Update the EML model + this.model.set("keywordSets", newKeywordSets); - //Add a new row when the user has added a new keyword just now - if(row.is(".new")){ - row.removeClass("new"); - row.append(this.createRemoveButton(null, "keywordSets", "div.keyword-row", "div.keywords")); - this.addKeyword(); + if(e){ + var row = $(e.target).parent(".keyword-row"); + + //Add a new row when the user has added a new keyword just now + if(row.is(".new")){ + row.removeClass("new"); + row.append(this.createRemoveButton(null, "keywordSets", "div.keyword-row", "div.keywords")); + this.addKeyword(); + } } }, From b3600316d4052e440d6fa1a85c50c442a178975c Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 21 Sep 2017 16:02:59 -0400 Subject: [PATCH 423/560] Remove the funding input error messages from the editor once the user starts typing Closes #192 --- .../main/webapp/js/views/metadata/EML211View.js | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/metacatui/src/main/webapp/js/views/metadata/EML211View.js b/metacatui/src/main/webapp/js/views/metadata/EML211View.js index 601d45266..668f5f296 100644 --- a/metacatui/src/main/webapp/js/views/metadata/EML211View.js +++ b/metacatui/src/main/webapp/js/views/metadata/EML211View.js @@ -69,6 +69,7 @@ define(['underscore', 'jquery', 'backbone', "keyup .funding.new" : "addFunding", "mouseover .funding-row .remove" : "previewFundingRemove", "mouseout .funding-row .remove" : "previewFundingRemove", + "keyup .funding.error" : "handleFundingTyping", "keyup .eml-party.new" : "handlePersonTyping", @@ -794,6 +795,20 @@ define(['underscore', 'jquery', 'backbone', $(e.target).parents(".funding-row").toggleClass("remove-preview"); }, + handleFundingTyping: function(e){ + var fundingInput = $(e.target); + + //If the funding value is at least one character + if(fundingInput.val().length > 0){ + //Get rid of the error styling in this row + fundingInput.parent(".funding-row").children().removeClass("error"); + + //If this was the only funding input with an error, we can safely remove the error message + if( !this.$("input.funding.error").length ) + this.$("[data-category='funding'] .notification").removeClass("error").text(""); + } + }, + addKeyword: function(keyword, thesaurus){ if(typeof keyword != "string" || !keyword){ var keyword = ""; From 8f67f1a15a674951c453df4b6afa2a99af11a4a1 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Fri, 22 Sep 2017 18:20:03 -0400 Subject: [PATCH 424/560] Change EMLAttribute model defaults to a function to avoid using the same arrays across model instances. Closes #253 --- .../js/models/metadata/eml211/EMLAttribute.js | 65 ++++++++++--------- 1 file changed, 33 insertions(+), 32 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLAttribute.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLAttribute.js index c9cd26d1b..3b32d6c15 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EMLAttribute.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EMLAttribute.js @@ -12,38 +12,39 @@ define(["jquery", "underscore", "backbone", var EMLAttribute = Backbone.Model.extend({ /* Attributes of an EML attribute object */ - defaults: { - - /* Attributes from EML */ - xmlID: null, // The XML id of the attribute - attributeName: null, - attributeLabel: [], // Zero or more human readable labels - attributeDefinition: null, - storageType: [], // Zero or more storage types - typeSystem: [], // Zero or more system types for storage type - measurementScale: null, // An EML{Non}NumericDomain or EMLDateTimeDomain object - missingValueCode: [], // Zero or more {code: value, definition: value} objects - accuracy: null, // An EMLAccuracy object - coverage: null, // an EMLCoverage object - methods: [], // Zero or more EMLMethods objects - references: null, // A reference to another EMLAttribute by id (needs work) - - /* Attributes not from EML */ - type: "attribute", // The element type in the DOM - parentModel: null, // The parent model this attribute belongs to - objectXML: null, // The serialized XML of this EML attribute - objectDOM: null, // The DOM of this EML attribute - nodeOrder: [ // The order of the top level XML element nodes - "attributeName", - "attributeLabel", - "attributeDefinition", - "storageType", - "measurementScale", - "missingValueCode", - "accuracy", - "coverage", - "methods" - ] + defaults: function(){ + return { + /* Attributes from EML */ + xmlID: null, // The XML id of the attribute + attributeName: null, + attributeLabel: [], // Zero or more human readable labels + attributeDefinition: null, + storageType: [], // Zero or more storage types + typeSystem: [], // Zero or more system types for storage type + measurementScale: null, // An EML{Non}NumericDomain or EMLDateTimeDomain object + missingValueCode: [], // Zero or more {code: value, definition: value} objects + accuracy: null, // An EMLAccuracy object + coverage: null, // an EMLCoverage object + methods: [], // Zero or more EMLMethods objects + references: null, // A reference to another EMLAttribute by id (needs work) + + /* Attributes not from EML */ + type: "attribute", // The element type in the DOM + parentModel: null, // The parent model this attribute belongs to + objectXML: null, // The serialized XML of this EML attribute + objectDOM: null, // The DOM of this EML attribute + nodeOrder: [ // The order of the top level XML element nodes + "attributeName", + "attributeLabel", + "attributeDefinition", + "storageType", + "measurementScale", + "missingValueCode", + "accuracy", + "coverage", + "methods" + ] + } }, /* From 41c35add12e760722ed1bcf084a8cb9e7f9c2bf2 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Wed, 11 Oct 2017 14:25:52 -0400 Subject: [PATCH 425/560] Added the ability to copy parties to another role. The copy and remove buttons have been consolidated to a single menu in the EMLPartyView, which is accessed via a vertical ellipsis menu icon. Closes #227 --- .../src/main/webapp/css/metacatui-common.css | 61 ++++- .../main/webapp/img/ellipsis-menu-icon.png | Bin 0 -> 255 bytes .../js/models/metadata/eml211/EML211.js | 17 ++ .../js/templates/metadata/EMLParty.html | 59 +++-- .../templates/metadata/EMLPartyCopyMenu.html | 50 ++++ .../webapp/js/themes/arctic/css/metacatui.css | 7 +- .../webapp/js/views/metadata/EML211View.js | 220 ++++++++++++++++-- .../webapp/js/views/metadata/EMLPartyView.js | 7 +- 8 files changed, 371 insertions(+), 50 deletions(-) create mode 100644 metacatui/src/main/webapp/img/ellipsis-menu-icon.png create mode 100644 metacatui/src/main/webapp/js/templates/metadata/EMLPartyCopyMenu.html diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 9fc00b6c9..1bacba57d 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3515,6 +3515,10 @@ textarea.xlarge{ padding: 0px; height: auto; } +.checkbox .disabled, +.checkbox .disabled + .text{ + opacity: .5; +} .Editor input.error, .Editor select.error, .Editor textarea.error{ @@ -3734,6 +3738,59 @@ textarea.xlarge{ padding: 5px; height: 3em; } +.subtle-btn-group button, +.subtle-btn-group button:hover { + border-width: 0px; + box-shadow: none; + -webkit-box-shadow: none; + -moz-box-shadow: none; + background-color: transparent; +} +.subtle-btn-group .icon-ellipsis-vertical { + font-size: 1.2em; +} +.subtle-btn-group .dropdown-toggle:hover, +.subtle-btn-group .dropdown-toggle:focus { + background-color: #DDD; + border-width: 0px; +} +.eml-party .party-menu { + position: absolute; + top: 5px; + right: 10px; +} +.eml-party.new .party-menu{ + display: none; +} +.eml-party .party-menu .dropdown-menu { + margin-left: -142px; + width: 160px; + background-color: #FFF; + border: 1px solid #CCC; + box-shadow: 8px 6px 24px -1px #ccc; + -moz-box-shadow: 8px 6px 24px -1px #ccc; + -webkit-box-shadow: 8px 6px 24px -1px #ccc; +} +.eml-party .party-menu .dropdown-menu li { + border-bottom: 1px solid #ccc; +} +.eml-party .party-menu .dropdown-menu li:hover{ + background-color: rgba(255, 255, 255, 0.57); +} +.eml-party .party-menu .dropdown-menu>li>a:hover { + background-color: transparent; + background-image: none; +} +.eml-party .party-menu .remove, +.eml-party .party-menu .remove:hover, +.eml-party .party-menu .remove a, +.eml-party .party-menu .remove a:hover { + font-size: inherit; + position: relative; + margin: 0px; + color: red; + max-width: 100%; +} /* ---- Keywords ---- */ .metadata-container .keywords .span2{ @@ -3804,10 +3861,6 @@ textarea.xlarge{ cursor: pointer; color: #FF0000; } -.metadata-container .eml-party .remove{ - right: 10px; - top: 5px; -} .taxonomic-coverage-row .remove{ position: relative; diff --git a/metacatui/src/main/webapp/img/ellipsis-menu-icon.png b/metacatui/src/main/webapp/img/ellipsis-menu-icon.png new file mode 100644 index 0000000000000000000000000000000000000000..ee642d56f99717f036de04d4a0eb14e182ff5a3b GIT binary patch literal 255 zcmeAS@N?(olHy`uVBq!ia0vp^Y(Ol{0V3mD{_z4S$r9IylHmNblJdl&R0hYC{G?O` z&)mfH)S%SFl*+=BsWw1G3q4&NLn>}1{rUgjp4sfckp^agX){c-r!fdvANbLuVBNsP z=DQtb9g;-DI*%!7t{U&wDTI@L00Ro`H#nLGYM;Zzopr0Ix<^ A4gdfE literal 0 HcmV?d00001 diff --git a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js index 89f5f91cb..0c9e2d14b 100644 --- a/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js +++ b/metacatui/src/main/webapp/js/models/metadata/eml211/EML211.js @@ -1292,6 +1292,23 @@ define(['jquery', 'underscore', 'backbone', 'uuid', }, + /* + * removeParty - removes the given EMLParty model from this EML211 model's attributes + */ + removeParty: function(partyModel){ + //The list of attributes this EMLParty might be stored in + var possibleAttr = ["creator", "contact", "metadataProvider", "publisher", "associatedParty"]; + + // Iterate over each possible attribute + _.each(possibleAttr, function(attr){ + + if( _.contains(this.get(attr), partyModel) ){ + this.set( attr, _.without(this.get(attr), partyModel) ); + } + + }, this); + }, + createUnits: function(){ var units = new Units(); units.fetch(); diff --git a/metacatui/src/main/webapp/js/templates/metadata/EMLParty.html b/metacatui/src/main/webapp/js/templates/metadata/EMLParty.html index 407367554..ac2ed7391 100644 --- a/metacatui/src/main/webapp/js/templates/metadata/EMLParty.html +++ b/metacatui/src/main/webapp/js/templates/metadata/EMLParty.html @@ -3,46 +3,73 @@
                    - - + + + +
                    - + +
                    - + +
                    - + +
                    - + +
                    - - + + + + +
                    + - +
                    - + +
                    - + +
                    - - + + + + +
                    - - + + + + +
                    -
                    \ No newline at end of file +
                  + \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/templates/metadata/EMLPartyCopyMenu.html b/metacatui/src/main/webapp/js/templates/metadata/EMLPartyCopyMenu.html new file mode 100644 index 000000000..68896d135 --- /dev/null +++ b/metacatui/src/main/webapp/js/templates/metadata/EMLPartyCopyMenu.html @@ -0,0 +1,50 @@ + \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index 88e99a4b5..101a302b0 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -549,13 +549,13 @@ footer .logos a:hover, a:focus{ /* EDITOR ----------------------- */ -.Editor .dropdown-menu li { +.Editor #data-package-table .dropdown-menu li { float: left; position: relative; width: 100%; } -.Editor .dropdown-menu li a { +.Editor #data-package-table .dropdown-menu li a { background-color: #1F254F; background-image: none; color: #FFF; @@ -597,6 +597,9 @@ footer .logos a:hover, a:focus{ .attribute-menu-item .remove{ background-color: rgba(49, 61, 129, .6); } +.eml-party .party-menu .dropdown-menu>li>a:hover { + color: #12238e; +} /* MAPS --------------------------------- */ diff --git a/metacatui/src/main/webapp/js/views/metadata/EML211View.js b/metacatui/src/main/webapp/js/views/metadata/EML211View.js index 668f5f296..1a44a4eed 100644 --- a/metacatui/src/main/webapp/js/views/metadata/EML211View.js +++ b/metacatui/src/main/webapp/js/views/metadata/EML211View.js @@ -13,6 +13,7 @@ define(['underscore', 'jquery', 'backbone', 'models/metadata/eml211/EMLTemporalCoverage', 'models/metadata/eml211/EMLMethods', 'text!templates/metadata/eml.html', + 'text!templates/metadata/EMLPartyCopyMenu.html', 'text!templates/metadata/metadataOverview.html', 'text!templates/metadata/dates.html', 'text!templates/metadata/locationsSection.html', @@ -21,7 +22,7 @@ define(['underscore', 'jquery', 'backbone', 'text!templates/metadata/taxonomicClassificationRow.html'], function(_, $, Backbone, ScienceMetadataView, EMLGeoCoverageView, EMLPartyView, EMLMethodsView, EML, EMLGeoCoverage, EMLKeywordSet, EMLParty, EMLProject, EMLText, EMLTaxonCoverage, - EMLTemporalCoverage, EMLMethods, Template, OverviewTemplate, + EMLTemporalCoverage, EMLMethods, Template, EMLPartyCopyMenuTemplate, OverviewTemplate, DatesTemplate, LocationsTemplate, TaxonomicCoverageTemplate, TaxonomicClassificationTable, TaxonomicClassificationRow){ @@ -70,14 +71,16 @@ define(['underscore', 'jquery', 'backbone', "mouseover .funding-row .remove" : "previewFundingRemove", "mouseout .funding-row .remove" : "previewFundingRemove", "keyup .funding.error" : "handleFundingTyping", - - "keyup .eml-party.new" : "handlePersonTyping", - + "click .side-nav-item" : "switchSection", - - "change #new-party-menu" : "chooseNewPersonType", - "click .remove" : "handleRemove" + "keyup .eml-party.new" : "handlePersonTyping", + "change #new-party-menu" : "chooseNewPersonType", + "click .eml-party .copy" : "showCopyPersonMenu", + "click #copy-party-save" : "copyPerson", + "click .eml-party .remove" : "removePerson", + + "click .remove" : "handleRemove" }, /* A list of the subviews */ @@ -100,6 +103,7 @@ define(['underscore', 'jquery', 'backbone', taxonomicCoverageTemplate: _.template(TaxonomicCoverageTemplate), taxonomicClassificationTableTemplate: _.template(TaxonomicClassificationTable), taxonomicClassificationRowTemplate: _.template(TaxonomicClassificationRow), + copyPersonMenuTemplate: _.template(EMLPartyCopyMenuTemplate), initialize: function(options) { @@ -253,13 +257,13 @@ define(['underscore', 'jquery', 'backbone', var emptyTypes = []; this.partyTypeMap = { - "collaboratingPrincipalInvestigator" : "Collborating-Principal Investigators", + "collaboratingPrincipalInvestigator" : "Collaborating-Principal Investigators", "coPrincipalInvestigator" : "Co-Principal Investigators", "principalInvestigator" : "Principal Investigators", "creator" : "Dataset Creators (Authors/Owners/Originators)", "contact" : "Contacts", "metadataProvider" : "Metadata Provider", - "custodianSteward" : "Custodian/Steward", + "custodianSteward" : "Custodians/Stewards", "publisher" : "Publisher", "user" : "Users" } @@ -427,15 +431,35 @@ define(['underscore', 'jquery', 'backbone', if(!partyType || typeof partyType != "string") var partyType = emlParty.get("role") || emlParty.get("type"); } + + + //Find the container section for this party type + var container = this.$(".section.people").find('[data-attribute="' + partyType + '"]'); + //See if this view already exists + if( !isNew && container.length && emlParty ){ + var partyView; + + _.each(container.find(".eml-party"), function(singlePartyEl){ + + //If this EMLPartyView element is for the current model, then get the View + if( $(singlePartyEl).data("model") == emlParty ) + partyView = $(singlePartyEl).data("view"); + }); + + //If a partyView was found, just rerender it and exit + if(partyView){ + partyView.render(); + return; + } + } + + //If there still is no partyView found, create a new one var partyView = new EMLPartyView({ model: emlParty, edit: this.edit, isNew: isNew - }); - - //Find the container section for this party type - var container = this.$(".section.people").find('[data-attribute="' + partyType + '"]'); + }); //If this person type is not on the page yet, add it if(!container.length){ @@ -450,9 +474,6 @@ define(['underscore', 'jquery', 'backbone', container.find(".new").before(partyView.render().el); else container.append(partyView.render().el); - - // Add in a remove button - $(container).find("div.eml-party").append(this.createRemoveButton(null, partyType, "div.eml-party", "div.row-striped")); } }, @@ -467,9 +488,6 @@ define(['underscore', 'jquery', 'backbone', if(this.$("[data-attribute='" + partyType + "'] .eml-party.new").length > 1) return; - // Add in a remove button - $(container).append(this.createRemoveButton(null, partyType, "div.eml-party", "div.row-striped")); - //Render a new person if(partyType != "publisher") this.renderPerson(null, partyType); @@ -529,7 +547,7 @@ define(['underscore', 'jquery', 'backbone', }, /* - * Gets the party type chosen by the user and adds that section to the view + * addNewPersonType - Adds a header and container to the People section for the given party type/role, */ addNewPersonType: function(partyType){ if(!partyType) return; @@ -539,16 +557,16 @@ define(['underscore', 'jquery', 'backbone', // Add a new header for the party type var header = $(document.createElement("h4")).text(this.partyTypeMap[partyType]); - $(partyContainer).append(header); + $(partyTypeContainer).append(header); //Remove this type from the dropdown menu this.$("#new-party-menu").find("[value='" + partyType + "']").remove(); //Add the new party container - var partyContainer = $(document.createElement("div")) + var partyRow = $(document.createElement("div")) .attr("data-attribute", partyType) .addClass("row-striped"); - partyTypeContainer.append(partyContainer); + partyTypeContainer.append(partyRow); // Add in the new party type container just before the dropdown this.$("#new-party-menu").before(partyTypeContainer); @@ -557,6 +575,160 @@ define(['underscore', 'jquery', 'backbone', this.renderPerson(null, partyType); }, + /* + * showCopyPersonMenu: Displays a modal window to the user with a list of roles that they can + * copy this person to + */ + showCopyPersonMenu: function(e){ + + //Get the EMLParty to copy + var partyToCopy = $(e.target).parents(".eml-party").data("model"), + menu = this.$("#copy-person-menu"); + + //Check if the modal window menu has been created already + if( !menu.length ){ + + //Create the modal window menu from the template + menu = $(this.copyPersonMenuTemplate()); + + //Add to the DOM + this.$el.append(menu); + + //Initialize the modal + menu.modal(); + } + else{ + //Reset all the checkboxes + menu.find("input:checked").prop("checked", false); + menu.find(".disabled") + .prop("disabled", false) + .removeClass("disabled") + .parent(".checkbox") + .attr("title", ""); + } + + //Disable the roles this person is already in + var currentRole = partyToCopy.get("role") || partyToCopy.get("type") || ""; + menu.find("input[value='" + currentRole + "']") + .prop("disabled", "disabled") + .addClass("disabled") + .parent(".checkbox") + .attr("title", "This person is already in the " + this.partyTypeMap[currentRole] + " list."); + + //If there is already one publisher, disable that option + if( this.model.get("publisher").length ){ + var publisherName = this.model.get("publisher")[0].get("individualName") ? + this.model.get("publisher")[0].get("individualName").givenName + " " + + this.model.get("publisher")[0].get("individualName").surName : + this.model.get("publisher")[0].get("organizationName") || + this.model.get("publisher")[0].get("positionName") || + "Someone"; + + menu.find("input[value='publisher']") + .prop("disabled", "disabled") + .addClass("disabled") + .parent(".checkbox") + .attr("title", publisherName + " is already listed as the publisher. (There can be only one)."); + + } + + //Attach the EMLParty to the menu DOMs + menu.data({ + EMLParty: partyToCopy + }); + + //Show the modal window menu now + menu.modal("show"); + }, + + /* + * copyPerson: Gets the selected checkboxes from the copy person menu and copies the EMLParty + * to those new roles + */ + copyPerson: function(){ + + //Get all the checked boxes + var checkedBoxes = this.$("#copy-person-menu input:checked"), + //Get the EMLParty to copy + partyToCopy = this.$("#copy-person-menu").data("EMLParty"); + + //For each selected role, + _.each(checkedBoxes, function(checkedBox){ + + //Get the roles + var role = $(checkedBox).val(), + isAssocParty = _.contains(partyToCopy.get("roleOptions"), role); + + //If this are no associated parties yet... + if( isAssocParty ){ + + //If there are no parties in this role yet, + // then add this person type to the view + if( !this.model.get("associatedParty").length ) + this.addNewPersonType(role); + else if( !_.find(this.model.get("associatedParty"), function(p){ + return p.get("role") == role; + }) ){ + this.addNewPersonType(role); + } + + //Create all the attributes for the new person. We're only changing the role + var options = partyToCopy.toJSON(); + options.type = "associatedParty"; + options.role = role; + + //Create a new EMLParty model + var newPerson = new EMLParty(options); + + //Add this new EMLParty to the EML model + this.model.get("associatedParty").push(newPerson); + + //Render this new person + this.renderPerson(newPerson, role); + } + //If this person type is not an associated party... + else{ + //If there are no parties in this role yet, + // then add this person type to the view + if( !this.model.get(role).length ) + this.addNewPersonType(role); + + //Create all the attributes for the new person. We're only changing the type + var options = partyToCopy.toJSON(); + options.type = role; + + //Create a new EMLParty model + var newPerson = new EMLParty(options); + + //Add this new EMLParty to the EML model + this.model.get(role).push(newPerson); + + //Render this new person + this.renderPerson(newPerson, role); + } + + }, this); + }, + + removePerson: function(e){ + e.preventDefault(); + + //Get the party view el, view, and model + var partyEl = $(e.target).parents(".eml-party"), + partyView = partyEl.data("view"), + partyToRemove = partyEl.data("model"); + + //If there is no model found, we have nothing to do, so exit + if(!partyToRemove) return false; + + //Call removeParty on the EML211 model to remove this EMLParty + this.model.removeParty(partyToRemove); + + //Let the EMLPartyView remove itself + partyView.remove(); + + }, + /* * Renders the Dates section of the page */ @@ -1207,7 +1379,6 @@ define(['underscore', 'jquery', 'backbone', this.model.set('pubDate', $(e.target).val().trim()); this.model.trigger("change"); - console.log(this.model.get('pubDate')); // Trigger a change on the entire package MetacatUI.rootDataPackage.packageModel.set("changed", true); }, @@ -1801,7 +1972,6 @@ define(['underscore', 'jquery', 'backbone', $("#metadata-container input").change(); $("#metadata-container textarea").change(); $("#metadata-container select").change(); - console.log("changes fired"); }, /* Creates "Remove" buttons for removing non-required sections diff --git a/metacatui/src/main/webapp/js/views/metadata/EMLPartyView.js b/metacatui/src/main/webapp/js/views/metadata/EMLPartyView.js index 734cac027..58f5555fd 100644 --- a/metacatui/src/main/webapp/js/views/metadata/EMLPartyView.js +++ b/metacatui/src/main/webapp/js/views/metadata/EMLPartyView.js @@ -76,8 +76,9 @@ define(['underscore', 'jquery', 'backbone', 'models/metadata/eml211/EMLParty', fax : this.model.get("fax").length? this.model.get("fax")[0] : "", email : this.model.get("email").length? this.model.get("email")[0] : "", website : this.model.get("onlineUrl").length? this.model.get("onlineUrl")[0] : "", - userId : Array.isArray(this.model.get("userId"))? this.model.get("userId")[0] : this.model.get("userId") || "" - })); + userId : Array.isArray(this.model.get("userId"))? this.model.get("userId")[0] : this.model.get("userId") || "", + uniqueId : this.model.cid + })); } //If this EML Party is new/empty, then add the new class @@ -274,7 +275,7 @@ define(['underscore', 'jquery', 'backbone', 'models/metadata/eml211/EMLParty', }, previewRemove: function(){ - this.$el.toggleClass("remove-preview"); + this.$("input, img, label").toggleClass("remove-preview"); }, /* From 2b8e18fb4cc7a440b2e0b456a5c0f7aee168b84c Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Wed, 11 Oct 2017 14:28:27 -0400 Subject: [PATCH 426/560] Moved around some of the code in NodeModel and added comments --- .../src/main/webapp/js/models/NodeModel.js | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/NodeModel.js b/metacatui/src/main/webapp/js/models/NodeModel.js index d6e955e03..8b41d9e40 100644 --- a/metacatui/src/main/webapp/js/models/NodeModel.js +++ b/metacatui/src/main/webapp/js/models/NodeModel.js @@ -152,16 +152,25 @@ define(['jquery', 'underscore', 'backbone'], thisModel.set('coordinators', coordList); thisModel.trigger('change:coordinators'); - //Find the node we are currently querying, if there is one + //If we don't have a current member node yet, find it if(!thisModel.get("currentMemberNode")){ + + // Find the current member node by matching the current DataONE MN API base URL + // with the DataONE MN API base URLs in the member list var thisMember = _.findWhere(thisModel.get("members"), { baseURL: (MetacatUI.appModel.get("baseUrl") + MetacatUI.appModel.get('context') + MetacatUI.appModel.get("d1Service")).replace("/v2", "").replace("/v1", "") }); - if(thisMember !== undefined) + + if(thisMember !== undefined){ + //If a matching member node is found, set the node ID thisModel.set("currentMemberNode", thisMember.identifier); + + //If the node ID is not set in the appModel user the matching MN we found + if(!MetacatUI.appModel.get("nodeId")) + MetacatUI.appModel.set("nodeId", thisMember.identifier); + } + //Trigger a change so the rest of the app knows we at least looked for the current MN thisModel.trigger("change:currentMemberNode"); - - if(!MetacatUI.appModel.get("nodeId")) - MetacatUI.appModel.set("nodeId", thisMember.identifier); + } }); } From 05bb839b1374f387b6e33f44389e2a8c4474ed62 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Wed, 11 Oct 2017 16:26:13 -0400 Subject: [PATCH 427/560] Fix bug where not found message was covering up the app navigation Closes #296 --- metacatui/src/main/webapp/css/metacatui-common.css | 3 +++ metacatui/src/main/webapp/js/views/EditorView.js | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 1bacba57d..e316fbcd2 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3480,6 +3480,9 @@ textarea.xlarge{ .Editor .dropdown-menu li a i { vertical-align: middle; } +#editor-body .alert { + position: relative; +} .Editor #Content > .alert-container{ position: fixed; left: 0px; diff --git a/metacatui/src/main/webapp/js/views/EditorView.js b/metacatui/src/main/webapp/js/views/EditorView.js index 28fcc370c..4d853bb02 100644 --- a/metacatui/src/main/webapp/js/views/EditorView.js +++ b/metacatui/src/main/webapp/js/views/EditorView.js @@ -553,7 +553,7 @@ define(['underscore', "
                • The content was removed because it was invalid.
                  • " + "
                "; this.hideLoading(); - MetacatUI.appView.showAlert(msg, "alert-error", this.$el, null, {remove: true}); + MetacatUI.appView.showAlert(msg, "alert-error", this.$("#editor-body"), null, {remove: true}); }, From 58cc76b124a90e6df014e862d2ddb94059874aae Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 12 Oct 2017 14:59:13 -0400 Subject: [PATCH 428/560] Make sure the MetacatUI.rootDataPackage.packageModel uploadStatus gets set back to "q" (queued) when there are validation errors preventing it from being saved. Closes #291 --- metacatui/src/main/webapp/js/collections/DataPackage.js | 1 + 1 file changed, 1 insertion(+) diff --git a/metacatui/src/main/webapp/js/collections/DataPackage.js b/metacatui/src/main/webapp/js/collections/DataPackage.js index 5aa56b705..8081070ae 100644 --- a/metacatui/src/main/webapp/js/collections/DataPackage.js +++ b/metacatui/src/main/webapp/js/collections/DataPackage.js @@ -544,6 +544,7 @@ define(['jquery', 'underscore', 'backbone', 'rdflib', "uuid", "md5", return model.get("uploadStatus"); } ), "e") ) { this.packageModel.set("changed", false); + this.packageModel.set("uploadStatus", "q"); this.trigger("cancelSave"); return; } From 9a4b6b52d98ab6f415e7f9b4a49c8dee2b41070f Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 12 Oct 2017 15:26:22 -0400 Subject: [PATCH 429/560] Change #share routes to #submit Closes #298 --- metacatui/src/main/webapp/js/routers/router.js | 3 ++- metacatui/src/main/webapp/js/templates/about.html | 6 +++--- metacatui/src/main/webapp/js/templates/editMetadata.html | 2 +- metacatui/src/main/webapp/js/templates/insertProgress.html | 2 +- metacatui/src/main/webapp/js/templates/navbar.html | 4 ++-- metacatui/src/main/webapp/js/templates/noResults.html | 2 +- .../src/main/webapp/js/themes/arctic/routers/router.js | 3 ++- .../src/main/webapp/js/themes/arctic/templates/about.html | 6 +++--- .../webapp/js/themes/arctic/templates/insertProgress.html | 2 +- .../main/webapp/js/themes/arctic/templates/mainContent.html | 2 +- .../src/main/webapp/js/themes/arctic/templates/navbar.html | 4 ++-- .../main/webapp/js/themes/arctic/templates/noResults.html | 2 +- metacatui/src/main/webapp/js/themes/goa/routers/router.js | 3 ++- .../src/main/webapp/js/themes/goa/templates/navbar.html | 2 +- .../src/main/webapp/js/themes/knb/templates/about.html | 6 +++--- .../main/webapp/js/themes/knb/templates/mainContent.html | 2 +- .../src/main/webapp/js/themes/knb/templates/navbar.html | 6 +++--- .../src/main/webapp/js/themes/nceas/models/AppModel.js | 2 +- metacatui/src/main/webapp/js/themes/nceas/routers/router.js | 3 ++- metacatui/src/main/webapp/js/views/EditorView.js | 4 ++-- metacatui/src/main/webapp/js/views/NavbarView.js | 2 +- 21 files changed, 36 insertions(+), 32 deletions(-) diff --git a/metacatui/src/main/webapp/js/routers/router.js b/metacatui/src/main/webapp/js/routers/router.js index 08459d77a..01e102268 100644 --- a/metacatui/src/main/webapp/js/routers/router.js +++ b/metacatui/src/main/webapp/js/routers/router.js @@ -26,6 +26,7 @@ function ($, _, Backbone) { "signinsuccess" : "renderSignInSuccess", "signinldaperror" : "renderLdapSignInError", 'share(/*pid)' : 'renderEditor', // registry page + 'submit(/*pid)' : 'renderEditor', // registry page 'quality(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'api(/:anchorId)' : 'renderAPI' // API page }, @@ -139,7 +140,7 @@ function ($, _, Backbone) { package identifier will be queried and then rendered. */ renderEditor: function (pid) { - this.routeHistory.push("share"); + this.routeHistory.push("submit"); if( ! MetacatUI.appView.editorView ){ require(['views/EditorView'], function(EditorView) { diff --git a/metacatui/src/main/webapp/js/templates/about.html b/metacatui/src/main/webapp/js/templates/about.html index 8e6d7f2a1..a44b31009 100644 --- a/metacatui/src/main/webapp/js/templates/about.html +++ b/metacatui/src/main/webapp/js/templates/about.html @@ -46,13 +46,13 @@

                Submitting your data is easy. Here are two ways to get started:

                - + KNB Online Data Registry Form

                On the web

                -

                Upload your data on this website using a simple online form.

                -

                Upload now

                +

                Upload your data on this website using a simple online form.

                +

                Upload now

                diff --git a/metacatui/src/main/webapp/js/templates/editMetadata.html b/metacatui/src/main/webapp/js/templates/editMetadata.html index e919743f9..c3fbf93a5 100644 --- a/metacatui/src/main/webapp/js/templates/editMetadata.html +++ b/metacatui/src/main/webapp/js/templates/editMetadata.html @@ -1 +1 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/templates/insertProgress.html b/metacatui/src/main/webapp/js/templates/insertProgress.html index 15107d7d5..d80dd7e66 100644 --- a/metacatui/src/main/webapp/js/templates/insertProgress.html +++ b/metacatui/src/main/webapp/js/templates/insertProgress.html @@ -33,7 +33,7 @@

                Thank you for your submission

                -
                Your submission could not be completed. Please try again or +
                Your submission could not be completed. Please try again or contact us at <%=MetacatUI.appModel.get("emailContact")%> for assistance.
                diff --git a/metacatui/src/main/webapp/js/templates/navbar.html b/metacatui/src/main/webapp/js/templates/navbar.html index 1eaee84a6..19cbc5246 100644 --- a/metacatui/src/main/webapp/js/templates/navbar.html +++ b/metacatui/src/main/webapp/js/templates/navbar.html @@ -28,7 +28,7 @@ '
                  ', '
                • ', formattedName, '
                  • ', '
                • ', - '
                • Submit data
                  • ', + '
                • Submit data
                  • ', '
                • My Profile
                  • ', '
                • My datasets
                  • ', '
                • ', @@ -38,7 +38,7 @@ ); } else { print( - '' + '' ); } %> diff --git a/metacatui/src/main/webapp/js/templates/noResults.html b/metacatui/src/main/webapp/js/templates/noResults.html index a515e7887..36f2bc8db 100644 --- a/metacatui/src/main/webapp/js/templates/noResults.html +++ b/metacatui/src/main/webapp/js/templates/noResults.html @@ -9,7 +9,7 @@ <% if(username){ %> <% } %> diff --git a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js index a89689ced..3a28e4d06 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js @@ -19,6 +19,7 @@ function ($, _, Backbone) { 'signin' : 'renderTokenSignIn', "signinsuccess" : "renderSignInSuccess", 'share(/*pid)' : 'renderEditor', // registry page + 'submit(/*pid)' : 'renderEditor', // registry page 'quality(/s=:suiteId)(/:pid)' : 'renderMdqRun', // MDQ page 'api(/:anchorId)' : 'renderAPI' // API page }, @@ -260,7 +261,7 @@ function ($, _, Backbone) { package identifier will be queried and then rendered. */ renderEditor: function (pid) { - this.routeHistory.push("share"); + this.routeHistory.push("submit"); if( ! MetacatUI.appView.editorView ){ require(['views/EditorView'], function(EditorView) { diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/about.html b/metacatui/src/main/webapp/js/themes/arctic/templates/about.html index 7eca43a51..f656c986c 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/about.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/about.html @@ -69,13 +69,13 @@

                  Submitting your data to Arctica is easy. Here are two ways to get started:

                  - + Arctica Online Data Registry Form

                  On the web

                  -

                  Upload your data on the Arctica website using a simple online form.

                  -

                  Upload now

                  +

                  Upload your data on the Arctica website using a simple online form.

                  +

                  Upload now

                  diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/insertProgress.html b/metacatui/src/main/webapp/js/themes/arctic/templates/insertProgress.html index 1eb603e49..23b60d176 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/insertProgress.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/insertProgress.html @@ -35,7 +35,7 @@

                  Thank you for your submission

                -
                Your submission could not be completed. Please try again or +
                Your submission could not be completed. Please try again or contact us at <%=MetacatUI.appModel.get("emailContact")%> for assistance.
                diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/mainContent.html b/metacatui/src/main/webapp/js/themes/arctic/templates/mainContent.html index 192ea91df..484add143 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/mainContent.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/mainContent.html @@ -9,7 +9,7 @@

                Store and confidently share.

                Store up to 5GB of data for free. Arctica also supports DOIs to permanently publish your data sets.

                - Share your data + Share your data
                diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html b/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html index 86b62ae20..a567c404f 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html @@ -35,12 +35,12 @@
              • History
              • -
            • Submit Data
              • +
            • Submit Data
              • <% if (loggedIn) { %>
            • <%=formattedName%>
                -
              • Submit data
                • +
              • Submit data
              • My profile
              • My groups
              • My data sets
                • diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/noResults.html b/metacatui/src/main/webapp/js/themes/arctic/templates/noResults.html index 7b2ea2a30..8ab3c7702 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/noResults.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/noResults.html @@ -9,7 +9,7 @@ <% if(username){ %>

                - Submit data now. + Submit data now.

                Where are my data sets?

                If you are a previous ACADIS Gateway user, you will need to take additional steps to access your data sets diff --git a/metacatui/src/main/webapp/js/themes/goa/routers/router.js b/metacatui/src/main/webapp/js/themes/goa/routers/router.js index ef06fb972..5fa3c3a6f 100644 --- a/metacatui/src/main/webapp/js/themes/goa/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/goa/routers/router.js @@ -20,7 +20,8 @@ function ($, _, Backbone) { 'signout' : 'logout', // logout the user 'signin' : "renderSignIn", "signinldaperror" : "renderLdapSignInError", - 'share(/*pid)' : 'renderEditor' // registry page + 'share(/*pid)' : 'renderEditor', // registry page + 'submit(/*pid)' : 'renderEditor' // registry page }, helpPages: { diff --git a/metacatui/src/main/webapp/js/themes/goa/templates/navbar.html b/metacatui/src/main/webapp/js/themes/goa/templates/navbar.html index 5d4c34df6..af0eb4ac6 100644 --- a/metacatui/src/main/webapp/js/themes/goa/templates/navbar.html +++ b/metacatui/src/main/webapp/js/themes/goa/templates/navbar.html @@ -51,7 +51,7 @@ ); } else{ %> -

              • Sign in
                • +
              • Sign in
                • <% } %>
              diff --git a/metacatui/src/main/webapp/js/themes/knb/templates/about.html b/metacatui/src/main/webapp/js/themes/knb/templates/about.html index 246836774..c1c6eae47 100644 --- a/metacatui/src/main/webapp/js/themes/knb/templates/about.html +++ b/metacatui/src/main/webapp/js/themes/knb/templates/about.html @@ -71,13 +71,13 @@

              Submitting your data to the KNB is easy. Here are two ways to get started:

              - + KNB Online Data Registry Form

              On the web

              -

              Upload your data on the KNB website using a simple online form.

              -

              Upload now

              +

              Upload your data on the KNB website using a simple online form.

              +

              Upload now

              diff --git a/metacatui/src/main/webapp/js/themes/knb/templates/mainContent.html b/metacatui/src/main/webapp/js/themes/knb/templates/mainContent.html index 73419b7e7..c60d04a68 100644 --- a/metacatui/src/main/webapp/js/themes/knb/templates/mainContent.html +++ b/metacatui/src/main/webapp/js/themes/knb/templates/mainContent.html @@ -20,7 +20,7 @@

              Store and confidently share.

              Store up to 5GB of data for free. The KNB also supports DOIs to permanently publish your data sets.

              - Share your data + Share your data
              diff --git a/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html b/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html index 6575fb031..004a9aea5 100644 --- a/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html +++ b/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html @@ -11,7 +11,7 @@
            • Summary

            • -
          • Share
            • +
          • Submit
          • Tools
            • <% } else { %> -
          • Sign In
            • +
          • Sign In
            • <% } %>
          diff --git a/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js b/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js index 8550f0cf2..46822127a 100644 --- a/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js @@ -66,7 +66,7 @@ define(['jquery', 'underscore', 'backbone'], accountsUrl: null }, - defaultView: "share", + defaultView: "submit", initialize: function() { diff --git a/metacatui/src/main/webapp/js/themes/nceas/routers/router.js b/metacatui/src/main/webapp/js/themes/nceas/routers/router.js index fe833e876..c807f9569 100644 --- a/metacatui/src/main/webapp/js/themes/nceas/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/nceas/routers/router.js @@ -15,7 +15,8 @@ function ($, _, Backbone) { 'signup' : 'renderLdap', // use ldapweb for registration "signinldaperror" : "renderLdapSignInError", 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI - 'share(/*pid)' : 'renderEditor' // metadata Editor + 'share(/*pid)' : 'renderEditor', // metadata Editor + 'submit(/*pid)' : 'renderEditor' // metadata Editor }, initialize: function(){ diff --git a/metacatui/src/main/webapp/js/views/EditorView.js b/metacatui/src/main/webapp/js/views/EditorView.js index 4d853bb02..13d96840c 100644 --- a/metacatui/src/main/webapp/js/views/EditorView.js +++ b/metacatui/src/main/webapp/js/views/EditorView.js @@ -479,7 +479,7 @@ define(['underscore', if(savedObject.type != "DataPackage") return; //Change the URL to the new id - MetacatUI.uiRouter.navigate("#share/" + this.model.get("id"), { trigger: false, replace: true }); + MetacatUI.uiRouter.navigate("#submit/" + this.model.get("id"), { trigger: false, replace: true }); this.toggleControls(); @@ -572,7 +572,7 @@ define(['underscore', view.model = null; //Update the URL - MetacatUI.uiRouter.navigate("#share/" + view.pid, { trigger: false, replace: true }); + MetacatUI.uiRouter.navigate("#submit/" + view.pid, { trigger: false, replace: true }); //Render the new model view.render(); diff --git a/metacatui/src/main/webapp/js/views/NavbarView.js b/metacatui/src/main/webapp/js/views/NavbarView.js index 195993eab..364bf8f0a 100644 --- a/metacatui/src/main/webapp/js/views/NavbarView.js +++ b/metacatui/src/main/webapp/js/views/NavbarView.js @@ -96,7 +96,7 @@ define(['jquery', 'underscore', 'backbone', 'views/SignInView', 'text!templates/ MetacatUI.appView.showView(MetacatUI.appView.registryView); //Otherwise, just navigate to it else - MetacatUI.uiRouter.navigate("share", { trigger: true }); + MetacatUI.uiRouter.navigate("submit", { trigger: true }); }, hideDropdown: function(){ From 71df20cb0e0f8caed309915c4d1e04748dd9fa41 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 12 Oct 2017 15:27:45 -0400 Subject: [PATCH 430/560] Started some changes to KNB styling for the Editor Related to #278 --- metacatui/src/main/webapp/css/metacatui-common.css | 5 +++++ metacatui/src/main/webapp/js/themes/knb/css/metacatui.css | 6 ++++++ 2 files changed, 11 insertions(+) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index e316fbcd2..1aeb74fe9 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3199,6 +3199,11 @@ Editor View height: 15px; margin-bottom: 5px; } +.editor-view { + margin: 0px; + width: 100%; + max-width: 100%; +} .Editor #Content { padding-top: 70px; max-width: 100%; diff --git a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css index 7bcbaa684..f781643cb 100644 --- a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css @@ -173,7 +173,13 @@ div.row-fluid > a[name] { margin: 35px auto auto auto; } + +/* Editor +-------------------------------------------------- */ +.Editor #Content { + padding-top: 0px; +} /* MDQ -------------------------------------------------- */ From 79bd1a4486bdcbfa06c6413199128722fb082ead Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Mon, 16 Oct 2017 17:49:48 -0400 Subject: [PATCH 431/560] Merge changes from 1.14 branch to the profile view, and add some minor adjustments/fixes --- .../src/main/webapp/css/metacatui-common.css | 34 ++- .../src/main/webapp/js/models/AppModel.js | 2 +- .../src/main/webapp/js/models/NodeModel.js | 7 + metacatui/src/main/webapp/js/models/Stats.js | 220 +++++++++++++++- .../src/main/webapp/js/templates/profile.html | 66 +++-- .../webapp/js/themes/arctic/css/metacatui.css | 1 + .../js/themes/arctic/models/AppModel.js | 2 +- .../js/themes/dataone/css/metacatui.css | 1 + .../js/themes/default/css/metacatui.css | 2 +- .../main/webapp/js/views/CircleBadgeView.js | 40 ++- .../main/webapp/js/views/DataCatalogView.js | 2 +- .../src/main/webapp/js/views/LineChartView.js | 69 +++-- .../src/main/webapp/js/views/StatsView.js | 238 +++++++++++++++++- .../src/main/webapp/js/views/UserView.js | 25 +- 14 files changed, 639 insertions(+), 70 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 1aeb74fe9..a1f9e24df 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -2420,6 +2420,13 @@ address.email-container:before{ stroke: #CCC; fill: #CCC; } +.profile .circle-badge circle.no-activity{ + stroke: #CCC; + fill: transparent; +} +.profile .circle-badge text.no-activity{ + fill: #CCC; +} .profile .chart-title{ float: left; } @@ -2430,14 +2437,22 @@ address.email-container:before{ } .profile .stripe{ clear: both; + min-height: 200px; +} +.profile .chart-title{ + height: 100%; } .profile .chart-title.uploads{ width: 100%; } +.profile .quick-stats, +.profile .quick-stats .badge-container{ + height: 280px; +}s .profile .downloads .chart-title, .profile .uploads .chart-title{ width: 100%; - min-width: 300px; + min-width: 250px; } .profile #downloads-title, .profile #uploads-title{ @@ -2455,9 +2470,25 @@ address.email-container:before{ padding-bottom: 20px; padding-top: 20px; } +.profile .packages p { + color: #333; +} +.no-activity .profile .packages p{ + color: inherit; +} .temporal-coverage-chart{ width: calc(100% - 300px); } +.profile .circle-badge circle{ + fill: transparent; +} +.profile .quick-stats .circle-badge .count{ + font-size: 27px; +} +.profile .quick-stats .circle-badge .title{ + font-size: 18px; +} + /**** Bar Charts ******/ .bar-chart .bar-label.bg{ fill: rgba(0,0,0,0.8); @@ -3131,6 +3162,7 @@ input.subtle:focus .jump-width-input{ transition: width 1000s; } +.nav .input-submit{ margin-left: 10px; height: 1em; diff --git a/metacatui/src/main/webapp/js/models/AppModel.js b/metacatui/src/main/webapp/js/models/AppModel.js index 9bd4d9cf4..f220caa53 100644 --- a/metacatui/src/main/webapp/js/models/AppModel.js +++ b/metacatui/src/main/webapp/js/models/AppModel.js @@ -130,7 +130,7 @@ define(['jquery', 'underscore', 'backbone'], } if(typeof this.get("d1LogServiceUrl") != "undefined") - this.set('d1LogServiceUrl', this.get('d1CNBaseUrl') + this.get('d1CNService') + '/query/logsolr/'); + this.set('d1LogServiceUrl', this.get('d1CNBaseUrl') + this.get('d1CNService') + '/query/logsolr/?'); this.set("nodeServiceUrl", this.get("d1CNBaseUrl") + this.get("d1CNService") + "/node/"); this.set('resolveServiceUrl', this.get('d1CNBaseUrl') + this.get('d1CNService') + '/resolve/'); diff --git a/metacatui/src/main/webapp/js/models/NodeModel.js b/metacatui/src/main/webapp/js/models/NodeModel.js index 8b41d9e40..18702b59a 100644 --- a/metacatui/src/main/webapp/js/models/NodeModel.js +++ b/metacatui/src/main/webapp/js/models/NodeModel.js @@ -173,6 +173,13 @@ define(['jquery', 'underscore', 'backbone'], } }); + }, + + /* + * Returns true if the given nodeId is a Coordinating Node + */ + isCN: function(nodeId){ + return _.findWhere(this.get("coordinators"), { identifier: nodeId }); } }); diff --git a/metacatui/src/main/webapp/js/models/Stats.js b/metacatui/src/main/webapp/js/models/Stats.js index f84fd9556..3b17bcdaa 100644 --- a/metacatui/src/main/webapp/js/models/Stats.js +++ b/metacatui/src/main/webapp/js/models/Stats.js @@ -12,6 +12,7 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], metadataCount: 0, dataCount: 0, + totalCount: 0, metadataFormatIDs: [], //Uses same structure as Solr facet counts: ["text/csv", 5] dataFormatIDs: [], //Uses same structure as Solr facet counts: ["text/csv", 5] @@ -22,6 +23,11 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], metadataUploadDates: null, dataUploadDates: null, + //Number of updates to content for each time period + firstUpdate: 0, + dataUpdateDates: null, + metadataUpdateDates: null, + downloads: 0, metadataDownloads: null, dataDownloads: null, @@ -91,12 +97,16 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], this.listenToOnce(this, 'change:lastEndDate', this.getCollectionYearFacets); this.listenToOnce(this, 'change:dataCount', this.getDataFormatIDs); this.listenToOnce(this, 'change:metadataCount', this.getMetadataFormatIDs); + this.listenToOnce(this, 'change:firstUpload', this.getUpdateDates); this.getFirstBeginDate(); + this.getFirstUpload(); + this.getFormatTypes(); - this.getUploads(); + this.getDownloadDates(); + this.getMdqStatsTotal(); //this.getDataDownloadDates(); //this.getMetadataDownloadDates(); @@ -229,6 +239,8 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], "&group=true" + "&group.field=formatType" + "&group.limit=0" + + "&stats=true" + + "&stats.field=size" + "&sort=formatType%20desc" + "&wt=json"; @@ -258,6 +270,8 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], //Store falsey data model.set('dataCount', 0); model.set('metadataCount', 0); + model.set("totalCount", 0); + model.trigger("change:totalCount"); model.set('metadataFormatIDs', ["", 0]); model.set('dataFormatIDs', ["", 0]); @@ -268,6 +282,10 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], model.set('metadataCount', formats[0].doclist.numFound); model.set('dataCount', formats[1].doclist.numFound); } + + //Get the total size of all the files in the index + var totalSize = data.stats.stats_fields.size.sum; + model.set("totalSize", totalSize); } } @@ -329,11 +347,192 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], } }, + /* + * getUpdateDates will get the number of newest-version science metadata and data + * objects uploaded in each month + */ + getUpdateDates: function(){ + + //If the node model hasn't been retrieved yet, then wait - because we need to know + //if the first update date should be based on the DataONE time frame (started in 2012) + //or a metacat timeframe (as early as 2001) + if( !MetacatUI.nodeModel.get("coordinators").length ){ + this.listenToOnce(MetacatUI.nodeModel, "change:coordinators", this.getUpdateDates); + return; + } + + // If there has never been an update, there are no dates to get + if( !this.get("firstUpload") ){ + this.set('firstUpdate', null); + + this.set("metadataUpdateDates", []); + this.set("dataUpdateDates", []); + + return; + } + + var model = this; + + var now = new Date(); + + var dataQuery = "q=" + model.get('query') + + "+-obsoletedBy:*+formatType:DATA"; + + var metadataQuery = "q=" + model.get('query') + + "+-obsoletedBy:*+formatType:METADATA"; + + var firstPossibleUpdate = MetacatUI.nodeModel.isCN(MetacatUI.nodeModel.get("currentMemberNode"))? + this.firstPossibleDataONEDate : model.get("firstUpload"); + + var facets = "&rows=1" + + "&sort=dateUploaded+asc" + + "&facet=true" + + "&facet.missing=true" + //Include months that have 0 uploads + "&facet.limit=-1" + + "&facet.range=dateUploaded" + + "&facet.range.start=" + firstPossibleUpdate + + "&facet.range.end=" + now.toISOString() + + "&facet.range.gap=%2B1MONTH" + + "&wt=json"; + + //Run the query + var requestSettings = { + url: MetacatUI.appModel.get('queryServiceUrl') + metadataQuery + facets, + dataType: "json", + type: "GET", + success: function(data, textStatus, xhr) { + + if( !data.response.numFound ){ + model.set('firstUpdate', null); + + model.set("metadataUpdateDates", []); + + } + else{ + // Save the earliest dateUploaded and total found in our model + model.set('firstUpdate', data.response.docs[0].dateUploaded); + + //Remove all the empty facet counts at the beginning of the array + var updateDates = data.facet_counts.facet_ranges.dateUploaded.counts; + + while(updateDates[1] == 0){ + + updateDates.splice(0, 2); + + } + + //Save the dateUploaded facets for metadata objects + model.set("metadataUpdateDates", updateDates); + } + + var requestSettings = { + url: MetacatUI.appModel.get('queryServiceUrl') + dataQuery + facets, + type: 'GET', + dataType: "json", + success: function(data, textStatus, xhr) { + if( !data.response.numFound ){ + model.set("dataUpdateDates", []); + } + else{ + + // Save the earliest dateUploaded and total found in our model + if(data.response.docs[0].dateUploaded < model.set("firstUpdate")) + model.set('firstUpdate', data.response.docs[0].dateUploaded); + + //Remove all the empty facet counts at the beginning of the array + var updateDates = data.facet_counts.facet_ranges.dateUploaded.counts; + + while(updateDates[1] == 0){ + + updateDates.splice(0, 2); + + } + + //Save the dateUploaded facets for data objects + model.set("dataUpdateDates", updateDates); + } + } + } + + $.ajax(_.extend(requestSettings, MetacatUI.appUserModel.createAjaxSettings())); + } + } + + $.ajax(_.extend(requestSettings, MetacatUI.appUserModel.createAjaxSettings())); + + }, + + /* + * Gets the earliest dateUploaded from the solr index + */ + getFirstUpload: function(){ + //If the node model hasn't been retrieved yet, then wait - because we need to know + //if the first update date should be based on the DataONE time frame (started in 2012) + //or a metacat timeframe (as early as 2001) + if( !MetacatUI.nodeModel.get("coordinators").length ){ + this.listenToOnce(MetacatUI.nodeModel, "change:coordinators", this.getFirstUpload); + return; + } + + var now = new Date(), + model = this, + firstPossibleUpload = MetacatUI.nodeModel.isCN(MetacatUI.appModel.get("nodeId") || MetacatUI.nodeModel.get("currentMemberNode"))? + this.firstPossibleDataONEDate : this.firstPossibleUpload; + + //Get the earliest upload date + var query = "q=" + this.get('query') + + "+formatType:(METADATA OR DATA)" + //Weeds out resource maps and annotations + "+dateUploaded:[" + firstPossibleUpload + "%20TO%20" + now.toISOString() + "]" + //Weeds out badly formatted dates + "+-obsoletes:*"+ //Only count one version of a revision chain + "&fl=dateUploaded" + + "&rows=1" + + "&sort=dateUploaded+asc" + + "&wt=json"; + + //Run the query + var requestSettings = { + url: MetacatUI.appModel.get('queryServiceUrl') + query, + type: "GET", + dataType: "json", + success: function(data, textStatus, xhr) { + if(!data.response.numFound){ + //Save some falsey values if none are found + model.set('totalUploads', 0); + model.trigger("change:totalUploads"); + + model.set('firstUpload', null); + + model.set("dataUploads", 0); + model.set("metadataUploads", 0); + model.set('metadataUploadDates', []); + model.set('dataUploadDates', []); + } + else{ + // Save the earliest dateUploaded and total found in our model + model.set('firstUpload', data.response.docs[0].dateUploaded); + model.set('totalUploads', data.response.numFound); + + //model.getUploadDates(); + } + } + } + + $.ajax(_.extend(requestSettings, MetacatUI.appUserModel.createAjaxSettings())); + + }, + /** * getUploads will get the files uploaded statistics */ getUploads: function() { + if( !this.get("firstUpload") ){ + this.set('totalUploads', 0); + this.trigger("change:totalUploads"); + + return; + } + var model = this; var now = new Date(); @@ -555,7 +754,11 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], */ getDataDownloadDates: function(){ - if(!MetacatUI.appModel.get("d1LogServiceUrl")) return; + if(!MetacatUI.appModel.get("d1LogServiceUrl")){ + this.set("downloads", 0); + this.trigger("change:downloads"); + return; + } var model = this; @@ -589,7 +792,12 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], }, getMetadataDownloadDates: function(){ - if(!MetacatUI.appModel.get("d1LogServiceUrl")) return; + if(!MetacatUI.appModel.get("d1LogServiceUrl")){ + this.set("downloads", 0); + this.trigger("change:downloads"); + + return; + } var model = this; @@ -624,7 +832,11 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], }, getDownloadDates: function(){ - if(!MetacatUI.appModel.get("d1LogServiceUrl")) return; + if(!MetacatUI.appModel.get("d1LogServiceUrl")){ + this.set("downloads", 0); + this.trigger("change:downloads"); + return; + } var model = this; diff --git a/metacatui/src/main/webapp/js/templates/profile.html b/metacatui/src/main/webapp/js/templates/profile.html index 96781ba57..18ad067bd 100644 --- a/metacatui/src/main/webapp/js/templates/profile.html +++ b/metacatui/src/main/webapp/js/templates/profile.html @@ -4,24 +4,41 @@

          <%=title%>

          <% if(typeof description == "string"){ %>

          <%=description%>

          <% } %> -
          -
          -
          -

          Metadata quality metrics

          -

          A summary of the MDQ scores are included below

          -
          -
          +
          +
          +
          +
          +
          +

          + The total number of publicly-available metadata records. + Only the latest version of each metadata record is counted. + A "dataset" here is defined by a single metadata record which + may be packaged with one or more data files. +

          +
          +
          +
          +
          +
          +

          + The sum of all publicly-available metadata and data files + in this repository. Only the latest version of each file is + included. +

          +
          -
          -
          -

          Downloads

          -

          The number of individual metadata and data files downloaded over time. These download counts are partially - COUNTER compliant, meaning that downloads from some Internet robots and - repeat downloads within a certain time window are excluded.

          +
          +
          +
          +

          Downloads

          +

          The number of individual metadata and data files downloaded over time. These download counts are partially + COUNTER compliant, meaning that downloads from some Internet robots and + repeat downloads within a certain time window are excluded.

          +
          @@ -29,13 +46,14 @@

          Downloads

          -
          -
          -

          Uploads

          -

          The number of individual metadata and data files uploaded over time. Only the most recent version of each file is counted.

          +
          +

          Latest Updates

          +

          When datasets were last updated, separated by content type (science metadata or data).

          +
          +
          +
          +
          -
          -
          @@ -64,5 +82,15 @@

          Time period of data

          +
          \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index 101a302b0..072fb95e6 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -1003,6 +1003,7 @@ svg .packages, .profile .packages{ color: #146660; fill: #146660; + stroke: #146660; } .profile .bar-label.packages{ fill: inherit; diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js index ed60a1182..1c3144e6c 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js @@ -106,7 +106,7 @@ define(['jquery', 'underscore', 'backbone'], this.set('viewServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/views/metacatui/'); this.set('publishServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/publish/'); this.set('authServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/isAuthorized/'); - this.set('queryServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/query/solr/'); + this.set('queryServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/query/solr/?'); this.set('metaServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/meta/'); this.set('objectServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/object/'); this.set('registryServiceUrl', this.get('baseUrl') + this.get('context') + '/cgi-bin/register-dataset.cgi'); diff --git a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css index 1691722ca..9162030b3 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css @@ -1728,6 +1728,7 @@ svg .packages, .profile .packages{ color: #FF6633; fill: #FF6633; + stroke: #FF6633; } .profile .bar-label.packages{ diff --git a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css index ca9dc5db2..fdc047a89 100644 --- a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css @@ -1472,7 +1472,7 @@ li.ui-menu-item > a:hover, } .mapMode #results-container { width: 40%; - width: calc(100% - 33% - 229px); + width: calc(66.66% - 227px); overflow-x: hidden; overflow-y: scroll; -webkit-transform: translate3d(0,0,1); diff --git a/metacatui/src/main/webapp/js/views/CircleBadgeView.js b/metacatui/src/main/webapp/js/views/CircleBadgeView.js index 0f5801425..acc5b27c9 100644 --- a/metacatui/src/main/webapp/js/views/CircleBadgeView.js +++ b/metacatui/src/main/webapp/js/views/CircleBadgeView.js @@ -32,6 +32,8 @@ define(['jquery', 'underscore', 'backbone', 'd3'], this.useGlobalR = options.useGlobalR || false; this.className = options.className || ""; this.margin = options.margin || 20; + this.titlePlacement = options.titlePlacement || null; + this.height = options.height || null; }, // http://stackoverflow.com/questions/9651167/svg-not-rendering-properly-as-a-backbone-view @@ -123,6 +125,9 @@ define(['jquery', 'underscore', 'backbone', 'd3'], var svg = d3.select(this.el) .attr("class", "circle-badge " + this.className); + if(this.height) + svg.attr("height", this.height); + //Draw the circles var circle = svg.selectAll("circle") .data(this.data) @@ -166,20 +171,39 @@ define(['jquery', 'underscore', 'backbone', 'd3'], .selectAll("text") .data(this.data) .enter().append("svg:text") - .text(function(d){ return MetacatUI.appView.commaSeparateNumber(d.count) || 0; }) + .text(function(d){ return typeof d.count == "string" ? d.count : MetacatUI.appView.commaSeparateNumber(d.count) || 0; }) .attr("transform", function(d, i){ - return "translate(" + d.x + "," + (d.r+12) + ")"; + + var y = (viewRef.titlePlacement == "inside")? d.r-12 : d.r+12; + + return "translate(" + d.x + "," + y + ")"; }) .attr("class", function(d){ return d.className + " count"; }) .attr("text-anchor", "middle"); if(this.title){ - //Draw the title next to the circles at the end - svg.append("text") - .text(this.title) - .attr("class", "title") - .attr("transform", function(d, i){ return "translate(" + (viewRef.data[viewRef.data.length-1].x + viewRef.data[viewRef.data.length-1].r + viewRef.margin) + "," + (viewRef.data[viewRef.data.length-1].r + 5) + ")"; }) - .attr("text-anchor", "left"); + + if(this.titlePlacement == "inside"){ + + //Draw the title next to the circles at the end + var title = svg.append("text") + .data(this.data) + .text(this.title) + .attr("class", "title") + .attr("text-anchor", "middle") + .attr("transform", function(d, i){ + return "translate(" + d.x + "," + (d.r + 30) + ")"; + }); + + } + else{ + //Draw the title next to the circles at the end + svg.append("text") + .text(this.title) + .attr("class", "title") + .attr("transform", function(d, i){ return "translate(" + (viewRef.data[viewRef.data.length-1].x + viewRef.data[viewRef.data.length-1].r + viewRef.margin) + "," + (viewRef.data[viewRef.data.length-1].r + 5) + ")"; }) + .attr("text-anchor", "left"); + } } return this; diff --git a/metacatui/src/main/webapp/js/views/DataCatalogView.js b/metacatui/src/main/webapp/js/views/DataCatalogView.js index 289db1911..09215a34c 100644 --- a/metacatui/src/main/webapp/js/views/DataCatalogView.js +++ b/metacatui/src/main/webapp/js/views/DataCatalogView.js @@ -2668,7 +2668,7 @@ define(['jquery', this.$results.html('

          No results found.

          '); if(MetacatUI.theme == "arctic"){ //When we get new results, check if the user is searching for their own datasets and display a message - if((MetacatUI.appView.dataCatalogView.searchModel.getQuery() == MetacatUI.appUserModel.get("searchModel").getQuery()) && !MetacatUI.appSearchResults.length){ + if((MetacatUI.appView.dataCatalogView && MetacatUI.appView.dataCatalogView.searchModel.getQuery() == MetacatUI.appUserModel.get("searchModel").getQuery()) && !MetacatUI.appSearchResults.length){ $("#no-results-found").after("

          Where are my data sets?

          If you are a previous ACADIS Gateway user, " + "you will need to take additional steps to access your data sets in the new NSF Arctic Data Center." + "Send us a message at support@arcticdata.io with your old ACADIS " + diff --git a/metacatui/src/main/webapp/js/views/LineChartView.js b/metacatui/src/main/webapp/js/views/LineChartView.js index 9da7fa674..398126b00 100644 --- a/metacatui/src/main/webapp/js/views/LineChartView.js +++ b/metacatui/src/main/webapp/js/views/LineChartView.js @@ -44,11 +44,11 @@ define(['jquery', 'underscore', 'backbone', 'd3'], this.frequency = options.frequency || 1; //Use 0 to not add any points if(!options.data) this.frequency = 0; //If no data is provided, do not draw any points (otherwise, one point at 0,0 will be drawn) this.yLabel = options.yLabel || ""; - this.labelValue = options.labelValue || "Value: "; - this.labelWidth = options.labelWidth || 130; + this.labelValue = options.labelValue || ""; + this.labelWidth = options.labelWidth || (this.labelValue.length * 7) + (this.yLabel.length * 7) + 60; this.radius = options.radius || 6; this.width = options.width || 650; - this.height = options.height || 250; + this.height = options.height || 300; this.formatFromSolrFacets = options.formatFromSolrFacets || false; this.cumulative = options.cumulative || false; @@ -112,7 +112,7 @@ define(['jquery', 'underscore', 'backbone', 'd3'], if(!this.data) return this; - var margin = {top: 20, right: 50, bottom: 30, left: 80}; + var margin = {top: 20, right: 50, bottom: 50, left: 80}; this.margin = margin; this.width = this.width - margin.left - margin.right; this.height = this.height - margin.top - margin.bottom; @@ -120,27 +120,42 @@ define(['jquery', 'underscore', 'backbone', 'd3'], var min = d3.min(this.data, function(d) { return d.count; }), max = d3.max(this.data, function(d) { return d.count; }), difference = max - min; + + //Format the data + this.data.forEach(function(d) { + d.date = viewRef.parseDate(d.date); + d.count = +d.count; + }); + //Set the y scale /*if((difference > 30000) || ((min < 10) && (difference > 10000))){ this.y = d3.scale.log() - .range([this.height, 0]); + .range([this.height, 0]) + .domain([1, max]); + var log = true; this.className += " log-scale"; } else{*/ this.y = d3.scale.linear() - .range([this.height, 0]); + .range([this.height, 0]) + .domain([0, max]); var log = false; //} - this.x = d3.time.scale().range([0, this.width]); - + //Set the x scale + this.x = d3.time.scale() + .range([0, this.width]) + .domain(d3.extent(this.data, function(d) { return d.date; })); + + //Set up the x axis var xAxis = d3.svg.axis() .scale(this.x) .orient("bottom") .ticks(this.xTicks) .tickFormat(this.xTickFormat); + //Set up the y axis var yAxis = d3.svg.axis() .scale(this.y) .orient("left") @@ -155,15 +170,6 @@ define(['jquery', 'underscore', 'backbone', 'd3'], .attr("height", this.height + margin.top + margin.bottom) .append("g") .attr("transform", "translate(" + margin.left + "," + margin.top + ")"); - - this.data.forEach(function(d) { - d.date = viewRef.parseDate(d.date); - d.count = +d.count; - }); - - this.x = this.x.domain(d3.extent(this.data, function(d) { return d.date; })); - if(log) this.y = this.y.domain([1, max]); //y axis is always 1 - max y value - else this.y = this.y.domain([0, max]); /* * ======================================================================== @@ -179,6 +185,12 @@ define(['jquery', 'underscore', 'backbone', 'd3'], .attr("class", "y axis") .call(yAxis); + svg.selectAll(".x.axis .tick text") + .style("text-anchor", 'end') + .attr("dx", "-.8em") + .attr("dy", ".15em") + .attr("transform", "rotate(-65)"); + /* * ======================================================================== * Draw the y-axis title @@ -202,7 +214,6 @@ define(['jquery', 'underscore', 'backbone', 'd3'], var line = d3.svg.line() .x(function(d) { return viewRef.x(d.date); }) .y(function(d) { return viewRef.y(d.count); }); - //.interpolate("linear"); svg.append("path") @@ -382,7 +393,7 @@ define(['jquery', 'underscore', 'backbone', 'd3'], //Don't let our label bleed off the edge if(xPos < 0) xPos = xPos + labelWidth; - return xPos + labelXPadding;; }) + return xPos + labelXPadding; }) .attr("y", function(d, i){ var yPos = viewRef.y(d.count) + viewRef.radius; //Don't let our label bleed off the edge @@ -397,7 +408,7 @@ define(['jquery', 'underscore', 'backbone', 'd3'], labels.append("text") .text(function(d, i){ - return viewRef.labelValue + MetacatUI.appView.commaSeparateNumber(d.count); + return viewRef.labelValue + MetacatUI.appView.commaSeparateNumber(d.count) + " " + viewRef.yLabel; }) .attr("x", function(d, i){ var xPos = viewRef.x(d.date) - (labelWidth/2); @@ -443,15 +454,23 @@ define(['jquery', 'underscore', 'backbone', 'd3'], //Format the data for a cumulative time series chart //We will take only the first 10 characters of the date //To make it a cumulative chart, we will keep adding to the count - var uploadData = []; - var lastCount = 0; + var newData = []; + var totalCount = 0; + for(var i=0; i < counts.length; i+=2){ - uploadData.push({date: counts[i].substr(0, 10), count: lastCount + counts[i+1]}); - if(this.cumulative) lastCount += counts[i+1]; + if(this.cumulative) + totalCount += counts[i+1]; + else + totalCount = counts[i+1]; + + newData.push({ + date: counts[i].substr(0, 10), + count: totalCount + }); } - return uploadData; + return newData; } }); diff --git a/metacatui/src/main/webapp/js/views/StatsView.js b/metacatui/src/main/webapp/js/views/StatsView.js index 741308268..7933e20f4 100644 --- a/metacatui/src/main/webapp/js/views/StatsView.js +++ b/metacatui/src/main/webapp/js/views/StatsView.js @@ -30,21 +30,27 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'LineChart', 'BarChart', 'Donu //Only trigger the functions that draw SVG charts if d3 loaded correctly if(d3){ - this.listenTo(MetacatUI.statsModel, 'change:dataUploadDates', this.drawUploadChart); + //this.listenTo(MetacatUI.statsModel, 'change:dataUploadDates', this.drawUploadChart); this.listenTo(MetacatUI.statsModel, 'change:temporalCoverage', this.drawCoverageChart); this.listenTo(MetacatUI.statsModel, 'change:metadataDownloadDates', this.drawDownloadsChart); this.listenTo(MetacatUI.statsModel, 'change:dataDownloadDates', this.drawDownloadsChart); this.listenTo(MetacatUI.statsModel, 'change:downloadDates', this.drawDownloadsChart); + this.listenTo(MetacatUI.statsModel, "change:dataUpdateDates", this.drawUpdatesChart); + this.listenTo(MetacatUI.statsModel, "change:totalSize", this.drawTotalSize); + this.listenTo(MetacatUI.statsModel, 'change:metadataCount', this.drawTotalCount); + this.listenTo(MetacatUI.statsModel, 'change:dataFormatIDs', this.drawDataCountChart); + this.listenTo(MetacatUI.statsModel, 'change:metadataFormatIDs', this.drawMetadataCountChart); + + //this.listenTo(MetacatUI.statsModel, 'change:dataUploads', this.drawUploadTitle); } - this.listenTo(MetacatUI.statsModel, 'change:dataUploads', this.drawUploadTitle); this.listenTo(MetacatUI.statsModel, 'change:downloads', this.drawDownloadTitle); - this.listenTo(MetacatUI.statsModel, 'change:dataFormatIDs', this.drawDataCountChart); - this.listenTo(MetacatUI.statsModel, 'change:metadataFormatIDs', this.drawMetadataCountChart); this.listenTo(MetacatUI.statsModel, 'change:lastEndDate', this.drawCoverageChartTitle); // mdq this.listenTo(MetacatUI.statsModel, 'change:mdqStats', this.drawMdqStats); + + this.listenTo(MetacatUI.statsModel, "change:totalCount", this.showNoActivity); // set the header type MetacatUI.appModel.set('headerType', 'default'); @@ -177,6 +183,41 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'LineChart', 'BarChart', 'Donu this.$('.format-charts-metadata').html(donut.render().el); }, + drawFirstUpload: function(){ + + var className = ""; + + if( !MetacatUI.statsModel.get("firstUpload") ){ + var chartData = [{ + count: "N/A", + className: "packages no-activity" + }]; + } + else{ + var firstUpload = new Date(MetacatUI.statsModel.get("firstUpload")), + readableDate = firstUpload.toDateString(); + + readableDate = readableDate.substring(readableDate.indexOf(" ") + 1); + + var chartData = [{ + count: readableDate, + className: "packages" + }]; + } + + //Create the circle badge + var dateBadge = new CircleBadge({ + id: "first-upload-badge", + data: chartData, + title: "first upload", + titlePlacement: "inside", + useGlobalR: true, + globalR: 100 + }); + + this.$("#first-upload").html(dateBadge.render().el); + }, + //drawUploadChart will get the upload stats from the stats model and draw a time series cumulative chart drawUploadChart: function(){ //Get the width of the chart by using the parent container width @@ -310,6 +351,151 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'LineChart', 'BarChart', 'Donu this.$('#uploads-title').prepend(uploadChartTitle.render().el); }, + /* + * drawTotalCount - draws a simple count of total metadata files/datasets + */ + drawTotalCount: function(){ + + var className = ""; + + if( !MetacatUI.statsModel.get("metadataCount") && !MetacatUI.statsModel.get("dataCount") ) + className += " no-activity"; + + var chartData = [{ + count: MetacatUI.statsModel.get("metadataCount"), + className: "packages" + className + }]; + + //Create the circle badge + var countBadge = new CircleBadge({ + id: "total-datasets-title", + data: chartData, + title: "datasets", + titlePlacement: "inside", + useGlobalR: true, + globalR: 100, + height: 220 + }); + + this.$('#total-datasets').html(countBadge.render().el); + }, + + /* + * drawTotalSize draws a CircleBadgeView with the total file size of + * all current metadata and data files + */ + drawTotalSize: function(){ + + if( !MetacatUI.statsModel.get("totalSize") ){ + var chartData = [{ + count: "0 bytes", + className: "packages no-activity" + }]; + + } + else{ + var chartData = [{ + count: this.bytesToSize( MetacatUI.statsModel.get("totalSize") ), + className: "packages" + }]; + } + + //Create the circle badge + var sizeBadge = new CircleBadge({ + id: "total-size-title", + data: chartData, + title: "of content", + titlePlacement: "inside", + useGlobalR: true, + globalR: 100, + height: 220 + }); + + this.$('#total-size').html(sizeBadge.render().el); + }, + + /* + * drawUpdatesChart - draws a line chart representing the latest updates over time + */ + drawUpdatesChart: function(){ + + //If there was no first upload, draw a blank chart and exit + if(!MetacatUI.statsModel.get('firstUpdate')){ + + var lineChartView = new LineChart( + { id: "updates-chart", + yLabel: "files updated", + frequency: 0, + cumulative: false, + width: this.$('.metadata-updates-chart').width() + }); + + this.$('.metadata-updates-chart').html(lineChartView.render().el); + + return; + } + + //Set the frequency of our points + var frequency = 12; + + //If there isn't a lot of points to graph, draw points more frequently on the line + if(MetacatUI.statsModel.get("metadataUpdateDates").length < 40) frequency = 1; + + //Create the line chart for metadata updates + var metadataLineChart = new LineChart( + { data: MetacatUI.statsModel.get('metadataUpdateDates'), + formatFromSolrFacets: true, + cumulative: false, + id: "updates-chart", + className: "metadata", + yLabel: "metadata files updated", + // frequency: frequency, + radius: 2, + width: this.$('.metadata-updates-chart').width(), + labelDate: "M-y" + }); + + this.$('.metadata-updates-chart').html(metadataLineChart.render().el); + + //Only draw the data updates chart if there was at least one uploaded + if(MetacatUI.statsModel.get("dataCount")){ + //Create the line chart for data updates + var dataLineChart = new LineChart( + { data: MetacatUI.statsModel.get('dataUpdateDates'), + formatFromSolrFacets: true, + cumulative: false, + id: "updates-chart", + className: "data", + yLabel: "data files updated", + // frequency: frequency, + radius: 2, + width: this.$('.data-updates-chart').width(), + labelDate: "M-y" + }); + + this.$('.data-updates-chart').html(dataLineChart.render().el); + + } + else{ + //Create the line chart for data updates + var dataLineChart = new LineChart( + { data: null, + formatFromSolrFacets: true, + cumulative: false, + id: "updates-chart", + className: "data no-activity", + yLabel: "data files updated", + // frequency: frequency, + radius: 2, + width: this.$('.data-updates-chart').width(), + labelDate: "M-y" + }); + + this.$('.data-updates-chart').html(dataLineChart.render().el); + } + + }, + /* * drawDownloadsChart - draws a line chart representing the downloads over time */ @@ -563,6 +749,50 @@ define(['jquery', 'underscore', 'backbone', 'd3', 'LineChart', 'BarChart', 'Donu }, + /* + * Shows that this person/group/node has no activity + */ + showNoActivity: function(){ + this.$(".show-loading .loading").remove(); + + this.$el.addClass("no-activity"); + }, + + /** + * Convert number of bytes into human readable format + * + * @param integer bytes Number of bytes to convert + * @param integer precision Number of digits after the decimal separator + * @return string + */ + bytesToSize: function(bytes, precision){ + var kilobyte = 1024; + var megabyte = kilobyte * 1024; + var gigabyte = megabyte * 1024; + var terabyte = gigabyte * 1024; + + if(typeof bytes === "undefined") var bytes = this.get("size"); + + if ((bytes >= 0) && (bytes < kilobyte)) { + return bytes + ' B'; + + } else if ((bytes >= kilobyte) && (bytes < megabyte)) { + return (bytes / kilobyte).toFixed(precision) + ' KB'; + + } else if ((bytes >= megabyte) && (bytes < gigabyte)) { + return (bytes / megabyte).toFixed(precision) + ' MB'; + + } else if ((bytes >= gigabyte) && (bytes < terabyte)) { + return (bytes / gigabyte).toFixed(precision) + ' GB'; + + } else if (bytes >= terabyte) { + return (bytes / terabyte).toFixed(precision) + ' TB'; + + } else { + return bytes + ' B'; + } + }, + onClose: function () { //Clear the template this.$el.html(""); diff --git a/metacatui/src/main/webapp/js/views/UserView.js b/metacatui/src/main/webapp/js/views/UserView.js index 5e0ef5bb2..5392e1ca6 100644 --- a/metacatui/src/main/webapp/js/views/UserView.js +++ b/metacatui/src/main/webapp/js/views/UserView.js @@ -355,8 +355,7 @@ define(['jquery', 'underscore', 'backbone', 'clipboard', 'collections/UserGroup' insertStats: function(){ if(this.model.noActivity && this.statsView){ this.statsView.$el.addClass("no-activity"); - this.$("#total-upload-container").text("0"); - this.$("#total-download-container").text("0"); + this.$("#total-download-wrapper, section.downloads").hide(); return; } @@ -365,11 +364,16 @@ define(['jquery', 'underscore', 'backbone', 'clipboard', 'collections/UserGroup' //Insert a couple stats into the profile this.listenToOnce(MetacatUI.statsModel, "change:firstUpload", this.insertFirstUpload); + this.listenToOnce(MetacatUI.statsModel, "change:totalUploads", function(){ view.$("#total-upload-container").text(MetacatUI.appView.commaSeparateNumber(MetacatUI.statsModel.get("totalUploads"))); }); + MetacatUI.statsModel.once("change:downloads", function(){ - view.$("#total-download-container").text(MetacatUI.appView.commaSeparateNumber(this.get("downloads"))); + if( !this.get("downloads") ) + view.$("#total-download-wrapper, section.downloads").hide(); + else + view.$("#total-download-container").text(MetacatUI.appView.commaSeparateNumber(this.get("downloads"))); }); //Create a base query for the statistics @@ -470,8 +474,19 @@ define(['jquery', 'underscore', 'backbone', 'clipboard', 'collections/UserGroup' // Get the first upload or first operational date if(this.model.get("type") == "node"){ - var node = _.findWhere(MetacatUI.nodeModel.get("members"), {identifier: "urn:node:" + this.model.get("username") }), - firstUpload = node.memberSince? new Date(node.memberSince.substring(0, node.memberSince.indexOf("T"))) : new Date(); + + //Get the member node object + var node = _.findWhere(MetacatUI.nodeModel.get("members"), {identifier: "urn:node:" + this.model.get("username") }); + + //If there is no memberSince date, then hide this statistic and exit + if( !node.memberSince ){ + this.$("#first-upload-container, #first-upload-year-container").hide(); + return; + } + else{ + var firstUpload = node.memberSince? new Date(node.memberSince.substring(0, node.memberSince.indexOf("T"))) : new Date(); + } + } else{ var firstUpload = new Date(MetacatUI.statsModel.get("firstUpload")); From 66a17203d14a0d5c1e985803e3c7d4a79adf8c99 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Thu, 19 Oct 2017 18:49:28 -0400 Subject: [PATCH 432/560] Merge changes from 1.14 branch --- metacatui/src/main/webapp/css/metacatui-common.css | 11 ++++++++++- metacatui/src/main/webapp/js/models/Stats.js | 11 +++++++++-- .../main/webapp/js/themes/arctic/routers/router.js | 4 ++-- .../main/webapp/js/themes/dataone/routers/router.js | 2 +- .../main/webapp/js/themes/default/css/metacatui.css | 7 +++++++ metacatui/src/main/webapp/js/views/SignInView.js | 12 +++++++++++- 6 files changed, 40 insertions(+), 7 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index a1f9e24df..9200eec40 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -271,6 +271,9 @@ header .citation { .btn.download.complete.btn-primary{ color: white; } +.downloading.icon-spin.hidden{ + display: none; +} /****************************************** ** Notifications and Alerts *** @@ -499,6 +502,7 @@ img.icon{ } .result-row .tooltip{ z-index: 99999; + min-width: 100px; } .result-row .info-icons .label { background-color: #FFF; @@ -514,6 +518,10 @@ img.icon{ .result-row .tooltip-inner{ font-size: 1.2em; } +.result-row .download-icon-placeholder{ + width: 16px; + display: inline-block; +} /****************************************** ** Provenance flow-charts *** ******************************************/ @@ -2083,7 +2091,7 @@ table.download-contents .name{ } table.download-contents .btn-container, table.download-contents .btn-container .btn{ - width: 115px; + width: 140px; } .download-contents.service .btn-container .btn{ width: 135px; @@ -2622,6 +2630,7 @@ svg .no-activity, } .list-group-header.list-group-item{ background-color: #ECF1F5; + min-width: auto; } .panel>.list-group .list-group-item.active{ border-left-width: 5px; diff --git a/metacatui/src/main/webapp/js/models/Stats.js b/metacatui/src/main/webapp/js/models/Stats.js index 3b17bcdaa..0a844ef24 100644 --- a/metacatui/src/main/webapp/js/models/Stats.js +++ b/metacatui/src/main/webapp/js/models/Stats.js @@ -255,12 +255,14 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], if(formats.length == 1){ //Only one format type was found if(formats[0].groupValue == "METADATA"){ //That one format type is metadata - model.set('metadataCount', formats[0].doclist.numFound); model.set('dataCount', 0); + model.trigger("change:dataCount"); + model.set('metadataCount', formats[0].doclist.numFound); model.set('dataFormatIDs', ["", 0]); }else{ model.set('dataCount', formats[0].doclist.numFound); model.set('metadataCount', 0); + model.trigger("change:metadataCount"); model.set('metadataFormatIDs', ["", 0]); } } @@ -269,9 +271,14 @@ define(['jquery', 'underscore', 'backbone', 'models/LogsSearch'], //Store falsey data model.set('dataCount', 0); - model.set('metadataCount', 0); + model.trigger("change:dataCount"); + model.set("totalCount", 0); model.trigger("change:totalCount"); + + model.set('metadataCount', 0); + model.trigger("change:metadataCount"); + model.set('metadataFormatIDs', ["", 0]); model.set('dataFormatIDs', ["", 0]); diff --git a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js index 3a28e4d06..6f34fc7bb 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js @@ -171,7 +171,7 @@ function ($, _, Backbone) { var seriesId; //Check for a seriesId - if(MetacatUI.appModel.get("useSeriesId") && (pid.indexOf("version:") > -1)){ + if(pid.indexOf("version:") > -1){ seriesId = pid.substr(0, pid.indexOf(", version:")); pid = pid.substr(pid.indexOf(", version: ") + ", version: ".length); @@ -321,7 +321,7 @@ function ($, _, Backbone) { if(!MetacatUI.appView.signInView){ require(['views/SignInView'], function(SignInView){ - MetacatUI.appView.signInView = new SignInView({ el: "#Content"}); + MetacatUI.appView.signInView = new SignInView({ el: "#Content", fullPage: true}); MetacatUI.appView.showView(MetacatUI.appView.signInView); }); } diff --git a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js index fadcd2a82..b82460bb9 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/dataone/routers/router.js @@ -316,7 +316,7 @@ function ($, _, Backbone) { if(!MetacatUI.appView.signInView){ require(["views/SignInView"], function(SignInView){ - MetacatUI.appView.signInView = new SignInView({ el: "#Content"}); + MetacatUI.appView.signInView = new SignInView({ el: "#Content", fullPage: true }); MetacatUI.appView.showView(MetacatUI.appView.signInView); }); } diff --git a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css index fdc047a89..056275377 100644 --- a/metacatui/src/main/webapp/js/themes/default/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/default/css/metacatui.css @@ -1865,6 +1865,13 @@ svg .title{ fill: #445200; } +.no-activity .donut > g:first-child .donut-arc, +.no-activity .donut > g .donut-arc-label, +.no-activity .donut > g .donut-title-text, +.no-activity .donut > g .donut-title-count{ + fill: #CCC; +} + .donut.default .donut-labels{ visibility: hidden; diff --git a/metacatui/src/main/webapp/js/views/SignInView.js b/metacatui/src/main/webapp/js/views/SignInView.js index a57e3d7d9..af2a44c96 100644 --- a/metacatui/src/main/webapp/js/views/SignInView.js +++ b/metacatui/src/main/webapp/js/views/SignInView.js @@ -16,10 +16,20 @@ define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.ht ldapError: false, + /* Set to true if this SignInView is the only thing on the page */ + fullPage: false, + + /* Set to true if this SignInView is in a modal window */ + inPlace: false, + + /*A message to display at the top of the view */ + topMessage: "", + initialize: function(options){ if(typeof options !== "undefined"){ this.inPlace = options.inPlace; this.topMessage = options.topMessage; + this.fullPage = options.fullPage; } }, @@ -88,7 +98,7 @@ define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.ht else{ //If it's a full-page sign-in view, then empty it first - if(this.el == MetacatUI.appView.el){ + if(this.el == MetacatUI.appView.el || this.fullPage){ this.$el.empty(); var container = document.createElement("div"); container.className = "container login"; From 114e31bd02a39d369026b6eea3e1c0cc9c8323e2 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Fri, 20 Oct 2017 15:53:28 -0400 Subject: [PATCH 433/560] Moved all these to token login, including the default theme. LDAP login will not be supported in 2.0.0 unless it is the ecoinformatics LDAP that is built into the DataONE portal. Changed the SignInView to use Backbone modal windows instead of Fancybox, which is an extra unneeded library for that view. If a logged-in user navigates to #signin, either directly or after being redirected from the DataONE portal, we will redirect them to their profile. --- .../src/main/webapp/css/metacatui-common.css | 171 ++++-------------- metacatui/src/main/webapp/index.html | 2 +- .../src/main/webapp/js/models/UserModel.js | 1 - .../src/main/webapp/js/routers/router.js | 32 +++- .../src/main/webapp/js/templates/login.html | 57 +++--- .../webapp/js/templates/loginButtons.html | 4 +- .../src/main/webapp/js/templates/navbar.html | 2 +- .../webapp/js/themes/arctic/css/metacatui.css | 7 - .../webapp/js/themes/arctic/routers/router.js | 33 +++- .../js/themes/arctic/templates/altHeader.html | 15 -- .../js/themes/arctic/templates/navbar.html | 2 +- .../js/themes/dataone/css/metacatui.css | 19 +- .../js/themes/dataone/templates/login.html | 135 +++++++------- .../webapp/js/themes/goa/routers/router.js | 34 +++- .../js/themes/goa/templates/navbar.html | 2 +- .../webapp/js/themes/knb/css/metacatui.css | 8 +- .../js/themes/knb/templates/altHeader.html | 4 +- .../js/themes/knb/templates/navbar.html | 2 +- .../webapp/js/themes/nceas/routers/router.js | 16 +- .../src/main/webapp/js/views/SignInView.js | 23 ++- 20 files changed, 251 insertions(+), 318 deletions(-) diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 9200eec40..363d1d2a8 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -1290,133 +1290,12 @@ img.icon{ /****************************************** ************ Popup Login ************** ******************************************/ -.fancybox-inline{ - background-color: #FFF; - padding: 20px; - display: none; -} -.fancybox-inline h2 { - font-size: 1.2em; - text-align: center; -} -.fancybox-inline h3.subtitle{ - font-size: 1em; - font-weight: lighter; - line-height: 1.5em; - font-style: italic; -} -.fancybox-inline h4{ - font-size: 1em; -} -.fancybox-inline > form .input-group, .fancybox-inline form .btn { - max-width: 296px; - left: 22%; - position: relative; -} -.fancybox-inline > form input{ - width: 90%; - width: calc(100% - 20px); - margin-bottom: 5px; -} -.fancybox-inline > form select{ - width: calc(100% - 6px); - margin-bottom: 5px; -} -.fancybox-inline > form input.btn{ - width: 95%; - width: calc(100% - 5px); - margin-top: 20px; -} -.fancybox-inline .divider-text{ - position: absolute; - top: 50%; - left: 40%; - background-color: white; - padding: 5px; - color: #AAA; -} + .nav.list-group > .list-group-item img.icon{ width: 32px; height: auto; padding: 16px; } -.fancybox-inline .notification { - min-height: 150px; -} -.fancybox-inline { - min-width: 550px; - padding: 5px; -} -.fancybox-inline h3{ - font-size: .9em; - font-weight: normal; - margin-top: 0px; - line-height: 1.1em; -} -.fancybox-inline .well ul{ - font-size: .9em; - list-style: none; - margin-left: 0px; -} -.fancybox-inline .well ul li{ - border-bottom: 1px solid #DDD; - padding: 3px; - font-size: .9em; -} -.fancybox-inline > .row-fluid > .span7{ - border-left: 1px solid #DDD; - padding-left: 20px; -} -.fancybox-inline .btn.ldap{ - width: 220px; - left: 0; -} -.orcid-signin a > span{ - padding: 11px; - display: inline-block; - height: 1.5em; - color: #8FAF10; - border-top-right-radius: 4px; - border-bottom-right-radius: 4px; - border-left-width: 0px; - border: 1px solid #aacf14; - border-left-width: 0px; -} -.orcid-signin a { - padding: 0px; - border-radius: 4px; - padding-left: 0px; -} -.fancybox-inline .signin{ - display: inline-block; - width: auto; - padding: 0px; - margin-bottom: 10px; -} -.fancybox-inline .orcid-signin a:hover, -.fancybox-inline .orcid-signin a:hover > img{ - background-color: #aacf14; - cursor: pointer; - transition: all 500ms; - -} -.fancybox-inline .orcid-signin a:hover > span{ - color: white; -} -.fancybox-inline .well{ - border-color: #CCC; -} -.fancybox-inline .span12 .well .btn{ - width: 300px; - margin-left: auto; - margin-right: auto; - display: block; - margin-bottom: 20px; -} -.fancybox-inline .remember{ - height: 1.2em; - overflow: hidden; -} .scroll-y{ overflow-y: scroll; -webkit-transform: translate3d(0,0,0); @@ -1431,26 +1310,9 @@ img.icon{ margin-right: 10px; margin-left: 30%; } -.orcid-signin img { - height: 1.5em; - background-color: #FFF; - padding: 11px; - border-radius: 4px; - border: 1px solid #aacf14; - display: inline-block; - margin-right: -4px; - margin-top: -1px; - border-bottom-right-radius: 0px; - border-top-right-radius: 0px; - border-right-width: 0px; -} #signInPopup .orcid-signin { margin-top: 10%; } -.fancybox-inline > .row-fluid > .span6:first-child { - border-right: 1px solid #CCC; - min-height: 265px; -} .modal.container{ padding: 20px 20px 40px 20px; } @@ -1458,6 +1320,37 @@ img.icon{ width: auto; margin-bottom: 20px; } +.sign-in.modal .close { + font-size: 2em; +} +/** The ORCID Sign In button **/ +.orcid-btn{ + border: 1px solid #aacf14; + border-radius: 4px; + -moz-border-radius: 4px; + -webkit-border-radius: 4px; + background-color: #FFF; + padding: 15px 20px; + color: #aacf14; + text-decoration: none; + margin-bottom: 10px; + margin-top: 10px; + display: inline-block; + font-weight: bold; +} +.orcid-btn img { + height: 1.5em; + margin-right: 5px; +} +.orcid-btn:hover{ + background-color: #aacf14; + transition: all 500ms; + text-decoration: none; +} +.orcid-btn:hover > span{ + color: #FFF; + text-decoration: none; +} /****************************************** ** The Metadata and MetadataIndex View ** ******************************************/ diff --git a/metacatui/src/main/webapp/index.html b/metacatui/src/main/webapp/index.html index b109db57a..bbedd3ba4 100644 --- a/metacatui/src/main/webapp/index.html +++ b/metacatui/src/main/webapp/index.html @@ -12,7 +12,7 @@ diff --git a/metacatui/src/main/webapp/js/models/UserModel.js b/metacatui/src/main/webapp/js/models/UserModel.js index 112d66b7c..b6e3caed9 100644 --- a/metacatui/src/main/webapp/js/models/UserModel.js +++ b/metacatui/src/main/webapp/js/models/UserModel.js @@ -531,7 +531,6 @@ define(['jquery', 'underscore', 'backbone', 'jws', 'models/Search', "collections }, getToken: function(customCallback) { - var tokenUrl = MetacatUI.appModel.get('tokenUrl'); var model = this; diff --git a/metacatui/src/main/webapp/js/routers/router.js b/metacatui/src/main/webapp/js/routers/router.js index 01e102268..8627b2357 100644 --- a/metacatui/src/main/webapp/js/routers/router.js +++ b/metacatui/src/main/webapp/js/routers/router.js @@ -22,7 +22,7 @@ function ($, _, Backbone) { 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI 'logout' : 'logout', // logout the user 'signout' : 'logout', // logout the user - 'signin' : 'renderTokenSignIn', // logout the user + 'signin' : 'renderSignIn', // logout the user "signinsuccess" : "renderSignInSuccess", "signinldaperror" : "renderLdapSignInError", 'share(/*pid)' : 'renderEditor', // registry page @@ -341,13 +341,13 @@ function ($, _, Backbone) { renderMyProfile: function(section, subsection){ if(MetacatUI.appUserModel.get("checked") && !MetacatUI.appUserModel.get("loggedIn")) - this.renderTokenSignIn(); + this.renderSignIn(); else if(!MetacatUI.appUserModel.get("checked")){ this.listenToOnce(MetacatUI.appUserModel, "change:checked", function(){ if(MetacatUI.appUserModel.get("loggedIn")) this.renderProfile(MetacatUI.appUserModel.get("username"), section, subsection); else - this.renderTokenSignIn(); + this.renderSignIn(); }); } else if(MetacatUI.appUserModel.get("checked") && MetacatUI.appUserModel.get("loggedIn")){ @@ -374,18 +374,34 @@ function ($, _, Backbone) { } }, - renderTokenSignIn: function(){ - this.routeHistory.push("signin"); + renderSignIn: function(){ + var router = this; + + //If there is no SignInView yet, create one if(!MetacatUI.appView.signInView){ require(['views/SignInView'], function(SignInView){ - MetacatUI.appView.signInView = new SignInView({ el: "#Content"}); - MetacatUI.appView.showView(MetacatUI.appView.signInView); + MetacatUI.appView.signInView = new SignInView({ el: "#Content", fullPage: true }); + router.renderSignIn(); }); + + return; } - else{ + + //If the user status has been checked and they are already logged in, we will forward them to their profile + if( MetacatUI.appUserModel.get("checked") && MetacatUI.appUserModel.get("loggedIn") ){ + this.navigate("my-profile", { trigger: true }); + return; + } + //If the user status has been checked and they are NOT logged in, show the SignInView + else if( MetacatUI.appUserModel.get("checked") && !MetacatUI.appUserModel.get("loggedIn") ){ + this.routeHistory.push("signin"); MetacatUI.appView.showView(MetacatUI.appView.signInView); } + //If the user status has not been checked yet, wait for it + else if( !MetacatUI.appUserModel.get("checked") ){ + this.listenToOnce(MetacatUI.appUserModel, "change:checked", this.renderSignIn); + } }, renderSignInSuccess: function(){ diff --git a/metacatui/src/main/webapp/js/templates/login.html b/metacatui/src/main/webapp/js/templates/login.html index cb56ddebd..c5bd9b8c4 100644 --- a/metacatui/src/main/webapp/js/templates/login.html +++ b/metacatui/src/main/webapp/js/templates/login.html @@ -3,19 +3,20 @@ else var linkAttr = ''; %> -

          -
          -

          Sign Up

          -
          -
          - <% if(signInUrlOrcid) { %> -

          There's no need to create a new account - just use your existing ORCID account now or create a new one.

          - - <% } %> -
          + + +
          \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/templates/loginButtons.html b/metacatui/src/main/webapp/js/templates/loginButtons.html index e38a35009..d1546eafe 100644 --- a/metacatui/src/main/webapp/js/templates/loginButtons.html +++ b/metacatui/src/main/webapp/js/templates/loginButtons.html @@ -1,3 +1,3 @@ - + or - Sign up + Sign up diff --git a/metacatui/src/main/webapp/js/templates/navbar.html b/metacatui/src/main/webapp/js/templates/navbar.html index 19cbc5246..ee91b1d92 100644 --- a/metacatui/src/main/webapp/js/templates/navbar.html +++ b/metacatui/src/main/webapp/js/templates/navbar.html @@ -38,7 +38,7 @@ ); } else { print( - '' + '' ); } %> diff --git a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css index 072fb95e6..13e15d55a 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/arctic/css/metacatui.css @@ -1979,13 +1979,6 @@ MDQ items color: #FFF; background-color: #00AAFF; } - - -#signinPopup{ - width: auto; - min-width: 210px; - max-width: 210px; -} /*-------------- DOCUMENTATION CSS -----------------------------*/ /* ---------------------------------------------------- */ diff --git a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js index 6f34fc7bb..0d66a873c 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/arctic/routers/router.js @@ -16,7 +16,7 @@ function ($, _, Backbone) { 'my-profile(/s=:section)(/s=:subsection)' : 'renderMyProfile', 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI 'signout' : 'logout', - 'signin' : 'renderTokenSignIn', + 'signin' : 'renderSignIn', "signinsuccess" : "renderSignInSuccess", 'share(/*pid)' : 'renderEditor', // registry page 'submit(/*pid)' : 'renderEditor', // registry page @@ -241,13 +241,13 @@ function ($, _, Backbone) { renderMyProfile: function(section, subsection){ if(MetacatUI.appUserModel.get("checked") && !MetacatUI.appUserModel.get("loggedIn")) - this.renderTokenSignIn(); + this.renderSignIn(); else if(!MetacatUI.appUserModel.get("checked")){ this.listenToOnce(appUserModel, "change:checked", function(){ if(MetacatUI.appUserModel.get("loggedIn")) this.renderProfile(MetacatUI.appUserModel.get("username"), section, subsection); else - this.renderTokenSignIn(); + this.renderSignIn(); }); } else if(MetacatUI.appUserModel.get("checked") && MetacatUI.appUserModel.get("loggedIn")){ @@ -316,18 +316,35 @@ function ($, _, Backbone) { } }, - renderTokenSignIn: function(){ - this.routeHistory.push("signin"); + + renderSignIn: function(){ + + var router = this; + //If there is no SignInView yet, create one if(!MetacatUI.appView.signInView){ require(['views/SignInView'], function(SignInView){ - MetacatUI.appView.signInView = new SignInView({ el: "#Content", fullPage: true}); - MetacatUI.appView.showView(MetacatUI.appView.signInView); + MetacatUI.appView.signInView = new SignInView({ el: "#Content", fullPage: true }); + router.renderSignIn(); }); + + return; } - else{ + + //If the user status has been checked and they are already logged in, we will forward them to their profile + if( MetacatUI.appUserModel.get("checked") && MetacatUI.appUserModel.get("loggedIn") ){ + this.navigate("my-profile", { trigger: true }); + return; + } + //If the user status has been checked and they are NOT logged in, show the SignInView + else if( MetacatUI.appUserModel.get("checked") && !MetacatUI.appUserModel.get("loggedIn") ){ + this.routeHistory.push("signin"); MetacatUI.appView.showView(MetacatUI.appView.signInView); } + //If the user status has not been checked yet, wait for it + else if( !MetacatUI.appUserModel.get("checked") ){ + this.listenToOnce(MetacatUI.appUserModel, "change:checked", this.renderSignIn); + } }, renderSignInSuccess: function(){ diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/altHeader.html b/metacatui/src/main/webapp/js/themes/arctic/templates/altHeader.html index 04edade64..e69de29bb 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/altHeader.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/altHeader.html @@ -1,15 +0,0 @@ -
          - -
          diff --git a/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html b/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html index a567c404f..0b28ab17f 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html +++ b/metacatui/src/main/webapp/js/themes/arctic/templates/navbar.html @@ -49,7 +49,7 @@
          • <% } else { %>
        • - +
          • <% } %>
        diff --git a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css index 9162030b3..4745e824d 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/dataone/css/metacatui.css @@ -702,21 +702,14 @@ table th.btn-container .btn{ .navbar .nav>li>.dropdown-menu:after{ display: none; } + /** The login form from the navbar **/ -.fancybox-inline{ - width: 315px; -} -.fancybox-inline > a{ - color: rgb(102, 0, 51); -} -.fancybox-inline .alert{ - width: auto; - width: calc(100% - 73px); - margin-left: auto; - margin-right: auto; - margin-bottom: 10px; - font-size: .9em; +.sign-in .divider-text { + margin-top: 30px; + font-weight: bold; } + + .list-group > .divider { list-style: none; border-bottom: 1px solid #DDD; diff --git a/metacatui/src/main/webapp/js/themes/dataone/templates/login.html b/metacatui/src/main/webapp/js/themes/dataone/templates/login.html index f1add9177..9853f4aaf 100644 --- a/metacatui/src/main/webapp/js/themes/dataone/templates/login.html +++ b/metacatui/src/main/webapp/js/themes/dataone/templates/login.html @@ -3,86 +3,83 @@ else var linkAttr = ''; %> -
      diff --git a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css index f781643cb..858dfff9f 100644 --- a/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css +++ b/metacatui/src/main/webapp/js/themes/knb/css/metacatui.css @@ -889,11 +889,6 @@ img[src*="gstatic.com/"], img[src*="googleapis.com/"] { float: right; } - #signupPopup { - max-width: 350px; - min-width: 350px; - } - .dropdown-header { display: block; padding: 3px 20px; @@ -1172,6 +1167,9 @@ svg .packages, color: #0E69A1; fill: #0E69A1; } +.profile .quick-stats circle{ + stroke: #0E69A1; +} .profile .bar-label.packages{ fill: inherit; } diff --git a/metacatui/src/main/webapp/js/themes/knb/templates/altHeader.html b/metacatui/src/main/webapp/js/themes/knb/templates/altHeader.html index 15a07f9d7..fcb72a70c 100644 --- a/metacatui/src/main/webapp/js/themes/knb/templates/altHeader.html +++ b/metacatui/src/main/webapp/js/themes/knb/templates/altHeader.html @@ -7,7 +7,7 @@

      Store, share, and collaborate.

      Team up by sharing research data through the KNB repository.

      - Sign up + Submit data
@@ -17,7 +17,7 @@

Store, share, and collaborate.

Find and repurpose.

Drive your next meta analysis with data and partners through the KNB.

- Sign up + Submit data
diff --git a/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html b/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html index 004a9aea5..e53d2f996 100644 --- a/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html +++ b/metacatui/src/main/webapp/js/themes/knb/templates/navbar.html @@ -36,7 +36,7 @@ <% } else { %> -
  • Sign In
    • +
  • Sign In
    • <% } %> diff --git a/metacatui/src/main/webapp/js/themes/nceas/routers/router.js b/metacatui/src/main/webapp/js/themes/nceas/routers/router.js index c807f9569..5ca575a53 100644 --- a/metacatui/src/main/webapp/js/themes/nceas/routers/router.js +++ b/metacatui/src/main/webapp/js/themes/nceas/routers/router.js @@ -12,7 +12,7 @@ function ($, _, Backbone) { 'view/*pid' : 'renderMetadata', // metadata page 'logout' : 'logout', // logout the user 'signout' : 'logout', // logout the user - 'signup' : 'renderLdap', // use ldapweb for registration + 'signup' : 'renderTokenSignIn', // use ldapweb for registration "signinldaperror" : "renderLdapSignInError", 'external(/*url)' : 'renderExternal', // renders the content of the given url in our UI 'share(/*pid)' : 'renderEditor', // metadata Editor @@ -145,6 +145,20 @@ function ($, _, Backbone) { } }, + renderTokenSignIn: function(){ + this.routeHistory.push("signin"); + + if(!MetacatUI.appView.signInView){ + require(['views/SignInView'], function(SignInView){ + MetacatUI.appView.signInView = new SignInView({ el: "#Content"}); + MetacatUI.appView.showView(MetacatUI.appView.signInView); + }); + } + else{ + MetacatUI.appView.showView(MetacatUI.appView.signInView); + } + }, + logout: function (param) { //Clear our browsing history when we log out this.routeHistory.length = 0; diff --git a/metacatui/src/main/webapp/js/views/SignInView.js b/metacatui/src/main/webapp/js/views/SignInView.js index af2a44c96..fae024fbf 100644 --- a/metacatui/src/main/webapp/js/views/SignInView.js +++ b/metacatui/src/main/webapp/js/views/SignInView.js @@ -1,7 +1,7 @@ /*global define */ -define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.html', 'text!templates/alert.html', 'text!templates/loginButtons.html', 'text!templates/loginOptions.html'], - function($, _, Backbone, fancybox, LoginTemplate, AlertTemplate, LoginButtonsTemplate, LoginOptionsTemplate) { +define(['jquery', 'underscore', 'backbone', 'text!templates/login.html', 'text!templates/alert.html', 'text!templates/loginButtons.html', 'text!templates/loginOptions.html'], + function($, _, Backbone, LoginTemplate, AlertTemplate, LoginButtonsTemplate, LoginOptionsTemplate) { 'use strict'; var SignInView = Backbone.View.extend({ @@ -126,7 +126,12 @@ define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.ht window.location.href.replace("#signinldaperror", "") : window.location.href })); + this.setUpPopup(); } + + //Open the Sign In modal window + if(this.fullPage) + $("#signinPopup").modal("show"); //If there is an error message in the URL, it means authentication has failed if(this.ldapError){ @@ -151,9 +156,9 @@ define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.ht //If this is a full-page sign-in view, then take the from and insert it into the page if(this.$el.attr("id") == "Content") $("#Content").html( $("#ldap-login").html() ); - //Else, just show the login in the fancybox modal window + //Else, just show the login in the modal window else{ - $.fancybox.open("#SignIn"); + $("#signinPopup").modal("show"); } //Show the LDAP login form @@ -163,15 +168,15 @@ define(['jquery', 'underscore', 'backbone', 'fancybox', 'text!templates/login.ht setUpPopup: function(){ var view = this; - //Initialize the fancybox elements - this.$(".fancybox").fancybox({ - transitionIn: "elastic", - afterShow: function(){ + //Initialize the modal elements + $("#signupPopup, #signinPopup").modal({ + show: false, + shown: function(){ //Update the sign-in URLs so we are redirected back to the previous page after authentication $("a.update-sign-in-url").attr("href", MetacatUI.appModel.get("signInUrl") + encodeURIComponent(window.location.href)); $("a.update-orcid-sign-in-url").attr("href", MetacatUI.appModel.get("signInUrlOrcid") + encodeURIComponent(window.location.href)); - $("a.update-ldap-sign-in-url").attr("href", MetacatUI.appModel.get("signInUrlLdap") + encodeURIComponent(window.location.href)); + } }); }, From 2954a76728f4b49cbaeb453f0a5f7a0e8a6d00c7 Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Fri, 20 Oct 2017 16:54:48 -0400 Subject: [PATCH 434/560] Add a start message to the data package table at the top of the Editor to get users started in the right direction. --- .../src/main/webapp/css/metacatui-common.css | 14 ++++++++++ .../main/webapp/js/models/DataONEObject.js | 3 +++ .../webapp/js/templates/dataPackageStart.html | 13 ++++++++++ .../src/main/webapp/js/views/DataItemView.js | 5 +++- .../main/webapp/js/views/DataPackageView.js | 26 ++++++++++++++++--- .../src/main/webapp/js/views/EditorView.js | 2 +- 6 files changed, 57 insertions(+), 6 deletions(-) create mode 100644 metacatui/src/main/webapp/js/templates/dataPackageStart.html diff --git a/metacatui/src/main/webapp/css/metacatui-common.css b/metacatui/src/main/webapp/css/metacatui-common.css index 363d1d2a8..d649b70b9 100644 --- a/metacatui/src/main/webapp/css/metacatui-common.css +++ b/metacatui/src/main/webapp/css/metacatui-common.css @@ -3320,6 +3320,20 @@ ul.side-nav-items { .data-package-item.remove-preview .type-icon{ opacity: .3; } +.data-package-item.message-row td{ + padding-top: 150px; +} +.data-package-item.message-row:hover td{ + background-color: #FFF; +} +.data-package-item.message-row h2{ + font-size: 2.1em; +} +.data-package-item.message-row button{ + font-size: 1.2em; + margin-top: 10px; + display: block; +} /* Editor package table status column */ .data-package-item .status{ width: 60px; diff --git a/metacatui/src/main/webapp/js/models/DataONEObject.js b/metacatui/src/main/webapp/js/models/DataONEObject.js index 3a0c9c47d..25beb1adf 100644 --- a/metacatui/src/main/webapp/js/models/DataONEObject.js +++ b/metacatui/src/main/webapp/js/models/DataONEObject.js @@ -90,6 +90,9 @@ define(['jquery', 'underscore', 'backbone', 'uuid', 'collections/ObjectFormats', }, initialize: function(attrs, options) { + if(typeof attrs == "undefined") var attrs = {}; + if(typeof options == "undefined") var options = {}; + this.on("change:size", this.bytesToSize); if(attrs.size) this.bytesToSize(); diff --git a/metacatui/src/main/webapp/js/templates/dataPackageStart.html b/metacatui/src/main/webapp/js/templates/dataPackageStart.html new file mode 100644 index 000000000..e242d054d --- /dev/null +++ b/metacatui/src/main/webapp/js/templates/dataPackageStart.html @@ -0,0 +1,13 @@ + + +

    Add files to start your dataset

    + + + + + + + \ No newline at end of file diff --git a/metacatui/src/main/webapp/js/views/DataItemView.js b/metacatui/src/main/webapp/js/views/DataItemView.js index 1e9501a3f..baf8d25d3 100644 --- a/metacatui/src/main/webapp/js/views/DataItemView.js +++ b/metacatui/src/main/webapp/js/views/DataItemView.js @@ -43,8 +43,11 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', /* Initialize the object - post constructor */ initialize: function(options) { + if(typeof options == "undefined") var options = {}; + + this.model = options.model || new DataONEObject(); this.id = this.model.get("id"); - + }, /* Render the template into the DOM */ diff --git a/metacatui/src/main/webapp/js/views/DataPackageView.js b/metacatui/src/main/webapp/js/views/DataPackageView.js index 66e1f3273..9f5021206 100644 --- a/metacatui/src/main/webapp/js/views/DataPackageView.js +++ b/metacatui/src/main/webapp/js/views/DataPackageView.js @@ -8,9 +8,9 @@ define([ 'models/metadata/ScienceMetadata', 'models/metadata/eml211/EML211', 'views/DataItemView', 'text!templates/dataPackage.html', - 'text!templates/loading.html'], + 'text!templates/dataPackageStart.html'], function($, _, Backbone, DataPackage, DataONEObject, ScienceMetadata, EML211, DataItemView, - DataPackageTemplate) { + DataPackageTemplate, DataPackageStartTemplate) { 'use strict'; /* @@ -26,13 +26,14 @@ define([ id: "data-package-table", events: { - "click .toggle-rows" : "toggleRows" // Show/hide rows associated with event's metadata row - + "click .toggle-rows" : "toggleRows", // Show/hide rows associated with event's metadata row + "click .message-row .addFiles" : "handleAddFiles" }, subviews: {}, template: _.template(DataPackageTemplate), + startMessageTemplate: _.template(DataPackageStartTemplate), // Models waiting for their parent folder to be rendered, hashed by parent id: // {'parentid': [model1, model2, ...]} @@ -74,6 +75,18 @@ define([ // Render the current set of models in the DataPackage this.addAll(); + + //If this is a new data package, then display a message and button + if((this.dataPackage.length == 1 && this.dataPackage.models[0].isNew()) || !this.dataPackage.length){ + + var messageRow = this.startMessageTemplate(); + + this.$("tbody").append(messageRow); + + this.listenTo(this.dataPackage, "add", function(){ + this.$(".message-row").remove(); + }); + } return this; }, @@ -180,6 +193,11 @@ define([ }, + handleAddFiles: function(e){ + //Pass this on to the DataItemView for the root data package + this.$(".data-package-item.folder").first().data("view").handleAddFiles(e); + }, + /* * Close subviews as needed */ diff --git a/metacatui/src/main/webapp/js/views/EditorView.js b/metacatui/src/main/webapp/js/views/EditorView.js index 13d96840c..5eeb1d3d3 100644 --- a/metacatui/src/main/webapp/js/views/EditorView.js +++ b/metacatui/src/main/webapp/js/views/EditorView.js @@ -280,7 +280,7 @@ define(['underscore', view.emlView.resizeTOC(); } }); - $packageTableContainer.css("height", "200px"); + $packageTableContainer.css("height", "500px"); var table = this.dataPackageView.$el; this.listenTo(this.dataPackageView, "addOne", function(){ From 3e5c8b36a59cc38058de429c869a34cbb122292c Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Fri, 20 Oct 2017 17:44:16 -0400 Subject: [PATCH 435/560] Move the title to the Overview section and remove the content editable table cell for metadata titles Closes #308 --- .../src/main/webapp/js/models/AppModel.js | 3 +- .../main/webapp/js/templates/dataItem.html | 6 +-- .../templates/metadata/metadataOverview.html | 7 ++++ .../js/themes/arctic/models/AppModel.js | 3 +- .../webapp/js/themes/knb/models/AppModel.js | 3 +- .../webapp/js/themes/nceas/models/AppModel.js | 3 +- .../src/main/webapp/js/views/DataItemView.js | 10 +++-- .../webapp/js/views/metadata/EML211View.js | 40 +++++++++++-------- 8 files changed, 48 insertions(+), 27 deletions(-) diff --git a/metacatui/src/main/webapp/js/models/AppModel.js b/metacatui/src/main/webapp/js/models/AppModel.js index f220caa53..90a36bd49 100644 --- a/metacatui/src/main/webapp/js/models/AppModel.js +++ b/metacatui/src/main/webapp/js/models/AppModel.js @@ -48,7 +48,8 @@ define(['jquery', 'underscore', 'backbone'], samplingDescription: false, studyExtentDescription: false, taxonCoverage: false, - temporalCoverage: true + temporalCoverage: true, + title: true }, baseUrl: window.location.origin || (window.location.protocol + "//" + window.location.host), diff --git a/metacatui/src/main/webapp/js/templates/dataItem.html b/metacatui/src/main/webapp/js/templates/dataItem.html index 5c3975b5c..8f6430012 100644 --- a/metacatui/src/main/webapp/js/templates/dataItem.html +++ b/metacatui/src/main/webapp/js/templates/dataItem.html @@ -13,8 +13,8 @@ - data-category="title" <% } %> > - <% if(uploadStatus != "l" && uploadStatus != "p"){ %> + + <% if(uploadStatus != "l" && uploadStatus != "p" && type != "Metadata"){ %>
    <% } else { %>
    @@ -24,7 +24,7 @@ <% } else if ( typeof fileName != "undefined" && fileName) { %> <%= fileName %> <% } else if(type == "Metadata"){ %> - Untitled dataset: Add a descriptive title for your dataset + Untitled dataset <% } else { %> <%= id %> <% } %> diff --git a/metacatui/src/main/webapp/js/templates/metadata/metadataOverview.html b/metacatui/src/main/webapp/js/templates/metadata/metadataOverview.html index fddb66776..4b99a40d3 100644 --- a/metacatui/src/main/webapp/js/templates/metadata/metadataOverview.html +++ b/metacatui/src/main/webapp/js/templates/metadata/metadataOverview.html @@ -1,5 +1,12 @@

    Overview

    +
    +
    Title
    +

    A brief but meaningful title for this dataset. A good title includes the topic, geographic location, dates, and scale of the data.

    +

    +
    +
    +
    Abstract

    Short summary of the purpose and content of this data set.

    diff --git a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js index 1c3144e6c..db5f0b4c6 100644 --- a/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/arctic/models/AppModel.js @@ -48,7 +48,8 @@ define(['jquery', 'underscore', 'backbone'], samplingDescription: false, studyExtentDescription: false, taxonCoverage: false, - temporalCoverage: true + temporalCoverage: true, + title: true }, baseUrl: window.location.origin || (window.location.protocol + "//" + window.location.host), diff --git a/metacatui/src/main/webapp/js/themes/knb/models/AppModel.js b/metacatui/src/main/webapp/js/themes/knb/models/AppModel.js index f7ec7fb4c..1e3b411e4 100644 --- a/metacatui/src/main/webapp/js/themes/knb/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/knb/models/AppModel.js @@ -48,7 +48,8 @@ define(['jquery', 'underscore', 'backbone'], samplingDescription: false, studyExtentDescription: false, taxonCoverage: false, - temporalCoverage: true + temporalCoverage: true, + title: true }, baseUrl: window.location.origin || (window.location.protocol + "//" + window.location.host), diff --git a/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js b/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js index 46822127a..722f1b9db 100644 --- a/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js +++ b/metacatui/src/main/webapp/js/themes/nceas/models/AppModel.js @@ -35,7 +35,8 @@ define(['jquery', 'underscore', 'backbone'], samplingDescription: false, studyExtentDescription: false, taxonCoverage: false, - temporalCoverage: true + temporalCoverage: true, + title: true }, baseUrl: "https://knb.ecoinformatics.org", diff --git a/metacatui/src/main/webapp/js/views/DataItemView.js b/metacatui/src/main/webapp/js/views/DataItemView.js index baf8d25d3..af15f0ba7 100644 --- a/metacatui/src/main/webapp/js/views/DataItemView.js +++ b/metacatui/src/main/webapp/js/views/DataItemView.js @@ -24,7 +24,7 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', /* Events this view listens to */ events: { "focusout .name" : "updateName", - "click .name" : "emptyName", + //"click .name" : "emptyName", /* "click .rename" : "rename", */ "click .duplicate" : "duplicate", // Edit dropdown, duplicate scimeta/rdf "click .addFolder" : "handleAddFolder", // Edit dropdown, add nested scimeta/rdf @@ -282,7 +282,7 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', // Don't set the title if it hasn't changed or is empty if (enteredText !== "" && currentTitle !== enteredText && - enteredText !== "Untitled dataset: Add a descriptive title for your dataset") { + enteredText !== "Untitled dataset") { // Set the new title, upgrading any title attributes // that aren't Arrays into Arrays if ((Array.isArray(title) && title.length < 2) || typeof title == "string") { @@ -666,7 +666,11 @@ define(['underscore', 'jquery', 'backbone', 'models/DataONEObject', hideSaving: function(){ this.$("button").prop("disabled", false); this.$(".disable-layer").remove(); - this.$(".name > div").prop("contenteditable", true); + + //Make the name cell editable again + if(this.model.get("type") != "Metadata") + this.$(".name > div").prop("contenteditable", true); + this.$el.removeClass("error-saving"); }, diff --git a/metacatui/src/main/webapp/js/views/metadata/EML211View.js b/metacatui/src/main/webapp/js/views/metadata/EML211View.js index 1a44a4eed..eaa41bbcb 100644 --- a/metacatui/src/main/webapp/js/views/metadata/EML211View.js +++ b/metacatui/src/main/webapp/js/views/metadata/EML211View.js @@ -191,12 +191,10 @@ define(['underscore', 'jquery', 'backbone', var overviewEl = this.$container.find(".overview"); $(overviewEl).html(this.overviewTemplate()); - // pubDate - // BDM: This isn't a createBasicText call because that helper - // assumes multiple values for the category - // TODO: Consider a re-factor of createBasicText - var pubDateInput = $(overviewEl).find("input.pubDate").val(this.model.get("pubDate")); - + //Title + var titleEl = this.createBasicTextFields("title", "Example: Greater Yellowstone Rivers from 1:126,700 U.S. Forest Service Visitor Maps (1961-1983)", false); + $(overviewEl).find(".title-container").append(titleEl); + //Abstract _.each(this.model.get("abstract"), function(abs){ var abstractEl = this.createEMLText(abs, edit, "abstract"); @@ -236,6 +234,13 @@ define(['underscore', 'jquery', 'backbone', //Funding this.renderFunding(); + + // pubDate + // BDM: This isn't a createBasicText call because that helper + // assumes multiple values for the category + // TODO: Consider a re-factor of createBasicText + var pubDateInput = $(overviewEl).find("input.pubDate").val(this.model.get("pubDate")); + //Initialize all the tooltips this.$(".tooltip-this").tooltip(); @@ -1276,15 +1281,12 @@ define(['underscore', 'jquery', 'backbone', /* * Creates and returns an array of basic text input field for editing */ - createBasicTextFields: function(category, placeholder, appendNew){ + createBasicTextFields: function(category, placeholder){ var textContainer = $(document.createElement("div")).addClass("text-container"), modelValues = this.model.get(category), textRow; // Holds the DOM for each field - - if(typeof appendNew === "undefined") - var appendNew = true; - + //Format as an array if(!Array.isArray(modelValues) && modelValues) modelValues = [modelValues]; @@ -1301,7 +1303,7 @@ define(['underscore', 'jquery', 'backbone', textContainer.append(textRow); //At the end, append an empty input for the user to add a new one - if(i+1 == allModelValues.length && appendNew) { + if(i+1 == allModelValues.length && category != "title") { var newRow = $($(document.createElement("div")).addClass("basic-text-row")); newRow.append(input.clone().addClass("new").attr("placeholder", placeholder || "Add a new " + category)); textContainer.append(newRow); @@ -1349,19 +1351,20 @@ define(['underscore', 'jquery', 'backbone', var position = $(e.target).parents("div.text-container").first().children("div").index($(e.target).parent()); currentValue[position] = value; model.set(category, currentValue); - model.trigger("change"); + model.trigger("change:" + category); } //Update the model if the current value is a string else if(typeof currentValue == "string"){ model.set(category, [currentValue, value]); - model.trigger("change"); + model.trigger("change:" + category); } else if(!currentValue) { model.set(category, [value]); + model.trigger("change:" + category); } //Add another blank text input - if($(e.target).is(".new") && value != ''){ + if($(e.target).is(".new") && value != '' && category != "title"){ $(e.target).removeClass("new"); this.addBasicText(e); } @@ -1390,11 +1393,14 @@ define(['underscore', 'jquery', 'backbone', var category = $(e.target).attr("data-category"), allBasicTexts = $(".basic-text.new[data-category='" + category + "']"); - //Only show one new keyword row at a time + //Only show one new row at a time if((allBasicTexts.length == 1) && !allBasicTexts.val()) return; else if(allBasicTexts.length > 1) return; + //We are only supporting one title right now + else if(category == "title") + return; //Add another blank text input var newRow = $(document.createElement("div")).addClass("basic-text-row"); @@ -1407,7 +1413,7 @@ define(['underscore', 'jquery', 'backbone', $(e.target).parent().after(newRow); - $(e.target).after(this.createRemoveButton(null, 'alternateIdentifier', '.basic-text-row', "div.text-container")); + $(e.target).after(this.createRemoveButton(null, category, '.basic-text-row', "div.text-container")); }, previewTextRemove: function(e){ From bb54be1a95c4b186d4269060a11626125e1a237b Mon Sep 17 00:00:00 2001 From: laurenwalker Date: Mon, 23 Oct 2017 14:32:21 -0400 Subject: [PATCH 436/560] Show the required red asterisk icon in the Editor vertical navigation / table of contents Closes #302 --- .../src/main/webapp/js/templates/dataItem.html | 2 +- .../src/main/webapp/js/templates/metadata/eml.html | 6 ++++++ .../main/webapp/js/views/metadata/EML211View.js | 14 ++++++++++++-- 3 files changed, 19 insertions(+), 3 deletions(-) diff --git a/metacatui/src/main/webapp/js/templates/dataItem.html b/metacatui/src/main/webapp/js/templates/dataItem.html index 8f6430012..d4f4356e0 100644 --- a/metacatui/src/main/webapp/js/templates/dataItem.html +++ b/metacatui/src/main/webapp/js/templates/dataItem.html @@ -57,7 +57,7 @@ <% } else if( type != "Metadata" && numAttributes > 0 && hasAttributeChanges && entityIsValid ) { %> <% } else if( type != "Metadata" && !entityIsValid ) { %> - + <% } else if( uploadStatus == "c" ) { %> <% } else if( uploadStatus == "e" ) { %> diff --git a/metacatui/src/main/webapp/js/templates/metadata/eml.html b/metacatui/src/main/webapp/js/templates/metadata/eml.html index 5c5f8cbd6..fcd9d0989 100644 --- a/metacatui/src/main/webapp/js/templates/metadata/eml.html +++ b/metacatui/src/main/webapp/js/templates/metadata/eml.html @@ -5,36 +5,42 @@ Overview +
  • People +
  • Dates +
  • Locations +
  • Taxa +
  • Methods +