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Allow adding, removing, and changing the "canonical dataset" in the Editor #2551

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218 changes: 167 additions & 51 deletions src/js/collections/metadata/eml/EMLAnnotations.js
Original file line number Diff line number Diff line change
@@ -1,75 +1,191 @@
"use strict";

define([
"jquery",
"underscore",
"backbone",
"models/metadata/eml211/EMLAnnotation",
], function ($, _, Backbone, EMLAnnotation) {
define(["underscore", "backbone", "models/metadata/eml211/EMLAnnotation"], (
_,
Backbone,
EMLAnnotation,
) => {
const SCHEMA_ORG_SAME_AS = "http://www.w3.org/2002/07/owl#sameAs";
const PROV_WAS_DERIVED_FROM = "http://www.w3.org/ns/prov#wasDerivedFrom";
/**
* @class EMLAnnotations
* @classdesc A collection of EMLAnnotations.
* @classcategory Collections/Metadata/EML
* @since 2.19.0
* @extends Backbone.Collection
* @augments Backbone.Collection
*/
var EMLAnnotations = Backbone.Collection.extend(
const EMLAnnotations = Backbone.Collection.extend(
/** @lends EMLAnnotations.prototype */
{
/** @inheritdoc */
model: EMLAnnotation,

/**
* The reference to the model class that this collection is made of.
* @type EMLAnnotation
* @since 2.19.0
* Checks if this collection already has an annotation for the same
* property URI.
* @param {EMLAnnotation} annotation The EMLAnnotation to compare against
* the annotations already in this collection.
* @returns {boolean} Returns true is this collection already has an
* annotation for this property.
*/
model: EMLAnnotation,
hasDuplicateOf(annotation) {
// If there is at least one model in this collection and there is a
// propertyURI set on the given model,
if (this.length && annotation.get("propertyURI")) {
// Return whether or not there is a duplicate
const properties = this.pluck("propertyURI");
return properties.includes(annotation.get("propertyURI"));
}
// If this collection is empty or the propertyURI is falsey, return
// false
return false;
},

/**
* Checks if this collection already has an annotation for the same property URI.
* @param {EMLAnnotation} annotation The EMLAnnotation to compare against the annotations already in this collection.
* @returns {Boolean} Returns true is this collection already has an annotation for this property.
* @since 2.19.0
* Removes the EMLAnnotation from this collection that has the same
* propertyURI as the given annotation. Then adds the given annotation to
* the collection. If no duplicate is found, the given annotation is still
* added to the collection.
* @param {EMLAnnotation} annotation The EMLAnnotation to replace
* duplicates with.
*/
hasDuplicateOf: function (annotation) {
try {
//If there is at least one model in this collection and there is a propertyURI set on the given model,
if (this.length && annotation.get("propertyURI")) {
//Return whether or not there is a duplicate
let properties = this.pluck("propertyURI");
return properties.includes(annotation.get("propertyURI"));
}
//If this collection is empty or the propertyURI is falsey, return false
else {
return false;
}
} catch (e) {
console.error("Could not check for a duplicate annotation: ", e);
return false;
replaceDuplicateWith(annotation) {
if (this.length && annotation.get("propertyURI")) {
const duplicates = this.findWhere({
propertyURI: annotation.get("propertyURI"),
});
this.remove(duplicates);
}
this.add(annotation);
},

/**
* Find all annotations with the given propertyURI.
* @param {string} propertyURI The propertyURI to search for.
* @returns {EMLAnnotation[]} An array of EMLAnnotations with the given
* propertyURI.
* @since 0.0.0
*/
findByProperty(propertyURI) {
return this.where({ propertyURI });
},

/**
* Removes the EMLAnnotation from this collection that has the same propertyURI as the given annotation.
* Then adds the given annotation to the collection. If no duplicate is found, the given annotation is still added
* to the collection.
* @param {EMLAnnotation} annotation
* @since 2.19.0
* Adds canonical dataset annotations to this collection. A canonical
* dataset is the one that is considered the authoritative version; the
* current EML doc being essentially a duplicate version.
* @param {string} sourceId The DOI or URL of the canonical dataset.
* @returns {void}
* @since 0.0.0
*/
replaceDuplicateWith: function (annotation) {
try {
if (this.length && annotation.get("propertyURI")) {
let duplicates = this.findWhere({
propertyURI: annotation.get("propertyURI"),
});
this.remove(duplicates);
}

this.add(annotation);
} catch (e) {
console.error(
"Could not replace the EMLAnnotation in the collection: ",
e,
);
addCanonicalDatasetAnnotation(sourceId) {
if (!sourceId) return null;
// TODO: Check that sourceId is a valid DOI or URL

// TODO: Check that there is not already a canonical dataset annotation
// before adding a new one, since there should only be one.
return this.add([
{
propertyLabel: "derivedFrom",
propertyURI: PROV_WAS_DERIVED_FROM,
valueLabel: sourceId,
valueURI: sourceId,
},
{
propertyLabel: "sameAs",
propertyURI: SCHEMA_ORG_SAME_AS,
valueLabel: sourceId,
valueURI: sourceId,
},
]);
},

/**
* Find the annotations that make up the canonical dataset annotation. A
* canonical dataset is identified by having both a "derivedFrom" and a
* "sameAs" annotation with the same DOI or URL for the valueURI.
* @returns {object} An object with the derivedFrom and sameAs
* annotations.
* @since 0.0.0
*/
findCanonicalDatasetAnnotation() {
// There must be at least one derivedFrom and one sameAs annotation
// for this to have a canonical dataset annotation
if (!this.length) return null;
const derivedFrom = this.findByProperty(PROV_WAS_DERIVED_FROM);
if (!derivedFrom?.length) return null;
const sameAs = this.findByProperty(SCHEMA_ORG_SAME_AS);
if (!sameAs?.length) return null;

// Find all pairs that have matching valueURIs
const pairs = [];
derivedFrom.forEach((derived) => {
sameAs.forEach((same) => {
if (derived.get("valueURI") === same.get("valueURI")) {
// TODO? Check that the URI is a valid DOI or URL
pairs.push({ derived, same, uri: derived.get("valueURI") });
}
});
});

// If there are multiple pairs, we cannot determine which is the
// canonical dataset.
if (pairs.length > 1 || !pairs.length) return null;

// There is only one pair, so return it
return pairs[0];
},

/**
* Updates the canonical dataset annotations to have the given ID. If
* there is no canonical dataset annotation, one is added. If the ID is a
* falsy value, the canonical dataset annotation is removed.
* @param {string} newSourceId The DOI or URL of the canonical dataset.
* @returns {object} An object with the derivedFrom and sameAs annotations
* if the canonical dataset annotations were updated.
* @since 0.0.0
*/
updateCanonicalDataset(newSourceId) {
if (!newSourceId) {
this.removeCanonicalDatasetAnnotation();
return null;
}
const canonical = this.findCanonicalDatasetAnnotation();
if (!canonical) {
return this.addCanonicalDatasetAnnotation(newSourceId);
}

const { derived, same, uri } = canonical;
if (uri === newSourceId) return null;

derived.set("valueURI", newSourceId);
derived.set("valueLabel", newSourceId);
same.set("valueURI", newSourceId);
same.set("valueLabel", newSourceId);

return [derived, same];
},

/**
* Removes the canonical dataset annotations from this collection.
* @returns {EMLAnnotation[]} The canonical dataset annotations that were
* removed.
* @since 0.0.0
*/
removeCanonicalDatasetAnnotation() {
const canonical = this.findCanonicalDatasetAnnotation();
if (!canonical) return null;
return this.remove([canonical.derived, canonical.same]);
},

/**
* Returns the URI of the canonical dataset.
* @returns {string} The URI of the canonical dataset.
* @since 0.0.0
*/
getCanonicalURI() {
const canonical = this.findCanonicalDatasetAnnotation();
return canonical?.uri;
},
},
);
Expand Down
29 changes: 29 additions & 0 deletions src/js/models/metadata/eml211/EML211.js
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🚫 [eslint] <prefer-arrow-callback> reported by reviewdog 🐶
Unexpected function expression.

], function (
$,
_,
Backbone,
uuid,
Units,
ScienceMetadata,
DataONEObject,
EMLGeoCoverage,
EMLKeywordSet,
EMLTaxonCoverage,
EMLTemporalCoverage,
EMLDistribution,
EMLEntity,
EMLDataTable,
EMLOtherEntity,
EMLParty,
EMLProject,
EMLText,
EMLMethods,
EMLAnnotations,
EMLAnnotation,
) {
/**
* @class EML211
* @classdesc An EML211 object represents an Ecological Metadata Language
* document, version 2.1.1
* @classcategory Models/Metadata/EML211
* @extends ScienceMetadata
*/
var EML211 = ScienceMetadata.extend(
/** @lends EML211.prototype */ {
type: "EML",
defaults: function () {
return _.extend(ScienceMetadata.prototype.defaults(), {
id: "urn:uuid:" + uuid.v4(),
formatId: "https://eml.ecoinformatics.org/eml-2.2.0",
objectXML: null,
isEditable: false,
alternateIdentifier: [],
shortName: null,
title: [],
creator: [], // array of EMLParty objects
metadataProvider: [], // array of EMLParty objects
associatedParty: [], // array of EMLParty objects
contact: [], // array of EMLParty objects
publisher: [], // array of EMLParty objects
pubDate: null,
language: null,
series: null,
abstract: [], //array of EMLText objects
keywordSets: [], //array of EMLKeywordSet objects
additionalInfo: [],
intellectualRights:
"This work is dedicated to the public domain under the Creative Commons Universal 1.0 Public Domain Dedication. To view a copy of this dedication, visit https://creativecommons.org/publicdomain/zero/1.0/.",
distribution: [], // array of EMLDistribution objects
geoCoverage: [], //an array for EMLGeoCoverages
temporalCoverage: [], //an array of EMLTempCoverage models
taxonCoverage: [], //an array of EMLTaxonCoverages
purpose: [],
entities: [], //An array of EMLEntities
pubplace: null,
methods: new EMLMethods(), // An EMLMethods objects
project: null, // An EMLProject object,
annotations: null, // Dataset-level annotations
canonicalDataset: null,
dataSensitivityPropertyURI:
"http://purl.dataone.org/odo/SENSO_00000005",
nodeOrder: [
"alternateidentifier",
"shortname",
"title",
"creator",
"metadataprovider",
"associatedparty",
"pubdate",
"language",
"series",
"abstract",
"keywordset",
"additionalinfo",
"intellectualrights",
"licensed",
"distribution",
"coverage",
"annotation",
"purpose",
"introduction",
"gettingstarted",
"acknowledgements",
"maintenance",
"contact",
"publisher",
"pubplace",
"methods",
"project",
"datatable",
"spatialraster",
"spatialvector",
"storedprocedure",
"view",
"otherentity",
"referencepublications",
"usagecitations",
"literaturecited",
],
});
},
units: new Units(),
initialize: function (attributes) {
// Call initialize for the super class
ScienceMetadata.prototype.initialize.call(this, attributes);
// EML211-specific init goes here
// this.set("objectXML", this.createXML());
this.parse(this.createXML());
this.on("sync", function () {
this.set("synced", true);
});
this.stopListening(this, "change:canonicalDataset");
this.listenTo(
this,
"change:canonicalDataset",
this.updateCanonicalDataset,
);
//Create a Unit collection
if (!this.units.length) this.createUnits();
},
url: function (options) {
var identifier;
if (options && options.update) {
identifier = this.get("oldPid") || this.get("seriesid");
} else {
identifier = this.get("id") || this.get("seriesid");
}
return (
MetacatUI.appModel.get("objectServiceUrl") +
encodeURIComponent(identifier)
);
},
updateCanonicalDataset() {
let uri = this.get("canonicalDataset");
uri = uri?.length ? uri[0] : null;
let annotations = this.get("annotations");
if (!annotations) {
annotations = new EMLAnnotations();
this.set("annotations", annotations);
}
annotations.updateCanonicalDataset(uri);
},
/*
* Maps the lower-case EML node names (valid in HTML DOM) to the camel-cased EML node names (valid in EML).
* Used during parse() and serialize()
*/
nodeNameMap: function () {
return _.extend(
this.constructor.__super__.nodeNameMap(),
EMLDistribution.prototype.nodeNameMap(),
EMLGeoCoverage.prototype.nodeNameMap(),
EMLKeywordSet.prototype.nodeNameMap(),
EMLParty.prototype.nodeNameMap(),
EMLProject.prototype.nodeNameMap(),
EMLTaxonCoverage.prototype.nodeNameMap(),
EMLTemporalCoverage.prototype.nodeNameMap(),
EMLMethods.prototype.nodeNameMap(),
{
accuracyreport: "accuracyReport",
actionlist: "actionList",
additionalclassifications: "additionalClassifications",
additionalinfo: "additionalInfo",
additionallinks: "additionalLinks",
additionalmetadata: "additionalMetadata",
allowfirst: "allowFirst",
alternateidentifier: "alternateIdentifier",
altitudedatumname: "altitudeDatumName",
altitudedistanceunits: "altitudeDistanceUnits",
altituderesolution: "altitudeResolution",
altitudeencodingmethod: "altitudeEncodingMethod",
altitudesysdef: "altitudeSysDef",
asneeded: "asNeeded",
associatedparty: "associatedParty",
attributeaccuracyexplanation: "attributeAccuracyExplanation",
attributeaccuracyreport: "attributeAccuracyReport",
attributeaccuracyvalue: "attributeAccuracyValue",
attributedefinition: "attributeDefinition",
attributelabel: "attributeLabel",
attributelist: "attributeList",
attributename: "attributeName",
attributeorientation: "attributeOrientation",
attributereference: "attributeReference",
awardnumber: "awardNumber",
awardurl: "awardUrl",
audiovisual: "audioVisual",
authsystem: "authSystem",
banddescription: "bandDescription",
bilinearfit: "bilinearFit",
binaryrasterformat: "binaryRasterFormat",
blockedmembernode: "blockedMemberNode",
booktitle: "bookTitle",
cameracalibrationinformationavailability:
"cameraCalibrationInformationAvailability",
casesensitive: "caseSensitive",
cellgeometry: "cellGeometry",
cellsizexdirection: "cellSizeXDirection",
cellsizeydirection: "cellSizeYDirection",
changehistory: "changeHistory",
changedate: "changeDate",
changescope: "changeScope",
chapternumber: "chapterNumber",
characterencoding: "characterEncoding",
checkcondition: "checkCondition",
checkconstraint: "checkConstraint",
childoccurences: "childOccurences",
citableclassificationsystem: "citableClassificationSystem",
cloudcoverpercentage: "cloudCoverPercentage",
codedefinition: "codeDefinition",
codeexplanation: "codeExplanation",
codesetname: "codesetName",
codeseturl: "codesetURL",
collapsedelimiters: "collapseDelimiters",
communicationtype: "communicationType",
compressiongenerationquality: "compressionGenerationQuality",
compressionmethod: "compressionMethod",
conferencedate: "conferenceDate",
conferencelocation: "conferenceLocation",
conferencename: "conferenceName",
conferenceproceedings: "conferenceProceedings",
constraintdescription: "constraintDescription",
constraintname: "constraintName",
constanttosi: "constantToSI",
controlpoint: "controlPoint",
cornerpoint: "cornerPoint",
customunit: "customUnit",
dataformat: "dataFormat",
datasetgpolygon: "datasetGPolygon",
datasetgpolygonoutergring: "datasetGPolygonOuterGRing",
datasetgpolygonexclusiongring: "datasetGPolygonExclusionGRing",
datatable: "dataTable",
datatype: "dataType",
datetime: "dateTime",
datetimedomain: "dateTimeDomain",
datetimeprecision: "dateTimePrecision",
defaultvalue: "defaultValue",
definitionattributereference: "definitionAttributeReference",
denomflatratio: "denomFlatRatio",
depthsysdef: "depthSysDef",
depthdatumname: "depthDatumName",
depthdistanceunits: "depthDistanceUnits",
depthencodingmethod: "depthEncodingMethod",
depthresolution: "depthResolution",
descriptorvalue: "descriptorValue",
dictref: "dictRef",
diskusage: "diskUsage",
domainDescription: "domainDescription",
editedbook: "editedBook",
encodingmethod: "encodingMethod",
endcondition: "endCondition",
entitycodelist: "entityCodeList",
entitydescription: "entityDescription",
entityname: "entityName",
entityreference: "entityReference",
entitytype: "entityType",
enumerateddomain: "enumeratedDomain",
errorbasis: "errorBasis",
errorvalues: "errorValues",
externalcodeset: "externalCodeSet",
externallydefinedformat: "externallyDefinedFormat",
fielddelimiter: "fieldDelimiter",
fieldstartcolumn: "fieldStartColumn",
fieldwidth: "fieldWidth",
filmdistortioninformationavailability:
"filmDistortionInformationAvailability",
foreignkey: "foreignKey",
formatname: "formatName",
formatstring: "formatString",
formatversion: "formatVersion",
fractiondigits: "fractionDigits",
fundername: "funderName",
funderidentifier: "funderIdentifier",
gettingstarted: "gettingStarted",
gring: "gRing",
gringpoint: "gRingPoint",
gringlatitude: "gRingLatitude",
gringlongitude: "gRingLongitude",
geogcoordsys: "geogCoordSys",
geometricobjectcount: "geometricObjectCount",
georeferenceinfo: "georeferenceInfo",
highwavelength: "highWavelength",
horizontalaccuracy: "horizontalAccuracy",
horizcoordsysdef: "horizCoordSysDef",
horizcoordsysname: "horizCoordSysName",
identifiername: "identifierName",
illuminationazimuthangle: "illuminationAzimuthAngle",
illuminationelevationangle: "illuminationElevationAngle",
imagingcondition: "imagingCondition",
imagequalitycode: "imageQualityCode",
imageorientationangle: "imageOrientationAngle",
intellectualrights: "intellectualRights",
imagedescription: "imageDescription",
isbn: "ISBN",
issn: "ISSN",
joincondition: "joinCondition",
keywordtype: "keywordType",
languagevalue: "LanguageValue",
languagecodestandard: "LanguageCodeStandard",
lensdistortioninformationavailability:
"lensDistortionInformationAvailability",
licensename: "licenseName",
licenseurl: "licenseURL",
linenumber: "lineNumber",
literalcharacter: "literalCharacter",
literallayout: "literalLayout",
literaturecited: "literatureCited",
lowwavelength: "lowWaveLength",
machineprocessor: "machineProcessor",
maintenanceupdatefrequency: "maintenanceUpdateFrequency",
matrixtype: "matrixType",
maxexclusive: "maxExclusive",
maxinclusive: "maxInclusive",
maxlength: "maxLength",
maxrecordlength: "maxRecordLength",
maxvalues: "maxValues",
measurementscale: "measurementScale",
metadatalist: "metadataList",
methodstep: "methodStep",
minexclusive: "minExclusive",
mininclusive: "minInclusive",
minlength: "minLength",
minvalues: "minValues",
missingvaluecode: "missingValueCode",
moduledocs: "moduleDocs",
modulename: "moduleName",
moduledescription: "moduleDescription",
multiband: "multiBand",
multipliertosi: "multiplierToSI",
nonnumericdomain: "nonNumericDomain",
notnullconstraint: "notNullConstraint",
notplanned: "notPlanned",
numberofbands: "numberOfBands",
numbertype: "numberType",
numericdomain: "numericDomain",
numfooterlines: "numFooterLines",
numheaderlines: "numHeaderLines",
numberofrecords: "numberOfRecords",
numberofvolumes: "numberOfVolumes",
numphysicallinesperrecord: "numPhysicalLinesPerRecord",
objectname: "objectName",
oldvalue: "oldValue",
operatingsystem: "operatingSystem",
orderattributereference: "orderAttributeReference",
originalpublication: "originalPublication",
otherentity: "otherEntity",
othermaintenanceperiod: "otherMaintenancePeriod",
parameterdefinition: "parameterDefinition",
packageid: "packageId",
pagerange: "pageRange",
parentoccurences: "parentOccurences",
parentsi: "parentSI",
peakresponse: "peakResponse",
personalcommunication: "personalCommunication",
physicallinedelimiter: "physicalLineDelimiter",
pointinpixel: "pointInPixel",
preferredmembernode: "preferredMemberNode",
preprocessingtypecode: "preProcessingTypeCode",
primarykey: "primaryKey",
primemeridian: "primeMeridian",
proceduralstep: "proceduralStep",
programminglanguage: "programmingLanguage",
projcoordsys: "projCoordSys",
projectionlist: "projectionList",
propertyuri: "propertyURI",
pubdate: "pubDate",
pubplace: "pubPlace",
publicationplace: "publicationPlace",
quantitativeaccuracyreport: "quantitativeAccuracyReport",
quantitativeaccuracyvalue: "quantitativeAccuracyValue",
quantitativeaccuracymethod: "quantitativeAccuracyMethod",
quantitativeattributeaccuracyassessment:
"quantitativeAttributeAccuracyAssessment",
querystatement: "queryStatement",
quotecharacter: "quoteCharacter",
radiometricdataavailability: "radiometricDataAvailability",
rasterorigin: "rasterOrigin",
recommendedunits: "recommendedUnits",
recommendedusage: "recommendedUsage",
referencedkey: "referencedKey",
referencetype: "referenceType",
relatedentry: "relatedEntry",
relationshiptype: "relationshipType",
reportnumber: "reportNumber",
reprintedition: "reprintEdition",
researchproject: "researchProject",
researchtopic: "researchTopic",
recorddelimiter: "recordDelimiter",
referencepublication: "referencePublication",
revieweditem: "reviewedItem",
rowcolumnorientation: "rowColumnOrientation",
runtimememoryusage: "runtimeMemoryUsage",
samplingdescription: "samplingDescription",
scalefactor: "scaleFactor",
sequenceidentifier: "sequenceIdentifier",
semiaxismajor: "semiAxisMajor",
shortname: "shortName",
simpledelimited: "simpleDelimited",
spatialraster: "spatialRaster",
spatialreference: "spatialReference",
spatialvector: "spatialVector",
standalone: "standAlone",
standardunit: "standardUnit",
startcondition: "startCondition",
studyareadescription: "studyAreaDescription",
storagetype: "storageType",
studyextent: "studyExtent",
studytype: "studyType",
textdelimited: "textDelimited",
textdomain: "textDomain",
textfixed: "textFixed",
textformat: "textFormat",
topologylevel: "topologyLevel",
tonegradation: "toneGradation",
totaldigits: "totalDigits",
totalfigures: "totalFigures",
totalpages: "totalPages",
totaltables: "totalTables",
triangulationindicator: "triangulationIndicator",
typesystem: "typeSystem",
uniquekey: "uniqueKey",
unittype: "unitType",
unitlist: "unitList",
usagecitation: "usageCitation",
valueuri: "valueURI",
valueattributereference: "valueAttributeReference",
verticalaccuracy: "verticalAccuracy",
vertcoordsys: "vertCoordSys",
virtualmachine: "virtualMachine",
wavelengthunits: "waveLengthUnits",
whitespace: "whiteSpace",
xintercept: "xIntercept",
xcoordinate: "xCoordinate",
"xsi:schemalocation": "xsi:schemaLocation",
xslope: "xSlope",
ycoordinate: "yCoordinate",
yintercept: "yIntercept",
yslope: "ySlope",
},
);
},
/**
* Fetch the EML from the MN object service
* @param {object} [options] - A set of options for this fetch()
* @property {boolean} [options.systemMetadataOnly=false] - If true, only the system metadata will be fetched.
* If false, the system metadata AND EML document will be fetched.
*/
fetch: function (options) {
if (!options) var options = {};
//Add the authorization header and other AJAX settings
_.extend(options, MetacatUI.appUserModel.createAjaxSettings(), {
dataType: "text",
});
// Merge the system metadata into the object first
_.extend(options, { merge: true });
this.fetchSystemMetadata(options);
//If we are retrieving system metadata only, then exit now
if (options.systemMetadataOnly) return;
//Call Backbone.Model.fetch to retrieve the info
return Backbone.Model.prototype.fetch.call(this, options);
},
/*
Deserialize an EML 2.1.1 XML document
*/
parse: function (response) {
// Save a reference to this model for use in setting the
// parentModel inside anonymous functions
var model = this;
//If the response is XML
if (typeof response == "string" && response.indexOf("<") == 0) {
//Look for a system metadata tag and call DataONEObject parse instead
if (response.indexOf("systemMetadata>") > -1)
return DataONEObject.prototype.parse.call(this, response);
response = this.cleanUpXML(response);
response = this.dereference(response);
this.set("objectXML", response);
var emlElement = $($.parseHTML(response)).filter("eml\\:eml");
}
var datasetEl;
if (emlElement[0]) datasetEl = $(emlElement[0]).find("dataset");
if (!datasetEl || !datasetEl.length) return {};
var emlParties = [
"metadataprovider",
"associatedparty",
"creator",
"contact",
"publisher",
],
emlDistribution = ["distribution"],
emlEntities = [
"datatable",
"otherentity",
"spatialvector",
"spatialraster",
"storedprocedure",
"view",
],
emlText = ["abstract", "additionalinfo"],
emlMethods = ["methods"];
var nodes = datasetEl.children(),
modelJSON = {};
for (var i = 0; i < nodes.length; i++) {
var thisNode = nodes[i];
var convertedName =
this.nodeNameMap()[thisNode.localName] || thisNode.localName;
//EML Party modules are stored in EMLParty models
if (_.contains(emlParties, thisNode.localName)) {
if (thisNode.localName == "metadataprovider")
var attributeName = "metadataProvider";
else if (thisNode.localName == "associatedparty")
var attributeName = "associatedParty";
else var attributeName = thisNode.localName;
if (typeof modelJSON[attributeName] == "undefined")
modelJSON[attributeName] = [];
modelJSON[attributeName].push(
new EMLParty({
objectDOM: thisNode,
parentModel: model,
type: attributeName,
}),
);
}
//EML Distribution modules are stored in EMLDistribution models
else if (_.contains(emlDistribution, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] == "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName].push(
new EMLDistribution(
{
objectDOM: thisNode,
parentModel: model,
},
{ parse: true },
),
);
}
//The EML Project is stored in the EMLProject model
else if (thisNode.localName == "project") {
modelJSON.project = new EMLProject({
objectDOM: thisNode,
parentModel: model,
});
}
//EML Temporal, Taxonomic, and Geographic Coverage modules are stored in their own models
else if (thisNode.localName == "coverage") {
var temporal = $(thisNode).children("temporalcoverage"),
geo = $(thisNode).children("geographiccoverage"),
taxon = $(thisNode).children("taxonomiccoverage");
if (temporal.length) {
modelJSON.temporalCoverage = [];
_.each(temporal, function (t) {
modelJSON.temporalCoverage.push(
new EMLTemporalCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
if (geo.length) {
modelJSON.geoCoverage = [];
_.each(geo, function (g) {
modelJSON.geoCoverage.push(
new EMLGeoCoverage({
objectDOM: g,
parentModel: model,
}),
);
});
}
if (taxon.length) {
modelJSON.taxonCoverage = [];
_.each(taxon, function (t) {
modelJSON.taxonCoverage.push(
new EMLTaxonCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
}
//Parse EMLText modules
else if (_.contains(emlText, thisNode.localName)) {
if (typeof modelJSON[convertedName] == "undefined")
modelJSON[convertedName] = [];
modelJSON[convertedName].push(
new EMLText({
objectDOM: thisNode,
parentModel: model,
}),
);
} else if (_.contains(emlMethods, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] === "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName] = new EMLMethods({
objectDOM: thisNode,
parentModel: model,
});
}
//Parse keywords
else if (thisNode.localName == "keywordset") {
//Start an array of keyword sets
if (typeof modelJSON["keywordSets"] == "undefined")
modelJSON["keywordSets"] = [];
modelJSON["keywordSets"].push(
new EMLKeywordSet({
objectDOM: thisNode,
parentModel: model,
}),
);
}
//Parse intellectual rights
else if (thisNode.localName == "intellectualrights") {
var value = "";
if ($(thisNode).children("para").length == 1)
value = $(thisNode).children("para").first().text().trim();
else $(thisNode).text().trim();
//If the value is one of our pre-defined options, then add it to the model
//if(_.contains(this.get("intellRightsOptions"), value))
modelJSON["intellectualRights"] = value;
}
//Parse Entities
else if (_.contains(emlEntities, thisNode.localName)) {
//Start an array of Entities
if (typeof modelJSON["entities"] == "undefined")
modelJSON["entities"] = [];
//Create the model
var entityModel;
if (thisNode.localName == "otherentity") {
entityModel = new EMLOtherEntity(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else if (thisNode.localName == "datatable") {
entityModel = new EMLDataTable(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else {
entityModel = new EMLEntity(
{
objectDOM: thisNode,
parentModel: model,
entityType: "application/octet-stream",
type: thisNode.localName,
},
{
parse: true,
},
);
}
modelJSON["entities"].push(entityModel);
}
//Parse dataset-level annotations
else if (thisNode.localName === "annotation") {
if (!modelJSON["annotations"]) {
modelJSON["annotations"] = new EMLAnnotations();
}
var annotationModel = new EMLAnnotation(
{
objectDOM: thisNode,
},
{ parse: true },
);
modelJSON["annotations"].add(annotationModel);
} else {
//Is this a multi-valued field in EML?
if (Array.isArray(this.get(convertedName))) {
//If we already have a value for this field, then add this value to the array
if (Array.isArray(modelJSON[convertedName]))
modelJSON[convertedName].push(this.toJson(thisNode));
//If it's the first value for this field, then create a new array
else modelJSON[convertedName] = [this.toJson(thisNode)];
} else modelJSON[convertedName] = this.toJson(thisNode);
}
}
// Once all the nodes have been parsed, check if any of the annotations
// make up a canonical dataset reference
const annotations = modelJSON["annotations"];
if (annotations) {
const canonicalDataset = annotations.getCanonicalURI();
if (canonicalDataset) {
modelJSON["canonicalDataset"] = canonicalDataset;
}
}
return modelJSON;
},
/*
* Retireves the model attributes and serializes into EML XML, to produce the new or modified EML document.
* Returns the EML XML as a string.
*/
serialize: function () {
//Get the EML document
var xmlString = this.get("objectXML"),
html = $.parseHTML(xmlString),
eml = $(html).filter("eml\\:eml"),
datasetNode = $(eml).find("dataset");
//Update the packageId on the eml node with the EML id
$(eml).attr("packageId", this.get("id"));
// Set id attribute on dataset node if needed
if (this.get("xmlID")) {
$(datasetNode).attr("id", this.get("xmlID"));
}
// Set schema version
$(eml).attr(
"xmlns:eml",
MetacatUI.appModel.get("editorSerializationFormat") ||
"https://eml.ecoinformatics.org/eml-2.2.0",
);
// Set formatID
this.set(
"formatId",
MetacatUI.appModel.get("editorSerializationFormat") ||
"https://eml.ecoinformatics.org/eml-2.2.0",
);
// Ensure xsi:schemaLocation has a value for the current format
eml = this.setSchemaLocation(eml);
var nodeNameMap = this.nodeNameMap();
//Serialize the basic text fields
var basicText = ["alternateIdentifier", "title"];
_.each(
basicText,
function (fieldName) {
var basicTextValues = this.get(fieldName);
if (!Array.isArray(basicTextValues))
basicTextValues = [basicTextValues];
// Remove existing nodes
datasetNode.children(fieldName.toLowerCase()).remove();
// Create new nodes
var nodes = _.map(basicTextValues, function (value) {
if (value) {
var node = document.createElement(fieldName.toLowerCase());
$(node).text(value);
return node;
} else {
return "";
}
});
var insertAfter = this.getEMLPosition(eml, fieldName.toLowerCase());
if (insertAfter) {
insertAfter.after(nodes);
} else {
datasetNode.prepend(nodes);
}
},
this,
);
// Serialize pubDate
// This one is special because it has a default behavior, unlike
// the others: When no pubDate is set, it should be set to
// the current year
var pubDate = this.get("pubDate");
datasetNode.find("pubdate").remove();
if (pubDate != null && pubDate.length > 0) {
var pubDateEl = document.createElement("pubdate");
$(pubDateEl).text(pubDate);
this.getEMLPosition(eml, "pubdate").after(pubDateEl);
}
// Serialize the parts of EML that are eml-text modules
var textFields = ["abstract", "additionalInfo"];
_.each(
textFields,
function (field) {
var fieldName = this.nodeNameMap()[field] || field;
// Get the EMLText model
var emlTextModels = Array.isArray(this.get(field))
? this.get(field)
: [this.get(field)];
if (!emlTextModels.length) return;
// Get the node from the EML doc
var nodes = datasetNode.find(fieldName);
// Update the DOMs for each model
_.each(
emlTextModels,
function (thisTextModel, i) {
//Don't serialize falsey values
if (!thisTextModel) return;
var node;
//Get the existing node or create a new one
if (nodes.length < i + 1) {
node = document.createElement(fieldName);
this.getEMLPosition(eml, fieldName).after(node);
} else {
node = nodes[i];
}
$(node).html($(thisTextModel.updateDOM()).html());
},
this,
);
// Remove the extra nodes
this.removeExtraNodes(nodes, emlTextModels);
},
this,
);
//Create a <coverage> XML node if there isn't one
if (datasetNode.children("coverage").length === 0) {
var coverageNode = $(document.createElement("coverage")),
coveragePosition = this.getEMLPosition(eml, "coverage");
if (coveragePosition) coveragePosition.after(coverageNode);
else datasetNode.append(coverageNode);
} else {
var coverageNode = datasetNode.children("coverage").first();
}
//Serialize the geographic coverage
if (
typeof this.get("geoCoverage") !== "undefined" &&
this.get("geoCoverage").length > 0
) {
// Don't serialize if geoCoverage is invalid
var validCoverages = _.filter(
this.get("geoCoverage"),
function (cov) {
return cov.isValid();
},
);
//Get the existing geo coverage nodes from the EML
var existingGeoCov = datasetNode.find("geographiccoverage");
//Update the DOM of each model
_.each(
validCoverages,
function (cov, position) {
//Update the existing node if it exists
if (existingGeoCov.length - 1 >= position) {
$(existingGeoCov[position]).replaceWith(cov.updateDOM());
}
//Or, append new nodes
else {
var insertAfter = existingGeoCov.length
? datasetNode.find("geographiccoverage").last()
: null;
if (insertAfter) insertAfter.after(cov.updateDOM());
else coverageNode.append(cov.updateDOM());
}
},
this,
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(
datasetNode.find("geographiccoverage"),
validCoverages,
);
} else {
//If there are no geographic coverages, remove the nodes
coverageNode.children("geographiccoverage").remove();
}
//Serialize the taxonomic coverage
if (
typeof this.get("taxonCoverage") !== "undefined" &&
this.get("taxonCoverage").length > 0
) {
// Group the taxonomic coverage models into empty and non-empty
var sortedTaxonModels = _.groupBy(
this.get("taxonCoverage"),
function (t) {
if (_.flatten(t.get("taxonomicClassification")).length > 0) {
return "notEmpty";
} else {
return "empty";
}
},
);
//Get the existing taxon coverage nodes from the EML
var existingTaxonCov = coverageNode.children("taxonomiccoverage");
//Iterate over each taxon coverage and update it's DOM
if (
sortedTaxonModels["notEmpty"] &&
sortedTaxonModels["notEmpty"].length > 0
) {
//Update the DOM of each model
_.each(
sortedTaxonModels["notEmpty"],
function (taxonCoverage, position) {
//Update the existing taxonCoverage node if it exists
if (existingTaxonCov.length - 1 >= position) {
$(existingTaxonCov[position]).replaceWith(
taxonCoverage.updateDOM(),
);
}
//Or, append new nodes
else {
coverageNode.append(taxonCoverage.updateDOM());
}
},
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(existingTaxonCov, this.get("taxonCoverage"));
}
//If all the taxon coverages are empty, remove the parent taxonomicCoverage node
else if (
!sortedTaxonModels["notEmpty"] ||
sortedTaxonModels["notEmpty"].length == 0
) {
existingTaxonCov.remove();
}
}
//Serialize the temporal coverage
var existingTemporalCoverages = datasetNode.find("temporalcoverage");
//Update the DOM of each model
_.each(
this.get("temporalCoverage"),
function (temporalCoverage, position) {
//Update the existing temporalCoverage node if it exists
if (existingTemporalCoverages.length - 1 >= position) {
$(existingTemporalCoverages[position]).replaceWith(
temporalCoverage.updateDOM(),
);
}
//Or, append new nodes
else {
coverageNode.append(temporalCoverage.updateDOM());
}
},
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(
existingTemporalCoverages,
this.get("temporalCoverage"),
);
//Remove the temporal coverage if it is empty
if (!coverageNode.children("temporalcoverage").children().length) {
coverageNode.children("temporalcoverage").remove();
}
//Remove the <coverage> node if it's empty
if (coverageNode.children().length == 0) {
coverageNode.remove();
}
// Dataset-level annotations
datasetNode.children("annotation").remove();
if (this.get("annotations")) {
this.get("annotations").each(function (annotation) {
if (annotation.isEmpty()) {
return;
}
var after = this.getEMLPosition(eml, "annotation");
$(after).after(annotation.updateDOM());
}, this);
//Since there is at least one annotation, the dataset node needs to have an id attribute.
datasetNode.attr("id", this.getUniqueEntityId(this));
}
//If there is no creator, create one from the user
if (!this.get("creator").length) {
var party = new EMLParty({ parentModel: this, type: "creator" });
party.createFromUser();
this.set("creator", [party]);
}
//Serialize the creators
this.serializeParties(eml, "creator");
//Serialize the metadata providers
this.serializeParties(eml, "metadataProvider");
//Serialize the associated parties
this.serializeParties(eml, "associatedParty");
//Serialize the contacts
this.serializeParties(eml, "contact");
//Serialize the publishers
this.serializeParties(eml, "publisher");
// Serialize methods
if (this.get("methods")) {
//If the methods model is empty, remove it from the EML
if (this.get("methods").isEmpty())
datasetNode.find("methods").remove();
else {
//Serialize the methods model
var methodsEl = this.get("methods").updateDOM();
//If the methodsEl is an empty string or other falsey value, then remove the methods node
if (!methodsEl || !$(methodsEl).children().length) {
datasetNode.find("methods").remove();
} else {
//Add the <methods> node to the EML
datasetNode.find("methods").detach();
var insertAfter = this.getEMLPosition(eml, "methods");
if (insertAfter) insertAfter.after(methodsEl);
else datasetNode.append(methodsEl);
}
}
}
//If there are no methods, then remove the methods nodes
else {
if (datasetNode.find("methods").length > 0) {
datasetNode.find("methods").remove();
}
}
//Serialize the keywords
this.serializeKeywords(eml, "keywordSets");
//Serialize the intellectual rights
if (this.get("intellectualRights")) {
if (datasetNode.find("intellectualRights").length)
datasetNode
.find("intellectualRights")
.html("<para>" + this.get("intellectualRights") + "</para>");
else {
this.getEMLPosition(eml, "intellectualrights").after(
$(document.createElement("intellectualRights")).html(
"<para>" + this.get("intellectualRights") + "</para>",
),
);
}
}
// Serialize the distribution
const distributions = this.get("distribution");
if (distributions && distributions.length > 0) {
// Remove existing nodes
datasetNode.children("distribution").remove();
// Get the updated DOMs
const distributionDOMs = distributions.map((d) => d.updateDOM());
// Insert the updated DOMs in their correct positions
distributionDOMs.forEach((dom, i) => {
const insertAfter = this.getEMLPosition(eml, "distribution");
if (insertAfter) {
insertAfter.after(dom);
} else {
datasetNode.append(dom);
}
});
}
//Detach the project elements from the DOM
if (datasetNode.find("project").length) {
datasetNode.find("project").detach();
}
//If there is an EMLProject, update its DOM
if (this.get("project")) {
this.getEMLPosition(eml, "project").after(
this.get("project").updateDOM(),
);
}
//Get the existing taxon coverage nodes from the EML
var existingEntities = datasetNode.find(
"otherEntity, dataTable, spatialRaster, spatialVector, storedProcedure, view",
);
//Serialize the entities
_.each(
this.get("entities"),
function (entity, position) {
//Update the existing node if it exists
if (existingEntities.length - 1 >= position) {
//Remove the entity from the EML
$(existingEntities[position]).detach();
//Insert it into the correct position
this.getEMLPosition(eml, entity.get("type").toLowerCase()).after(
entity.updateDOM(),
);
}
//Or, append new nodes
else {
//Inser the entity into the correct position
this.getEMLPosition(eml, entity.get("type").toLowerCase()).after(
entity.updateDOM(),
);
}
},
this,
);
//Remove extra entities that have been removed
var numExtraEntities =
existingEntities.length - this.get("entities").length;
for (
var i = existingEntities.length - numExtraEntities;
i < existingEntities.length;
i++
) {
$(existingEntities)[i].remove();
}
//Do a final check to make sure there are no duplicate ids in the EML
var elementsWithIDs = $(eml).find("[id]"),
//Get an array of all the ids in this EML doc
allIDs = _.map(elementsWithIDs, function (el) {
return $(el).attr("id");
});
//If there is at least one id in the EML...
if (allIDs && allIDs.length) {
//Boil the array down to just the unique values
var uniqueIDs = _.uniq(allIDs);
//If the unique array is shorter than the array of all ids,
// then there is a duplicate somewhere
if (uniqueIDs.length < allIDs.length) {
//For each element in the EML that has an id,
_.each(elementsWithIDs, function (el) {
//Get the id for this element
var id = $(el).attr("id");
//If there is more than one element in the EML with this id,
if ($(eml).find("[id='" + id + "']").length > 1) {
//And if it is not a unit node, which we don't want to change,
if (!$(el).is("unit"))
//Then change the id attribute to a random uuid
$(el).attr("id", "urn-uuid-" + uuid.v4());
}
});
}
}
//Camel-case the XML
var emlString = "";
_.each(
html,
function (rootEMLNode) {
emlString += this.formatXML(rootEMLNode);
},
this,
);
return emlString;
},
/*
* Given an EML DOM and party type, this function updated and/or adds the EMLParties to the EML
*/
serializeParties: function (eml, type) {
//Remove the nodes from the EML for this party type
$(eml).children("dataset").children(type.toLowerCase()).remove();
//Serialize each party of this type
_.each(
this.get(type),
function (party, i) {
//Get the last node of this type to insert after
var insertAfter = $(eml)
.children("dataset")
.children(type.toLowerCase())
.last();
//If there isn't a node found, find the EML position to insert after
if (!insertAfter.length) {
insertAfter = this.getEMLPosition(eml, type);
}
//Update the DOM of the EMLParty
var emlPartyDOM = party.updateDOM();
//Make sure we don't insert empty EMLParty nodes into the EML
if ($(emlPartyDOM).children().length) {
//Insert the party DOM at the insert position
if (insertAfter && insertAfter.length)
insertAfter.after(emlPartyDOM);
//If an insert position still hasn't been found, then just append to the dataset node
else $(eml).find("dataset").append(emlPartyDOM);
}
},
this,
);
//Create a certain parties from the current app user if none is given
if (type == "contact" && !this.get("contact").length) {
//Get the creators
var creators = this.get("creator"),
contacts = [];
_.each(
creators,
function (creator) {
//Clone the creator model and add it to the contacts array
var newModel = new EMLParty({ parentModel: this });
newModel.set(creator.toJSON());
newModel.set("type", type);
contacts.push(newModel);
},
this,
);
this.set(type, contacts);
//Call this function again to serialize the new models
this.serializeParties(eml, type);
}
},
serializeKeywords: function (eml) {
// Remove all existing keywordSets before appending
$(eml).find("dataset").find("keywordset").remove();
if (this.get("keywordSets").length == 0) return;
// Create the new keywordSets nodes
var nodes = _.map(this.get("keywordSets"), function (kwd) {
return kwd.updateDOM();
});
this.getEMLPosition(eml, "keywordset").after(nodes);
},
/*
* Remoes nodes from the EML that do not have an accompanying model
* (Were probably removed from the EML by the user during editing)
*/
removeExtraNodes: function (nodes, models) {
// Remove the extra nodes
var extraNodes = nodes.length - models.length;
if (extraNodes > 0) {
for (var i = models.length; i < nodes.length; i++) {
$(nodes[i]).remove();
}
}
},
/*
* Saves the EML document to the server using the DataONE API
*/
save: function (attributes, options) {
//Validate before we try anything else
if (!this.isValid()) {
this.trigger("invalid");
this.trigger("cancelSave");
return false;
} else {
this.trigger("valid");
}
this.setFileName();
//Set the upload transfer as in progress
this.set("uploadStatus", "p");
//Reset the draftSaved attribute
this.set("draftSaved", false);
//Create the creator from the current user if none is provided
if (!this.get("creator").length) {
var party = new EMLParty({ parentModel: this, type: "creator" });
party.createFromUser();
this.set("creator", [party]);
}
//Create the contact from the current user if none is provided
if (!this.get("contact").length) {
var party = new EMLParty({ parentModel: this, type: "contact" });
party.createFromUser();
this.set("contact", [party]);
}
//If this is an existing object and there is no system metadata, retrieve it
if (!this.isNew() && !this.get("sysMetaXML")) {
var model = this;
//When the system metadata is fetched, try saving again
var fetchOptions = {
success: function (response) {
model.set(DataONEObject.prototype.parse.call(model, response));
model.save(attributes, options);
},
};
//Fetch the system metadata now
this.fetchSystemMetadata(fetchOptions);
return;
}
//Create a FormData object to send data with our XHR
var formData = new FormData();
try {
//Add the identifier to the XHR data
if (this.isNew()) {
formData.append("pid", this.get("id"));
} else {
//Create a new ID
this.updateID();
//Add the ids to the form data
formData.append("newPid", this.get("id"));
formData.append("pid", this.get("oldPid"));
}
//Serialize the EML XML
var xml = this.serialize();
var xmlBlob = new Blob([xml], { type: "application/xml" });
//Get the size of the new EML XML
this.set("size", xmlBlob.size);
//Get the new checksum of the EML XML
var checksum = md5(xml);
this.set("checksum", checksum);
this.set("checksumAlgorithm", "MD5");
//Create the system metadata XML
var sysMetaXML = this.serializeSysMeta();
//Send the system metadata as a Blob
var sysMetaXMLBlob = new Blob([sysMetaXML], {
type: "application/xml",
});
//Add the object XML and System Metadata XML to the form data
//Append the system metadata first, so we can take advantage of Metacat's streaming multipart handler
formData.append("sysmeta", sysMetaXMLBlob, "sysmeta");
formData.append("object", xmlBlob);
} catch (error) {
//Reset the identifier since we didn't actually update the object
this.resetID();
this.set("uploadStatus", "e");
this.trigger("error");
this.trigger("cancelSave");
return false;
}
var model = this;
var saveOptions = options || {};
_.extend(
saveOptions,
{
data: formData,
cache: false,
contentType: false,
dataType: "text",
processData: false,
parse: false,
//Use the URL function to determine the URL
url: this.isNew() ? this.url() : this.url({ update: true }),
xhr: function () {
var xhr = new window.XMLHttpRequest();
//Upload progress
xhr.upload.addEventListener(
"progress",
function (evt) {
if (evt.lengthComputable) {
var percentComplete = (evt.loaded / evt.total) * 100;
model.set("uploadProgress", percentComplete);
}
},
false,
);
return xhr;
},
success: function (model, response, xhr) {
model.set("numSaveAttempts", 0);
model.set("uploadStatus", "c");
model.set("sysMetaXML", model.serializeSysMeta());
model.set("oldPid", null);
model.fetch({ merge: true, systemMetadataOnly: true });
model.trigger("successSaving", model);
},
error: function (model, response, xhr) {
model.set("numSaveAttempts", model.get("numSaveAttempts") + 1);
var numSaveAttempts = model.get("numSaveAttempts");
//Reset the identifier changes
model.resetID();
if (
numSaveAttempts < 3 &&
(response.status == 408 || response.status == 0)
) {
//Try saving again in 10, 40, and 90 seconds
setTimeout(
function () {
model.save.call(model);
},
numSaveAttempts * numSaveAttempts * 10000,
);
} else {
model.set("numSaveAttempts", 0);
//Get the error error information
var errorDOM = $($.parseHTML(response.responseText)),
errorContainer = errorDOM.filter("error"),
msgContainer = errorContainer.length
? errorContainer.find("description")
: errorDOM.not("style, title"),
errorMsg = msgContainer.length
? msgContainer.text()
: errorDOM;
//When there is no network connection (status == 0), there will be no response text
if (!errorMsg || response.status == 408 || response.status == 0)
errorMsg =
"There was a network issue that prevented your metadata from uploading. " +
"Make sure you are connected to a reliable internet connection.";
//Save the error message in the model
model.set("errorMessage", errorMsg);
//Set the model status as e for error
model.set("uploadStatus", "e");
//Save the EML as a plain text file, until drafts are a supported feature
var copy = model.createTextCopy();
//If the EML copy successfully saved, let the user know that there is a copy saved behind the scenes
model.listenToOnce(copy, "successSaving", function () {
model.set("draftSaved", true);
//Trigger the errorSaving event so other parts of the app know that the model failed to save
//And send the error message with it
model.trigger("errorSaving", errorMsg);
});
//If the EML copy fails to save too, then just display the usual error message
model.listenToOnce(copy, "errorSaving", function () {
//Trigger the errorSaving event so other parts of the app know that the model failed to save
//And send the error message with it
model.trigger("errorSaving", errorMsg);
});
//Save the EML plain text copy
copy.save();
// Track the error
MetacatUI.analytics?.trackException(
`EML save error: ${errorMsg}, EML draft: ${copy.get("id")}`,
model.get("id"),
true,
);
}
},
},
MetacatUI.appUserModel.createAjaxSettings(),
);
return Backbone.Model.prototype.save.call(
this,
attributes,
saveOptions,
);
},
/*
* Checks if this EML model has all the required values necessary to save to the server
*/
validate: function () {
let errors = {};
//A title is always required by EML
if (!this.get("title").length || !this.get("title")[0]) {
errors.title = "A title is required";
}
// Validate the publication date
if (this.get("pubDate") != null) {
if (!this.isValidYearDate(this.get("pubDate"))) {
errors["pubDate"] = [
"The value entered for publication date, '" +
this.get("pubDate") +
"' is not a valid value for this field. Enter with a year (e.g. 2017) or a date in the format YYYY-MM-DD.",
];
}
}
// Validate the temporal coverage
errors.temporalCoverage = [];
//If temporal coverage is required and there aren't any, return an error
if (
MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
!this.get("temporalCoverage").length
) {
errors.temporalCoverage = [{ beginDate: "Provide a begin date." }];
}
//If temporal coverage is required and they are all empty, return an error
else if (
MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
_.every(this.get("temporalCoverage"), function (tc) {
return tc.isEmpty();
})
) {
errors.temporalCoverage = [{ beginDate: "Provide a begin date." }];
}
//If temporal coverage is not required, validate each one
else if (
this.get("temporalCoverage").length ||
(MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
_.every(this.get("temporalCoverage"), function (tc) {
return tc.isEmpty();
}))
) {
//Iterate over each temporal coverage and add it's validation errors
_.each(this.get("temporalCoverage"), function (temporalCoverage) {
if (!temporalCoverage.isValid() && !temporalCoverage.isEmpty()) {
errors.temporalCoverage.push(temporalCoverage.validationError);
}
});
}
//Remove the temporalCoverage attribute if no errors were found
if (errors.temporalCoverage.length == 0) {
delete errors.temporalCoverage;
}
//Validate the EMLParty models
var partyTypes = [
"associatedParty",
"contact",
"creator",
"metadataProvider",
"publisher",
];
_.each(
partyTypes,
function (type) {
var people = this.get(type);
_.each(
people,
function (person, i) {
if (!person.isValid()) {
if (!errors[type]) errors[type] = [person.validationError];
else errors[type].push(person.validationError);
}
},
this,
);
},
this,
);
//Validate the EMLGeoCoverage models
_.each(
this.get("geoCoverage"),
function (geoCoverageModel, i) {
if (!geoCoverageModel.isValid()) {
if (!errors.geoCoverage)
errors.geoCoverage = [geoCoverageModel.validationError];
else errors.geoCoverage.push(geoCoverageModel.validationError);
}
},
this,
);
//Validate the EMLTaxonCoverage model
var taxonModel = this.get("taxonCoverage")[0];
if (!taxonModel.isEmpty() && !taxonModel.isValid()) {
errors = _.extend(errors, taxonModel.validationError);
} else if (
taxonModel.isEmpty() &&
this.get("taxonCoverage").length == 1 &&
MetacatUI.appModel.get("emlEditorRequiredFields").taxonCoverage
) {
taxonModel.isValid();
errors = _.extend(errors, taxonModel.validationError);
}
//Validate each EMLEntity model
_.each(this.get("entities"), function (entityModel) {
if (!entityModel.isValid()) {
if (!errors.entities)
errors.entities = [entityModel.validationError];
else errors.entities.push(entityModel.validationError);
}
});
//Validate the EML Methods
let emlMethods = this.get("methods");
if (emlMethods) {
if (!emlMethods.isValid()) {
errors.methods = emlMethods.validationError;
}
}
// Validate each EMLAnnotation model
if (this.get("annotations")) {
this.get("annotations").each(function (model) {
if (model.isValid()) {
return;
}
if (!errors.annotations) {
errors.annotations = [];
}
errors.annotations.push(model.validationError);
}, this);
}
//Check the required fields for this MetacatUI configuration
for ([field, isRequired] of Object.entries(
MetacatUI.appModel.get("emlEditorRequiredFields"),
)) {
//If it's not required, then go to the next field
if (!isRequired) continue;
if (field == "alternateIdentifier") {
if (
!this.get("alternateIdentifier").length ||
_.every(this.get("alternateIdentifier"), function (altId) {
return altId.trim() == "";
})
)
errors.alternateIdentifier =
"At least one alternate identifier is required.";
} else if (field == "generalTaxonomicCoverage") {
if (
!this.get("taxonCoverage").length ||
!this.get("taxonCoverage")[0].get("generalTaxonomicCoverage")
)
errors.generalTaxonomicCoverage =
"Provide a description of the general taxonomic coverage of this data set.";
} else if (field == "geoCoverage") {
if (!this.get("geoCoverage").length)
errors.geoCoverage = "At least one location is required.";
} else if (field == "intellectualRights") {
if (!this.get("intellectualRights"))
errors.intellectualRights =
"Select usage rights for this data set.";
} else if (field == "studyExtentDescription") {
if (
!this.get("methods") ||
!this.get("methods").get("studyExtentDescription")
)
errors.studyExtentDescription =
"Provide a study extent description.";
} else if (field == "samplingDescription") {
if (
!this.get("methods") ||
!this.get("methods").get("samplingDescription")
)
errors.samplingDescription = "Provide a sampling description.";
} else if (field == "temporalCoverage") {
if (!this.get("temporalCoverage").length)
errors.temporalCoverage =
"Provide the date(s) for this data set.";
} else if (field == "taxonCoverage") {
if (!this.get("taxonCoverage").length)
errors.taxonCoverage =
"At least one taxa rank and value is required.";
} else if (field == "keywordSets") {
if (!this.get("keywordSets").length)
errors.keywordSets = "Provide at least one keyword.";
}
//The EMLMethods model will validate itself for required fields, but
// this is a rudimentary check to make sure the EMLMethods model was created
// in the first place
else if (field == "methods") {
if (!this.get("methods"))
errors.methods = "At least one method step is required.";
} else if (field == "funding") {
// Note: Checks for either the funding or award element. award
// element is checked by the project's objectDOM for now until
// EMLProject fully supports the award element
if (
!this.get("project") ||
!(
this.get("project").get("funding").length ||
(this.get("project").get("objectDOM") &&
this.get("project").get("objectDOM").querySelectorAll &&
this.get("project").get("objectDOM").querySelectorAll("award")
.length > 0)
)
)
errors.funding =
"Provide at least one project funding number or name.";
} else if (field == "abstract") {
if (!this.get("abstract").length)
errors["abstract"] = "Provide an abstract.";
} else if (field == "dataSensitivity") {
if (!this.getDataSensitivity()) {
errors["dataSensitivity"] =
"Pick the category that best describes the level of sensitivity or restriction of the data.";
}
}
//If this is an EMLParty type, check that there is a party of this type in the model
else if (
EMLParty.prototype.partyTypes
.map((t) => t.dataCategory)
.includes(field)
) {
//If this is an associatedParty role
if (EMLParty.prototype.defaults().roleOptions?.includes(field)) {
if (
!this.get("associatedParty")
?.map((p) => p.get("roles"))
.flat()
.includes(field)
) {
errors[field] =
"Provide information about the people or organization(s) in the role: " +
EMLParty.prototype.partyTypes.find(
(t) => t.dataCategory == field,
)?.label;
}
} else if (!this.get(field)?.length) {
errors[field] =
"Provide information about the people or organization(s) in the role: " +
EMLParty.prototype.partyTypes.find(
(t) => t.dataCategory == field,
)?.label;
}
} else if (!this.get(field) || !this.get(field)?.length) {
errors[field] = "Provide a " + field + ".";
}
}
if (Object.keys(errors).length) return errors;
else {
return;
}
},
/* Returns a boolean for whether the argument 'value' is a valid
value for EML's yearDate type which is used in a few places.
Note that this method considers a zero-length String to be valid
because the EML211.serialize() method will properly handle a null
or zero-length String by serializing out the current year. */
isValidYearDate: function (value) {
return (
value === "" ||
/^\d{4}$/.test(value) ||
/^\d{4}-\d{2}-\d{2}$/.test(value)
);
},
/*
* Sends an AJAX request to fetch the system metadata for this EML object.
* Will not trigger a sync event since it does not use Backbone.Model.fetch
*/
fetchSystemMetadata: function (options) {
if (!options) var options = {};
else options = _.clone(options);
var model = this,
fetchOptions = _.extend(
{
url:
MetacatUI.appModel.get("metaServiceUrl") +
encodeURIComponent(this.get("id")),
dataType: "text",
success: function (response) {
model.set(DataONEObject.prototype.parse.call(model, response));
//Trigger a custom event that the sys meta was updated
model.trigger("sysMetaUpdated");
},
error: function () {
model.trigger("error");
},
},
options,
);
//Add the authorization header and other AJAX settings
_.extend(fetchOptions, MetacatUI.appUserModel.createAjaxSettings());
$.ajax(fetchOptions);
},
/*
* Returns the nofde in the given EML document that the given node type
* should be inserted after
*
* Returns false if either the node is not found in the and this should
* be handled by the caller.
*/
getEMLPosition: function (eml, nodeName) {
var nodeOrder = this.get("nodeOrder");
var position = _.indexOf(nodeOrder, nodeName.toLowerCase());
if (position == -1) {
return false;
}
// Go through each node in the node list and find the position where this
// node will be inserted after
for (var i = position - 1; i >= 0; i--) {
if ($(eml).find("dataset").children(nodeOrder[i]).length) {
return $(eml).find("dataset").children(nodeOrder[i]).last();
}
}
return false;
},
/*
* Checks if this model has updates that need to be synced with the server.
*/
hasUpdates: function () {
if (this.constructor.__super__.hasUpdates.call(this)) return true;
//If nothing else has been changed, then this object hasn't had any updates
return false;
},
/*
Add an entity into the EML 2.1.1 object
*/
addEntity: function (emlEntity, position) {
//Get the current list of entities
var currentEntities = this.get("entities");
if (typeof position == "undefined" || position == -1)
currentEntities.push(emlEntity);
//Add the entity model to the entity array
else currentEntities.splice(position, 0, emlEntity);
this.trigger("change:entities");
this.trickleUpChange();
return this;
},
/*
Remove an entity from the EML 2.1.1 object
*/
removeEntity: function (emlEntity) {
if (!emlEntity || typeof emlEntity != "object") return;
//Get the current list of entities
var entities = this.get("entities");
entities = _.without(entities, emlEntity);
this.set("entities", entities);
},
/*
* Find the entity model for a given DataONEObject
*/
getEntity: function (dataONEObj) {
//If an EMLEntity model has been found for this object before, then return it
if (dataONEObj.get("metadataEntity")) {
dataONEObj.get("metadataEntity").set("dataONEObject", dataONEObj);
return dataONEObj.get("metadataEntity");
}
var entity = _.find(
this.get("entities"),
function (e) {
//Matches of the checksum or identifier are definite matches
if (e.get("xmlID") == dataONEObj.getXMLSafeID()) return true;
else if (
e.get("physicalMD5Checksum") &&
e.get("physicalMD5Checksum") == dataONEObj.get("checksum") &&
dataONEObj.get("checksumAlgorithm").toUpperCase() == "MD5"
)
return true;
else if (
e.get("downloadID") &&
e.get("downloadID") == dataONEObj.get("id")
)
return true;
// Get the file name from the EML for this entity
var fileNameFromEML =
e.get("physicalObjectName") || e.get("entityName");
// If the EML file name matches the DataONEObject file name
if (
fileNameFromEML &&
dataONEObj.get("fileName") &&
(fileNameFromEML.toLowerCase() ==
dataONEObj.get("fileName").toLowerCase() ||
fileNameFromEML.replace(/ /g, "_").toLowerCase() ==
dataONEObj.get("fileName").toLowerCase())
) {
//Get an array of all the other entities in this EML
var otherEntities = _.without(this.get("entities"), e);
// If this entity name matches the dataone object file name, AND no other dataone object file name
// matches, then we can assume this is the entity element for this file.
var otherMatchingEntity = _.find(
otherEntities,
function (otherE) {
// Get the file name from the EML for the other entities
var otherFileNameFromEML =
otherE.get("physicalObjectName") ||
otherE.get("entityName");
// If the file names match, return true
if (
otherFileNameFromEML == dataONEObj.get("fileName") ||
otherFileNameFromEML.replace(/ /g, "_") ==
dataONEObj.get("fileName")
)
return true;
},
);
// If this entity's file name didn't match any other file names in the EML,
// then this entity is a match for the given dataONEObject
if (!otherMatchingEntity) return true;
}
},
this,
);
//If we found an entity, give it an ID and return it
if (entity) {
//If this entity has been matched to another DataONEObject already, then don't match it again
if (entity.get("dataONEObject") == dataONEObj) {
return entity;
}
//If this entity has been matched to a different DataONEObject already, then don't match it again.
//i.e. We will not override existing entity<->DataONEObject pairings
else if (entity.get("dataONEObject")) {
return;
} else {
entity.set("dataONEObject", dataONEObj);
}
//Create an XML-safe ID and set it on the Entity model
var entityID = this.getUniqueEntityId(dataONEObj);
entity.set("xmlID", entityID);
//Save a reference to this entity so we don't have to refind it later
dataONEObj.set("metadataEntity", entity);
return entity;
}
//See if one data object is of this type in the package
var matchingTypes = _.filter(this.get("entities"), function (e) {
return (
e.get("formatName") ==
(dataONEObj.get("formatId") || dataONEObj.get("mediaType"))
);
});
if (matchingTypes.length == 1) {
//Create an XML-safe ID and set it on the Entity model
matchingTypes[0].set("xmlID", dataONEObj.getXMLSafeID());
return matchingTypes[0];
}
//If this EML is in a DataPackage with only one other DataONEObject,
// and there is only one entity in the EML, then we can assume they are the same entity
if (this.get("entities").length == 1) {
if (
this.get("collections")[0] &&
this.get("collections")[0].type == "DataPackage" &&
this.get("collections")[0].length == 2 &&
_.contains(this.get("collections")[0].models, dataONEObj)
) {
return this.get("entities")[0];
}
}
return false;
},
createEntity: function (dataONEObject) {
// Add or append an entity to the parent's entity list
var entityModel = new EMLOtherEntity({
entityName: dataONEObject.get("fileName"),
entityType:
dataONEObject.get("formatId") ||
dataONEObject.get("mediaType") ||
"application/octet-stream",
dataONEObject: dataONEObject,
parentModel: this,
xmlID: dataONEObject.getXMLSafeID(),
});
this.addEntity(entityModel);
//If this DataONEObject fails to upload, remove the EML entity
this.listenTo(dataONEObject, "errorSaving", function () {
this.removeEntity(dataONEObject.get("metadataEntity"));
//Listen for a successful save so the entity can be added back
this.listenToOnce(dataONEObject, "successSaving", function () {
this.addEntity(dataONEObject.get("metadataEntity"));
});
});
},
/*
* Creates an XML-safe identifier that is unique to this EML document,
* based on the given DataONEObject model. It is intended for EML entity nodes in particular.
*
* @param {DataONEObject} - a DataONEObject model that this EML documents
* @return {string} - an identifier string unique to this EML document
*/
getUniqueEntityId: function (dataONEObject) {
var uniqueId = "";
uniqueId = dataONEObject.getXMLSafeID();
//Get the EML string, if there is one, to check if this id already exists
var emlString = this.get("objectXML");
//If this id already exists in the EML...
if (emlString && emlString.indexOf(' id="' + uniqueId + '"')) {
//Create a random uuid to use instead
uniqueId = "urn-uuid-" + uuid.v4();
}
return uniqueId;
},
/*
* 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,
);
},
/**
* Attempt to move a party one index forward within its sibling models
*
* @param {EMLParty} partyModel: The EMLParty model we're moving
*/
movePartyUp: function (partyModel) {
var possibleAttr = [
"creator",
"contact",
"metadataProvider",
"publisher",
"associatedParty",
];
// Iterate over each possible attribute
_.each(
possibleAttr,
function (attr) {
if (!_.contains(this.get(attr), partyModel)) {
return;
}
// Make a clone because we're going to use splice
var models = _.clone(this.get(attr));
// Find the index of the model we're moving
var index = _.findIndex(models, function (m) {
return m === partyModel;
});
if (index === 0) {
// Already first
return;
}
if (index === -1) {
// Couldn't find the model
return;
}
// Do the move using splice and update the model
models.splice(index - 1, 0, models.splice(index, 1)[0]);
this.set(attr, models);
this.trigger("change:" + attr);
},
this,
);
},
/**
* Attempt to move a party one index forward within its sibling models
*
* @param {EMLParty} partyModel: The EMLParty model we're moving
*/
movePartyDown: function (partyModel) {
var possibleAttr = [
"creator",
"contact",
"metadataProvider",
"publisher",
"associatedParty",
];
// Iterate over each possible attribute
_.each(
possibleAttr,
function (attr) {
if (!_.contains(this.get(attr), partyModel)) {
return;
}
// Make a clone because we're going to use splice
var models = _.clone(this.get(attr));
// Find the index of the model we're moving
var index = _.findIndex(models, function (m) {
return m === partyModel;
});
if (index === -1) {
// Couldn't find the model
return;
}
// Figure out where to put the new model
// Leave it in the same place if the next index doesn't exist
// Move one forward if it does
var newIndex = models.length <= index + 1 ? index : index + 1;
// Do the move using splice and update the model
models.splice(newIndex, 0, models.splice(index, 1)[0]);
this.set(attr, models);
this.trigger("change:" + attr);
},
this,
);
},
/*
* Adds the given EMLParty model to this EML211 model in the
* appropriate role array in the given position
*
* @param {EMLParty} - The EMLParty model to add
* @param {number} - The position in the role array in which to insert this EMLParty
* @return {boolean} - Returns true if the EMLParty was successfully added, false if it was cancelled
*/
addParty: function (partyModel, position) {
//If the EMLParty model is empty, don't add it to the EML211 model
if (partyModel.isEmpty()) return false;
//Get the role of this EMLParty
var role = partyModel.get("type") || "associatedParty";
//If this model already contains this EMLParty, then exit
if (_.contains(this.get(role), partyModel)) return false;
if (typeof position == "undefined") {
this.get(role).push(partyModel);
} else {
this.get(role).splice(position, 0, partyModel);
}
this.trigger("change:" + role);
return true;
},
/**
* getPartiesByType - Gets an array of EMLParty members that have a particular party type or role.
* @param {string} partyType - A string that represents either the role or the party type. For example, "contact", "creator", "principalInvestigator", etc.
* @since 2.15.0
*/
getPartiesByType: function (partyType) {
try {
if (!partyType) {
return false;
}
var associatedPartyTypes = new EMLParty().get("roleOptions"),
isAssociatedParty = associatedPartyTypes.includes(partyType),
parties = [];
// For "contact", "creator", "metadataProvider", "publisher", each party type has it's own
// array in the EML model
if (!isAssociatedParty) {
parties = this.get(partyType);
// For "custodianSteward", "principalInvestigator", "collaboratingPrincipalInvestigator", etc.,
// party members are listed in the EML model's associated parties array. Each associated party's
// party type is indicated in the role attribute.
} else {
parties = _.filter(
this.get("associatedParty"),
function (associatedParty) {
return associatedParty.get("roles").includes(partyType);
},
);
}
return parties;
} catch (error) {
console.log(
"Error trying to find a list of party members in an EML model by type. Error details: " +
error,
);
}
},
createUnits: function () {
this.units.fetch();
},
/* Initialize the object XML for brand spankin' new EML objects */
createXML: function () {
let emlSystem = MetacatUI.appModel.get("emlSystem");
emlSystem =
!emlSystem || typeof emlSystem != "string" ? "knb" : emlSystem;
var xml =
'<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0"></eml:eml>',
eml = $($.parseHTML(xml));
// Set base attributes
eml.attr("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
eml.attr("xmlns:stmml", "http://www.xml-cml.org/schema/stmml-1.1");
eml.attr(
"xsi:schemaLocation",
"https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd",
);
eml.attr("packageId", this.get("id"));
eml.attr("system", emlSystem);
// Add the dataset
eml.append(document.createElement("dataset"));
eml.find("dataset").append(document.createElement("title"));
var emlString = $(document.createElement("div"))
.append(eml.clone())
.html();
return emlString;
},
/*
Replace elements named "source" with "sourced" due to limitations
with using $.parseHTML() rather than $.parseXML()
@param xmlString The XML string to make the replacement in
*/
cleanUpXML: function (xmlString) {
xmlString.replace("<source>", "<sourced>");
xmlString.replace("</source>", "</sourced>");
return xmlString;
},
createTextCopy: function () {
var emlDraftText =
"EML draft for " +
this.get("id") +
"(" +
this.get("title") +
") by " +
MetacatUI.appUserModel.get("firstName") +
" " +
MetacatUI.appUserModel.get("lastName");
if (this.get("uploadStatus") == "e" && this.get("errorMessage")) {
emlDraftText +=
". This EML had the following save error: `" +
this.get("errorMessage") +
"` ";
} else {
emlDraftText += ": ";
}
emlDraftText += this.serialize();
var plainTextEML = new DataONEObject({
formatId: "text/plain",
fileName:
"eml_draft_" +
(MetacatUI.appUserModel.get("lastName") || "") +
".txt",
uploadFile: new Blob([emlDraftText], { type: "plain/text" }),
synced: true,
});
return plainTextEML;
},
/*
* Cleans up the given text so that it is XML-valid by escaping reserved characters, trimming white space, etc.
*
* @param {string} textString - The string to clean up
* @return {string} - The cleaned up string
*/
cleanXMLText: function (textString) {
if (typeof textString != "string") return;
textString = textString.trim();
//Check for XML/HTML elements
_.each(textString.match(/<\s*[^>]*>/g), function (xmlNode) {
//Encode <, >, and </ substrings
var tagName = xmlNode.replace(/>/g, "&gt;");
tagName = tagName.replace(/</g, "&lt;");
//Replace the xmlNode in the full text string
textString = textString.replace(xmlNode, tagName);
});
//Remove Unicode characters that are not valid XML characters
//Create a regular expression that matches any character that is not a valid XML character
// (see https://www.w3.org/TR/xml/#charsets)
var invalidCharsRegEx =
/[^\u0009\u000a\u000d\u0020-\uD7FF\uE000-\uFFFD]/g;
textString = textString.replace(invalidCharsRegEx, "");
return textString;
},
/*
Dereference "reference" elements and replace them with a cloned copy
of the referenced content
@param xmlString The XML string with reference elements to transform
*/
dereference: function (xmlString) {
var referencesList; // the array of references elements in the document
var referencedID; // The id of the referenced element
var referencesParentEl; // The parent of the given references element
var referencedEl; // The referenced DOM to be copied
var xmlDOM = $.parseXML(xmlString);
referencesList = xmlDOM.getElementsByTagName("references");
if (referencesList.length) {
// Process each references elements
_.each(
referencesList,
function (referencesEl, index, referencesList) {
// Can't rely on the passed referencesEl since the list length changes
// because of the remove() below. Reuse referencesList[0] for every item:
// referencedID = $(referencesEl).text(); // doesn't work
referencesEl = referencesList[0];
referencedID = $(referencesEl).text();
referencesParentEl = $(referencesEl).parent()[0];
if (typeof referencedID !== "undefined" && referencedID != "") {
referencedEl = xmlDOM.getElementById(referencedID);
if (typeof referencedEl != "undefined") {
// Clone the referenced element and replace the references element
var referencedClone = $(referencedEl).clone()[0];
$(referencesParentEl)
.children(referencesEl.localName)
.replaceWith($(referencedClone).children());
//$(referencesParentEl).append($(referencedClone).children());
$(referencesParentEl).attr("id", DataONEObject.generateId());
}
}
},
xmlDOM,
);
}
return new XMLSerializer().serializeToString(xmlDOM);
},
/*
* Uses the EML `title` to set the `fileName` attribute on this model.
*/
setFileName: function () {
var title = "";
// Get the title from the metadata
if (Array.isArray(this.get("title"))) {
title = this.get("title")[0];
} else if (typeof this.get("title") == "string") {
title = this.get("title");
}
//Max title length
var maxLength = 50;
//trim the string to the maximum length
var trimmedTitle = title.trim().substr(0, maxLength);
//re-trim if we are in the middle of a word
if (trimmedTitle.indexOf(" ") > -1) {
trimmedTitle = trimmedTitle.substr(
0,
Math.min(trimmedTitle.length, trimmedTitle.lastIndexOf(" ")),
);
}
//Replace all non alphanumeric characters with underscores
// and make sure there isn't more than one underscore in a row
trimmedTitle = trimmedTitle
.replace(/[^a-zA-Z0-9]/g, "_")
.replace(/_{2,}/g, "_");
//Set the fileName on the model
this.set("fileName", trimmedTitle + ".xml");
},
trickleUpChange: function () {
if (
!MetacatUI.rootDataPackage ||
!MetacatUI.rootDataPackage.packageModel
)
return;
//Mark the package as changed
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/**
* Sets the xsi:schemaLocation attribute on the passed-in Element
* depending on the application configuration.
*
* @param {Element} eml: The root eml:eml element to modify
* @return {Element} The element, possibly modified
*/
setSchemaLocation: function (eml) {
if (!MetacatUI || !MetacatUI.appModel) {
return eml;
}
var current = $(eml).attr("xsi:schemaLocation"),
format = MetacatUI.appModel.get("editorSerializationFormat"),
location = MetacatUI.appModel.get("editorSchemaLocation");
// Return now if we can't do anything anyway
if (!format || !location) {
return eml;
}
// Simply add if the attribute isn't present to begin with
if (!current || typeof current !== "string") {
$(eml).attr("xsi:schemaLocation", format + " " + location);
return eml;
}
// Don't append if it's already present
if (current.indexOf(format) >= 0) {
return eml;
}
$(eml).attr("xsi:schemaLocation", current + " " + location);
return eml;
},
createID: function () {
this.set("xmlID", uuid.v4());
},
/**
* Creates and adds an {@link EMLAnnotation} to this EML211 model with the given annotation data in JSON form.
* @param {object} annotationData The attribute data to set on the new {@link EMLAnnotation}. See {@link EMLAnnotation#defaults} for
* details on what attributes can be passed to the EMLAnnotation. In addition, there is an `elementName` property.
* @property {string} [annotationData.elementName] The name of the EML Element that this
annotation should be applied to. e.g. dataset, entity, attribute. Defaults to `dataset`. NOTE: Right now only dataset annotations are supported until
more annotation editing is added to the EML Editor.
* @property {Boolean} [annotationData.allowDuplicates] If false, this annotation will replace all annotations already set with the same propertyURI.
* By default, more than one annotation with a given propertyURI can be added (defaults to true)
*/
addAnnotation: function (annotationData) {
try {
if (!annotationData || typeof annotationData != "object") {
return;
}
//If no element name is provided, default to the dataset element.
let elementName = "";
if (!annotationData.elementName) {
elementName = "dataset";
} else {
elementName = annotationData.elementName;
}
//Remove the elementName property so it isn't set on the EMLAnnotation model later.
delete annotationData.elementName;
//Check if duplicates are allowed
let allowDuplicates = annotationData.allowDuplicates;
delete annotationData.allowDuplicates;
//Create a new EMLAnnotation model
let annotation = new EMLAnnotation(annotationData);
//Update annotations set on the dataset element
if (elementName == "dataset") {
let annotations = this.get("annotations");
//If the current annotations set on the EML model are not in Array form, change it to an array
if (!annotations) {
annotations = new EMLAnnotations();
}
if (allowDuplicates === false) {
//Add the EMLAnnotation to the collection, making sure to remove duplicates first
annotations.replaceDuplicateWith(annotation);
} else {
annotations.add(annotation);
}
//Set the annotations and force the change to be recognized by the model
this.set("annotations", annotations, { silent: true });
this.handleChange(this, { force: true });
} else {
/** @todo Add annotation support for other EML Elements */
}
} catch (e) {
console.error("Could not add Annotation to the EML: ", e);
}
},
/**
* Finds annotations that are of the `data sensitivity` property from the NCEAS SENSO ontology.
* Returns undefined if none are found. This function returns EMLAnnotation models because the data
* sensitivity is stored in the EML Model as EMLAnnotations and added to EML as semantic annotations.
* @returns {EMLAnnotation[]|undefined}
*/
getDataSensitivity: function () {
try {
let annotations = this.get("annotations");
if (annotations) {
let found = annotations.where({
propertyURI: this.get("dataSensitivityPropertyURI"),
});
if (!found || !found.length) {
return;
} else {
return found;
}
} else {
return;
}
} catch (e) {
console.error("Failed to get Data Sensitivity from EML model: ", e);
return;
}
},
},
);
return EML211;
});

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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

var EML211 = ScienceMetadata.extend(
/** @lends EML211.prototype */ {
type: "EML",
defaults: function () {
return _.extend(ScienceMetadata.prototype.defaults(), {
id: "urn:uuid:" + uuid.v4(),
formatId: "https://eml.ecoinformatics.org/eml-2.2.0",
objectXML: null,
isEditable: false,
alternateIdentifier: [],
shortName: null,
title: [],
creator: [], // array of EMLParty objects
metadataProvider: [], // array of EMLParty objects
associatedParty: [], // array of EMLParty objects
contact: [], // array of EMLParty objects
publisher: [], // array of EMLParty objects
pubDate: null,
language: null,
series: null,
abstract: [], //array of EMLText objects
keywordSets: [], //array of EMLKeywordSet objects
additionalInfo: [],
intellectualRights:
"This work is dedicated to the public domain under the Creative Commons Universal 1.0 Public Domain Dedication. To view a copy of this dedication, visit https://creativecommons.org/publicdomain/zero/1.0/.",
distribution: [], // array of EMLDistribution objects
geoCoverage: [], //an array for EMLGeoCoverages
temporalCoverage: [], //an array of EMLTempCoverage models
taxonCoverage: [], //an array of EMLTaxonCoverages
purpose: [],
entities: [], //An array of EMLEntities
pubplace: null,
methods: new EMLMethods(), // An EMLMethods objects
project: null, // An EMLProject object,
annotations: null, // Dataset-level annotations
canonicalDataset: null,
dataSensitivityPropertyURI:
"http://purl.dataone.org/odo/SENSO_00000005",
nodeOrder: [
"alternateidentifier",
"shortname",
"title",
"creator",
"metadataprovider",
"associatedparty",
"pubdate",
"language",
"series",
"abstract",
"keywordset",
"additionalinfo",
"intellectualrights",
"licensed",
"distribution",
"coverage",
"annotation",
"purpose",
"introduction",
"gettingstarted",
"acknowledgements",
"maintenance",
"contact",
"publisher",
"pubplace",
"methods",
"project",
"datatable",
"spatialraster",
"spatialvector",
"storedprocedure",
"view",
"otherentity",
"referencepublications",
"usagecitations",
"literaturecited",
],
});
},
units: new Units(),
initialize: function (attributes) {
// Call initialize for the super class
ScienceMetadata.prototype.initialize.call(this, attributes);
// EML211-specific init goes here
// this.set("objectXML", this.createXML());
this.parse(this.createXML());
this.on("sync", function () {
this.set("synced", true);
});
this.stopListening(this, "change:canonicalDataset");
this.listenTo(
this,
"change:canonicalDataset",
this.updateCanonicalDataset,
);
//Create a Unit collection
if (!this.units.length) this.createUnits();
},
url: function (options) {
var identifier;
if (options && options.update) {
identifier = this.get("oldPid") || this.get("seriesid");
} else {
identifier = this.get("id") || this.get("seriesid");
}
return (
MetacatUI.appModel.get("objectServiceUrl") +
encodeURIComponent(identifier)
);
},
updateCanonicalDataset() {
let uri = this.get("canonicalDataset");
uri = uri?.length ? uri[0] : null;
let annotations = this.get("annotations");
if (!annotations) {
annotations = new EMLAnnotations();
this.set("annotations", annotations);
}
annotations.updateCanonicalDataset(uri);
},
/*
* Maps the lower-case EML node names (valid in HTML DOM) to the camel-cased EML node names (valid in EML).
* Used during parse() and serialize()
*/
nodeNameMap: function () {
return _.extend(
this.constructor.__super__.nodeNameMap(),
EMLDistribution.prototype.nodeNameMap(),
EMLGeoCoverage.prototype.nodeNameMap(),
EMLKeywordSet.prototype.nodeNameMap(),
EMLParty.prototype.nodeNameMap(),
EMLProject.prototype.nodeNameMap(),
EMLTaxonCoverage.prototype.nodeNameMap(),
EMLTemporalCoverage.prototype.nodeNameMap(),
EMLMethods.prototype.nodeNameMap(),
{
accuracyreport: "accuracyReport",
actionlist: "actionList",
additionalclassifications: "additionalClassifications",
additionalinfo: "additionalInfo",
additionallinks: "additionalLinks",
additionalmetadata: "additionalMetadata",
allowfirst: "allowFirst",
alternateidentifier: "alternateIdentifier",
altitudedatumname: "altitudeDatumName",
altitudedistanceunits: "altitudeDistanceUnits",
altituderesolution: "altitudeResolution",
altitudeencodingmethod: "altitudeEncodingMethod",
altitudesysdef: "altitudeSysDef",
asneeded: "asNeeded",
associatedparty: "associatedParty",
attributeaccuracyexplanation: "attributeAccuracyExplanation",
attributeaccuracyreport: "attributeAccuracyReport",
attributeaccuracyvalue: "attributeAccuracyValue",
attributedefinition: "attributeDefinition",
attributelabel: "attributeLabel",
attributelist: "attributeList",
attributename: "attributeName",
attributeorientation: "attributeOrientation",
attributereference: "attributeReference",
awardnumber: "awardNumber",
awardurl: "awardUrl",
audiovisual: "audioVisual",
authsystem: "authSystem",
banddescription: "bandDescription",
bilinearfit: "bilinearFit",
binaryrasterformat: "binaryRasterFormat",
blockedmembernode: "blockedMemberNode",
booktitle: "bookTitle",
cameracalibrationinformationavailability:
"cameraCalibrationInformationAvailability",
casesensitive: "caseSensitive",
cellgeometry: "cellGeometry",
cellsizexdirection: "cellSizeXDirection",
cellsizeydirection: "cellSizeYDirection",
changehistory: "changeHistory",
changedate: "changeDate",
changescope: "changeScope",
chapternumber: "chapterNumber",
characterencoding: "characterEncoding",
checkcondition: "checkCondition",
checkconstraint: "checkConstraint",
childoccurences: "childOccurences",
citableclassificationsystem: "citableClassificationSystem",
cloudcoverpercentage: "cloudCoverPercentage",
codedefinition: "codeDefinition",
codeexplanation: "codeExplanation",
codesetname: "codesetName",
codeseturl: "codesetURL",
collapsedelimiters: "collapseDelimiters",
communicationtype: "communicationType",
compressiongenerationquality: "compressionGenerationQuality",
compressionmethod: "compressionMethod",
conferencedate: "conferenceDate",
conferencelocation: "conferenceLocation",
conferencename: "conferenceName",
conferenceproceedings: "conferenceProceedings",
constraintdescription: "constraintDescription",
constraintname: "constraintName",
constanttosi: "constantToSI",
controlpoint: "controlPoint",
cornerpoint: "cornerPoint",
customunit: "customUnit",
dataformat: "dataFormat",
datasetgpolygon: "datasetGPolygon",
datasetgpolygonoutergring: "datasetGPolygonOuterGRing",
datasetgpolygonexclusiongring: "datasetGPolygonExclusionGRing",
datatable: "dataTable",
datatype: "dataType",
datetime: "dateTime",
datetimedomain: "dateTimeDomain",
datetimeprecision: "dateTimePrecision",
defaultvalue: "defaultValue",
definitionattributereference: "definitionAttributeReference",
denomflatratio: "denomFlatRatio",
depthsysdef: "depthSysDef",
depthdatumname: "depthDatumName",
depthdistanceunits: "depthDistanceUnits",
depthencodingmethod: "depthEncodingMethod",
depthresolution: "depthResolution",
descriptorvalue: "descriptorValue",
dictref: "dictRef",
diskusage: "diskUsage",
domainDescription: "domainDescription",
editedbook: "editedBook",
encodingmethod: "encodingMethod",
endcondition: "endCondition",
entitycodelist: "entityCodeList",
entitydescription: "entityDescription",
entityname: "entityName",
entityreference: "entityReference",
entitytype: "entityType",
enumerateddomain: "enumeratedDomain",
errorbasis: "errorBasis",
errorvalues: "errorValues",
externalcodeset: "externalCodeSet",
externallydefinedformat: "externallyDefinedFormat",
fielddelimiter: "fieldDelimiter",
fieldstartcolumn: "fieldStartColumn",
fieldwidth: "fieldWidth",
filmdistortioninformationavailability:
"filmDistortionInformationAvailability",
foreignkey: "foreignKey",
formatname: "formatName",
formatstring: "formatString",
formatversion: "formatVersion",
fractiondigits: "fractionDigits",
fundername: "funderName",
funderidentifier: "funderIdentifier",
gettingstarted: "gettingStarted",
gring: "gRing",
gringpoint: "gRingPoint",
gringlatitude: "gRingLatitude",
gringlongitude: "gRingLongitude",
geogcoordsys: "geogCoordSys",
geometricobjectcount: "geometricObjectCount",
georeferenceinfo: "georeferenceInfo",
highwavelength: "highWavelength",
horizontalaccuracy: "horizontalAccuracy",
horizcoordsysdef: "horizCoordSysDef",
horizcoordsysname: "horizCoordSysName",
identifiername: "identifierName",
illuminationazimuthangle: "illuminationAzimuthAngle",
illuminationelevationangle: "illuminationElevationAngle",
imagingcondition: "imagingCondition",
imagequalitycode: "imageQualityCode",
imageorientationangle: "imageOrientationAngle",
intellectualrights: "intellectualRights",
imagedescription: "imageDescription",
isbn: "ISBN",
issn: "ISSN",
joincondition: "joinCondition",
keywordtype: "keywordType",
languagevalue: "LanguageValue",
languagecodestandard: "LanguageCodeStandard",
lensdistortioninformationavailability:
"lensDistortionInformationAvailability",
licensename: "licenseName",
licenseurl: "licenseURL",
linenumber: "lineNumber",
literalcharacter: "literalCharacter",
literallayout: "literalLayout",
literaturecited: "literatureCited",
lowwavelength: "lowWaveLength",
machineprocessor: "machineProcessor",
maintenanceupdatefrequency: "maintenanceUpdateFrequency",
matrixtype: "matrixType",
maxexclusive: "maxExclusive",
maxinclusive: "maxInclusive",
maxlength: "maxLength",
maxrecordlength: "maxRecordLength",
maxvalues: "maxValues",
measurementscale: "measurementScale",
metadatalist: "metadataList",
methodstep: "methodStep",
minexclusive: "minExclusive",
mininclusive: "minInclusive",
minlength: "minLength",
minvalues: "minValues",
missingvaluecode: "missingValueCode",
moduledocs: "moduleDocs",
modulename: "moduleName",
moduledescription: "moduleDescription",
multiband: "multiBand",
multipliertosi: "multiplierToSI",
nonnumericdomain: "nonNumericDomain",
notnullconstraint: "notNullConstraint",
notplanned: "notPlanned",
numberofbands: "numberOfBands",
numbertype: "numberType",
numericdomain: "numericDomain",
numfooterlines: "numFooterLines",
numheaderlines: "numHeaderLines",
numberofrecords: "numberOfRecords",
numberofvolumes: "numberOfVolumes",
numphysicallinesperrecord: "numPhysicalLinesPerRecord",
objectname: "objectName",
oldvalue: "oldValue",
operatingsystem: "operatingSystem",
orderattributereference: "orderAttributeReference",
originalpublication: "originalPublication",
otherentity: "otherEntity",
othermaintenanceperiod: "otherMaintenancePeriod",
parameterdefinition: "parameterDefinition",
packageid: "packageId",
pagerange: "pageRange",
parentoccurences: "parentOccurences",
parentsi: "parentSI",
peakresponse: "peakResponse",
personalcommunication: "personalCommunication",
physicallinedelimiter: "physicalLineDelimiter",
pointinpixel: "pointInPixel",
preferredmembernode: "preferredMemberNode",
preprocessingtypecode: "preProcessingTypeCode",
primarykey: "primaryKey",
primemeridian: "primeMeridian",
proceduralstep: "proceduralStep",
programminglanguage: "programmingLanguage",
projcoordsys: "projCoordSys",
projectionlist: "projectionList",
propertyuri: "propertyURI",
pubdate: "pubDate",
pubplace: "pubPlace",
publicationplace: "publicationPlace",
quantitativeaccuracyreport: "quantitativeAccuracyReport",
quantitativeaccuracyvalue: "quantitativeAccuracyValue",
quantitativeaccuracymethod: "quantitativeAccuracyMethod",
quantitativeattributeaccuracyassessment:
"quantitativeAttributeAccuracyAssessment",
querystatement: "queryStatement",
quotecharacter: "quoteCharacter",
radiometricdataavailability: "radiometricDataAvailability",
rasterorigin: "rasterOrigin",
recommendedunits: "recommendedUnits",
recommendedusage: "recommendedUsage",
referencedkey: "referencedKey",
referencetype: "referenceType",
relatedentry: "relatedEntry",
relationshiptype: "relationshipType",
reportnumber: "reportNumber",
reprintedition: "reprintEdition",
researchproject: "researchProject",
researchtopic: "researchTopic",
recorddelimiter: "recordDelimiter",
referencepublication: "referencePublication",
revieweditem: "reviewedItem",
rowcolumnorientation: "rowColumnOrientation",
runtimememoryusage: "runtimeMemoryUsage",
samplingdescription: "samplingDescription",
scalefactor: "scaleFactor",
sequenceidentifier: "sequenceIdentifier",
semiaxismajor: "semiAxisMajor",
shortname: "shortName",
simpledelimited: "simpleDelimited",
spatialraster: "spatialRaster",
spatialreference: "spatialReference",
spatialvector: "spatialVector",
standalone: "standAlone",
standardunit: "standardUnit",
startcondition: "startCondition",
studyareadescription: "studyAreaDescription",
storagetype: "storageType",
studyextent: "studyExtent",
studytype: "studyType",
textdelimited: "textDelimited",
textdomain: "textDomain",
textfixed: "textFixed",
textformat: "textFormat",
topologylevel: "topologyLevel",
tonegradation: "toneGradation",
totaldigits: "totalDigits",
totalfigures: "totalFigures",
totalpages: "totalPages",
totaltables: "totalTables",
triangulationindicator: "triangulationIndicator",
typesystem: "typeSystem",
uniquekey: "uniqueKey",
unittype: "unitType",
unitlist: "unitList",
usagecitation: "usageCitation",
valueuri: "valueURI",
valueattributereference: "valueAttributeReference",
verticalaccuracy: "verticalAccuracy",
vertcoordsys: "vertCoordSys",
virtualmachine: "virtualMachine",
wavelengthunits: "waveLengthUnits",
whitespace: "whiteSpace",
xintercept: "xIntercept",
xcoordinate: "xCoordinate",
"xsi:schemalocation": "xsi:schemaLocation",
xslope: "xSlope",
ycoordinate: "yCoordinate",
yintercept: "yIntercept",
yslope: "ySlope",
},
);
},
/**
* Fetch the EML from the MN object service
* @param {object} [options] - A set of options for this fetch()
* @property {boolean} [options.systemMetadataOnly=false] - If true, only the system metadata will be fetched.
* If false, the system metadata AND EML document will be fetched.
*/
fetch: function (options) {
if (!options) var options = {};
//Add the authorization header and other AJAX settings
_.extend(options, MetacatUI.appUserModel.createAjaxSettings(), {
dataType: "text",
});
// Merge the system metadata into the object first
_.extend(options, { merge: true });
this.fetchSystemMetadata(options);
//If we are retrieving system metadata only, then exit now
if (options.systemMetadataOnly) return;
//Call Backbone.Model.fetch to retrieve the info
return Backbone.Model.prototype.fetch.call(this, options);
},
/*
Deserialize an EML 2.1.1 XML document
*/
parse: function (response) {
// Save a reference to this model for use in setting the
// parentModel inside anonymous functions
var model = this;
//If the response is XML
if (typeof response == "string" && response.indexOf("<") == 0) {
//Look for a system metadata tag and call DataONEObject parse instead
if (response.indexOf("systemMetadata>") > -1)
return DataONEObject.prototype.parse.call(this, response);
response = this.cleanUpXML(response);
response = this.dereference(response);
this.set("objectXML", response);
var emlElement = $($.parseHTML(response)).filter("eml\\:eml");
}
var datasetEl;
if (emlElement[0]) datasetEl = $(emlElement[0]).find("dataset");
if (!datasetEl || !datasetEl.length) return {};
var emlParties = [
"metadataprovider",
"associatedparty",
"creator",
"contact",
"publisher",
],
emlDistribution = ["distribution"],
emlEntities = [
"datatable",
"otherentity",
"spatialvector",
"spatialraster",
"storedprocedure",
"view",
],
emlText = ["abstract", "additionalinfo"],
emlMethods = ["methods"];
var nodes = datasetEl.children(),
modelJSON = {};
for (var i = 0; i < nodes.length; i++) {
var thisNode = nodes[i];
var convertedName =
this.nodeNameMap()[thisNode.localName] || thisNode.localName;
//EML Party modules are stored in EMLParty models
if (_.contains(emlParties, thisNode.localName)) {
if (thisNode.localName == "metadataprovider")
var attributeName = "metadataProvider";
else if (thisNode.localName == "associatedparty")
var attributeName = "associatedParty";
else var attributeName = thisNode.localName;
if (typeof modelJSON[attributeName] == "undefined")
modelJSON[attributeName] = [];
modelJSON[attributeName].push(
new EMLParty({
objectDOM: thisNode,
parentModel: model,
type: attributeName,
}),
);
}
//EML Distribution modules are stored in EMLDistribution models
else if (_.contains(emlDistribution, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] == "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName].push(
new EMLDistribution(
{
objectDOM: thisNode,
parentModel: model,
},
{ parse: true },
),
);
}
//The EML Project is stored in the EMLProject model
else if (thisNode.localName == "project") {
modelJSON.project = new EMLProject({
objectDOM: thisNode,
parentModel: model,
});
}
//EML Temporal, Taxonomic, and Geographic Coverage modules are stored in their own models
else if (thisNode.localName == "coverage") {
var temporal = $(thisNode).children("temporalcoverage"),
geo = $(thisNode).children("geographiccoverage"),
taxon = $(thisNode).children("taxonomiccoverage");
if (temporal.length) {
modelJSON.temporalCoverage = [];
_.each(temporal, function (t) {
modelJSON.temporalCoverage.push(
new EMLTemporalCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
if (geo.length) {
modelJSON.geoCoverage = [];
_.each(geo, function (g) {
modelJSON.geoCoverage.push(
new EMLGeoCoverage({
objectDOM: g,
parentModel: model,
}),
);
});
}
if (taxon.length) {
modelJSON.taxonCoverage = [];
_.each(taxon, function (t) {
modelJSON.taxonCoverage.push(
new EMLTaxonCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
}
//Parse EMLText modules
else if (_.contains(emlText, thisNode.localName)) {
if (typeof modelJSON[convertedName] == "undefined")
modelJSON[convertedName] = [];
modelJSON[convertedName].push(
new EMLText({
objectDOM: thisNode,
parentModel: model,
}),
);
} else if (_.contains(emlMethods, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] === "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName] = new EMLMethods({
objectDOM: thisNode,
parentModel: model,
});
}
//Parse keywords
else if (thisNode.localName == "keywordset") {
//Start an array of keyword sets
if (typeof modelJSON["keywordSets"] == "undefined")
modelJSON["keywordSets"] = [];
modelJSON["keywordSets"].push(
new EMLKeywordSet({
objectDOM: thisNode,
parentModel: model,
}),
);
}
//Parse intellectual rights
else if (thisNode.localName == "intellectualrights") {
var value = "";
if ($(thisNode).children("para").length == 1)
value = $(thisNode).children("para").first().text().trim();
else $(thisNode).text().trim();
//If the value is one of our pre-defined options, then add it to the model
//if(_.contains(this.get("intellRightsOptions"), value))
modelJSON["intellectualRights"] = value;
}
//Parse Entities
else if (_.contains(emlEntities, thisNode.localName)) {
//Start an array of Entities
if (typeof modelJSON["entities"] == "undefined")
modelJSON["entities"] = [];
//Create the model
var entityModel;
if (thisNode.localName == "otherentity") {
entityModel = new EMLOtherEntity(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else if (thisNode.localName == "datatable") {
entityModel = new EMLDataTable(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else {
entityModel = new EMLEntity(
{
objectDOM: thisNode,
parentModel: model,
entityType: "application/octet-stream",
type: thisNode.localName,
},
{
parse: true,
},
);
}
modelJSON["entities"].push(entityModel);
}
//Parse dataset-level annotations
else if (thisNode.localName === "annotation") {
if (!modelJSON["annotations"]) {
modelJSON["annotations"] = new EMLAnnotations();
}
var annotationModel = new EMLAnnotation(
{
objectDOM: thisNode,
},
{ parse: true },
);
modelJSON["annotations"].add(annotationModel);
} else {
//Is this a multi-valued field in EML?
if (Array.isArray(this.get(convertedName))) {
//If we already have a value for this field, then add this value to the array
if (Array.isArray(modelJSON[convertedName]))
modelJSON[convertedName].push(this.toJson(thisNode));
//If it's the first value for this field, then create a new array
else modelJSON[convertedName] = [this.toJson(thisNode)];
} else modelJSON[convertedName] = this.toJson(thisNode);
}
}
// Once all the nodes have been parsed, check if any of the annotations
// make up a canonical dataset reference
const annotations = modelJSON["annotations"];
if (annotations) {
const canonicalDataset = annotations.getCanonicalURI();
if (canonicalDataset) {
modelJSON["canonicalDataset"] = canonicalDataset;
}
}
return modelJSON;
},
/*
* Retireves the model attributes and serializes into EML XML, to produce the new or modified EML document.
* Returns the EML XML as a string.
*/
serialize: function () {
//Get the EML document
var xmlString = this.get("objectXML"),
html = $.parseHTML(xmlString),
eml = $(html).filter("eml\\:eml"),
datasetNode = $(eml).find("dataset");
//Update the packageId on the eml node with the EML id
$(eml).attr("packageId", this.get("id"));
// Set id attribute on dataset node if needed
if (this.get("xmlID")) {
$(datasetNode).attr("id", this.get("xmlID"));
}
// Set schema version
$(eml).attr(
"xmlns:eml",
MetacatUI.appModel.get("editorSerializationFormat") ||
"https://eml.ecoinformatics.org/eml-2.2.0",
);
// Set formatID
this.set(
"formatId",
MetacatUI.appModel.get("editorSerializationFormat") ||
"https://eml.ecoinformatics.org/eml-2.2.0",
);
// Ensure xsi:schemaLocation has a value for the current format
eml = this.setSchemaLocation(eml);
var nodeNameMap = this.nodeNameMap();
//Serialize the basic text fields
var basicText = ["alternateIdentifier", "title"];
_.each(
basicText,
function (fieldName) {
var basicTextValues = this.get(fieldName);
if (!Array.isArray(basicTextValues))
basicTextValues = [basicTextValues];
// Remove existing nodes
datasetNode.children(fieldName.toLowerCase()).remove();
// Create new nodes
var nodes = _.map(basicTextValues, function (value) {
if (value) {
var node = document.createElement(fieldName.toLowerCase());
$(node).text(value);
return node;
} else {
return "";
}
});
var insertAfter = this.getEMLPosition(eml, fieldName.toLowerCase());
if (insertAfter) {
insertAfter.after(nodes);
} else {
datasetNode.prepend(nodes);
}
},
this,
);
// Serialize pubDate
// This one is special because it has a default behavior, unlike
// the others: When no pubDate is set, it should be set to
// the current year
var pubDate = this.get("pubDate");
datasetNode.find("pubdate").remove();
if (pubDate != null && pubDate.length > 0) {
var pubDateEl = document.createElement("pubdate");
$(pubDateEl).text(pubDate);
this.getEMLPosition(eml, "pubdate").after(pubDateEl);
}
// Serialize the parts of EML that are eml-text modules
var textFields = ["abstract", "additionalInfo"];
_.each(
textFields,
function (field) {
var fieldName = this.nodeNameMap()[field] || field;
// Get the EMLText model
var emlTextModels = Array.isArray(this.get(field))
? this.get(field)
: [this.get(field)];
if (!emlTextModels.length) return;
// Get the node from the EML doc
var nodes = datasetNode.find(fieldName);
// Update the DOMs for each model
_.each(
emlTextModels,
function (thisTextModel, i) {
//Don't serialize falsey values
if (!thisTextModel) return;
var node;
//Get the existing node or create a new one
if (nodes.length < i + 1) {
node = document.createElement(fieldName);
this.getEMLPosition(eml, fieldName).after(node);
} else {
node = nodes[i];
}
$(node).html($(thisTextModel.updateDOM()).html());
},
this,
);
// Remove the extra nodes
this.removeExtraNodes(nodes, emlTextModels);
},
this,
);
//Create a <coverage> XML node if there isn't one
if (datasetNode.children("coverage").length === 0) {
var coverageNode = $(document.createElement("coverage")),
coveragePosition = this.getEMLPosition(eml, "coverage");
if (coveragePosition) coveragePosition.after(coverageNode);
else datasetNode.append(coverageNode);
} else {
var coverageNode = datasetNode.children("coverage").first();
}
//Serialize the geographic coverage
if (
typeof this.get("geoCoverage") !== "undefined" &&
this.get("geoCoverage").length > 0
) {
// Don't serialize if geoCoverage is invalid
var validCoverages = _.filter(
this.get("geoCoverage"),
function (cov) {
return cov.isValid();
},
);
//Get the existing geo coverage nodes from the EML
var existingGeoCov = datasetNode.find("geographiccoverage");
//Update the DOM of each model
_.each(
validCoverages,
function (cov, position) {
//Update the existing node if it exists
if (existingGeoCov.length - 1 >= position) {
$(existingGeoCov[position]).replaceWith(cov.updateDOM());
}
//Or, append new nodes
else {
var insertAfter = existingGeoCov.length
? datasetNode.find("geographiccoverage").last()
: null;
if (insertAfter) insertAfter.after(cov.updateDOM());
else coverageNode.append(cov.updateDOM());
}
},
this,
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(
datasetNode.find("geographiccoverage"),
validCoverages,
);
} else {
//If there are no geographic coverages, remove the nodes
coverageNode.children("geographiccoverage").remove();
}
//Serialize the taxonomic coverage
if (
typeof this.get("taxonCoverage") !== "undefined" &&
this.get("taxonCoverage").length > 0
) {
// Group the taxonomic coverage models into empty and non-empty
var sortedTaxonModels = _.groupBy(
this.get("taxonCoverage"),
function (t) {
if (_.flatten(t.get("taxonomicClassification")).length > 0) {
return "notEmpty";
} else {
return "empty";
}
},
);
//Get the existing taxon coverage nodes from the EML
var existingTaxonCov = coverageNode.children("taxonomiccoverage");
//Iterate over each taxon coverage and update it's DOM
if (
sortedTaxonModels["notEmpty"] &&
sortedTaxonModels["notEmpty"].length > 0
) {
//Update the DOM of each model
_.each(
sortedTaxonModels["notEmpty"],
function (taxonCoverage, position) {
//Update the existing taxonCoverage node if it exists
if (existingTaxonCov.length - 1 >= position) {
$(existingTaxonCov[position]).replaceWith(
taxonCoverage.updateDOM(),
);
}
//Or, append new nodes
else {
coverageNode.append(taxonCoverage.updateDOM());
}
},
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(existingTaxonCov, this.get("taxonCoverage"));
}
//If all the taxon coverages are empty, remove the parent taxonomicCoverage node
else if (
!sortedTaxonModels["notEmpty"] ||
sortedTaxonModels["notEmpty"].length == 0
) {
existingTaxonCov.remove();
}
}
//Serialize the temporal coverage
var existingTemporalCoverages = datasetNode.find("temporalcoverage");
//Update the DOM of each model
_.each(
this.get("temporalCoverage"),
function (temporalCoverage, position) {
//Update the existing temporalCoverage node if it exists
if (existingTemporalCoverages.length - 1 >= position) {
$(existingTemporalCoverages[position]).replaceWith(
temporalCoverage.updateDOM(),
);
}
//Or, append new nodes
else {
coverageNode.append(temporalCoverage.updateDOM());
}
},
);
//Remove existing taxon coverage nodes that don't have an accompanying model
this.removeExtraNodes(
existingTemporalCoverages,
this.get("temporalCoverage"),
);
//Remove the temporal coverage if it is empty
if (!coverageNode.children("temporalcoverage").children().length) {
coverageNode.children("temporalcoverage").remove();
}
//Remove the <coverage> node if it's empty
if (coverageNode.children().length == 0) {
coverageNode.remove();
}
// Dataset-level annotations
datasetNode.children("annotation").remove();
if (this.get("annotations")) {
this.get("annotations").each(function (annotation) {
if (annotation.isEmpty()) {
return;
}
var after = this.getEMLPosition(eml, "annotation");
$(after).after(annotation.updateDOM());
}, this);
//Since there is at least one annotation, the dataset node needs to have an id attribute.
datasetNode.attr("id", this.getUniqueEntityId(this));
}
//If there is no creator, create one from the user
if (!this.get("creator").length) {
var party = new EMLParty({ parentModel: this, type: "creator" });
party.createFromUser();
this.set("creator", [party]);
}
//Serialize the creators
this.serializeParties(eml, "creator");
//Serialize the metadata providers
this.serializeParties(eml, "metadataProvider");
//Serialize the associated parties
this.serializeParties(eml, "associatedParty");
//Serialize the contacts
this.serializeParties(eml, "contact");
//Serialize the publishers
this.serializeParties(eml, "publisher");
// Serialize methods
if (this.get("methods")) {
//If the methods model is empty, remove it from the EML
if (this.get("methods").isEmpty())
datasetNode.find("methods").remove();
else {
//Serialize the methods model
var methodsEl = this.get("methods").updateDOM();
//If the methodsEl is an empty string or other falsey value, then remove the methods node
if (!methodsEl || !$(methodsEl).children().length) {
datasetNode.find("methods").remove();
} else {
//Add the <methods> node to the EML
datasetNode.find("methods").detach();
var insertAfter = this.getEMLPosition(eml, "methods");
if (insertAfter) insertAfter.after(methodsEl);
else datasetNode.append(methodsEl);
}
}
}
//If there are no methods, then remove the methods nodes
else {
if (datasetNode.find("methods").length > 0) {
datasetNode.find("methods").remove();
}
}
//Serialize the keywords
this.serializeKeywords(eml, "keywordSets");
//Serialize the intellectual rights
if (this.get("intellectualRights")) {
if (datasetNode.find("intellectualRights").length)
datasetNode
.find("intellectualRights")
.html("<para>" + this.get("intellectualRights") + "</para>");
else {
this.getEMLPosition(eml, "intellectualrights").after(
$(document.createElement("intellectualRights")).html(
"<para>" + this.get("intellectualRights") + "</para>",
),
);
}
}
// Serialize the distribution
const distributions = this.get("distribution");
if (distributions && distributions.length > 0) {
// Remove existing nodes
datasetNode.children("distribution").remove();
// Get the updated DOMs
const distributionDOMs = distributions.map((d) => d.updateDOM());
// Insert the updated DOMs in their correct positions
distributionDOMs.forEach((dom, i) => {
const insertAfter = this.getEMLPosition(eml, "distribution");
if (insertAfter) {
insertAfter.after(dom);
} else {
datasetNode.append(dom);
}
});
}
//Detach the project elements from the DOM
if (datasetNode.find("project").length) {
datasetNode.find("project").detach();
}
//If there is an EMLProject, update its DOM
if (this.get("project")) {
this.getEMLPosition(eml, "project").after(
this.get("project").updateDOM(),
);
}
//Get the existing taxon coverage nodes from the EML
var existingEntities = datasetNode.find(
"otherEntity, dataTable, spatialRaster, spatialVector, storedProcedure, view",
);
//Serialize the entities
_.each(
this.get("entities"),
function (entity, position) {
//Update the existing node if it exists
if (existingEntities.length - 1 >= position) {
//Remove the entity from the EML
$(existingEntities[position]).detach();
//Insert it into the correct position
this.getEMLPosition(eml, entity.get("type").toLowerCase()).after(
entity.updateDOM(),
);
}
//Or, append new nodes
else {
//Inser the entity into the correct position
this.getEMLPosition(eml, entity.get("type").toLowerCase()).after(
entity.updateDOM(),
);
}
},
this,
);
//Remove extra entities that have been removed
var numExtraEntities =
existingEntities.length - this.get("entities").length;
for (
var i = existingEntities.length - numExtraEntities;
i < existingEntities.length;
i++
) {
$(existingEntities)[i].remove();
}
//Do a final check to make sure there are no duplicate ids in the EML
var elementsWithIDs = $(eml).find("[id]"),
//Get an array of all the ids in this EML doc
allIDs = _.map(elementsWithIDs, function (el) {
return $(el).attr("id");
});
//If there is at least one id in the EML...
if (allIDs && allIDs.length) {
//Boil the array down to just the unique values
var uniqueIDs = _.uniq(allIDs);
//If the unique array is shorter than the array of all ids,
// then there is a duplicate somewhere
if (uniqueIDs.length < allIDs.length) {
//For each element in the EML that has an id,
_.each(elementsWithIDs, function (el) {
//Get the id for this element
var id = $(el).attr("id");
//If there is more than one element in the EML with this id,
if ($(eml).find("[id='" + id + "']").length > 1) {
//And if it is not a unit node, which we don't want to change,
if (!$(el).is("unit"))
//Then change the id attribute to a random uuid
$(el).attr("id", "urn-uuid-" + uuid.v4());
}
});
}
}
//Camel-case the XML
var emlString = "";
_.each(
html,
function (rootEMLNode) {
emlString += this.formatXML(rootEMLNode);
},
this,
);
return emlString;
},
/*
* Given an EML DOM and party type, this function updated and/or adds the EMLParties to the EML
*/
serializeParties: function (eml, type) {
//Remove the nodes from the EML for this party type
$(eml).children("dataset").children(type.toLowerCase()).remove();
//Serialize each party of this type
_.each(
this.get(type),
function (party, i) {
//Get the last node of this type to insert after
var insertAfter = $(eml)
.children("dataset")
.children(type.toLowerCase())
.last();
//If there isn't a node found, find the EML position to insert after
if (!insertAfter.length) {
insertAfter = this.getEMLPosition(eml, type);
}
//Update the DOM of the EMLParty
var emlPartyDOM = party.updateDOM();
//Make sure we don't insert empty EMLParty nodes into the EML
if ($(emlPartyDOM).children().length) {
//Insert the party DOM at the insert position
if (insertAfter && insertAfter.length)
insertAfter.after(emlPartyDOM);
//If an insert position still hasn't been found, then just append to the dataset node
else $(eml).find("dataset").append(emlPartyDOM);
}
},
this,
);
//Create a certain parties from the current app user if none is given
if (type == "contact" && !this.get("contact").length) {
//Get the creators
var creators = this.get("creator"),
contacts = [];
_.each(
creators,
function (creator) {
//Clone the creator model and add it to the contacts array
var newModel = new EMLParty({ parentModel: this });
newModel.set(creator.toJSON());
newModel.set("type", type);
contacts.push(newModel);
},
this,
);
this.set(type, contacts);
//Call this function again to serialize the new models
this.serializeParties(eml, type);
}
},
serializeKeywords: function (eml) {
// Remove all existing keywordSets before appending
$(eml).find("dataset").find("keywordset").remove();
if (this.get("keywordSets").length == 0) return;
// Create the new keywordSets nodes
var nodes = _.map(this.get("keywordSets"), function (kwd) {
return kwd.updateDOM();
});
this.getEMLPosition(eml, "keywordset").after(nodes);
},
/*
* Remoes nodes from the EML that do not have an accompanying model
* (Were probably removed from the EML by the user during editing)
*/
removeExtraNodes: function (nodes, models) {
// Remove the extra nodes
var extraNodes = nodes.length - models.length;
if (extraNodes > 0) {
for (var i = models.length; i < nodes.length; i++) {
$(nodes[i]).remove();
}
}
},
/*
* Saves the EML document to the server using the DataONE API
*/
save: function (attributes, options) {
//Validate before we try anything else
if (!this.isValid()) {
this.trigger("invalid");
this.trigger("cancelSave");
return false;
} else {
this.trigger("valid");
}
this.setFileName();
//Set the upload transfer as in progress
this.set("uploadStatus", "p");
//Reset the draftSaved attribute
this.set("draftSaved", false);
//Create the creator from the current user if none is provided
if (!this.get("creator").length) {
var party = new EMLParty({ parentModel: this, type: "creator" });
party.createFromUser();
this.set("creator", [party]);
}
//Create the contact from the current user if none is provided
if (!this.get("contact").length) {
var party = new EMLParty({ parentModel: this, type: "contact" });
party.createFromUser();
this.set("contact", [party]);
}
//If this is an existing object and there is no system metadata, retrieve it
if (!this.isNew() && !this.get("sysMetaXML")) {
var model = this;
//When the system metadata is fetched, try saving again
var fetchOptions = {
success: function (response) {
model.set(DataONEObject.prototype.parse.call(model, response));
model.save(attributes, options);
},
};
//Fetch the system metadata now
this.fetchSystemMetadata(fetchOptions);
return;
}
//Create a FormData object to send data with our XHR
var formData = new FormData();
try {
//Add the identifier to the XHR data
if (this.isNew()) {
formData.append("pid", this.get("id"));
} else {
//Create a new ID
this.updateID();
//Add the ids to the form data
formData.append("newPid", this.get("id"));
formData.append("pid", this.get("oldPid"));
}
//Serialize the EML XML
var xml = this.serialize();
var xmlBlob = new Blob([xml], { type: "application/xml" });
//Get the size of the new EML XML
this.set("size", xmlBlob.size);
//Get the new checksum of the EML XML
var checksum = md5(xml);
this.set("checksum", checksum);
this.set("checksumAlgorithm", "MD5");
//Create the system metadata XML
var sysMetaXML = this.serializeSysMeta();
//Send the system metadata as a Blob
var sysMetaXMLBlob = new Blob([sysMetaXML], {
type: "application/xml",
});
//Add the object XML and System Metadata XML to the form data
//Append the system metadata first, so we can take advantage of Metacat's streaming multipart handler
formData.append("sysmeta", sysMetaXMLBlob, "sysmeta");
formData.append("object", xmlBlob);
} catch (error) {
//Reset the identifier since we didn't actually update the object
this.resetID();
this.set("uploadStatus", "e");
this.trigger("error");
this.trigger("cancelSave");
return false;
}
var model = this;
var saveOptions = options || {};
_.extend(
saveOptions,
{
data: formData,
cache: false,
contentType: false,
dataType: "text",
processData: false,
parse: false,
//Use the URL function to determine the URL
url: this.isNew() ? this.url() : this.url({ update: true }),
xhr: function () {
var xhr = new window.XMLHttpRequest();
//Upload progress
xhr.upload.addEventListener(
"progress",
function (evt) {
if (evt.lengthComputable) {
var percentComplete = (evt.loaded / evt.total) * 100;
model.set("uploadProgress", percentComplete);
}
},
false,
);
return xhr;
},
success: function (model, response, xhr) {
model.set("numSaveAttempts", 0);
model.set("uploadStatus", "c");
model.set("sysMetaXML", model.serializeSysMeta());
model.set("oldPid", null);
model.fetch({ merge: true, systemMetadataOnly: true });
model.trigger("successSaving", model);
},
error: function (model, response, xhr) {
model.set("numSaveAttempts", model.get("numSaveAttempts") + 1);
var numSaveAttempts = model.get("numSaveAttempts");
//Reset the identifier changes
model.resetID();
if (
numSaveAttempts < 3 &&
(response.status == 408 || response.status == 0)
) {
//Try saving again in 10, 40, and 90 seconds
setTimeout(
function () {
model.save.call(model);
},
numSaveAttempts * numSaveAttempts * 10000,
);
} else {
model.set("numSaveAttempts", 0);
//Get the error error information
var errorDOM = $($.parseHTML(response.responseText)),
errorContainer = errorDOM.filter("error"),
msgContainer = errorContainer.length
? errorContainer.find("description")
: errorDOM.not("style, title"),
errorMsg = msgContainer.length
? msgContainer.text()
: errorDOM;
//When there is no network connection (status == 0), there will be no response text
if (!errorMsg || response.status == 408 || response.status == 0)
errorMsg =
"There was a network issue that prevented your metadata from uploading. " +
"Make sure you are connected to a reliable internet connection.";
//Save the error message in the model
model.set("errorMessage", errorMsg);
//Set the model status as e for error
model.set("uploadStatus", "e");
//Save the EML as a plain text file, until drafts are a supported feature
var copy = model.createTextCopy();
//If the EML copy successfully saved, let the user know that there is a copy saved behind the scenes
model.listenToOnce(copy, "successSaving", function () {
model.set("draftSaved", true);
//Trigger the errorSaving event so other parts of the app know that the model failed to save
//And send the error message with it
model.trigger("errorSaving", errorMsg);
});
//If the EML copy fails to save too, then just display the usual error message
model.listenToOnce(copy, "errorSaving", function () {
//Trigger the errorSaving event so other parts of the app know that the model failed to save
//And send the error message with it
model.trigger("errorSaving", errorMsg);
});
//Save the EML plain text copy
copy.save();
// Track the error
MetacatUI.analytics?.trackException(
`EML save error: ${errorMsg}, EML draft: ${copy.get("id")}`,
model.get("id"),
true,
);
}
},
},
MetacatUI.appUserModel.createAjaxSettings(),
);
return Backbone.Model.prototype.save.call(
this,
attributes,
saveOptions,
);
},
/*
* Checks if this EML model has all the required values necessary to save to the server
*/
validate: function () {
let errors = {};
//A title is always required by EML
if (!this.get("title").length || !this.get("title")[0]) {
errors.title = "A title is required";
}
// Validate the publication date
if (this.get("pubDate") != null) {
if (!this.isValidYearDate(this.get("pubDate"))) {
errors["pubDate"] = [
"The value entered for publication date, '" +
this.get("pubDate") +
"' is not a valid value for this field. Enter with a year (e.g. 2017) or a date in the format YYYY-MM-DD.",
];
}
}
// Validate the temporal coverage
errors.temporalCoverage = [];
//If temporal coverage is required and there aren't any, return an error
if (
MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
!this.get("temporalCoverage").length
) {
errors.temporalCoverage = [{ beginDate: "Provide a begin date." }];
}
//If temporal coverage is required and they are all empty, return an error
else if (
MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
_.every(this.get("temporalCoverage"), function (tc) {
return tc.isEmpty();
})
) {
errors.temporalCoverage = [{ beginDate: "Provide a begin date." }];
}
//If temporal coverage is not required, validate each one
else if (
this.get("temporalCoverage").length ||
(MetacatUI.appModel.get("emlEditorRequiredFields").temporalCoverage &&
_.every(this.get("temporalCoverage"), function (tc) {
return tc.isEmpty();
}))
) {
//Iterate over each temporal coverage and add it's validation errors
_.each(this.get("temporalCoverage"), function (temporalCoverage) {
if (!temporalCoverage.isValid() && !temporalCoverage.isEmpty()) {
errors.temporalCoverage.push(temporalCoverage.validationError);
}
});
}
//Remove the temporalCoverage attribute if no errors were found
if (errors.temporalCoverage.length == 0) {
delete errors.temporalCoverage;
}
//Validate the EMLParty models
var partyTypes = [
"associatedParty",
"contact",
"creator",
"metadataProvider",
"publisher",
];
_.each(
partyTypes,
function (type) {
var people = this.get(type);
_.each(
people,
function (person, i) {
if (!person.isValid()) {
if (!errors[type]) errors[type] = [person.validationError];
else errors[type].push(person.validationError);
}
},
this,
);
},
this,
);
//Validate the EMLGeoCoverage models
_.each(
this.get("geoCoverage"),
function (geoCoverageModel, i) {
if (!geoCoverageModel.isValid()) {
if (!errors.geoCoverage)
errors.geoCoverage = [geoCoverageModel.validationError];
else errors.geoCoverage.push(geoCoverageModel.validationError);
}
},
this,
);
//Validate the EMLTaxonCoverage model
var taxonModel = this.get("taxonCoverage")[0];
if (!taxonModel.isEmpty() && !taxonModel.isValid()) {
errors = _.extend(errors, taxonModel.validationError);
} else if (
taxonModel.isEmpty() &&
this.get("taxonCoverage").length == 1 &&
MetacatUI.appModel.get("emlEditorRequiredFields").taxonCoverage
) {
taxonModel.isValid();
errors = _.extend(errors, taxonModel.validationError);
}
//Validate each EMLEntity model
_.each(this.get("entities"), function (entityModel) {
if (!entityModel.isValid()) {
if (!errors.entities)
errors.entities = [entityModel.validationError];
else errors.entities.push(entityModel.validationError);
}
});
//Validate the EML Methods
let emlMethods = this.get("methods");
if (emlMethods) {
if (!emlMethods.isValid()) {
errors.methods = emlMethods.validationError;
}
}
// Validate each EMLAnnotation model
if (this.get("annotations")) {
this.get("annotations").each(function (model) {
if (model.isValid()) {
return;
}
if (!errors.annotations) {
errors.annotations = [];
}
errors.annotations.push(model.validationError);
}, this);
}
//Check the required fields for this MetacatUI configuration
for ([field, isRequired] of Object.entries(
MetacatUI.appModel.get("emlEditorRequiredFields"),
)) {
//If it's not required, then go to the next field
if (!isRequired) continue;
if (field == "alternateIdentifier") {
if (
!this.get("alternateIdentifier").length ||
_.every(this.get("alternateIdentifier"), function (altId) {
return altId.trim() == "";
})
)
errors.alternateIdentifier =
"At least one alternate identifier is required.";
} else if (field == "generalTaxonomicCoverage") {
if (
!this.get("taxonCoverage").length ||
!this.get("taxonCoverage")[0].get("generalTaxonomicCoverage")
)
errors.generalTaxonomicCoverage =
"Provide a description of the general taxonomic coverage of this data set.";
} else if (field == "geoCoverage") {
if (!this.get("geoCoverage").length)
errors.geoCoverage = "At least one location is required.";
} else if (field == "intellectualRights") {
if (!this.get("intellectualRights"))
errors.intellectualRights =
"Select usage rights for this data set.";
} else if (field == "studyExtentDescription") {
if (
!this.get("methods") ||
!this.get("methods").get("studyExtentDescription")
)
errors.studyExtentDescription =
"Provide a study extent description.";
} else if (field == "samplingDescription") {
if (
!this.get("methods") ||
!this.get("methods").get("samplingDescription")
)
errors.samplingDescription = "Provide a sampling description.";
} else if (field == "temporalCoverage") {
if (!this.get("temporalCoverage").length)
errors.temporalCoverage =
"Provide the date(s) for this data set.";
} else if (field == "taxonCoverage") {
if (!this.get("taxonCoverage").length)
errors.taxonCoverage =
"At least one taxa rank and value is required.";
} else if (field == "keywordSets") {
if (!this.get("keywordSets").length)
errors.keywordSets = "Provide at least one keyword.";
}
//The EMLMethods model will validate itself for required fields, but
// this is a rudimentary check to make sure the EMLMethods model was created
// in the first place
else if (field == "methods") {
if (!this.get("methods"))
errors.methods = "At least one method step is required.";
} else if (field == "funding") {
// Note: Checks for either the funding or award element. award
// element is checked by the project's objectDOM for now until
// EMLProject fully supports the award element
if (
!this.get("project") ||
!(
this.get("project").get("funding").length ||
(this.get("project").get("objectDOM") &&
this.get("project").get("objectDOM").querySelectorAll &&
this.get("project").get("objectDOM").querySelectorAll("award")
.length > 0)
)
)
errors.funding =
"Provide at least one project funding number or name.";
} else if (field == "abstract") {
if (!this.get("abstract").length)
errors["abstract"] = "Provide an abstract.";
} else if (field == "dataSensitivity") {
if (!this.getDataSensitivity()) {
errors["dataSensitivity"] =
"Pick the category that best describes the level of sensitivity or restriction of the data.";
}
}
//If this is an EMLParty type, check that there is a party of this type in the model
else if (
EMLParty.prototype.partyTypes
.map((t) => t.dataCategory)
.includes(field)
) {
//If this is an associatedParty role
if (EMLParty.prototype.defaults().roleOptions?.includes(field)) {
if (
!this.get("associatedParty")
?.map((p) => p.get("roles"))
.flat()
.includes(field)
) {
errors[field] =
"Provide information about the people or organization(s) in the role: " +
EMLParty.prototype.partyTypes.find(
(t) => t.dataCategory == field,
)?.label;
}
} else if (!this.get(field)?.length) {
errors[field] =
"Provide information about the people or organization(s) in the role: " +
EMLParty.prototype.partyTypes.find(
(t) => t.dataCategory == field,
)?.label;
}
} else if (!this.get(field) || !this.get(field)?.length) {
errors[field] = "Provide a " + field + ".";
}
}
if (Object.keys(errors).length) return errors;
else {
return;
}
},
/* Returns a boolean for whether the argument 'value' is a valid
value for EML's yearDate type which is used in a few places.
Note that this method considers a zero-length String to be valid
because the EML211.serialize() method will properly handle a null
or zero-length String by serializing out the current year. */
isValidYearDate: function (value) {
return (
value === "" ||
/^\d{4}$/.test(value) ||
/^\d{4}-\d{2}-\d{2}$/.test(value)
);
},
/*
* Sends an AJAX request to fetch the system metadata for this EML object.
* Will not trigger a sync event since it does not use Backbone.Model.fetch
*/
fetchSystemMetadata: function (options) {
if (!options) var options = {};
else options = _.clone(options);
var model = this,
fetchOptions = _.extend(
{
url:
MetacatUI.appModel.get("metaServiceUrl") +
encodeURIComponent(this.get("id")),
dataType: "text",
success: function (response) {
model.set(DataONEObject.prototype.parse.call(model, response));
//Trigger a custom event that the sys meta was updated
model.trigger("sysMetaUpdated");
},
error: function () {
model.trigger("error");
},
},
options,
);
//Add the authorization header and other AJAX settings
_.extend(fetchOptions, MetacatUI.appUserModel.createAjaxSettings());
$.ajax(fetchOptions);
},
/*
* Returns the nofde in the given EML document that the given node type
* should be inserted after
*
* Returns false if either the node is not found in the and this should
* be handled by the caller.
*/
getEMLPosition: function (eml, nodeName) {
var nodeOrder = this.get("nodeOrder");
var position = _.indexOf(nodeOrder, nodeName.toLowerCase());
if (position == -1) {
return false;
}
// Go through each node in the node list and find the position where this
// node will be inserted after
for (var i = position - 1; i >= 0; i--) {
if ($(eml).find("dataset").children(nodeOrder[i]).length) {
return $(eml).find("dataset").children(nodeOrder[i]).last();
}
}
return false;
},
/*
* Checks if this model has updates that need to be synced with the server.
*/
hasUpdates: function () {
if (this.constructor.__super__.hasUpdates.call(this)) return true;
//If nothing else has been changed, then this object hasn't had any updates
return false;
},
/*
Add an entity into the EML 2.1.1 object
*/
addEntity: function (emlEntity, position) {
//Get the current list of entities
var currentEntities = this.get("entities");
if (typeof position == "undefined" || position == -1)
currentEntities.push(emlEntity);
//Add the entity model to the entity array
else currentEntities.splice(position, 0, emlEntity);
this.trigger("change:entities");
this.trickleUpChange();
return this;
},
/*
Remove an entity from the EML 2.1.1 object
*/
removeEntity: function (emlEntity) {
if (!emlEntity || typeof emlEntity != "object") return;
//Get the current list of entities
var entities = this.get("entities");
entities = _.without(entities, emlEntity);
this.set("entities", entities);
},
/*
* Find the entity model for a given DataONEObject
*/
getEntity: function (dataONEObj) {
//If an EMLEntity model has been found for this object before, then return it
if (dataONEObj.get("metadataEntity")) {
dataONEObj.get("metadataEntity").set("dataONEObject", dataONEObj);
return dataONEObj.get("metadataEntity");
}
var entity = _.find(
this.get("entities"),
function (e) {
//Matches of the checksum or identifier are definite matches
if (e.get("xmlID") == dataONEObj.getXMLSafeID()) return true;
else if (
e.get("physicalMD5Checksum") &&
e.get("physicalMD5Checksum") == dataONEObj.get("checksum") &&
dataONEObj.get("checksumAlgorithm").toUpperCase() == "MD5"
)
return true;
else if (
e.get("downloadID") &&
e.get("downloadID") == dataONEObj.get("id")
)
return true;
// Get the file name from the EML for this entity
var fileNameFromEML =
e.get("physicalObjectName") || e.get("entityName");
// If the EML file name matches the DataONEObject file name
if (
fileNameFromEML &&
dataONEObj.get("fileName") &&
(fileNameFromEML.toLowerCase() ==
dataONEObj.get("fileName").toLowerCase() ||
fileNameFromEML.replace(/ /g, "_").toLowerCase() ==
dataONEObj.get("fileName").toLowerCase())
) {
//Get an array of all the other entities in this EML
var otherEntities = _.without(this.get("entities"), e);
// If this entity name matches the dataone object file name, AND no other dataone object file name
// matches, then we can assume this is the entity element for this file.
var otherMatchingEntity = _.find(
otherEntities,
function (otherE) {
// Get the file name from the EML for the other entities
var otherFileNameFromEML =
otherE.get("physicalObjectName") ||
otherE.get("entityName");
// If the file names match, return true
if (
otherFileNameFromEML == dataONEObj.get("fileName") ||
otherFileNameFromEML.replace(/ /g, "_") ==
dataONEObj.get("fileName")
)
return true;
},
);
// If this entity's file name didn't match any other file names in the EML,
// then this entity is a match for the given dataONEObject
if (!otherMatchingEntity) return true;
}
},
this,
);
//If we found an entity, give it an ID and return it
if (entity) {
//If this entity has been matched to another DataONEObject already, then don't match it again
if (entity.get("dataONEObject") == dataONEObj) {
return entity;
}
//If this entity has been matched to a different DataONEObject already, then don't match it again.
//i.e. We will not override existing entity<->DataONEObject pairings
else if (entity.get("dataONEObject")) {
return;
} else {
entity.set("dataONEObject", dataONEObj);
}
//Create an XML-safe ID and set it on the Entity model
var entityID = this.getUniqueEntityId(dataONEObj);
entity.set("xmlID", entityID);
//Save a reference to this entity so we don't have to refind it later
dataONEObj.set("metadataEntity", entity);
return entity;
}
//See if one data object is of this type in the package
var matchingTypes = _.filter(this.get("entities"), function (e) {
return (
e.get("formatName") ==
(dataONEObj.get("formatId") || dataONEObj.get("mediaType"))
);
});
if (matchingTypes.length == 1) {
//Create an XML-safe ID and set it on the Entity model
matchingTypes[0].set("xmlID", dataONEObj.getXMLSafeID());
return matchingTypes[0];
}
//If this EML is in a DataPackage with only one other DataONEObject,
// and there is only one entity in the EML, then we can assume they are the same entity
if (this.get("entities").length == 1) {
if (
this.get("collections")[0] &&
this.get("collections")[0].type == "DataPackage" &&
this.get("collections")[0].length == 2 &&
_.contains(this.get("collections")[0].models, dataONEObj)
) {
return this.get("entities")[0];
}
}
return false;
},
createEntity: function (dataONEObject) {
// Add or append an entity to the parent's entity list
var entityModel = new EMLOtherEntity({
entityName: dataONEObject.get("fileName"),
entityType:
dataONEObject.get("formatId") ||
dataONEObject.get("mediaType") ||
"application/octet-stream",
dataONEObject: dataONEObject,
parentModel: this,
xmlID: dataONEObject.getXMLSafeID(),
});
this.addEntity(entityModel);
//If this DataONEObject fails to upload, remove the EML entity
this.listenTo(dataONEObject, "errorSaving", function () {
this.removeEntity(dataONEObject.get("metadataEntity"));
//Listen for a successful save so the entity can be added back
this.listenToOnce(dataONEObject, "successSaving", function () {
this.addEntity(dataONEObject.get("metadataEntity"));
});
});
},
/*
* Creates an XML-safe identifier that is unique to this EML document,
* based on the given DataONEObject model. It is intended for EML entity nodes in particular.
*
* @param {DataONEObject} - a DataONEObject model that this EML documents
* @return {string} - an identifier string unique to this EML document
*/
getUniqueEntityId: function (dataONEObject) {
var uniqueId = "";
uniqueId = dataONEObject.getXMLSafeID();
//Get the EML string, if there is one, to check if this id already exists
var emlString = this.get("objectXML");
//If this id already exists in the EML...
if (emlString && emlString.indexOf(' id="' + uniqueId + '"')) {
//Create a random uuid to use instead
uniqueId = "urn-uuid-" + uuid.v4();
}
return uniqueId;
},
/*
* 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,
);
},
/**
* Attempt to move a party one index forward within its sibling models
*
* @param {EMLParty} partyModel: The EMLParty model we're moving
*/
movePartyUp: function (partyModel) {
var possibleAttr = [
"creator",
"contact",
"metadataProvider",
"publisher",
"associatedParty",
];
// Iterate over each possible attribute
_.each(
possibleAttr,
function (attr) {
if (!_.contains(this.get(attr), partyModel)) {
return;
}
// Make a clone because we're going to use splice
var models = _.clone(this.get(attr));
// Find the index of the model we're moving
var index = _.findIndex(models, function (m) {
return m === partyModel;
});
if (index === 0) {
// Already first
return;
}
if (index === -1) {
// Couldn't find the model
return;
}
// Do the move using splice and update the model
models.splice(index - 1, 0, models.splice(index, 1)[0]);
this.set(attr, models);
this.trigger("change:" + attr);
},
this,
);
},
/**
* Attempt to move a party one index forward within its sibling models
*
* @param {EMLParty} partyModel: The EMLParty model we're moving
*/
movePartyDown: function (partyModel) {
var possibleAttr = [
"creator",
"contact",
"metadataProvider",
"publisher",
"associatedParty",
];
// Iterate over each possible attribute
_.each(
possibleAttr,
function (attr) {
if (!_.contains(this.get(attr), partyModel)) {
return;
}
// Make a clone because we're going to use splice
var models = _.clone(this.get(attr));
// Find the index of the model we're moving
var index = _.findIndex(models, function (m) {
return m === partyModel;
});
if (index === -1) {
// Couldn't find the model
return;
}
// Figure out where to put the new model
// Leave it in the same place if the next index doesn't exist
// Move one forward if it does
var newIndex = models.length <= index + 1 ? index : index + 1;
// Do the move using splice and update the model
models.splice(newIndex, 0, models.splice(index, 1)[0]);
this.set(attr, models);
this.trigger("change:" + attr);
},
this,
);
},
/*
* Adds the given EMLParty model to this EML211 model in the
* appropriate role array in the given position
*
* @param {EMLParty} - The EMLParty model to add
* @param {number} - The position in the role array in which to insert this EMLParty
* @return {boolean} - Returns true if the EMLParty was successfully added, false if it was cancelled
*/
addParty: function (partyModel, position) {
//If the EMLParty model is empty, don't add it to the EML211 model
if (partyModel.isEmpty()) return false;
//Get the role of this EMLParty
var role = partyModel.get("type") || "associatedParty";
//If this model already contains this EMLParty, then exit
if (_.contains(this.get(role), partyModel)) return false;
if (typeof position == "undefined") {
this.get(role).push(partyModel);
} else {
this.get(role).splice(position, 0, partyModel);
}
this.trigger("change:" + role);
return true;
},
/**
* getPartiesByType - Gets an array of EMLParty members that have a particular party type or role.
* @param {string} partyType - A string that represents either the role or the party type. For example, "contact", "creator", "principalInvestigator", etc.
* @since 2.15.0
*/
getPartiesByType: function (partyType) {
try {
if (!partyType) {
return false;
}
var associatedPartyTypes = new EMLParty().get("roleOptions"),
isAssociatedParty = associatedPartyTypes.includes(partyType),
parties = [];
// For "contact", "creator", "metadataProvider", "publisher", each party type has it's own
// array in the EML model
if (!isAssociatedParty) {
parties = this.get(partyType);
// For "custodianSteward", "principalInvestigator", "collaboratingPrincipalInvestigator", etc.,
// party members are listed in the EML model's associated parties array. Each associated party's
// party type is indicated in the role attribute.
} else {
parties = _.filter(
this.get("associatedParty"),
function (associatedParty) {
return associatedParty.get("roles").includes(partyType);
},
);
}
return parties;
} catch (error) {
console.log(
"Error trying to find a list of party members in an EML model by type. Error details: " +
error,
);
}
},
createUnits: function () {
this.units.fetch();
},
/* Initialize the object XML for brand spankin' new EML objects */
createXML: function () {
let emlSystem = MetacatUI.appModel.get("emlSystem");
emlSystem =
!emlSystem || typeof emlSystem != "string" ? "knb" : emlSystem;
var xml =
'<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0"></eml:eml>',
eml = $($.parseHTML(xml));
// Set base attributes
eml.attr("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
eml.attr("xmlns:stmml", "http://www.xml-cml.org/schema/stmml-1.1");
eml.attr(
"xsi:schemaLocation",
"https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd",
);
eml.attr("packageId", this.get("id"));
eml.attr("system", emlSystem);
// Add the dataset
eml.append(document.createElement("dataset"));
eml.find("dataset").append(document.createElement("title"));
var emlString = $(document.createElement("div"))
.append(eml.clone())
.html();
return emlString;
},
/*
Replace elements named "source" with "sourced" due to limitations
with using $.parseHTML() rather than $.parseXML()
@param xmlString The XML string to make the replacement in
*/
cleanUpXML: function (xmlString) {
xmlString.replace("<source>", "<sourced>");
xmlString.replace("</source>", "</sourced>");
return xmlString;
},
createTextCopy: function () {
var emlDraftText =
"EML draft for " +
this.get("id") +
"(" +
this.get("title") +
") by " +
MetacatUI.appUserModel.get("firstName") +
" " +
MetacatUI.appUserModel.get("lastName");
if (this.get("uploadStatus") == "e" && this.get("errorMessage")) {
emlDraftText +=
". This EML had the following save error: `" +
this.get("errorMessage") +
"` ";
} else {
emlDraftText += ": ";
}
emlDraftText += this.serialize();
var plainTextEML = new DataONEObject({
formatId: "text/plain",
fileName:
"eml_draft_" +
(MetacatUI.appUserModel.get("lastName") || "") +
".txt",
uploadFile: new Blob([emlDraftText], { type: "plain/text" }),
synced: true,
});
return plainTextEML;
},
/*
* Cleans up the given text so that it is XML-valid by escaping reserved characters, trimming white space, etc.
*
* @param {string} textString - The string to clean up
* @return {string} - The cleaned up string
*/
cleanXMLText: function (textString) {
if (typeof textString != "string") return;
textString = textString.trim();
//Check for XML/HTML elements
_.each(textString.match(/<\s*[^>]*>/g), function (xmlNode) {
//Encode <, >, and </ substrings
var tagName = xmlNode.replace(/>/g, "&gt;");
tagName = tagName.replace(/</g, "&lt;");
//Replace the xmlNode in the full text string
textString = textString.replace(xmlNode, tagName);
});
//Remove Unicode characters that are not valid XML characters
//Create a regular expression that matches any character that is not a valid XML character
// (see https://www.w3.org/TR/xml/#charsets)
var invalidCharsRegEx =
/[^\u0009\u000a\u000d\u0020-\uD7FF\uE000-\uFFFD]/g;
textString = textString.replace(invalidCharsRegEx, "");
return textString;
},
/*
Dereference "reference" elements and replace them with a cloned copy
of the referenced content
@param xmlString The XML string with reference elements to transform
*/
dereference: function (xmlString) {
var referencesList; // the array of references elements in the document
var referencedID; // The id of the referenced element
var referencesParentEl; // The parent of the given references element
var referencedEl; // The referenced DOM to be copied
var xmlDOM = $.parseXML(xmlString);
referencesList = xmlDOM.getElementsByTagName("references");
if (referencesList.length) {
// Process each references elements
_.each(
referencesList,
function (referencesEl, index, referencesList) {
// Can't rely on the passed referencesEl since the list length changes
// because of the remove() below. Reuse referencesList[0] for every item:
// referencedID = $(referencesEl).text(); // doesn't work
referencesEl = referencesList[0];
referencedID = $(referencesEl).text();
referencesParentEl = $(referencesEl).parent()[0];
if (typeof referencedID !== "undefined" && referencedID != "") {
referencedEl = xmlDOM.getElementById(referencedID);
if (typeof referencedEl != "undefined") {
// Clone the referenced element and replace the references element
var referencedClone = $(referencedEl).clone()[0];
$(referencesParentEl)
.children(referencesEl.localName)
.replaceWith($(referencedClone).children());
//$(referencesParentEl).append($(referencedClone).children());
$(referencesParentEl).attr("id", DataONEObject.generateId());
}
}
},
xmlDOM,
);
}
return new XMLSerializer().serializeToString(xmlDOM);
},
/*
* Uses the EML `title` to set the `fileName` attribute on this model.
*/
setFileName: function () {
var title = "";
// Get the title from the metadata
if (Array.isArray(this.get("title"))) {
title = this.get("title")[0];
} else if (typeof this.get("title") == "string") {
title = this.get("title");
}
//Max title length
var maxLength = 50;
//trim the string to the maximum length
var trimmedTitle = title.trim().substr(0, maxLength);
//re-trim if we are in the middle of a word
if (trimmedTitle.indexOf(" ") > -1) {
trimmedTitle = trimmedTitle.substr(
0,
Math.min(trimmedTitle.length, trimmedTitle.lastIndexOf(" ")),
);
}
//Replace all non alphanumeric characters with underscores
// and make sure there isn't more than one underscore in a row
trimmedTitle = trimmedTitle
.replace(/[^a-zA-Z0-9]/g, "_")
.replace(/_{2,}/g, "_");
//Set the fileName on the model
this.set("fileName", trimmedTitle + ".xml");
},
trickleUpChange: function () {
if (
!MetacatUI.rootDataPackage ||
!MetacatUI.rootDataPackage.packageModel
)
return;
//Mark the package as changed
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/**
* Sets the xsi:schemaLocation attribute on the passed-in Element
* depending on the application configuration.
*
* @param {Element} eml: The root eml:eml element to modify
* @return {Element} The element, possibly modified
*/
setSchemaLocation: function (eml) {
if (!MetacatUI || !MetacatUI.appModel) {
return eml;
}
var current = $(eml).attr("xsi:schemaLocation"),
format = MetacatUI.appModel.get("editorSerializationFormat"),
location = MetacatUI.appModel.get("editorSchemaLocation");
// Return now if we can't do anything anyway
if (!format || !location) {
return eml;
}
// Simply add if the attribute isn't present to begin with
if (!current || typeof current !== "string") {
$(eml).attr("xsi:schemaLocation", format + " " + location);
return eml;
}
// Don't append if it's already present
if (current.indexOf(format) >= 0) {
return eml;
}
$(eml).attr("xsi:schemaLocation", current + " " + location);
return eml;
},
createID: function () {
this.set("xmlID", uuid.v4());
},
/**
* Creates and adds an {@link EMLAnnotation} to this EML211 model with the given annotation data in JSON form.
* @param {object} annotationData The attribute data to set on the new {@link EMLAnnotation}. See {@link EMLAnnotation#defaults} for
* details on what attributes can be passed to the EMLAnnotation. In addition, there is an `elementName` property.
* @property {string} [annotationData.elementName] The name of the EML Element that this
annotation should be applied to. e.g. dataset, entity, attribute. Defaults to `dataset`. NOTE: Right now only dataset annotations are supported until
more annotation editing is added to the EML Editor.
* @property {Boolean} [annotationData.allowDuplicates] If false, this annotation will replace all annotations already set with the same propertyURI.
* By default, more than one annotation with a given propertyURI can be added (defaults to true)
*/
addAnnotation: function (annotationData) {
try {
if (!annotationData || typeof annotationData != "object") {
return;
}
//If no element name is provided, default to the dataset element.
let elementName = "";
if (!annotationData.elementName) {
elementName = "dataset";
} else {
elementName = annotationData.elementName;
}
//Remove the elementName property so it isn't set on the EMLAnnotation model later.
delete annotationData.elementName;
//Check if duplicates are allowed
let allowDuplicates = annotationData.allowDuplicates;
delete annotationData.allowDuplicates;
//Create a new EMLAnnotation model
let annotation = new EMLAnnotation(annotationData);
//Update annotations set on the dataset element
if (elementName == "dataset") {
let annotations = this.get("annotations");
//If the current annotations set on the EML model are not in Array form, change it to an array
if (!annotations) {
annotations = new EMLAnnotations();
}
if (allowDuplicates === false) {
//Add the EMLAnnotation to the collection, making sure to remove duplicates first
annotations.replaceDuplicateWith(annotation);
} else {
annotations.add(annotation);
}
//Set the annotations and force the change to be recognized by the model
this.set("annotations", annotations, { silent: true });
this.handleChange(this, { force: true });
} else {
/** @todo Add annotation support for other EML Elements */
}
} catch (e) {
console.error("Could not add Annotation to the EML: ", e);
}
},
/**
* Finds annotations that are of the `data sensitivity` property from the NCEAS SENSO ontology.
* Returns undefined if none are found. This function returns EMLAnnotation models because the data
* sensitivity is stored in the EML Model as EMLAnnotations and added to EML as semantic annotations.
* @returns {EMLAnnotation[]|undefined}
*/
getDataSensitivity: function () {
try {
let annotations = this.get("annotations");
if (annotations) {
let found = annotations.where({
propertyURI: this.get("dataSensitivityPropertyURI"),
});
if (!found || !found.length) {
return;
} else {
return found;
}
} else {
return;
}
} catch (e) {
console.error("Failed to get Data Sensitivity from EML model: ", e);
return;
}
},
},
);

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

defaults: function () {
return _.extend(ScienceMetadata.prototype.defaults(), {
id: "urn:uuid:" + uuid.v4(),
formatId: "https://eml.ecoinformatics.org/eml-2.2.0",
objectXML: null,
isEditable: false,
alternateIdentifier: [],
shortName: null,
title: [],
creator: [], // array of EMLParty objects
metadataProvider: [], // array of EMLParty objects
associatedParty: [], // array of EMLParty objects
contact: [], // array of EMLParty objects
publisher: [], // array of EMLParty objects
pubDate: null,
language: null,
series: null,
abstract: [], //array of EMLText objects
keywordSets: [], //array of EMLKeywordSet objects
additionalInfo: [],
intellectualRights:
"This work is dedicated to the public domain under the Creative Commons Universal 1.0 Public Domain Dedication. To view a copy of this dedication, visit https://creativecommons.org/publicdomain/zero/1.0/.",
distribution: [], // array of EMLDistribution objects
geoCoverage: [], //an array for EMLGeoCoverages
temporalCoverage: [], //an array of EMLTempCoverage models
taxonCoverage: [], //an array of EMLTaxonCoverages
purpose: [],
entities: [], //An array of EMLEntities
pubplace: null,
methods: new EMLMethods(), // An EMLMethods objects
project: null, // An EMLProject object,
annotations: null, // Dataset-level annotations
canonicalDataset: null,
dataSensitivityPropertyURI:
"http://purl.dataone.org/odo/SENSO_00000005",
nodeOrder: [
"alternateidentifier",
"shortname",
"title",
"creator",
"metadataprovider",
"associatedparty",
"pubdate",
"language",
"series",
"abstract",
"keywordset",
"additionalinfo",
"intellectualrights",
"licensed",
"distribution",
"coverage",
"annotation",
"purpose",
"introduction",
"gettingstarted",
"acknowledgements",
"maintenance",
"contact",
"publisher",
"pubplace",
"methods",
"project",
"datatable",
"spatialraster",
"spatialvector",
"storedprocedure",
"view",
"otherentity",
"referencepublications",
"usagecitations",
"literaturecited",
],
});
},

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

initialize: function (attributes) {
// Call initialize for the super class
ScienceMetadata.prototype.initialize.call(this, attributes);
// EML211-specific init goes here
// this.set("objectXML", this.createXML());
this.parse(this.createXML());
this.on("sync", function () {
this.set("synced", true);
});
this.stopListening(this, "change:canonicalDataset");
this.listenTo(
this,
"change:canonicalDataset",
this.updateCanonicalDataset,
);
//Create a Unit collection
if (!this.units.length) this.createUnits();
},

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

url: function (options) {
var identifier;
if (options && options.update) {
identifier = this.get("oldPid") || this.get("seriesid");
} else {
identifier = this.get("id") || this.get("seriesid");
}
return (
MetacatUI.appModel.get("objectServiceUrl") +
encodeURIComponent(identifier)
);
},

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

parse: function (response) {
// Save a reference to this model for use in setting the
// parentModel inside anonymous functions
var model = this;
//If the response is XML
if (typeof response == "string" && response.indexOf("<") == 0) {
//Look for a system metadata tag and call DataONEObject parse instead
if (response.indexOf("systemMetadata>") > -1)
return DataONEObject.prototype.parse.call(this, response);
response = this.cleanUpXML(response);
response = this.dereference(response);
this.set("objectXML", response);
var emlElement = $($.parseHTML(response)).filter("eml\\:eml");
}
var datasetEl;
if (emlElement[0]) datasetEl = $(emlElement[0]).find("dataset");
if (!datasetEl || !datasetEl.length) return {};
var emlParties = [
"metadataprovider",
"associatedparty",
"creator",
"contact",
"publisher",
],
emlDistribution = ["distribution"],
emlEntities = [
"datatable",
"otherentity",
"spatialvector",
"spatialraster",
"storedprocedure",
"view",
],
emlText = ["abstract", "additionalinfo"],
emlMethods = ["methods"];
var nodes = datasetEl.children(),
modelJSON = {};
for (var i = 0; i < nodes.length; i++) {
var thisNode = nodes[i];
var convertedName =
this.nodeNameMap()[thisNode.localName] || thisNode.localName;
//EML Party modules are stored in EMLParty models
if (_.contains(emlParties, thisNode.localName)) {
if (thisNode.localName == "metadataprovider")
var attributeName = "metadataProvider";
else if (thisNode.localName == "associatedparty")
var attributeName = "associatedParty";
else var attributeName = thisNode.localName;
if (typeof modelJSON[attributeName] == "undefined")
modelJSON[attributeName] = [];
modelJSON[attributeName].push(
new EMLParty({
objectDOM: thisNode,
parentModel: model,
type: attributeName,
}),
);
}
//EML Distribution modules are stored in EMLDistribution models
else if (_.contains(emlDistribution, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] == "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName].push(
new EMLDistribution(
{
objectDOM: thisNode,
parentModel: model,
},
{ parse: true },
),
);
}
//The EML Project is stored in the EMLProject model
else if (thisNode.localName == "project") {
modelJSON.project = new EMLProject({
objectDOM: thisNode,
parentModel: model,
});
}
//EML Temporal, Taxonomic, and Geographic Coverage modules are stored in their own models
else if (thisNode.localName == "coverage") {
var temporal = $(thisNode).children("temporalcoverage"),
geo = $(thisNode).children("geographiccoverage"),
taxon = $(thisNode).children("taxonomiccoverage");
if (temporal.length) {
modelJSON.temporalCoverage = [];
_.each(temporal, function (t) {
modelJSON.temporalCoverage.push(
new EMLTemporalCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
if (geo.length) {
modelJSON.geoCoverage = [];
_.each(geo, function (g) {
modelJSON.geoCoverage.push(
new EMLGeoCoverage({
objectDOM: g,
parentModel: model,
}),
);
});
}
if (taxon.length) {
modelJSON.taxonCoverage = [];
_.each(taxon, function (t) {
modelJSON.taxonCoverage.push(
new EMLTaxonCoverage({
objectDOM: t,
parentModel: model,
}),
);
});
}
}
//Parse EMLText modules
else if (_.contains(emlText, thisNode.localName)) {
if (typeof modelJSON[convertedName] == "undefined")
modelJSON[convertedName] = [];
modelJSON[convertedName].push(
new EMLText({
objectDOM: thisNode,
parentModel: model,
}),
);
} else if (_.contains(emlMethods, thisNode.localName)) {
if (typeof modelJSON[thisNode.localName] === "undefined")
modelJSON[thisNode.localName] = [];
modelJSON[thisNode.localName] = new EMLMethods({
objectDOM: thisNode,
parentModel: model,
});
}
//Parse keywords
else if (thisNode.localName == "keywordset") {
//Start an array of keyword sets
if (typeof modelJSON["keywordSets"] == "undefined")
modelJSON["keywordSets"] = [];
modelJSON["keywordSets"].push(
new EMLKeywordSet({
objectDOM: thisNode,
parentModel: model,
}),
);
}
//Parse intellectual rights
else if (thisNode.localName == "intellectualrights") {
var value = "";
if ($(thisNode).children("para").length == 1)
value = $(thisNode).children("para").first().text().trim();
else $(thisNode).text().trim();
//If the value is one of our pre-defined options, then add it to the model
//if(_.contains(this.get("intellRightsOptions"), value))
modelJSON["intellectualRights"] = value;
}
//Parse Entities
else if (_.contains(emlEntities, thisNode.localName)) {
//Start an array of Entities
if (typeof modelJSON["entities"] == "undefined")
modelJSON["entities"] = [];
//Create the model
var entityModel;
if (thisNode.localName == "otherentity") {
entityModel = new EMLOtherEntity(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else if (thisNode.localName == "datatable") {
entityModel = new EMLDataTable(
{
objectDOM: thisNode,
parentModel: model,
},
{
parse: true,
},
);
} else {
entityModel = new EMLEntity(
{
objectDOM: thisNode,
parentModel: model,
entityType: "application/octet-stream",
type: thisNode.localName,
},
{
parse: true,
},
);
}
modelJSON["entities"].push(entityModel);
}
//Parse dataset-level annotations
else if (thisNode.localName === "annotation") {
if (!modelJSON["annotations"]) {
modelJSON["annotations"] = new EMLAnnotations();
}
var annotationModel = new EMLAnnotation(
{
objectDOM: thisNode,
},
{ parse: true },
);
modelJSON["annotations"].add(annotationModel);
} else {
//Is this a multi-valued field in EML?
if (Array.isArray(this.get(convertedName))) {
//If we already have a value for this field, then add this value to the array
if (Array.isArray(modelJSON[convertedName]))
modelJSON[convertedName].push(this.toJson(thisNode));
//If it's the first value for this field, then create a new array
else modelJSON[convertedName] = [this.toJson(thisNode)];
} else modelJSON[convertedName] = this.toJson(thisNode);
}
}
// Once all the nodes have been parsed, check if any of the annotations
// make up a canonical dataset reference
const annotations = modelJSON["annotations"];
if (annotations) {
const canonicalDataset = annotations.getCanonicalURI();
if (canonicalDataset) {
modelJSON["canonicalDataset"] = canonicalDataset;
}
}
return modelJSON;
},

Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,7 @@ define([
methods: new EMLMethods(), // An EMLMethods objects
project: null, // An EMLProject object,
annotations: null, // Dataset-level annotations
canonicalDataset: null,
dataSensitivityPropertyURI:
"http://purl.dataone.org/odo/SENSO_00000005",
nodeOrder: [
Expand Down Expand Up @@ -143,6 +144,13 @@ define([
this.set("synced", true);
});

this.stopListening(this, "change:canonicalDataset");
this.listenTo(
this,
"change:canonicalDataset",
this.updateCanonicalDataset,
);

//Create a Unit collection
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Create a Unit collection
// Create a Unit collection

if (!this.units.length) this.createUnits();
},
Expand All @@ -160,6 +168,17 @@ define([
);
},

updateCanonicalDataset() {
let uri = this.get("canonicalDataset");
uri = uri?.length ? uri[0] : null;
let annotations = this.get("annotations");
if (!annotations) {
annotations = new EMLAnnotations();
this.set("annotations", annotations);
}
annotations.updateCanonicalDataset(uri);
},

/*
* Maps the lower-case EML node names (valid in HTML DOM) to the camel-cased EML node names (valid in EML).
* Used during parse() and serialize()
Expand Down Expand Up @@ -734,6 +753,16 @@ define([
}
}

// Once all the nodes have been parsed, check if any of the annotations
// make up a canonical dataset reference
const annotations = modelJSON["annotations"];
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🚫 [eslint] <prefer-destructuring> reported by reviewdog 🐶
Use object destructuring.

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🚫 [eslint] <dot-notation> reported by reviewdog 🐶
["annotations"] is better written in dot notation.

Suggested change
const annotations = modelJSON["annotations"];
const annotations = modelJSON.annotations;

if (annotations) {
const canonicalDataset = annotations.getCanonicalURI();
if (canonicalDataset) {
modelJSON["canonicalDataset"] = canonicalDataset;
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🚫 [eslint] <dot-notation> reported by reviewdog 🐶
["canonicalDataset"] is better written in dot notation.

Suggested change
modelJSON["canonicalDataset"] = canonicalDataset;
modelJSON.canonicalDataset = canonicalDataset;

}
}

return modelJSON;
},

Expand Down
5 changes: 3 additions & 2 deletions src/js/models/metadata/eml211/EMLAnnotation.js
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🚫 [eslint] <prefer-arrow-callback> reported by reviewdog 🐶
Unexpected function expression.

define(["jquery", "underscore", "backbone"], function ($, _, Backbone) {
/**
* @class EMLAnnotation
* @classdesc Stores EML SemanticAnnotation elements.
* @classcategory Models/Metadata/EML211
* @see https://eml.ecoinformatics.org/eml-2.2.0/eml-semantics.xsd
* @extends Backbone.Model
*/
var EMLAnnotation = Backbone.Model.extend(
/** @lends EMLAnnotation.prototype */ {
type: "EMLAnnotation",
defaults: function () {
return {
isNew: true,
propertyLabel: null,
propertyURI: null,
valueLabel: null,
valueURI: null,
objectDOM: null,
objectXML: null,
};
},
initialize: function (attributes, opions) {
this.stopListening(this, "change", this.trickleUpChange);
this.listenTo(this, "change", this.trickleUpChange);
},
parse: function (attributes, options) {
// If parsing, this is an existing annotation so it's not isNew
attributes.isNew = false;
var propertyURI = $(attributes.objectDOM).find("propertyuri");
var valueURI = $(attributes.objectDOM).find("valueuri");
if (propertyURI.length !== 1 || valueURI.length !== 1) {
return;
}
attributes.propertyURI = $(propertyURI).text().trim();
attributes.valueURI = $(valueURI).text().trim();
var propertyLabel = $(propertyURI).attr("label");
var valueLabel = $(valueURI).attr("label");
if (!propertyLabel || !valueLabel) {
return;
}
attributes.propertyLabel = propertyLabel.trim();
attributes.valueLabel = valueLabel.trim();
return attributes;
},
validate: function () {
var errors = [];
if (this.isEmpty()) {
this.trigger("valid");
return;
}
var propertyURI = this.get("propertyURI");
if (!propertyURI || propertyURI.length <= 0) {
errors.push({
category: "propertyURI",
message: "Property URI must be set.",
});
} else if (propertyURI.match(/http[s]?:\/\/.+/) === null) {
errors.push({
category: "propertyURI",
message: "Property URI should be an HTTP(S) URI.",
});
}
var propertyLabel = this.get("propertyLabel");
if (!propertyLabel || propertyLabel.length <= 0) {
errors.push({
category: "propertyLabel",
message: "Property Label must be set.",
});
}
var valueURI = this.get("valueURI");
if (!valueURI || valueURI.length <= 0) {
errors.push({
category: "valueURI",
message: "Value URI must be set.",
});
} else if (valueURI.match(/http[s]?:\/\/.+/) === null) {
errors.push({
category: "valueURI",
message: "Value URI should be an HTTP(S) URI.",
});
}
var valueLabel = this.get("valueLabel");
if (!valueLabel || valueLabel.length <= 0) {
errors.push({
category: "valueLabel",
message: "Value Label must be set.",
});
}
if (errors.length === 0) {
this.trigger("valid");
return;
}
return errors;
},
updateDOM: function (objectDOM) {
objectDOM = document.createElement("annotation");
if (this.get("propertyURI")) {
var propertyURIEl = document.createElement("propertyuri");
$(propertyURIEl).html(this.get("propertyURI"));
if (this.get("propertyLabel")) {
$(propertyURIEl).attr("label", this.get("propertyLabel"));
}
$(objectDOM).append(propertyURIEl);
}
if (this.get("valueURI")) {
var valueURIEl = document.createElement("valueuri");
$(valueURIEl).html(this.get("valueURI"));
if (this.get("valueLabel")) {
$(valueURIEl).attr("label", this.get("valueLabel"));
}
$(objectDOM).append(valueURIEl);
}
return objectDOM;
},
formatXML: function (xmlString) {
return DataONEObject.prototype.formatXML.call(this, xmlString);
},
/**
* isEmpty
*
* Check whether the model's properties are all empty for the purpose
* of skipping the model during serialization to avoid invalid EML
* documents.
*
* @return {boolean} - Returns true if all child elements have no
* content
*/
isEmpty: function () {
return (
(typeof this.get("propertyLabel") !== "string" ||
this.get("propertyLabel").length <= 0) &&
(typeof this.get("propertyURI") !== "string" ||
this.get("propertyURI").length <= 0) &&
(typeof this.get("valueLabel") !== "string" ||
this.get("valueLabel").length <= 0) &&
(typeof this.get("valueURI") !== "string" ||
this.get("valueURI").length <= 0)
);
},
/* Let the top level package know of attribute changes from this object */
trickleUpChange: function () {
MetacatUI.rootDataPackage.packageModel?.set("changed", true);
},
},
);
return EMLAnnotation;
});

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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

var EMLAnnotation = Backbone.Model.extend(
/** @lends EMLAnnotation.prototype */ {
type: "EMLAnnotation",
defaults: function () {
return {
isNew: true,
propertyLabel: null,
propertyURI: null,
valueLabel: null,
valueURI: null,
objectDOM: null,
objectXML: null,
};
},
initialize: function (attributes, opions) {
this.stopListening(this, "change", this.trickleUpChange);
this.listenTo(this, "change", this.trickleUpChange);
},
parse: function (attributes, options) {
// If parsing, this is an existing annotation so it's not isNew
attributes.isNew = false;
var propertyURI = $(attributes.objectDOM).find("propertyuri");
var valueURI = $(attributes.objectDOM).find("valueuri");
if (propertyURI.length !== 1 || valueURI.length !== 1) {
return;
}
attributes.propertyURI = $(propertyURI).text().trim();
attributes.valueURI = $(valueURI).text().trim();
var propertyLabel = $(propertyURI).attr("label");
var valueLabel = $(valueURI).attr("label");
if (!propertyLabel || !valueLabel) {
return;
}
attributes.propertyLabel = propertyLabel.trim();
attributes.valueLabel = valueLabel.trim();
return attributes;
},
validate: function () {
var errors = [];
if (this.isEmpty()) {
this.trigger("valid");
return;
}
var propertyURI = this.get("propertyURI");
if (!propertyURI || propertyURI.length <= 0) {
errors.push({
category: "propertyURI",
message: "Property URI must be set.",
});
} else if (propertyURI.match(/http[s]?:\/\/.+/) === null) {
errors.push({
category: "propertyURI",
message: "Property URI should be an HTTP(S) URI.",
});
}
var propertyLabel = this.get("propertyLabel");
if (!propertyLabel || propertyLabel.length <= 0) {
errors.push({
category: "propertyLabel",
message: "Property Label must be set.",
});
}
var valueURI = this.get("valueURI");
if (!valueURI || valueURI.length <= 0) {
errors.push({
category: "valueURI",
message: "Value URI must be set.",
});
} else if (valueURI.match(/http[s]?:\/\/.+/) === null) {
errors.push({
category: "valueURI",
message: "Value URI should be an HTTP(S) URI.",
});
}
var valueLabel = this.get("valueLabel");
if (!valueLabel || valueLabel.length <= 0) {
errors.push({
category: "valueLabel",
message: "Value Label must be set.",
});
}
if (errors.length === 0) {
this.trigger("valid");
return;
}
return errors;
},
updateDOM: function (objectDOM) {
objectDOM = document.createElement("annotation");
if (this.get("propertyURI")) {
var propertyURIEl = document.createElement("propertyuri");
$(propertyURIEl).html(this.get("propertyURI"));
if (this.get("propertyLabel")) {
$(propertyURIEl).attr("label", this.get("propertyLabel"));
}
$(objectDOM).append(propertyURIEl);
}
if (this.get("valueURI")) {
var valueURIEl = document.createElement("valueuri");
$(valueURIEl).html(this.get("valueURI"));
if (this.get("valueLabel")) {
$(valueURIEl).attr("label", this.get("valueLabel"));
}
$(objectDOM).append(valueURIEl);
}
return objectDOM;
},
formatXML: function (xmlString) {
return DataONEObject.prototype.formatXML.call(this, xmlString);
},
/**
* isEmpty
*
* Check whether the model's properties are all empty for the purpose
* of skipping the model during serialization to avoid invalid EML
* documents.
*
* @return {boolean} - Returns true if all child elements have no
* content
*/
isEmpty: function () {
return (
(typeof this.get("propertyLabel") !== "string" ||
this.get("propertyLabel").length <= 0) &&
(typeof this.get("propertyURI") !== "string" ||
this.get("propertyURI").length <= 0) &&
(typeof this.get("valueLabel") !== "string" ||
this.get("valueLabel").length <= 0) &&
(typeof this.get("valueURI") !== "string" ||
this.get("valueURI").length <= 0)
);
},
/* Let the top level package know of attribute changes from this object */
trickleUpChange: function () {
MetacatUI.rootDataPackage.packageModel?.set("changed", true);
},
},
);

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

defaults: function () {
return {
isNew: true,
propertyLabel: null,
propertyURI: null,
valueLabel: null,
valueURI: null,
objectDOM: null,
objectXML: null,
};
},

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

parse: function (attributes, options) {
// If parsing, this is an existing annotation so it's not isNew
attributes.isNew = false;
var propertyURI = $(attributes.objectDOM).find("propertyuri");
var valueURI = $(attributes.objectDOM).find("valueuri");
if (propertyURI.length !== 1 || valueURI.length !== 1) {
return;
}
attributes.propertyURI = $(propertyURI).text().trim();
attributes.valueURI = $(valueURI).text().trim();
var propertyLabel = $(propertyURI).attr("label");
var valueLabel = $(valueURI).attr("label");
if (!propertyLabel || !valueLabel) {
return;
}
attributes.propertyLabel = propertyLabel.trim();
attributes.valueLabel = valueLabel.trim();
return attributes;
},

Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,8 @@ define(["jquery", "underscore", "backbone"], function ($, _, Backbone) {
},

initialize: function (attributes, opions) {
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⚠️ [eslint] <func-names> reported by reviewdog 🐶
Unexpected unnamed method 'initialize'.

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

Suggested change
initialize: function (attributes, opions) {
initialize (attributes, opions) {

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🚫 [eslint] <no-unused-vars> reported by reviewdog 🐶
'attributes' is defined but never used. Allowed unused args must match /^_/u.

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🚫 [eslint] <no-unused-vars> reported by reviewdog 🐶
'opions' is defined but never used. Allowed unused args must match /^_/u.

this.on("change", this.trickleUpChange);
this.stopListening(this, "change", this.trickleUpChange);
this.listenTo(this, "change", this.trickleUpChange);
},

parse: function (attributes, options) {
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⚠️ [eslint] <func-names> reported by reviewdog 🐶
Unexpected unnamed method 'parse'.

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🚫 [eslint] <no-unused-vars> reported by reviewdog 🐶
'options' is defined but never used. Allowed unused args must match /^_/u.

Expand Down Expand Up @@ -175,7 +176,7 @@ define(["jquery", "underscore", "backbone"], function ($, _, Backbone) {

/* Let the top level package know of attribute changes from this object */
trickleUpChange: function () {
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⚠️ [eslint] <func-names> reported by reviewdog 🐶
Unexpected unnamed method 'trickleUpChange'.

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

Suggested change
trickleUpChange: function () {
trickleUpChange () {

MetacatUI.rootDataPackage.packageModel.set("changed", true);
MetacatUI.rootDataPackage.packageModel?.set("changed", true);
},
},
);
Expand Down
8 changes: 8 additions & 0 deletions src/js/templates/metadata/metadataOverview.html
Original file line number Diff line number Diff line change
Expand Up @@ -94,3 +94,11 @@ <h5>Alternate Identifiers <i class="required-icon hidden" data-category="alterna
list any additional identifiers that can be used to locate or label the dataset here.</p>
<p class="notification" data-category="alternateIdentifier"></p>
</div>

<div class="canonical-id basic-text-container" data-category="canonicalDataset">
<h5>Canonical Dataset <i class="required-icon hidden" data-category="canonicalDataset"></i></h5>
<p class="subtle">If this dataset is essentially a duplicate of a version
stored elsewhere, provide the ID of the original dataset here. This must be a
DOI or URL</p>
<p class="notification" data-category="canonicalDataset"></p>
</div>
26 changes: 21 additions & 5 deletions src/js/views/metadata/EML211View.js
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🚫 [eslint] <prefer-arrow-callback> reported by reviewdog 🐶
Unexpected function expression.

], function (
_,
$,
Backbone,
ScienceMetadataView,
EMLGeoCoverageView,
EMLPartyView,
EMLMethodsView,
EMLTempCoverageView,
EML,
EMLGeoCoverage,
EMLKeywordSet,
EMLParty,
EMLProject,
EMLText,
EMLTaxonCoverage,
EMLTemporalCoverage,
EMLMethods,
Template,
PeopleTemplate,
EMLPartyCopyMenuTemplate,
OverviewTemplate,
DatesTemplate,
LocationsTemplate,
TaxonomicCoverageTemplate,
TaxonomicClassificationTable,
TaxonomicClassificationRow,
DataSensitivityTemplate,
) {
/**
* @class EMLView
* @classdesc An EMLView renders an editable view of an EML 2.1.1 document
* @classcategory Views/Metadata
* @extends ScienceMetadataView
*/
var EMLView = ScienceMetadataView.extend(
/** @lends EMLView */ {
type: "EML211",
el: "#metadata-container",
events: {
"change .text": "updateText",
"change .basic-text": "updateBasicText",
"keyup .basic-text.new": "addBasicText",
"mouseover .basic-text-row .remove": "previewTextRemove",
"mouseout .basic-text-row .remove": "previewTextRemove",
"change .pubDate input": "updatePubDate",
"focusout .pubDate input": "showPubDateValidation",
"keyup .eml-geocoverage.new": "updateLocations",
"change .taxonomic-coverage": "updateTaxonCoverage",
"keyup .taxonomic-coverage .new input": "addNewTaxon",
"keyup .taxonomic-coverage .new select": "addNewTaxon",
"focusout .taxonomic-coverage tr": "showTaxonValidation",
"click .taxonomic-coverage-row .remove": "removeTaxonRank",
"mouseover .taxonomic-coverage .remove": "previewTaxonRemove",
"mouseout .taxonomic-coverage .remove": "previewTaxonRemove",
"change .keywords": "updateKeywords",
"keyup .keyword-row.new input": "addNewKeyword",
"mouseover .keyword-row .remove": "previewKeywordRemove",
"mouseout .keyword-row .remove": "previewKeywordRemove",
"change .usage": "updateRadioButtons",
"change .funding": "updateFunding",
"keyup .funding.new": "addFunding",
"mouseover .funding-row .remove": "previewFundingRemove",
"mouseout .funding-row .remove": "previewFundingRemove",
"keyup .funding.error": "handleFundingTyping",
"click .side-nav-item": "switchSection",
"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 .eml-party .move-up": "movePersonUp",
"click .eml-party .move-down": "movePersonDown",
"click input.annotation": "addAnnotation",
"click .remove": "handleRemove",
},
/* A list of the subviews */
subviews: [],
/* The active section in the view - can only be the section name (e.g. overview, people)
* The active section is highlighted in the table of contents and is scrolled to when the page loads
*/
activeSection: "overview",
/* The visible section in the view - can either be the section name (e.g. overview, people) or "all"
* The visible section is the ONLY section that is displayed. If set to all, all sections are displayed.
*/
visibleSection: "overview",
/* Templates */
template: _.template(Template),
overviewTemplate: _.template(OverviewTemplate),
dataSensitivityTemplate: _.template(DataSensitivityTemplate),
datesTemplate: _.template(DatesTemplate),
locationsTemplate: _.template(LocationsTemplate),
taxonomicCoverageTemplate: _.template(TaxonomicCoverageTemplate),
taxonomicClassificationTableTemplate: _.template(
TaxonomicClassificationTable,
),
taxonomicClassificationRowTemplate: _.template(
TaxonomicClassificationRow,
),
copyPersonMenuTemplate: _.template(EMLPartyCopyMenuTemplate),
peopleTemplate: _.template(PeopleTemplate),
/**
* jQuery selector for the element that contains the Data Sensitivity section.
* @type {string}
*/
dataSensitivityContainerSelector: "#data-sensitivity-container",
/**
* An array of literal objects to describe each type of EML Party. This property has been moved to
* {@link EMLParty#partyTypes} as of 2.21.0 and will soon be deprecated.
* @type {object[]}
* @deprecated
* @since 2.15.0
*/
partyTypes: EMLParty.prototype.partyTypes,
initialize: function (options) {
//Set up all the options
if (typeof options == "undefined") var options = {};
//The EML Model and ID
this.model = options.model || new EML();
if (!this.model.get("id") && options.id)
this.model.set("id", options.id);
//Get the current mode
this.edit = options.edit || false;
return this;
},
/* Render the view */
render: function () {
MetacatUI.appModel.set("headerType", "default");
//Render the basic structure of the page and table of contents
this.$el.html(
this.template({
activeSection: this.activeSection,
visibleSection: this.visibleSection,
}),
);
this.$container = this.$(".metadata-container");
//Render all the EML sections when the model is synced
this.renderAllSections();
if (!this.model.get("synced"))
this.listenToOnce(this.model, "sync", this.renderAllSections);
//Listen to updates on the data package collections
_.each(
this.model.get("collections"),
function (dataPackage) {
if (dataPackage.type != "DataPackage") return;
// When the data package has been saved, render the EML again.
// This is needed because the EML model validate & serialize functions may
// automatically make changes, such as adding a contact and creator
// if none is supplied by the user.
this.listenTo(
dataPackage.packageModel,
"successSaving",
this.renderAllSections,
);
},
this,
);
return this;
},
renderAllSections: function () {
this.renderOverview();
this.renderPeople();
this.renderDates();
this.renderLocations();
this.renderTaxa();
this.renderMethods();
this.renderProject();
this.renderSharing();
//Scroll to the active section
if (this.activeSection != "overview") {
MetacatUI.appView.scrollTo(this.$(".section." + this.activeSection));
}
//When scrolling through the metadata, highlight the side navigation
var view = this;
$(document).scroll(function () {
view.highlightTOC.call(view);
});
},
/*
* Renders the Overview section of the page
*/
renderOverview: function () {
//Get the overall view mode
var edit = this.edit;
var view = this;
//Append the empty layout
var overviewEl = this.$container.find(".overview");
$(overviewEl).html(this.overviewTemplate());
//Title
this.renderTitle();
this.listenTo(this.model, "change:title", this.renderTitle);
//Data Sensitivity
this.renderDataSensitivity();
//Abstract
_.each(
this.model.get("abstract"),
function (abs) {
var abstractEl = this.createEMLText(abs, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
},
this,
);
if (!this.model.get("abstract").length) {
var abstractEl = this.createEMLText(null, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
}
//Keywords
//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.get("thesaurus"));
},
this,
);
},
this,
);
//Add a new keyword row
this.addKeyword();
//Alternate Ids
var altIdsEls = this.createBasicTextFields(
"alternateIdentifier",
"Add a new alternate identifier",
);
$(overviewEl).find(".altids").append(altIdsEls);
// Canonical Identifier
const canonicalIdEl = this.createBasicTextFields(
"canonicalDataset",
"Add a new canonical identifier",
);
$(overviewEl).find(".canonical-id").append(canonicalIdEl);
//Usage
//Find the model value that matches a radio button and check it
// Note the replace() call removing newlines and replacing them with a single space
// character. This is a temporary hack to fix https://github.com/NCEAS/metacatui/issues/128
if (this.model.get("intellectualRights"))
this.$(
".checkbox .usage[value='" +
this.model.get("intellectualRights").replace(/\r?\n|\r/g, " ") +
"']",
).prop("checked", true);
//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();
},
renderTitle: function () {
var titleEl = this.createBasicTextFields(
"title",
"Example: Greater Yellowstone Rivers from 1:126,700 U.S. Forest Service Visitor Maps (1961-1983)",
false,
);
this.$container
.find(".overview")
.find(".title-container")
.html(titleEl);
},
/**
* Renders the Data Sensitivity section of the Editor using the data-sensitivity.html template.
* @fires EML211View#editorInputsAdded
*/
renderDataSensitivity: function () {
try {
//If Data Sensitivity questions are disabled in the AppConfig, exit before rendering
if (!MetacatUI.appModel.get("enableDataSensitivityInEditor")) {
return;
}
var container = this.$(this.dataSensitivityContainerSelector),
view = this;
if (!container.length) {
container = $(`<div id="data-sensitivity-container"></div>`);
this.$(".section.overview").append(container);
}
require([
"text!../img/icons/datatags/check-tag.svg",
"text!../img/icons/datatags/alert-tag.svg",
], function (checkTagIcon, alertTagIcon) {
container.html(
view.dataSensitivityTemplate({
checkTagIcon: checkTagIcon,
alertTagIcon: alertTagIcon,
}),
);
//Initialize all the tooltips
view.$(".tooltip-this").tooltip();
//Check the radio button that is already selected, per the EML
let annotations = view.model.getDataSensitivity();
if (
annotations &&
annotations.length &&
typeof annotations[0].get == "function"
) {
let annotationValue = annotations[0].get("valueURI");
container
.find("[value='" + annotationValue + "']")
.prop("checked", true);
}
//Trigger the editorInputsAdded event which will let other parts of the app,
// such as the EditorView, know that new inputs are on the page
view.trigger("editorInputsAdded");
});
} catch (e) {
console.error("Could not render the Data Sensitivity section: ", e);
}
},
/*
* Renders the People section of the page
*/
renderPeople: function () {
var view = this,
model = view.model;
this.peopleSection = this.$(".section[data-section='people']");
// Empty the people section in case we are re-rendering people
// Insert the people template
this.peopleSection.html(this.peopleTemplate());
// Create a dropdown menu for adding new person types
this.renderPeopleDropdown();
EMLParty.prototype.partyTypes.forEach(function (partyType) {
// Make sure that there are no container elements saved
// in the partyType array, since we may need to re-create the
// containers the hold the rendered EMLParty information.
partyType.containerEl = null;
// Any party type that is listed as a role in EMLParty "roleOptions" is saved
// in the EML model as an associated party. The isAssociatedParty property
// is used for other parts of the EML211View.
if (
new EMLParty().get("roleOptions").includes(partyType.dataCategory)
) {
partyType.isAssociatedParty = true;
} else {
partyType.isAssociatedParty = false;
}
// Get the array of party members for the given partyType from the EML model
var parties = this.model.getPartiesByType(partyType.dataCategory);
// If no parties exist for the given party type, but one is required,
// (e.g. for contact and creator), then create one from the user's information.
if (!parties?.length && partyType.createFromUser) {
var newParty = new EMLParty({
type: partyType.isAssociatedParty
? "associatedParty"
: partyType.dataCategory,
roles: partyType.isAssociatedParty
? [partyType.dataCategory]
: [],
parentModel: model,
});
newParty.createFromUser();
model.addParty(newParty);
parties = [newParty];
}
// Render each party of this type
if (parties.length) {
parties.forEach(function (party) {
this.renderPerson(party, partyType.dataCategory);
}, this);
}
//If there are no parties of this type but they are required, then render a new empty person for this type
else if (
MetacatUI.appModel.get("emlEditorRequiredFields")[
partyType.dataCategory
]
) {
this.renderPerson(null, partyType.dataCategory);
}
}, this);
// Render a new blank party form at the very bottom of the people section.
// This allows the user to start entering details for a person before they've
// selected the party type.
this.renderPerson(null, "new");
// Initialize the tooltips
this.$("input.tooltip-this").tooltip({
placement: "top",
title: function () {
return $(this).attr("data-title") || $(this).attr("placeholder");
},
delay: 1000,
});
},
/**
* Creates and renders the dropdown at the bottom of the people section
* that allows the user to create a new party type category. The dropdown
* menu is saved to the view as view.partyMenu.
* @since 2.15.0
*/
renderPeopleDropdown: function () {
try {
var helpText =
"Optionally add other contributors, collaborators, and maintainers of this dataset.",
placeholderText = "Choose new person or organization role ...";
this.partyMenu = $(document.createElement("select"))
.attr("id", "new-party-menu")
.addClass("header-dropdown");
//Add the first option to the menu, which works as a label
this.partyMenu.append(
$(document.createElement("option")).text(placeholderText),
);
//Add some help text for the menu
this.partyMenu.attr("title", helpText);
//Add a container element for the new party
this.newPartyContainer = $(document.createElement("div"))
.attr("data-attribute", "new")
.addClass("row-striped");
//For each party type, add it to the menu as an option
EMLParty.prototype.partyTypes.forEach(function (partyType) {
$(this.partyMenu).append(
$(document.createElement("option"))
.val(partyType.dataCategory)
.text(partyType.label),
);
}, this);
// Add the menu and new party element to the page
this.peopleSection.append(this.partyMenu, this.newPartyContainer);
} catch (error) {
console.log(
"Error creating the menu for adding new party categories, error message: " +
error,
);
}
},
/**
* Render the information provided for a given EML party in the party section.
*
* @param {EMLParty} emlParty - the EMLParty model to render. If set to null, a new EML party will be created for the given party type.
* @param {string} partyType - The party type for which to render a new EML party. E.g. "creator", "coPrincipalInvestigator", etc.
*/
renderPerson: function (emlParty, partyType) {
// Whether or not this is a new emlParty model
var isNew = false;
//If no model is given, create a new model
if (!emlParty) {
var emlParty = new EMLParty({
parentModel: this.model,
});
//Mark this model as new
isNew = true;
// Find the party type or role based on the type given.
// Update the model.
if (partyType) {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: partyType },
);
if (partyTypeProperties) {
if (partyTypeProperties.isAssociatedParty) {
var newRoles = _.clone(emlParty.get("roles"));
newRoles.push(partyType);
emlParty.set("roles", newRoles);
} else {
emlParty.set("type", partyType);
}
}
}
} else {
//Get the party type, if it was not sent as a parameter
if (!partyType || !partyType.length) {
var partyType = emlParty.get("type");
if (
partyType == "associatedParty" ||
!partyType ||
!partyType.length
) {
partyType = emlParty.get("roles");
}
}
}
// partyType is a string when if it's a 'type' and an array if it's 'roles'
// If it's a string, convert to an array for the subsequent _.each() function
if (typeof partyType == "string") {
partyType = [partyType];
}
_.each(
partyType,
function (partyType) {
// The container for this specific party type
var container = null;
if (partyType === "new") {
container = this.newPartyContainer;
} else {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: partyType },
);
if (partyTypeProperties) {
container = partyTypeProperties.containerEl;
}
}
//See if this view already exists
if (!isNew && container && 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 this person type is not on the page yet, add it.
// For now, this only adds the first role if person has multiple roles.
if (!container || !container.length) {
container = this.addNewPersonType(partyType);
}
//If there still is no partyView found, create a new one
var partyView = new EMLPartyView({
model: emlParty,
edit: this.edit,
isNew: isNew,
});
if (isNew) {
container.append(partyView.render().el);
} else {
if (container.find(".new").length)
container.find(".new").before(partyView.render().el);
else container.append(partyView.render().el);
}
},
this,
);
},
/*
* This function reacts to the user typing a new person in the person section (an EMLPartyView)
*/
handlePersonTyping: function (e) {
var container = $(e.target).parents(".eml-party"),
emlParty = container.length ? container.data("model") : null,
partyType =
container.length && emlParty
? emlParty.get("roles")[0] || emlParty.get("type")
: null;
(partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
})),
(numPartyForms = this.$(
"[data-attribute='" + partyType + "'] .eml-party",
).length),
(numNewPartyForms = this.$(
"[data-attribute='" + partyType + "'] .eml-party.new",
).length);
// If there is already a form to enter a new party for this party type, don't add another one
if (numNewPartyForms > 1) return;
// If there is a limit to how many party types can be added for this type,
// don't add more forms than is allowed
if (partyTypeProperties && partyTypeProperties.limit) {
return;
}
// Render a form to enter information for a new person
this.renderPerson(null, partyType);
},
/*
* This function is called when someone chooses a new person type from the dropdown list
*/
chooseNewPersonType: function (e) {
var partyType = $(e.target).val();
if (!partyType) return;
//Get the form and model
var partyForm = this.newPartyContainer,
partyModel = partyForm.find(".eml-party").data("model").clone(),
partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
});
// Remove this type from the dropdown menu
this.partyMenu.find("[value='" + partyType + "']").remove();
if (!partyModel.isEmpty()) {
//Update the model
if (partyTypeProperties.isAssociatedParty) {
var newRoles = _.clone(partyModel.get("roles"));
newRoles.push(partyType);
partyModel.set("roles", newRoles);
} else {
partyModel.set("type", partyType);
}
if (partyModel.isValid()) {
partyModel.mergeIntoParent();
// Add the person of that type (a section will be added if required)
this.renderPerson(partyModel, partyType);
// Clear and re-render the new person form
partyForm.empty();
this.renderPerson(null, "new");
} else {
partyForm.find(".eml-party").data("view").showValidation();
}
} else {
this.addNewPersonType(partyType);
}
},
/*
* addNewPersonType - Adds a header and container to the People section for the given party type/role,
* @return {JQuery} Returns the HTML element that contains each rendered EML Party for the given party type.
*/
addNewPersonType: function (partyType) {
if (!partyType) return;
var partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
});
if (!partyTypeProperties) {
return;
}
// If there is already a view for this person type, don't re-add it.
if (partyTypeProperties.containerEl) {
return;
}
// Container element to hold all parties of this type
var outerContainer = $(document.createElement("div")).addClass(
"party-type-container",
);
// Add a new header for the party type,
// plus an icon and spot for validation messages
var header = $(document.createElement("h4"))
.text(partyTypeProperties.label)
.append(
"<i class='required-icon hidden' data-category='" +
partyType +
"'></i>",
);
outerContainer.append(header);
// If there is a description, add that to the container as well
if (partyTypeProperties.description) {
outerContainer.append(
'<p class="subtle">' + partyTypeProperties.description + "</p>",
);
}
//Remove this type from the dropdown menu
this.partyMenu.find("[value='" + partyType + "']").remove();
//Add the new party container
partyTypeProperties.containerEl = $(document.createElement("div"))
.attr("data-attribute", partyType)
.attr("data-category", partyType)
.addClass("row-striped");
let notification = document.createElement("p");
notification.className = "notification";
notification.setAttribute("data-category", partyType);
partyTypeProperties.containerEl.append(notification);
outerContainer.append(partyTypeProperties.containerEl);
// Add in the new party type container just before the dropdown
this.partyMenu.before(outerContainer);
// Add a blank form to the new person type section, unless the max number
// for this party type has already been reached (e.g. when a new person type
// is added after copying from another type)
if (
typeof partyTypeProperties.limit !== "number" ||
this.model.getPartiesByType(partyType).length <
partyTypeProperties.limit
) {
this.renderPerson(null, partyType);
}
return partyTypeProperties.containerEl;
},
/*
* 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 currentRoles = partyToCopy.get("roles");
if (!currentRoles || !currentRoles.length) {
currentRoles = partyToCopy.get("type");
}
// "type" is a string and "roles" is an array.
// so that we can use _.each() on both, convert "type" to an array
if (typeof currentRoles === "string") {
currentRoles = [currentRoles];
}
_.each(
currentRoles,
function (currentRole) {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: currentRole },
),
label = partyTypeProperties ? partyTypeProperties.label : "";
menu
.find("input[value='" + currentRole + "']")
.prop("disabled", "disabled")
.addClass("disabled")
.parent(".checkbox")
.attr(
"title",
"This person is already in the " + label + " list.",
);
},
this,
);
// If the maximum number of parties has already been for this party type,
// then don't allow adding more.
var partiesWithLimits = _.filter(
EMLParty.prototype.partyTypes,
function (partyType) {
return typeof partyType.limit === "number";
},
);
partiesWithLimits.forEach(function (partyType) {
// See how many parties already exist for this type
var existingParties = this.model.getPartiesByType(
partyType.dataCategory,
);
if (
existingParties &&
existingParties.length &&
existingParties.length >= partyType.limit
) {
var names = _.map(existingParties, function (partyModel) {
var name = partyModel.getName();
if (name) {
return name;
} else {
return "Someone";
}
});
var sep = names.length === 2 ? " and " : ", ",
beVerbNames = names.length > 1 ? "are" : "is",
beVerbLimit = partyType.limit > 1 ? "are" : "is",
title =
names.join(sep) +
" " +
beVerbNames +
" already listed as " +
partyType.dataCategory +
". (Only " +
partyType.limit +
" " +
beVerbLimit +
" is allowed.)";
menu
.find("input[value='" + partyType.dataCategory + "']")
.prop("disabled", "disabled")
.addClass("disabled")
.parent(".checkbox")
.attr("title", title);
}
}, this);
//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(),
partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: role,
});
//Create a new EMLParty model
var newPerson = new EMLParty();
// Copy the attributes from the original person
// and set it on the new person
newPerson.set(partyToCopy.copyValues());
//If the new role is an associated party ...
if (partyTypeProperties.isAssociatedParty) {
newPerson.set("type", "associatedParty");
newPerson.set("roles", [role]);
}
//If the new role is not an associated party...
else {
newPerson.set("type", role);
newPerson.set("roles", newPerson.defaults().role);
}
//Add this new EMLParty to the EML model
this.model.addParty(newPerson);
// Add a view for the copied person
this.renderPerson(newPerson);
},
this,
);
//If there was at least one copy created, then trigger the change event
if (checkedBoxes.length) {
this.model.trickleUpChange();
}
},
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();
},
/**
* Attempt to move the current person (Party) one index backward (up).
*
* @param {EventHandler} e: The click event handler
*/
movePersonUp: function (e) {
e.preventDefault();
// Get the party view el, view, and model
var partyEl = $(e.target).parents(".eml-party"),
model = partyEl.data("model"),
next = $(partyEl).prev().not(".new");
if (next.length === 0) {
return;
}
// Remove current view, create and insert a new one for the model
$(partyEl).remove();
var newView = new EMLPartyView({
model: model,
edit: this.edit,
});
$(next).before(newView.render().el);
// Move the party down within the model too
this.model.movePartyUp(model);
this.model.trickleUpChange();
},
/**
* Attempt to move the current person (Party) one index forward (down).
*
* @param {EventHandler} e: The click event handler
*/
movePersonDown: function (e) {
e.preventDefault();
// Get the party view el, view, and model
var partyEl = $(e.target).parents(".eml-party"),
model = partyEl.data("model"),
next = $(partyEl).next().not(".new");
if (next.length === 0) {
return;
}
// Remove current view, create and insert a new one for the model
$(partyEl).remove();
var newView = new EMLPartyView({
model: model,
edit: this.edit,
});
$(next).after(newView.render().el);
// Move the party down within the model too
this.model.movePartyDown(model);
this.model.trickleUpChange();
},
/*
* Renders the Dates section of the page
*/
renderDates: function () {
//Add a header
this.$(".section.dates").html(
$(document.createElement("h2")).text("Dates"),
);
_.each(
this.model.get("temporalCoverage"),
function (model) {
var tempCovView = new EMLTempCoverageView({
model: model,
isNew: false,
edit: this.edit,
});
tempCovView.render();
this.$(".section.dates").append(tempCovView.el);
},
this,
);
if (!this.model.get("temporalCoverage").length) {
var tempCovView = new EMLTempCoverageView({
isNew: true,
edit: this.edit,
model: new EMLTemporalCoverage({ parentModel: this.model }),
});
tempCovView.render();
this.$(".section.dates").append(tempCovView.el);
}
},
/*
* Renders the Locations section of the page
*/
renderLocations: function () {
var locationsSection = this.$(".section.locations");
//Add the Locations header
locationsSection.html(this.locationsTemplate());
var locationsTable = locationsSection.find(".locations-table");
//Render an EMLGeoCoverage view for each EMLGeoCoverage model
_.each(
this.model.get("geoCoverage"),
function (geo, i) {
//Create an EMLGeoCoverageView
var geoView = new EMLGeoCoverageView({
model: geo,
edit: this.edit,
});
//Render the view
geoView.render();
geoView.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Add the locations section to the page
locationsTable.append(geoView.el);
//Listen to validation events
this.listenTo(geo, "valid", this.updateLocationsError);
//Save it in our subviews array
this.subviews.push(geoView);
},
this,
);
//Now add one empty row to enter a new geo coverage
if (this.edit) {
var newGeoModel = new EMLGeoCoverage({
parentModel: this.model,
isNew: true,
}),
newGeoView = new EMLGeoCoverageView({
edit: true,
model: newGeoModel,
isNew: true,
});
locationsTable.append(newGeoView.render().el);
newGeoView.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Listen to validation events
this.listenTo(newGeoModel, "valid", this.updateLocationsError);
}
},
/*
* Renders the Taxa section of the page
*/
renderTaxa: function () {
const view = this;
const taxaSectionEl = this.$(".section.taxa");
if (!taxaSectionEl) return;
taxaSectionEl.html($(document.createElement("h2")).text("Taxa"));
var taxonomy = this.model.get("taxonCoverage");
// Render a set of tables for each taxonomicCoverage
if (
typeof taxonomy !== "undefined" &&
Array.isArray(taxonomy) &&
taxonomy.length
) {
for (var i = 0; i < taxonomy.length; i++) {
taxaSectionEl.append(this.createTaxonomicCoverage(taxonomy[i]));
}
} else {
// Create a new one
var taxonCov = new EMLTaxonCoverage({
parentModel: this.model,
});
this.model.set("taxonCoverage", [taxonCov], { silent: true });
taxaSectionEl.append(this.createTaxonomicCoverage(taxonCov));
}
// updating the indexes of taxa-tables before rendering the information on page(view).
var taxaNums = this.$(".editor-header-index");
for (var i = 0; i < taxaNums.length; i++) {
$(taxaNums[i]).text(i + 1);
}
// Insert the quick-add taxon options, if any are configured for this
// theme. See {@link AppModel#quickAddTaxa}
view.renderTaxaQuickAdd();
// If duplicates are removed while saving, make sure to re-render the taxa
view.model.get("taxonCoverage").forEach(function (taxonCov) {
view.model.stopListening(taxonCov);
view.model.listenTo(
taxonCov,
"duplicateClassificationsRemoved",
function () {
view.renderTaxa();
},
);
}, view);
},
/*
* Renders the Methods section of the page
*/
renderMethods: function () {
var methodsModel = this.model.get("methods");
if (!methodsModel) {
methodsModel = new EMLMethods({
edit: this.edit,
parentModel: this.model,
});
}
this.$(".section.methods").html(
new EMLMethodsView({
model: methodsModel,
edit: this.edit,
parentEMLView: this,
}).render().el,
);
},
/*
* Renders the Projcet section of the page
*/
renderProject: function () {},
/*
* Renders the Sharing section of the page
*/
renderSharing: function () {},
/*
* Renders the funding field of the EML
*/
renderFunding: function () {
//Funding
var funding = this.model.get("project")
? this.model.get("project").get("funding")
: [];
//Clear the funding section
$(".section.overview .funding").empty();
//Create the funding input elements
_.each(
funding,
function (fundingItem, i) {
this.addFunding(fundingItem);
},
this,
);
//Add a blank funding input
this.addFunding();
},
/*
* Adds a single funding input row. Can either be called directly or used as an event callback
*/
addFunding: function (argument) {
if (this.edit) {
if (typeof argument == "string") var value = argument;
else if (!argument) var value = "";
//Don't add another new funding input if there already is one
else if (
!value &&
typeof argument == "object" &&
!$(argument.target).is(".new")
)
return;
else if (typeof argument == "object" && argument.target) {
var event = argument;
// Don't add a new funding row if the current one is empty
if ($(event.target).val().trim() === "") return;
}
var fundingInput = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", "funding")
.addClass("span12 funding hover-autocomplete-target")
.attr(
"placeholder",
"Search for NSF awards by keyword or enter custom funding information",
)
.val(value),
hiddenFundingInput = fundingInput
.clone()
.attr("type", "hidden")
.val(value)
.attr("id", "")
.addClass("hidden"),
loadingSpinner = $(document.createElement("i")).addClass(
"icon icon-spinner input-icon icon-spin subtle hidden",
);
//Append all the elements to a container
var containerEl = $(document.createElement("div"))
.addClass("ui-autocomplete-container funding-row")
.append(fundingInput, loadingSpinner, hiddenFundingInput);
if (!value) {
$(fundingInput).addClass("new");
if (event) {
$(event.target)
.parents("div.funding-row")
.append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
$(event.target).removeClass("new");
}
} else {
// Add a remove button if this is a non-new funding element
$(containerEl).append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
}
var view = this;
//Setup the autocomplete widget for the funding input
fundingInput.autocomplete({
source: function (request, response) {
var beforeRequest = function () {
loadingSpinner.show();
};
var afterRequest = function () {
loadingSpinner.hide();
};
return MetacatUI.appLookupModel.getGrantAutocomplete(
request,
response,
beforeRequest,
afterRequest,
);
},
select: function (e, ui) {
e.preventDefault();
var value =
"NSF Award " + ui.item.value + " (" + ui.item.label + ")";
hiddenFundingInput.val(value);
fundingInput.val(value);
$(".funding .ui-helper-hidden-accessible").hide();
view.updateFunding(e);
},
position: {
my: "left top",
at: "left bottom",
of: fundingInput,
collision: "fit",
},
appendTo: containerEl,
minLength: 3,
});
this.$(".funding-container").append(containerEl);
}
},
previewFundingRemove: function (e) {
$(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.$("[data-category='funding'] .notification")
.removeClass("error")
.text("");
}
},
addKeyword: function (keyword, thesaurus) {
if (typeof keyword != "string" || !keyword) {
var keyword = "";
//Only show one new keyword row at a time
if (
this.$(".keyword.new").length == 1 &&
!this.$(".keyword.new").val()
)
return;
else if (this.$(".keyword.new").length > 1) return;
}
//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",
),
thesOptionExists = false,
removeButton;
// Piece together the inputs
row.append(keywordInput, thesInput);
//Create the thesaurus options dropdown menu
_.each(MetacatUI.appModel.get("emlKeywordThesauri"), function (option) {
var optionEl = $(document.createElement("option"))
.val(option.thesaurus)
.text(option.label);
thesInput.append(optionEl);
if (option.thesaurus == thesaurus) {
optionEl.prop("selected", true);
thesOptionExists = true;
}
});
//Add a "None" option, which is always in the dropdown
thesInput.prepend(
$(document.createElement("option")).val("None").text("None"),
);
if (thesaurus == "None" || !thesaurus) {
thesInput.val("None");
}
//If this keyword is from a custom thesaurus that is NOT configured in this App, AND
// there is an option with the same label, then remove the option so it doesn't look like a duplicate.
else if (
!thesOptionExists &&
_.findWhere(MetacatUI.appModel.get("emlKeywordThesauri"), {
label: thesaurus,
})
) {
var duplicateOptions = thesInput.find(
"option:contains(" + thesaurus + ")",
);
duplicateOptions.each(function (i, option) {
if ($(option).text() == thesaurus && !$(option).prop("selected")) {
$(option).remove();
}
});
}
//If this keyword is from a custom thesaurus that is NOT configured in this App, then show it as a custom option
else if (!thesOptionExists) {
thesInput.append(
$(document.createElement("option"))
.val(thesaurus)
.text(thesaurus)
.prop("selected", true),
);
}
if (!keyword) row.addClass("new");
else {
//Set the keyword value on the text input
keywordInput.val(keyword);
// Add a remove button unless this is the .new keyword
row.append(
this.createRemoveButton(
null,
"keywordSets",
"div.keyword-row",
"div.keywords",
),
);
}
this.$(".keywords").append(row);
},
addNewKeyword: function (e) {
if ($(e.target).val().trim() === "") return;
$(e.target).parents(".keyword-row").first().removeClass("new");
// Add in a remove button
$(e.target)
.parents(".keyword-row")
.append(
this.createRemoveButton(
null,
"keywordSets",
"div.keyword-row",
"div.keywords",
),
);
var row = $(document.createElement("div"))
.addClass("row-fluid keyword-row new")
.data({ model: new EMLKeywordSet() }),
keywordInput = $(document.createElement("input"))
.attr("type", "text")
.addClass("keyword span10"),
thesInput = $(document.createElement("select")).addClass(
"thesaurus span2",
);
row.append(keywordInput, thesInput);
//Create the thesaurus options dropdown menu
_.each(MetacatUI.appModel.get("emlKeywordThesauri"), function (option) {
thesInput.append(
$(document.createElement("option"))
.val(option.thesaurus)
.text(option.label),
);
});
//Add a "None" option, which is always in the dropdown
thesInput.prepend(
$(document.createElement("option"))
.val("None")
.text("None")
.prop("selected", true),
);
this.$(".keywords").append(row);
},
previewKeywordRemove: function (e) {
var row = $(e.target)
.parents(".keyword-row")
.toggleClass("remove-preview");
},
/*
* Update the funding info when the form is changed
*/
updateFunding: function (e) {
if (!e) return;
var row = $(e.target).parent(".funding-row").first(),
rowNum = this.$(".funding-row").index(row),
input = $(row).find("input"),
isNew = $(row).is(".new");
var newValue = isNew
? $(e.target).siblings("input.hidden").val()
: $(e.target).val();
newValue = this.model.cleanXMLText(newValue);
if (typeof newValue == "string") {
newValue = newValue.trim();
}
//If there is no project model
if (!this.model.get("project")) {
var model = new EMLProject({ parentModel: this.model });
this.model.set("project", model);
} else var model = this.model.get("project");
var currentFundingValues = model.get("funding");
//If the new value is an empty string, then remove that index in the array
if (typeof newValue == "string" && newValue.trim().length == 0) {
currentFundingValues = currentFundingValues.splice(rowNum, 1);
} else {
currentFundingValues[rowNum] = newValue;
}
if (isNew && newValue != "") {
$(row).removeClass("new");
// Add in a remove button
$(e.target)
.parent()
.append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
this.addFunding();
}
this.model.trickleUpChange();
},
//TODO: Comma and semi-colon separate keywords
updateKeywords: function (e) {
var keywordSets = this.model.get("keywordSets"),
newKeywordSets = [];
//Get all the keywords in the view
_.each(
this.$(".keyword-row"),
function (thisRow) {
var thesaurus = this.model.cleanXMLText(
$(thisRow).find("select").val(),
),
keyword = this.model.cleanXMLText($(thisRow).find("input").val());
if (!keyword) return;
var keywordSet = _.find(newKeywordSets, function (keywordSet) {
return keywordSet.get("thesaurus") == thesaurus;
});
if (typeof keywordSet != "undefined") {
keywordSet.get("keywords").push(keyword);
} else {
newKeywordSets.push(
new EMLKeywordSet({
parentModel: this.model,
keywords: [keyword],
thesaurus: thesaurus,
}),
);
}
},
this,
);
//Update the EML model
this.model.set("keywordSets", newKeywordSets);
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();
}
}
},
/*
* Update the EML Geo Coverage models and views when the user interacts with the locations section
*/
updateLocations: function (e) {
if (!e) return;
e.preventDefault();
var viewEl = $(e.target).parents(".eml-geocoverage"),
geoCovModel = viewEl.data("model");
//If the EMLGeoCoverage is new
if (viewEl.is(".new")) {
if (this.$(".eml-geocoverage.new").length > 1) return;
//Render the new geo coverage view
var newGeo = new EMLGeoCoverageView({
edit: this.edit,
model: new EMLGeoCoverage({ parentModel: this.model, isNew: true }),
isNew: true,
});
this.$(".locations-table").append(newGeo.render().el);
newGeo.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Unmark the view as new
viewEl.data("view").notNew();
//Get the EMLGeoCoverage model attached to this EMlGeoCoverageView
var geoModel = viewEl.data("model"),
//Get the current EMLGeoCoverage models set on the parent EML model
currentCoverages = this.model.get("geoCoverage");
//Add this new geo coverage model to the parent EML model
if (Array.isArray(currentCoverages)) {
if (!_.contains(currentCoverages, geoModel)) {
currentCoverages.push(geoModel);
this.model.trigger("change:geoCoverage");
}
} else {
currentCoverages = [currentCoverages, geoModel];
this.model.set("geoCoverage", currentCoverages);
}
}
},
/*
* If all the EMLGeoCoverage models are valid, remove the error messages for the Locations section
*/
updateLocationsError: function () {
var allValid = _.every(
this.model.get("geoCoverage"),
function (geoCoverageModel) {
return geoCoverageModel.isValid();
},
);
if (allValid) {
this.$(".side-nav-item.error[data-category='geoCoverage']")
.removeClass("error")
.find(".icon.error")
.hide();
this.$(".section[data-section='locations'] .notification.error")
.removeClass("error")
.text("");
}
},
/*
* Creates the text elements
*/
createEMLText: function (textModel, edit, category) {
if (!textModel && edit) {
return $(document.createElement("textarea"))
.attr("data-category", category)
.addClass("xlarge text");
} else if (!textModel && !edit) {
return $(document.createElement("div")).attr(
"data-category",
category,
);
}
//Get the EMLText from the EML model
var finishedEl;
//Get the text attribute from the EMLText model
var paragraphs = textModel.get("text"),
paragraphsString = "";
//If the text should be editable,
if (edit) {
//Format the paragraphs with carriage returns between paragraphs
paragraphsString = paragraphs.join(String.fromCharCode(13));
//Create the textarea element
finishedEl = $(document.createElement("textarea"))
.addClass("xlarge text")
.attr("data-category", category)
.html(paragraphsString);
} else {
//Format the paragraphs with HTML
_.each(paragraphs, function (p) {
paragraphsString += "<p>" + p + "</p>";
});
//Create a div
finishedEl = $(document.createElement("div"))
.attr("data-category", category)
.append(paragraphsString);
}
$(finishedEl).data({ model: textModel });
//Return the finished DOM element
return finishedEl;
},
/*
* Updates a basic text field in the EML after the user changes the value
*/
updateText: function (e) {
if (!e) return false;
var category = $(e.target).attr("data-category"),
currentValue = this.model.get(category),
textModel = $(e.target).data("model"),
value = this.model.cleanXMLText($(e.target).val());
//We can't update anything without a category
if (!category) return false;
//Get the list of paragraphs - checking for carriage returns and line feeds
var paragraphsCR = value.split(String.fromCharCode(13));
var paragraphsLF = value.split(String.fromCharCode(10));
//Use the paragraph list that has the most
var paragraphs =
paragraphsCR > paragraphsLF ? paragraphsCR : paragraphsLF;
//If this category isn't set yet, then create a new EMLText model
if (!textModel) {
//Get the current value for this category and create a new EMLText model
var newTextModel = new EMLText({
text: paragraphs,
parentModel: this.model,
});
// Save the new model onto the underlying DOM node
$(e.target).data({ model: newTextModel });
//Set the new EMLText model on the EML model
if (Array.isArray(currentValue)) {
currentValue.push(newTextModel);
this.model.trigger("change:" + category);
this.model.trigger("change");
} else {
this.model.set(category, newTextModel);
}
}
//Update the existing EMLText model
else {
//If there are no paragraphs or all the paragraphs are empty...
if (
!paragraphs.length ||
_.every(paragraphs, function (p) {
return p.trim() == "";
})
) {
//Remove this text model from the array of text models since it is empty
var newValue = _.without(currentValue, textModel);
this.model.set(category, newValue);
} else {
textModel.set("text", paragraphs);
textModel.trigger("change:text");
//Is this text model set on the EML model?
if (
Array.isArray(currentValue) &&
!_.contains(currentValue, textModel)
) {
//Push this text model into the array of EMLText models
currentValue.push(textModel);
this.model.trigger("change:" + category);
this.model.trigger("change");
}
}
}
},
/*
* Creates and returns an array of basic text input field for editing
*/
createBasicTextFields: function (category, placeholder) {
var textContainer = $(document.createElement("div")).addClass(
"text-container",
),
modelValues = this.model.get(category),
textRow; // Holds the DOM for each field
//Format as an array
if (!Array.isArray(modelValues) && modelValues)
modelValues = [modelValues];
//For each value in this category, create an HTML element with the value inserted
_.each(
modelValues,
function (value, i, allModelValues) {
if (this.edit) {
var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");
textRow.append(input.clone().val(value));
if (category !== "title" && category !== "canonicalDataset")
textRow.append(
this.createRemoveButton(
null,
category,
"div.basic-text-row",
"div.text-container",
),
);
textContainer.append(textRow);
//At the end, append an empty input for the user to add a new one
if (
i + 1 == allModelValues.length &&
category !== "title" &&
category !== "canonicalDataset"
) {
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);
}
} else {
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.attr("data-category", category)
.text(value),
);
}
},
this,
);
if ((!modelValues || !modelValues.length) && this.edit) {
var input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text new")
.attr("placeholder", placeholder || "Add a new " + category);
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.append(input),
);
}
return textContainer;
},
updateBasicText: function (e) {
if (!e) return false;
//Get the category, new value, and model
var category = $(e.target).attr("data-category"),
value = this.model.cleanXMLText($(e.target).val()),
model = $(e.target).data("model") || this.model;
//We can't update anything without a category
if (!category) return false;
//Get the current value
var currentValue = model.get(category);
//Insert the new value into the array
if (Array.isArray(currentValue)) {
//Find the position this text input is in
var position = $(e.target)
.parents("div.text-container")
.first()
.children("div")
.index($(e.target).parent());
//Set the value in that position in the array
currentValue[position] = value;
//Set the changed array on this model
model.set(category, currentValue);
model.trigger("change:" + category);
}
//Update the model if the current value is a string
else if (typeof currentValue == "string") {
model.set(category, [value]);
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 != "" &&
category != "title" &&
category !== "canonicalDataset"
) {
$(e.target).removeClass("new");
this.addBasicText(e);
}
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/* One-off handler for updating pubDate on the model when the form
input changes. Fairly similar but just a pared down version of
updateBasicText. */
updatePubDate: function (e) {
if (!e) return false;
this.model.set("pubDate", $(e.target).val().trim());
this.model.trigger("change");
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/*
* Adds a basic text input
*/
addBasicText: function (e) {
var category = $(e.target).attr("data-category"),
allBasicTexts = $(
".basic-text.new[data-category='" + category + "']",
);
//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" || category === "canonicalDataset")
return;
//Add another blank text input
var newRow = $(document.createElement("div")).addClass(
"basic-text-row",
);
newRow.append(
$(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.attr("placeholder", $(e.target).attr("placeholder"))
.addClass("new basic-text"),
);
$(e.target).parent().after(newRow);
$(e.target).after(
this.createRemoveButton(
null,
category,
".basic-text-row",
"div.text-container",
),
);
},
previewTextRemove: function (e) {
$(e.target).parents(".basic-text-row").toggleClass("remove-preview");
},
// publication date validation.
isDateFormatValid: function (dateString) {
//Date strings that are four characters should be a full year. Make sure all characters are numbers
if (dateString.length == 4) {
var digits = dateString.match(/[0-9]/g);
return digits.length == 4;
}
//Date strings that are 10 characters long should be a valid date
else {
var dateParts = dateString.split("-");
if (
dateParts.length != 3 ||
dateParts[0].length != 4 ||
dateParts[1].length != 2 ||
dateParts[2].length != 2
)
return false;
dateYear = dateParts[0];
dateMonth = dateParts[1];
dateDay = dateParts[2];
// Validating the values for the date and month if in YYYY-MM-DD format.
if (dateMonth < 1 || dateMonth > 12) return false;
else if (dateDay < 1 || dateDay > 31) return false;
else if (
(dateMonth == 4 ||
dateMonth == 6 ||
dateMonth == 9 ||
dateMonth == 11) &&
dateDay == 31
)
return false;
else if (dateMonth == 2) {
// Validation for leap year dates.
var isleap =
dateYear % 4 == 0 && (dateYear % 100 != 0 || dateYear % 400 == 0);
if (dateDay > 29 || (dateDay == 29 && !isleap)) return false;
}
var digits = _.filter(dateParts, function (part) {
return part.match(/[0-9]/g).length == part.length;
});
return digits.length == 3;
}
},
/* Event handler for showing validation messaging for the pubDate input
which has to conform to the EML yearDate type (YYYY or YYYY-MM-DD) */
showPubDateValidation: function (e) {
var container = $(e.target).parents(".pubDate").first(),
input = $(e.target),
messageEl = $(container).find(".notification"),
value = input.val(),
errors = [];
// Remove existing error borders and notifications
input.removeClass("error");
messageEl.text("");
messageEl.removeClass("error");
if (value != "" && value.length > 0) {
if (!this.isDateFormatValid(value)) {
errors.push(
"The value entered for publication date, '" +
value +
"' is not a valid value for this field. Enter either a year (e.g. 2017) or a date in the format YYYY-MM-DD.",
);
input.addClass("error");
}
}
if (errors.length > 0) {
messageEl.text(errors[0]).addClass("error");
}
},
// Creates a table to hold a single EMLTaxonCoverage element (table) for
// each root-level taxonomicClassification
createTaxonomicCoverage: function (coverage) {
var finishedEls = $(
this.taxonomicCoverageTemplate({
generalTaxonomicCoverage:
coverage.get("generalTaxonomicCoverage") || "",
}),
),
coverageEl = finishedEls.filter(".taxonomic-coverage");
coverageEl.data({ model: coverage });
var classifications = coverage.get("taxonomicClassification");
// Makes a table... for the root level
for (var i = 0; i < classifications.length; i++) {
coverageEl.append(
this.createTaxonomicClassificationTable(classifications[i]),
);
}
// Create a new, blank table for another taxonomicClassification
var newTableEl = this.createTaxonomicClassificationTable();
coverageEl.append(newTableEl);
return finishedEls;
},
createTaxonomicClassificationTable: function (classification) {
// updating the taxonomic table indexes before adding a new table to the page.
var taxaNums = this.$(".editor-header-index");
for (var i = 0; i < taxaNums.length; i++) {
$(taxaNums[i]).text(i + 1);
}
// Adding the taxoSpeciesCounter to the table header for enhancement of the view
var finishedEl = $(
'<div class="row-striped root-taxonomic-classification-container"></div>',
);
$(finishedEl).append(
'<h6>Species <span class="editor-header-index">' +
(taxaNums.length + 1) +
"</span> </h6>",
);
// Add a remove button if this is not a new table
if (!(typeof classification === "undefined")) {
$(finishedEl).append(
this.createRemoveButton(
"taxonCoverage",
"taxonomicClassification",
".root-taxonomic-classification-container",
".taxonomic-coverage",
),
);
}
var tableEl = $(this.taxonomicClassificationTableTemplate());
var tableBodyEl = $(document.createElement("tbody"));
var queue = [classification],
rows = [],
cur;
while (queue.length > 0) {
cur = queue.pop();
// I threw this in here so I can this function without an
// argument to generate a new table from scratch
if (typeof cur === "undefined") {
continue;
}
cur.taxonRankName = cur.taxonRankName?.toLowerCase();
rows.push(cur);
if (cur.taxonomicClassification) {
for (var i = 0; i < cur.taxonomicClassification.length; i++) {
queue.push(cur.taxonomicClassification[i]);
}
}
}
for (var j = 0; j < rows.length; j++) {
tableBodyEl.append(this.makeTaxonomicClassificationRow(rows[j]));
}
var newRowEl = this.makeNewTaxonomicClassificationRow();
$(tableBodyEl).append(newRowEl);
$(tableEl).append(tableBodyEl);
// Add the new class to the entire table if it's a new one
if (typeof classification === "undefined") {
$(tableEl).addClass("new");
}
$(finishedEl).append(tableEl);
return finishedEl;
},
/**
* Create the HTML for a single row in a taxonomicClassification table
* @param {EMLTaxonCoverage#taxonomicClassification} classification A
* classification object from an EMLTaxonCoverage model, may include
* a taxonRank, taxonValue, taxonId, commonName, and nested
* taxonomicClassification objects
* @returns {jQuery} A jQuery object containing the HTML for a single
* row in a taxonomicClassification table
* @since 2.24.0
*/
makeTaxonomicClassificationRow: function (classification) {
try {
if (!classification) classification = {};
var finishedEl = $(
this.taxonomicClassificationRowTemplate({
taxonRankName: classification.taxonRankName || "",
taxonRankValue: classification.taxonRankValue || "",
}),
);
// Save a reference to other taxon attributes that we need to keep
// when serializing the model
if (classification.taxonId) {
$(finishedEl).data("taxonId", classification.taxonId);
}
if (classification.commonName) {
$(finishedEl).data("commonName", classification.commonName);
}
return finishedEl;
} catch (e) {
console.log("Error making taxonomic classification row: ", e);
}
},
/**
* Create the HTML for a new row in a taxonomicClassification table
* @returns {jQuery} A jQuery object containing the HTML for a new row
* in a taxonomicClassification table
* @since 2.24.0
*/
makeNewTaxonomicClassificationRow: function () {
const row = this.makeTaxonomicClassificationRow({});
$(row).addClass("new");
return row;
},
/* Update the underlying model and DOM for an EML TaxonomicCoverage
section. This method handles updating the underlying TaxonomicCoverage
models when the user changes form fields as well as inserting new
form fields automatically when the user needs them.
Since a dataset has multiple TaxonomicCoverage elements at the dataset
level, each Taxonomic Coverage is represented by a table element and
all taxonomicClassifications within are rows in that table.
TODO: Finish this function
TODO: Link this function into the DOM
*/
updateTaxonCoverage: function (options) {
if (options.target) {
// Ignore the event if the target is a quick add taxon UI element.
const quickAddEl = $(this.taxonQuickAddEl);
if (quickAddEl && quickAddEl.has(options.target).length) {
return;
}
var e = options;
/* Getting `model` here is different than in other places because
the thing being updated is an `input` or `select` element which
is part of a `taxonomicClassification`. The model is
`TaxonCoverage` which has one or more
`taxonomicClassifications`. So we have to walk up to the
hierarchy from input < td < tr < tbody < table < div to get at
the underlying TaxonCoverage model.
*/
var coverage = $(e.target).parents(".taxonomic-coverage"),
classificationEl = $(e.target).parents(
".root-taxonomic-classification",
),
model = $(coverage).data("model") || this.model,
category = $(e.target).attr("data-category"),
value = this.model.cleanXMLText($(e.target).val());
//We can't update anything without a coverage, or
//classification
if (!coverage) return false;
if (!classificationEl) return false;
// Use `category` to determine if we're updating the generalTaxonomicCoverage or
// the taxonomicClassification
if (category && category === "generalTaxonomicCoverage") {
model.set("generalTaxonomicCoverage", value);
return;
}
} else {
var coverage = options.coverage,
model = $(coverage).data("model");
}
// Find all of the root-level taxonomicClassifications
var classificationTables = $(coverage).find(
".root-taxonomic-classification",
);
if (!classificationTables) return false;
//TODO :This should probably (at least) be in its own View and
//definitely refactored into tidy functions.*/
var rows,
collectedClassifications = [];
for (var i = 0; i < classificationTables.length; i++) {
rows = $(classificationTables[i]).find("tbody tr");
if (!rows) continue;
var topLevelClassification = {},
classification = topLevelClassification,
currentRank,
currentValue;
for (var j = 0; j < rows.length; j++) {
const thisRow = rows[j];
currentRank =
this.model.cleanXMLText($(thisRow).find("select").val()) || "";
currentValue =
this.model.cleanXMLText($(thisRow).find("input").val()) || "";
// Maintain classification attributes that exist in the EML but are not visible in the editor
const taxonId = $(thisRow).data("taxonId");
const commonName = $(thisRow).data("commonName");
// Skip over rows with empty Rank or Value
if (!currentRank.length || !currentValue.length) {
continue;
}
//After the first row, start nesting taxonomicClassification objects
if (j > 0) {
classification.taxonomicClassification = [{}];
classification = classification.taxonomicClassification[0];
}
// Add it to the classification object
classification.taxonRankName = currentRank;
classification.taxonRankValue = currentValue;
classification.taxonId = taxonId;
classification.commonName = commonName;
}
//Add the top level classification to the array
if (Object.keys(topLevelClassification).length)
collectedClassifications.push(topLevelClassification);
}
if (
!_.isEqual(
collectedClassifications,
model.get("taxonomicClassification"),
)
) {
model.set("taxonomicClassification", collectedClassifications);
this.model.trigger("change");
}
// Handle adding new tables and rows
// Do nothing if the value isn't set
if (value) {
// Add a new row if this is itself a new row
if ($(e.target).parents("tr").first().is(".new")) {
var newRowEl = this.makeNewTaxonomicClassificationRow();
$(e.target).parents("tbody").first().append(newRowEl);
$(e.target).parents("tr").first().removeClass("new");
}
// Add a new classification table if this is itself a new table
if ($(classificationEl).is(".new")) {
$(classificationEl).removeClass("new");
$(classificationEl).append(
this.createRemoveButton(
"taxonCoverage",
"taxonomicClassification",
".root-taxonomic-classification-container",
".taxonomic-coverage",
),
);
$(coverage).append(this.createTaxonomicClassificationTable());
}
}
// update the quick add interface
this.updateQuickAddTaxa();
},
/**
* Update the options for the quick add taxon select interface. This
* ensures that only taxonomic classifications that are not already
* included in the taxonomic coverage are available for selection.
* @since 2.24.0
*/
updateQuickAddTaxa: function () {
const selects = this.taxonSelects;
if (!selects || !selects.length) return;
const taxa = this.getTaxonQuickAddOptions();
if (!taxa || !taxa.length) return;
selects.forEach((select, i) => {
select.updateOptions(taxa[i].options);
});
},
/*
* Adds a new row and/or table to the taxonomic coverage section
*/
addNewTaxon: function (e) {
// Don't do anything if the current classification doesn't have new content
if ($(e.target).val().trim() === "") return;
// If the row is new, add a new row to the table
if ($(e.target).parents("tr").is(".new")) {
var newRow = this.makeNewTaxonomicClassificationRow();
//Append the new row and remove the new class from the old row
$(e.target).parents("tr").removeClass("new").after(newRow);
}
},
/**
* Insert the "quick add" interface for adding common taxa to the
* taxonomic coverage section. Only renders if there is a list of taxa
* configured in the appModel.
*/
renderTaxaQuickAdd: function () {
try {
const view = this;
// To render the taxon select, the view must be in editor mode and we
// need a list of taxa configured for the theme
if (!view.edit) return;
// remove any existing quick add interface:
if (view.taxonQuickAddEl) view.taxonQuickAddEl.remove();
const quickAddTaxa = view.getTaxonQuickAddOptions();
if (!quickAddTaxa || !quickAddTaxa.length) {
// If the taxa are configured as SID for a dataObject, then wait
// for the dataObject to be loaded
this.listenToOnce(
MetacatUI.appModel,
"change:quickAddTaxa",
this.renderTaxaQuickAdd,
);
return;
}
// Create & insert the basic HTML for the taxon select interface
const template = `<div class="taxa-quick-add">
<p class="taxa-quick-add__text">
<b>⭐️ Quick Add Taxa:</b> Select one or more common taxa. Click "Add" to add them to the list.
</p>
<div class="taxa-quick-add__controls">
<div class="taxa-quick-add__selects"></div>
<button class="btn btn-primary taxa-quick-add__button">Add Taxa</button>
</div>
</div>`;
const parser = new DOMParser();
const doc = parser.parseFromString(template, "text/html");
const quickAddEl = doc.body.firstChild;
const button = quickAddEl.querySelector("button");
const container = quickAddEl.querySelector(
".taxa-quick-add__selects",
);
const rowSelector = ".root-taxonomic-classification-container";
const firstRow = document.querySelector(rowSelector);
firstRow.parentNode.insertBefore(quickAddEl, firstRow);
view.taxonQuickAddEl = quickAddEl;
// Update the taxon coverage when the button is clicked
const onButtonClick = () => {
const taxonSelects = view.taxonSelects;
if (!taxonSelects || !taxonSelects.length) return;
const selectedItems = taxonSelects
.map((select) => select.model.get("selected"))
.flat();
if (!selectedItems || !selectedItems.length) return;
const selectedItemObjs = selectedItems.map((item) => {
try {
// It will be encoded JSON if it's a pre-defined taxon
return JSON.parse(decodeURIComponent(item));
} catch (e) {
// Otherwise it will be a string a user typed in
return {
taxonRankName: "",
taxonRankValue: item,
};
}
});
view.addTaxa(selectedItemObjs);
taxonSelects.forEach((select) =>
select.model.setSelected([], { silent: true }),
);
};
button.removeEventListener("click", onButtonClick);
button.addEventListener("click", onButtonClick);
// Create the search selects
view.taxonSelects = [];
const componentPath = "views/searchSelect/SearchSelectView";
require([componentPath], function (SearchSelect) {
quickAddTaxa.forEach((taxaList, i) => {
try {
const taxaInput = new SearchSelect({
options: taxaList.options,
placeholderText: taxaList.placeholder,
inputLabel: taxaList.label,
allowMulti: true,
allowAdditions: true,
separatorTextOptions: false,
selected: [],
});
container.appendChild(taxaInput.el);
taxaInput.render();
view.taxonSelects.push(taxaInput);
} catch (e) {
console.log("Failed to create taxon select: ", e);
}
});
});
} catch (e) {
console.log("Failed to render taxon select: ", e);
}
},
/**
* Get the list of options for the taxon quick add interface. Filter
* out any that have already been added to the taxonomic coverage.
* @returns {Object[]} An array of search select options
* @since 2.24.0
*/
getTaxonQuickAddOptions: function () {
const quickAddTaxa = MetacatUI.appModel.getQuickAddTaxa();
if (!quickAddTaxa || !quickAddTaxa.length) return;
const coverages = this.model.get("taxonCoverage");
for (const taxaList of quickAddTaxa) {
const opts = [];
for (const taxon of taxaList.taxa) {
// check that it is not a duplicate in any coverages
let isDuplicate = false;
for (cov of coverages) {
if (cov.isDuplicate(taxon)) {
isDuplicate = true;
break;
}
}
if (!isDuplicate) {
opts.push(this.taxonOptionToSearchSelectItem(taxon));
}
}
taxaList.options = opts;
}
return quickAddTaxa;
},
/**
* Reformats a taxon option, as provided in the appModel
* {@link AppModel#quickAddTaxa}, as a search select item.
* @param {Object} option A single taxon classification with at least a
* taxonRankValue and taxonRankName. It may also have a taxonId (object
* with provider and value) and a commonName.
* @returns {Object} A search select item with label, value, and
* description properties.
*/
taxonOptionToSearchSelectItem: function (option) {
try {
// option must have a taxonRankValue and taxonRankName or it is invalid
if (!option.taxonRankValue || !option.taxonRankName) {
console.log("Invalid taxon option: ", option);
return null;
}
// Create a description
let description = option.taxonRankName + ": " + option.taxonRankValue;
if (option.taxonId) {
description +=
" (" +
option.taxonId.provider +
": " +
option.taxonId.value +
")";
}
// search select doesn't work with some of the json characters
const val = encodeURIComponent(JSON.stringify(option));
return {
label: option.commonName || option.taxonRankValue,
value: val,
description: description,
};
} catch (e) {
console.log(
"Failed to reformat taxon option as search select item: ",
e,
);
return null;
}
},
/**
* Add new taxa to the EML model and re-render the taxa section. The new
* taxa will be added to the first <taxonomicCoverage> element in the EML
* model. If there is no <taxonomicCoverage> element, one will be created.
* @param {Object[]} newClassifications - An array of objects with any of
* the following properties:
* - taxonRankName: (sting) The name of the taxonomic rank, e.g.
* "Kingdom"
* - taxonRankValue: (string) The value of the taxonomic rank, e.g.
* "Animalia"
* - commonName: (string) The common name of the taxon, e.g. "Animals"
* - taxonId: (object) The official ID of the taxon, including "provider"
* and "value".
* - taxonomicClassification: (array) An array of nested taxonomic
* classifications
* @since 2.24.0
* @example
* this.addTaxon([{
* taxonRankName: "Kingdom",
* taxonRankValue: "Animalia",
* commonName: "Animals",
* taxonId: {
* provider: "https://www.itis.gov/",
* value: "202423"
* }]);
*/
addTaxa: function (newClassifications) {
try {
// TODO: validate the new taxon before adding it to the model?
const taxonCoverages = this.model.get("taxonCoverage");
// We expect that there is already a taxonCoverage array on the model.
// If the EML was made in the editor, there can only be one
// <taxonomicCoverage> element. Add the new taxon to its
// <taxonomicClassification> array. If there is more than one, then the
// new taxon will be added to the first <taxonomicCoverage> element.
if (taxonCoverages && taxonCoverages.length >= 1) {
const taxonCoverage = taxonCoverages[0];
const classifications = taxonCoverage.get(
"taxonomicClassification",
);
const allClass = classifications.concat(newClassifications);
taxonCoverage.set("taxonomicClassification", allClass);
} else {
// If there is no <taxonomicCoverage> element for some reason,
// create one and add the new taxon to its <taxonomicClassification>
// array.
const newCov = new EMLTaxonCoverage({
taxonomicClassification: newClassifications,
parentModel: this.model,
});
this.model.set("taxonCoverage", [newCov]);
}
// Re-render the taxa section
this.renderTaxa();
} catch (e) {
console.log("Error adding taxon to EML model: ", e);
}
},
removeTaxonRank: function (e) {
var row = $(e.target).parents(".taxonomic-coverage-row"),
coverageEl = $(row).parents(".taxonomic-coverage"),
view = this;
//Animate the row away and then remove it
row.slideUp("fast", function () {
row.remove();
view.updateTaxonCoverage({ coverage: coverageEl });
});
},
/*
* After the user focuses out, show validation help, if needed
*/
showTaxonValidation: function (e) {
//Get the text inputs and select menus
var row = $(e.target).parents("tr"),
allInputs = row.find("input, select"),
tableContainer = $(e.target).parents("table"),
errorInputs = [];
//If none of the inputs have a value and this is a new row, then do nothing
if (
_.every(allInputs, function (i) {
return !i.value;
}) &&
row.is(".new")
)
return;
//Add the error styling to any input with no value
_.each(allInputs, function (input) {
// Keep track of the number of clicks of each input element so we only show the
// error message after the user has focused on both input elements
if (!input.value) errorInputs.push(input);
});
if (errorInputs.length) {
//Show the error message after a brief delay
setTimeout(function () {
//If the user focused on another element in the same row, don't do anything
if (_.contains(allInputs, document.activeElement)) return;
//Add the error styling
$(errorInputs).addClass("error");
//Add the error message
if (!tableContainer.prev(".notification").length) {
tableContainer.before(
$(document.createElement("p"))
.addClass("error notification")
.text("Enter a rank name AND value in each row."),
);
}
}, 200);
} else {
allInputs.removeClass("error");
if (!tableContainer.find(".error").length)
tableContainer.prev(".notification").remove();
}
},
previewTaxonRemove: function (e) {
var removeBtn = $(e.target);
if (removeBtn.parent().is(".root-taxonomic-classification")) {
removeBtn.parent().toggleClass("remove-preview");
} else {
removeBtn
.parents(".taxonomic-coverage-row")
.toggleClass("remove-preview");
}
},
updateRadioButtons: function (e) {
//Get the element of this radio button set that is checked
var choice = this.$(
"[name='" + $(e.target).attr("name") + "']:checked",
).val();
if (typeof choice == "undefined" || !choice)
this.model.set($(e.target).attr("data-category"), "");
else this.model.set($(e.target).attr("data-category"), choice);
this.model.trickleUpChange();
},
/*
* Switch to the given section
*/
switchSection: function (e) {
if (!e) return;
e.preventDefault();
var clickedEl = $(e.target),
section =
clickedEl.attr("data-section") ||
clickedEl.children("[data-section]").attr("data-section") ||
clickedEl.parents("[data-section]").attr("data-section");
if (this.visibleSection == "all") this.scrollToSection(section);
else {
this.$(".section." + this.activeSection).hide();
this.$(".section." + section).show();
this.highlightTOC(section);
this.activeSection = section;
this.visibleSection = section;
$("body").scrollTop(
this.$(".section." + section).offset().top - $("#Navbar").height(),
);
}
},
/*
* When a user clicks on the section names in the side tabs, jump to the section
*/
scrollToSection: function (e) {
if (!e) return false;
//Stop navigation
e.preventDefault();
var section = $(e.target).attr("data-section"),
sectionEl = this.$(".section." + section);
if (!sectionEl) return false;
//Temporarily unbind the scroll listener while we scroll to the clicked section
$(document).unbind("scroll");
var view = this;
setTimeout(function () {
$(document).scroll(view.highlightTOC.call(view));
}, 1500);
//Scroll to the section
if (sectionEl == section[0]) MetacatUI.appView.scrollToTop();
else MetacatUI.appView.scrollTo(sectionEl, $("#Navbar").outerHeight());
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
//Set the clicked item to active
$(".side-nav-item a[data-section='" + section + "']").addClass(
"active",
);
//Set the active section on this view
this.activeSection = section;
},
/*
* Highlight the given menu item.
* The first argument is either an event object or the section name
*/
highlightTOC: function (section) {
this.resizeTOC();
//Now change sections
if (typeof section == "string") {
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
$(".side-nav-item a[data-section='" + section + "']").addClass(
"active",
);
this.activeSection = section;
this.visibleSection = section;
return;
} else if (this.visibleSection == "all") {
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
//Get the section
var top = $(window).scrollTop() + $("#Navbar").outerHeight() + 70,
sections = $(".metadata-container .section");
//If we're somewhere in the middle, find the right section
for (var i = 0; i < sections.length; i++) {
if (
top > $(sections[i]).offset().top &&
top < $(sections[i + 1]).offset().top
) {
$($(".side-nav-item a")[i]).addClass("active");
this.activeSection = $(sections[i]).attr("data-section");
this.visibleSection = $(sections[i]).attr("data-section");
break;
}
}
}
},
/*
* Resizes the vertical table of contents so it's always the same height as the editor body
*/
resizeTOC: function () {
var tableBottomHandle = $("#editor-body .ui-resizable-handle");
if (!tableBottomHandle.length) return;
var tableBottom = tableBottomHandle[0].getBoundingClientRect().bottom,
navTop = tableBottom;
if (tableBottom < $("#Navbar").outerHeight()) {
if ($("#Navbar").css("position") == "fixed")
navTop = $("#Navbar").outerHeight();
else navTop = 0;
}
$(".metadata-toc").css("top", navTop);
},
/*
* -- This function is for development/testing purposes only --
* Trigger a change on all the form elements
* so that when values are changed by Javascript, we make sure the change event
* is fired. This is good for capturing changes by Javascript, or
* browser plugins that fill-in forms, etc.
*/
triggerChanges: function () {
$("#metadata-container input").change();
$("#metadata-container textarea").change();
$("#metadata-container select").change();
},
/* Creates "Remove" buttons for removing non-required sections
of the EML from the DOM */
createRemoveButton: function (submodel, attribute, selector, container) {
return $(document.createElement("span"))
.addClass("icon icon-remove remove pointer")
.attr("title", "Remove")
.data({
submodel: submodel,
attribute: attribute,
selector: selector,
container: container,
});
},
/* Generic event handler for removing sections of the EML (both
the DOM and inside the EML211Model) */
handleRemove: function (e) {
var submodel = $(e.target).data("submodel"), // Optional sub-model to remove attribute from
attribute = $(e.target).data("attribute"), // Attribute on the EML211 model we're removing from
selector = $(e.target).data("selector"), // Selector to find the parent DOM elemente we'll remove
container = $(e.target).data("container"), // Selector to find the parent container so we can remove by index
parentEl, // Element we'll remove
model; // Specific sub-model we're removing
if (!attribute) return;
if (!container) return;
// Find the element we'll remove from the DOM
if (selector) {
parentEl = $(e.target).parents(selector).first();
} else {
parentEl = $(e.target).parents().first();
}
if (parentEl.length == 0) return;
// Handle remove on a EML model / sub-model
if (submodel) {
model = this.model.get(submodel);
if (!model) return;
// Get the current value of the attribute so we can remove from it
var currentValue, submodelIndex;
if (Array.isArray(this.model.get(submodel))) {
// Stop now if there's nothing to remove in the first place
if (this.model.get(submodel).length == 0) return;
// For multi-valued submodels, find *which* submodel we are removing or
// removingn from
submodelIndex = $(container).index(
$(e.target).parents(container).first(),
);
if (submodelIndex === -1) return;
currentValue = this.model
.get(submodel)
[submodelIndex].get(attribute);
} else {
currentValue = this.model.get(submodel).get(attribute);
}
//FInd the position of this field in the list of fields
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index($(e.target).parents(selector));
// Remove from the EML Model
if (position >= 0) {
if (Array.isArray(this.model.get(submodel))) {
currentValue.splice(position, 1); // Splice returns the removed members
this.model
.get(submodel)
[submodelIndex].set(attribute, currentValue);
} else {
currentValue.splice(position, 1); // Splice returns the removed members
this.model.get(submodel).set(attribute, currentValue);
}
}
} else if (selector) {
// Find the index this attribute is in the DOM
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index($(e.target).parents(selector));
//Remove this index of the array
var currentValue = this.model.get(attribute);
if (Array.isArray(currentValue)) currentValue.splice(position, 1);
//Set the array on the model so the 'set' function is executed
this.model.set(attribute, currentValue);
}
// Handle remove on a basic text field
else {
// The DOM order matches the EML model attribute order so we can remove
// by that
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index(selector);
var currentValue = this.model.get(attribute);
// Remove from the EML Model
if (position >= 0) {
currentValue.splice(position, 1);
this.model.set(attribute, currentValue);
}
}
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
// Remove the DOM
$(parentEl).remove();
//updating the tablesIndex once the element has been removed
var tableNums = this.$(".editor-header-index");
for (var i = 0; i < tableNums.length; i++) {
$(tableNums[i]).text(i + 1);
}
// If this was a taxon, update the quickAdd interface
if (submodel === "taxonCoverage") {
this.updateQuickAddTaxa();
}
},
/**
* Adds an {@link EMLAnnotation} to the {@link EML211} model currently being edited.
* Attributes for the annotation are retreived from the HTML attributes from the HTML element
* that was interacted with.
* @param {Event} e - An Event on an Element that contains {@link EMLAnnotation} data
*/
addAnnotation: function (e) {
try {
if (!e || !e.target) {
return;
}
let annotationData = _.clone(e.target.dataset);
//If this is a radio button, we only want one annotation of this type.
if (e.target.getAttribute("type") == "radio") {
annotationData.allowDuplicates = false;
}
//Set the valueURI from the input value
annotationData.valueURI = $(e.target).val();
//Reformat the propertyURI property
if (annotationData.propertyUri) {
annotationData.propertyURI = annotationData.propertyUri;
delete annotationData.propertyUri;
}
this.model.addAnnotation(annotationData);
} catch (error) {
console.error("Couldn't add annotation: ", e);
}
},
/* Close the view and its sub views */
onClose: function () {
this.remove(); // remove for the DOM, stop listening
this.off(); // remove callbacks, prevent zombies
this.model.off();
//Remove the scroll event listeners
$(document).unbind("scroll");
this.model = null;
this.subviews = [];
window.onbeforeunload = null;
},
},
);
return EMLView;
});

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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

var EMLView = ScienceMetadataView.extend(
/** @lends EMLView */ {
type: "EML211",
el: "#metadata-container",
events: {
"change .text": "updateText",
"change .basic-text": "updateBasicText",
"keyup .basic-text.new": "addBasicText",
"mouseover .basic-text-row .remove": "previewTextRemove",
"mouseout .basic-text-row .remove": "previewTextRemove",
"change .pubDate input": "updatePubDate",
"focusout .pubDate input": "showPubDateValidation",
"keyup .eml-geocoverage.new": "updateLocations",
"change .taxonomic-coverage": "updateTaxonCoverage",
"keyup .taxonomic-coverage .new input": "addNewTaxon",
"keyup .taxonomic-coverage .new select": "addNewTaxon",
"focusout .taxonomic-coverage tr": "showTaxonValidation",
"click .taxonomic-coverage-row .remove": "removeTaxonRank",
"mouseover .taxonomic-coverage .remove": "previewTaxonRemove",
"mouseout .taxonomic-coverage .remove": "previewTaxonRemove",
"change .keywords": "updateKeywords",
"keyup .keyword-row.new input": "addNewKeyword",
"mouseover .keyword-row .remove": "previewKeywordRemove",
"mouseout .keyword-row .remove": "previewKeywordRemove",
"change .usage": "updateRadioButtons",
"change .funding": "updateFunding",
"keyup .funding.new": "addFunding",
"mouseover .funding-row .remove": "previewFundingRemove",
"mouseout .funding-row .remove": "previewFundingRemove",
"keyup .funding.error": "handleFundingTyping",
"click .side-nav-item": "switchSection",
"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 .eml-party .move-up": "movePersonUp",
"click .eml-party .move-down": "movePersonDown",
"click input.annotation": "addAnnotation",
"click .remove": "handleRemove",
},
/* A list of the subviews */
subviews: [],
/* The active section in the view - can only be the section name (e.g. overview, people)
* The active section is highlighted in the table of contents and is scrolled to when the page loads
*/
activeSection: "overview",
/* The visible section in the view - can either be the section name (e.g. overview, people) or "all"
* The visible section is the ONLY section that is displayed. If set to all, all sections are displayed.
*/
visibleSection: "overview",
/* Templates */
template: _.template(Template),
overviewTemplate: _.template(OverviewTemplate),
dataSensitivityTemplate: _.template(DataSensitivityTemplate),
datesTemplate: _.template(DatesTemplate),
locationsTemplate: _.template(LocationsTemplate),
taxonomicCoverageTemplate: _.template(TaxonomicCoverageTemplate),
taxonomicClassificationTableTemplate: _.template(
TaxonomicClassificationTable,
),
taxonomicClassificationRowTemplate: _.template(
TaxonomicClassificationRow,
),
copyPersonMenuTemplate: _.template(EMLPartyCopyMenuTemplate),
peopleTemplate: _.template(PeopleTemplate),
/**
* jQuery selector for the element that contains the Data Sensitivity section.
* @type {string}
*/
dataSensitivityContainerSelector: "#data-sensitivity-container",
/**
* An array of literal objects to describe each type of EML Party. This property has been moved to
* {@link EMLParty#partyTypes} as of 2.21.0 and will soon be deprecated.
* @type {object[]}
* @deprecated
* @since 2.15.0
*/
partyTypes: EMLParty.prototype.partyTypes,
initialize: function (options) {
//Set up all the options
if (typeof options == "undefined") var options = {};
//The EML Model and ID
this.model = options.model || new EML();
if (!this.model.get("id") && options.id)
this.model.set("id", options.id);
//Get the current mode
this.edit = options.edit || false;
return this;
},
/* Render the view */
render: function () {
MetacatUI.appModel.set("headerType", "default");
//Render the basic structure of the page and table of contents
this.$el.html(
this.template({
activeSection: this.activeSection,
visibleSection: this.visibleSection,
}),
);
this.$container = this.$(".metadata-container");
//Render all the EML sections when the model is synced
this.renderAllSections();
if (!this.model.get("synced"))
this.listenToOnce(this.model, "sync", this.renderAllSections);
//Listen to updates on the data package collections
_.each(
this.model.get("collections"),
function (dataPackage) {
if (dataPackage.type != "DataPackage") return;
// When the data package has been saved, render the EML again.
// This is needed because the EML model validate & serialize functions may
// automatically make changes, such as adding a contact and creator
// if none is supplied by the user.
this.listenTo(
dataPackage.packageModel,
"successSaving",
this.renderAllSections,
);
},
this,
);
return this;
},
renderAllSections: function () {
this.renderOverview();
this.renderPeople();
this.renderDates();
this.renderLocations();
this.renderTaxa();
this.renderMethods();
this.renderProject();
this.renderSharing();
//Scroll to the active section
if (this.activeSection != "overview") {
MetacatUI.appView.scrollTo(this.$(".section." + this.activeSection));
}
//When scrolling through the metadata, highlight the side navigation
var view = this;
$(document).scroll(function () {
view.highlightTOC.call(view);
});
},
/*
* Renders the Overview section of the page
*/
renderOverview: function () {
//Get the overall view mode
var edit = this.edit;
var view = this;
//Append the empty layout
var overviewEl = this.$container.find(".overview");
$(overviewEl).html(this.overviewTemplate());
//Title
this.renderTitle();
this.listenTo(this.model, "change:title", this.renderTitle);
//Data Sensitivity
this.renderDataSensitivity();
//Abstract
_.each(
this.model.get("abstract"),
function (abs) {
var abstractEl = this.createEMLText(abs, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
},
this,
);
if (!this.model.get("abstract").length) {
var abstractEl = this.createEMLText(null, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
}
//Keywords
//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.get("thesaurus"));
},
this,
);
},
this,
);
//Add a new keyword row
this.addKeyword();
//Alternate Ids
var altIdsEls = this.createBasicTextFields(
"alternateIdentifier",
"Add a new alternate identifier",
);
$(overviewEl).find(".altids").append(altIdsEls);
// Canonical Identifier
const canonicalIdEl = this.createBasicTextFields(
"canonicalDataset",
"Add a new canonical identifier",
);
$(overviewEl).find(".canonical-id").append(canonicalIdEl);
//Usage
//Find the model value that matches a radio button and check it
// Note the replace() call removing newlines and replacing them with a single space
// character. This is a temporary hack to fix https://github.com/NCEAS/metacatui/issues/128
if (this.model.get("intellectualRights"))
this.$(
".checkbox .usage[value='" +
this.model.get("intellectualRights").replace(/\r?\n|\r/g, " ") +
"']",
).prop("checked", true);
//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();
},
renderTitle: function () {
var titleEl = this.createBasicTextFields(
"title",
"Example: Greater Yellowstone Rivers from 1:126,700 U.S. Forest Service Visitor Maps (1961-1983)",
false,
);
this.$container
.find(".overview")
.find(".title-container")
.html(titleEl);
},
/**
* Renders the Data Sensitivity section of the Editor using the data-sensitivity.html template.
* @fires EML211View#editorInputsAdded
*/
renderDataSensitivity: function () {
try {
//If Data Sensitivity questions are disabled in the AppConfig, exit before rendering
if (!MetacatUI.appModel.get("enableDataSensitivityInEditor")) {
return;
}
var container = this.$(this.dataSensitivityContainerSelector),
view = this;
if (!container.length) {
container = $(`<div id="data-sensitivity-container"></div>`);
this.$(".section.overview").append(container);
}
require([
"text!../img/icons/datatags/check-tag.svg",
"text!../img/icons/datatags/alert-tag.svg",
], function (checkTagIcon, alertTagIcon) {
container.html(
view.dataSensitivityTemplate({
checkTagIcon: checkTagIcon,
alertTagIcon: alertTagIcon,
}),
);
//Initialize all the tooltips
view.$(".tooltip-this").tooltip();
//Check the radio button that is already selected, per the EML
let annotations = view.model.getDataSensitivity();
if (
annotations &&
annotations.length &&
typeof annotations[0].get == "function"
) {
let annotationValue = annotations[0].get("valueURI");
container
.find("[value='" + annotationValue + "']")
.prop("checked", true);
}
//Trigger the editorInputsAdded event which will let other parts of the app,
// such as the EditorView, know that new inputs are on the page
view.trigger("editorInputsAdded");
});
} catch (e) {
console.error("Could not render the Data Sensitivity section: ", e);
}
},
/*
* Renders the People section of the page
*/
renderPeople: function () {
var view = this,
model = view.model;
this.peopleSection = this.$(".section[data-section='people']");
// Empty the people section in case we are re-rendering people
// Insert the people template
this.peopleSection.html(this.peopleTemplate());
// Create a dropdown menu for adding new person types
this.renderPeopleDropdown();
EMLParty.prototype.partyTypes.forEach(function (partyType) {
// Make sure that there are no container elements saved
// in the partyType array, since we may need to re-create the
// containers the hold the rendered EMLParty information.
partyType.containerEl = null;
// Any party type that is listed as a role in EMLParty "roleOptions" is saved
// in the EML model as an associated party. The isAssociatedParty property
// is used for other parts of the EML211View.
if (
new EMLParty().get("roleOptions").includes(partyType.dataCategory)
) {
partyType.isAssociatedParty = true;
} else {
partyType.isAssociatedParty = false;
}
// Get the array of party members for the given partyType from the EML model
var parties = this.model.getPartiesByType(partyType.dataCategory);
// If no parties exist for the given party type, but one is required,
// (e.g. for contact and creator), then create one from the user's information.
if (!parties?.length && partyType.createFromUser) {
var newParty = new EMLParty({
type: partyType.isAssociatedParty
? "associatedParty"
: partyType.dataCategory,
roles: partyType.isAssociatedParty
? [partyType.dataCategory]
: [],
parentModel: model,
});
newParty.createFromUser();
model.addParty(newParty);
parties = [newParty];
}
// Render each party of this type
if (parties.length) {
parties.forEach(function (party) {
this.renderPerson(party, partyType.dataCategory);
}, this);
}
//If there are no parties of this type but they are required, then render a new empty person for this type
else if (
MetacatUI.appModel.get("emlEditorRequiredFields")[
partyType.dataCategory
]
) {
this.renderPerson(null, partyType.dataCategory);
}
}, this);
// Render a new blank party form at the very bottom of the people section.
// This allows the user to start entering details for a person before they've
// selected the party type.
this.renderPerson(null, "new");
// Initialize the tooltips
this.$("input.tooltip-this").tooltip({
placement: "top",
title: function () {
return $(this).attr("data-title") || $(this).attr("placeholder");
},
delay: 1000,
});
},
/**
* Creates and renders the dropdown at the bottom of the people section
* that allows the user to create a new party type category. The dropdown
* menu is saved to the view as view.partyMenu.
* @since 2.15.0
*/
renderPeopleDropdown: function () {
try {
var helpText =
"Optionally add other contributors, collaborators, and maintainers of this dataset.",
placeholderText = "Choose new person or organization role ...";
this.partyMenu = $(document.createElement("select"))
.attr("id", "new-party-menu")
.addClass("header-dropdown");
//Add the first option to the menu, which works as a label
this.partyMenu.append(
$(document.createElement("option")).text(placeholderText),
);
//Add some help text for the menu
this.partyMenu.attr("title", helpText);
//Add a container element for the new party
this.newPartyContainer = $(document.createElement("div"))
.attr("data-attribute", "new")
.addClass("row-striped");
//For each party type, add it to the menu as an option
EMLParty.prototype.partyTypes.forEach(function (partyType) {
$(this.partyMenu).append(
$(document.createElement("option"))
.val(partyType.dataCategory)
.text(partyType.label),
);
}, this);
// Add the menu and new party element to the page
this.peopleSection.append(this.partyMenu, this.newPartyContainer);
} catch (error) {
console.log(
"Error creating the menu for adding new party categories, error message: " +
error,
);
}
},
/**
* Render the information provided for a given EML party in the party section.
*
* @param {EMLParty} emlParty - the EMLParty model to render. If set to null, a new EML party will be created for the given party type.
* @param {string} partyType - The party type for which to render a new EML party. E.g. "creator", "coPrincipalInvestigator", etc.
*/
renderPerson: function (emlParty, partyType) {
// Whether or not this is a new emlParty model
var isNew = false;
//If no model is given, create a new model
if (!emlParty) {
var emlParty = new EMLParty({
parentModel: this.model,
});
//Mark this model as new
isNew = true;
// Find the party type or role based on the type given.
// Update the model.
if (partyType) {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: partyType },
);
if (partyTypeProperties) {
if (partyTypeProperties.isAssociatedParty) {
var newRoles = _.clone(emlParty.get("roles"));
newRoles.push(partyType);
emlParty.set("roles", newRoles);
} else {
emlParty.set("type", partyType);
}
}
}
} else {
//Get the party type, if it was not sent as a parameter
if (!partyType || !partyType.length) {
var partyType = emlParty.get("type");
if (
partyType == "associatedParty" ||
!partyType ||
!partyType.length
) {
partyType = emlParty.get("roles");
}
}
}
// partyType is a string when if it's a 'type' and an array if it's 'roles'
// If it's a string, convert to an array for the subsequent _.each() function
if (typeof partyType == "string") {
partyType = [partyType];
}
_.each(
partyType,
function (partyType) {
// The container for this specific party type
var container = null;
if (partyType === "new") {
container = this.newPartyContainer;
} else {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: partyType },
);
if (partyTypeProperties) {
container = partyTypeProperties.containerEl;
}
}
//See if this view already exists
if (!isNew && container && 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 this person type is not on the page yet, add it.
// For now, this only adds the first role if person has multiple roles.
if (!container || !container.length) {
container = this.addNewPersonType(partyType);
}
//If there still is no partyView found, create a new one
var partyView = new EMLPartyView({
model: emlParty,
edit: this.edit,
isNew: isNew,
});
if (isNew) {
container.append(partyView.render().el);
} else {
if (container.find(".new").length)
container.find(".new").before(partyView.render().el);
else container.append(partyView.render().el);
}
},
this,
);
},
/*
* This function reacts to the user typing a new person in the person section (an EMLPartyView)
*/
handlePersonTyping: function (e) {
var container = $(e.target).parents(".eml-party"),
emlParty = container.length ? container.data("model") : null,
partyType =
container.length && emlParty
? emlParty.get("roles")[0] || emlParty.get("type")
: null;
(partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
})),
(numPartyForms = this.$(
"[data-attribute='" + partyType + "'] .eml-party",
).length),
(numNewPartyForms = this.$(
"[data-attribute='" + partyType + "'] .eml-party.new",
).length);
// If there is already a form to enter a new party for this party type, don't add another one
if (numNewPartyForms > 1) return;
// If there is a limit to how many party types can be added for this type,
// don't add more forms than is allowed
if (partyTypeProperties && partyTypeProperties.limit) {
return;
}
// Render a form to enter information for a new person
this.renderPerson(null, partyType);
},
/*
* This function is called when someone chooses a new person type from the dropdown list
*/
chooseNewPersonType: function (e) {
var partyType = $(e.target).val();
if (!partyType) return;
//Get the form and model
var partyForm = this.newPartyContainer,
partyModel = partyForm.find(".eml-party").data("model").clone(),
partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
});
// Remove this type from the dropdown menu
this.partyMenu.find("[value='" + partyType + "']").remove();
if (!partyModel.isEmpty()) {
//Update the model
if (partyTypeProperties.isAssociatedParty) {
var newRoles = _.clone(partyModel.get("roles"));
newRoles.push(partyType);
partyModel.set("roles", newRoles);
} else {
partyModel.set("type", partyType);
}
if (partyModel.isValid()) {
partyModel.mergeIntoParent();
// Add the person of that type (a section will be added if required)
this.renderPerson(partyModel, partyType);
// Clear and re-render the new person form
partyForm.empty();
this.renderPerson(null, "new");
} else {
partyForm.find(".eml-party").data("view").showValidation();
}
} else {
this.addNewPersonType(partyType);
}
},
/*
* addNewPersonType - Adds a header and container to the People section for the given party type/role,
* @return {JQuery} Returns the HTML element that contains each rendered EML Party for the given party type.
*/
addNewPersonType: function (partyType) {
if (!partyType) return;
var partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: partyType,
});
if (!partyTypeProperties) {
return;
}
// If there is already a view for this person type, don't re-add it.
if (partyTypeProperties.containerEl) {
return;
}
// Container element to hold all parties of this type
var outerContainer = $(document.createElement("div")).addClass(
"party-type-container",
);
// Add a new header for the party type,
// plus an icon and spot for validation messages
var header = $(document.createElement("h4"))
.text(partyTypeProperties.label)
.append(
"<i class='required-icon hidden' data-category='" +
partyType +
"'></i>",
);
outerContainer.append(header);
// If there is a description, add that to the container as well
if (partyTypeProperties.description) {
outerContainer.append(
'<p class="subtle">' + partyTypeProperties.description + "</p>",
);
}
//Remove this type from the dropdown menu
this.partyMenu.find("[value='" + partyType + "']").remove();
//Add the new party container
partyTypeProperties.containerEl = $(document.createElement("div"))
.attr("data-attribute", partyType)
.attr("data-category", partyType)
.addClass("row-striped");
let notification = document.createElement("p");
notification.className = "notification";
notification.setAttribute("data-category", partyType);
partyTypeProperties.containerEl.append(notification);
outerContainer.append(partyTypeProperties.containerEl);
// Add in the new party type container just before the dropdown
this.partyMenu.before(outerContainer);
// Add a blank form to the new person type section, unless the max number
// for this party type has already been reached (e.g. when a new person type
// is added after copying from another type)
if (
typeof partyTypeProperties.limit !== "number" ||
this.model.getPartiesByType(partyType).length <
partyTypeProperties.limit
) {
this.renderPerson(null, partyType);
}
return partyTypeProperties.containerEl;
},
/*
* 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 currentRoles = partyToCopy.get("roles");
if (!currentRoles || !currentRoles.length) {
currentRoles = partyToCopy.get("type");
}
// "type" is a string and "roles" is an array.
// so that we can use _.each() on both, convert "type" to an array
if (typeof currentRoles === "string") {
currentRoles = [currentRoles];
}
_.each(
currentRoles,
function (currentRole) {
var partyTypeProperties = _.findWhere(
EMLParty.prototype.partyTypes,
{ dataCategory: currentRole },
),
label = partyTypeProperties ? partyTypeProperties.label : "";
menu
.find("input[value='" + currentRole + "']")
.prop("disabled", "disabled")
.addClass("disabled")
.parent(".checkbox")
.attr(
"title",
"This person is already in the " + label + " list.",
);
},
this,
);
// If the maximum number of parties has already been for this party type,
// then don't allow adding more.
var partiesWithLimits = _.filter(
EMLParty.prototype.partyTypes,
function (partyType) {
return typeof partyType.limit === "number";
},
);
partiesWithLimits.forEach(function (partyType) {
// See how many parties already exist for this type
var existingParties = this.model.getPartiesByType(
partyType.dataCategory,
);
if (
existingParties &&
existingParties.length &&
existingParties.length >= partyType.limit
) {
var names = _.map(existingParties, function (partyModel) {
var name = partyModel.getName();
if (name) {
return name;
} else {
return "Someone";
}
});
var sep = names.length === 2 ? " and " : ", ",
beVerbNames = names.length > 1 ? "are" : "is",
beVerbLimit = partyType.limit > 1 ? "are" : "is",
title =
names.join(sep) +
" " +
beVerbNames +
" already listed as " +
partyType.dataCategory +
". (Only " +
partyType.limit +
" " +
beVerbLimit +
" is allowed.)";
menu
.find("input[value='" + partyType.dataCategory + "']")
.prop("disabled", "disabled")
.addClass("disabled")
.parent(".checkbox")
.attr("title", title);
}
}, this);
//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(),
partyTypeProperties = _.findWhere(EMLParty.prototype.partyTypes, {
dataCategory: role,
});
//Create a new EMLParty model
var newPerson = new EMLParty();
// Copy the attributes from the original person
// and set it on the new person
newPerson.set(partyToCopy.copyValues());
//If the new role is an associated party ...
if (partyTypeProperties.isAssociatedParty) {
newPerson.set("type", "associatedParty");
newPerson.set("roles", [role]);
}
//If the new role is not an associated party...
else {
newPerson.set("type", role);
newPerson.set("roles", newPerson.defaults().role);
}
//Add this new EMLParty to the EML model
this.model.addParty(newPerson);
// Add a view for the copied person
this.renderPerson(newPerson);
},
this,
);
//If there was at least one copy created, then trigger the change event
if (checkedBoxes.length) {
this.model.trickleUpChange();
}
},
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();
},
/**
* Attempt to move the current person (Party) one index backward (up).
*
* @param {EventHandler} e: The click event handler
*/
movePersonUp: function (e) {
e.preventDefault();
// Get the party view el, view, and model
var partyEl = $(e.target).parents(".eml-party"),
model = partyEl.data("model"),
next = $(partyEl).prev().not(".new");
if (next.length === 0) {
return;
}
// Remove current view, create and insert a new one for the model
$(partyEl).remove();
var newView = new EMLPartyView({
model: model,
edit: this.edit,
});
$(next).before(newView.render().el);
// Move the party down within the model too
this.model.movePartyUp(model);
this.model.trickleUpChange();
},
/**
* Attempt to move the current person (Party) one index forward (down).
*
* @param {EventHandler} e: The click event handler
*/
movePersonDown: function (e) {
e.preventDefault();
// Get the party view el, view, and model
var partyEl = $(e.target).parents(".eml-party"),
model = partyEl.data("model"),
next = $(partyEl).next().not(".new");
if (next.length === 0) {
return;
}
// Remove current view, create and insert a new one for the model
$(partyEl).remove();
var newView = new EMLPartyView({
model: model,
edit: this.edit,
});
$(next).after(newView.render().el);
// Move the party down within the model too
this.model.movePartyDown(model);
this.model.trickleUpChange();
},
/*
* Renders the Dates section of the page
*/
renderDates: function () {
//Add a header
this.$(".section.dates").html(
$(document.createElement("h2")).text("Dates"),
);
_.each(
this.model.get("temporalCoverage"),
function (model) {
var tempCovView = new EMLTempCoverageView({
model: model,
isNew: false,
edit: this.edit,
});
tempCovView.render();
this.$(".section.dates").append(tempCovView.el);
},
this,
);
if (!this.model.get("temporalCoverage").length) {
var tempCovView = new EMLTempCoverageView({
isNew: true,
edit: this.edit,
model: new EMLTemporalCoverage({ parentModel: this.model }),
});
tempCovView.render();
this.$(".section.dates").append(tempCovView.el);
}
},
/*
* Renders the Locations section of the page
*/
renderLocations: function () {
var locationsSection = this.$(".section.locations");
//Add the Locations header
locationsSection.html(this.locationsTemplate());
var locationsTable = locationsSection.find(".locations-table");
//Render an EMLGeoCoverage view for each EMLGeoCoverage model
_.each(
this.model.get("geoCoverage"),
function (geo, i) {
//Create an EMLGeoCoverageView
var geoView = new EMLGeoCoverageView({
model: geo,
edit: this.edit,
});
//Render the view
geoView.render();
geoView.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Add the locations section to the page
locationsTable.append(geoView.el);
//Listen to validation events
this.listenTo(geo, "valid", this.updateLocationsError);
//Save it in our subviews array
this.subviews.push(geoView);
},
this,
);
//Now add one empty row to enter a new geo coverage
if (this.edit) {
var newGeoModel = new EMLGeoCoverage({
parentModel: this.model,
isNew: true,
}),
newGeoView = new EMLGeoCoverageView({
edit: true,
model: newGeoModel,
isNew: true,
});
locationsTable.append(newGeoView.render().el);
newGeoView.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Listen to validation events
this.listenTo(newGeoModel, "valid", this.updateLocationsError);
}
},
/*
* Renders the Taxa section of the page
*/
renderTaxa: function () {
const view = this;
const taxaSectionEl = this.$(".section.taxa");
if (!taxaSectionEl) return;
taxaSectionEl.html($(document.createElement("h2")).text("Taxa"));
var taxonomy = this.model.get("taxonCoverage");
// Render a set of tables for each taxonomicCoverage
if (
typeof taxonomy !== "undefined" &&
Array.isArray(taxonomy) &&
taxonomy.length
) {
for (var i = 0; i < taxonomy.length; i++) {
taxaSectionEl.append(this.createTaxonomicCoverage(taxonomy[i]));
}
} else {
// Create a new one
var taxonCov = new EMLTaxonCoverage({
parentModel: this.model,
});
this.model.set("taxonCoverage", [taxonCov], { silent: true });
taxaSectionEl.append(this.createTaxonomicCoverage(taxonCov));
}
// updating the indexes of taxa-tables before rendering the information on page(view).
var taxaNums = this.$(".editor-header-index");
for (var i = 0; i < taxaNums.length; i++) {
$(taxaNums[i]).text(i + 1);
}
// Insert the quick-add taxon options, if any are configured for this
// theme. See {@link AppModel#quickAddTaxa}
view.renderTaxaQuickAdd();
// If duplicates are removed while saving, make sure to re-render the taxa
view.model.get("taxonCoverage").forEach(function (taxonCov) {
view.model.stopListening(taxonCov);
view.model.listenTo(
taxonCov,
"duplicateClassificationsRemoved",
function () {
view.renderTaxa();
},
);
}, view);
},
/*
* Renders the Methods section of the page
*/
renderMethods: function () {
var methodsModel = this.model.get("methods");
if (!methodsModel) {
methodsModel = new EMLMethods({
edit: this.edit,
parentModel: this.model,
});
}
this.$(".section.methods").html(
new EMLMethodsView({
model: methodsModel,
edit: this.edit,
parentEMLView: this,
}).render().el,
);
},
/*
* Renders the Projcet section of the page
*/
renderProject: function () {},
/*
* Renders the Sharing section of the page
*/
renderSharing: function () {},
/*
* Renders the funding field of the EML
*/
renderFunding: function () {
//Funding
var funding = this.model.get("project")
? this.model.get("project").get("funding")
: [];
//Clear the funding section
$(".section.overview .funding").empty();
//Create the funding input elements
_.each(
funding,
function (fundingItem, i) {
this.addFunding(fundingItem);
},
this,
);
//Add a blank funding input
this.addFunding();
},
/*
* Adds a single funding input row. Can either be called directly or used as an event callback
*/
addFunding: function (argument) {
if (this.edit) {
if (typeof argument == "string") var value = argument;
else if (!argument) var value = "";
//Don't add another new funding input if there already is one
else if (
!value &&
typeof argument == "object" &&
!$(argument.target).is(".new")
)
return;
else if (typeof argument == "object" && argument.target) {
var event = argument;
// Don't add a new funding row if the current one is empty
if ($(event.target).val().trim() === "") return;
}
var fundingInput = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", "funding")
.addClass("span12 funding hover-autocomplete-target")
.attr(
"placeholder",
"Search for NSF awards by keyword or enter custom funding information",
)
.val(value),
hiddenFundingInput = fundingInput
.clone()
.attr("type", "hidden")
.val(value)
.attr("id", "")
.addClass("hidden"),
loadingSpinner = $(document.createElement("i")).addClass(
"icon icon-spinner input-icon icon-spin subtle hidden",
);
//Append all the elements to a container
var containerEl = $(document.createElement("div"))
.addClass("ui-autocomplete-container funding-row")
.append(fundingInput, loadingSpinner, hiddenFundingInput);
if (!value) {
$(fundingInput).addClass("new");
if (event) {
$(event.target)
.parents("div.funding-row")
.append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
$(event.target).removeClass("new");
}
} else {
// Add a remove button if this is a non-new funding element
$(containerEl).append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
}
var view = this;
//Setup the autocomplete widget for the funding input
fundingInput.autocomplete({
source: function (request, response) {
var beforeRequest = function () {
loadingSpinner.show();
};
var afterRequest = function () {
loadingSpinner.hide();
};
return MetacatUI.appLookupModel.getGrantAutocomplete(
request,
response,
beforeRequest,
afterRequest,
);
},
select: function (e, ui) {
e.preventDefault();
var value =
"NSF Award " + ui.item.value + " (" + ui.item.label + ")";
hiddenFundingInput.val(value);
fundingInput.val(value);
$(".funding .ui-helper-hidden-accessible").hide();
view.updateFunding(e);
},
position: {
my: "left top",
at: "left bottom",
of: fundingInput,
collision: "fit",
},
appendTo: containerEl,
minLength: 3,
});
this.$(".funding-container").append(containerEl);
}
},
previewFundingRemove: function (e) {
$(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.$("[data-category='funding'] .notification")
.removeClass("error")
.text("");
}
},
addKeyword: function (keyword, thesaurus) {
if (typeof keyword != "string" || !keyword) {
var keyword = "";
//Only show one new keyword row at a time
if (
this.$(".keyword.new").length == 1 &&
!this.$(".keyword.new").val()
)
return;
else if (this.$(".keyword.new").length > 1) return;
}
//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",
),
thesOptionExists = false,
removeButton;
// Piece together the inputs
row.append(keywordInput, thesInput);
//Create the thesaurus options dropdown menu
_.each(MetacatUI.appModel.get("emlKeywordThesauri"), function (option) {
var optionEl = $(document.createElement("option"))
.val(option.thesaurus)
.text(option.label);
thesInput.append(optionEl);
if (option.thesaurus == thesaurus) {
optionEl.prop("selected", true);
thesOptionExists = true;
}
});
//Add a "None" option, which is always in the dropdown
thesInput.prepend(
$(document.createElement("option")).val("None").text("None"),
);
if (thesaurus == "None" || !thesaurus) {
thesInput.val("None");
}
//If this keyword is from a custom thesaurus that is NOT configured in this App, AND
// there is an option with the same label, then remove the option so it doesn't look like a duplicate.
else if (
!thesOptionExists &&
_.findWhere(MetacatUI.appModel.get("emlKeywordThesauri"), {
label: thesaurus,
})
) {
var duplicateOptions = thesInput.find(
"option:contains(" + thesaurus + ")",
);
duplicateOptions.each(function (i, option) {
if ($(option).text() == thesaurus && !$(option).prop("selected")) {
$(option).remove();
}
});
}
//If this keyword is from a custom thesaurus that is NOT configured in this App, then show it as a custom option
else if (!thesOptionExists) {
thesInput.append(
$(document.createElement("option"))
.val(thesaurus)
.text(thesaurus)
.prop("selected", true),
);
}
if (!keyword) row.addClass("new");
else {
//Set the keyword value on the text input
keywordInput.val(keyword);
// Add a remove button unless this is the .new keyword
row.append(
this.createRemoveButton(
null,
"keywordSets",
"div.keyword-row",
"div.keywords",
),
);
}
this.$(".keywords").append(row);
},
addNewKeyword: function (e) {
if ($(e.target).val().trim() === "") return;
$(e.target).parents(".keyword-row").first().removeClass("new");
// Add in a remove button
$(e.target)
.parents(".keyword-row")
.append(
this.createRemoveButton(
null,
"keywordSets",
"div.keyword-row",
"div.keywords",
),
);
var row = $(document.createElement("div"))
.addClass("row-fluid keyword-row new")
.data({ model: new EMLKeywordSet() }),
keywordInput = $(document.createElement("input"))
.attr("type", "text")
.addClass("keyword span10"),
thesInput = $(document.createElement("select")).addClass(
"thesaurus span2",
);
row.append(keywordInput, thesInput);
//Create the thesaurus options dropdown menu
_.each(MetacatUI.appModel.get("emlKeywordThesauri"), function (option) {
thesInput.append(
$(document.createElement("option"))
.val(option.thesaurus)
.text(option.label),
);
});
//Add a "None" option, which is always in the dropdown
thesInput.prepend(
$(document.createElement("option"))
.val("None")
.text("None")
.prop("selected", true),
);
this.$(".keywords").append(row);
},
previewKeywordRemove: function (e) {
var row = $(e.target)
.parents(".keyword-row")
.toggleClass("remove-preview");
},
/*
* Update the funding info when the form is changed
*/
updateFunding: function (e) {
if (!e) return;
var row = $(e.target).parent(".funding-row").first(),
rowNum = this.$(".funding-row").index(row),
input = $(row).find("input"),
isNew = $(row).is(".new");
var newValue = isNew
? $(e.target).siblings("input.hidden").val()
: $(e.target).val();
newValue = this.model.cleanXMLText(newValue);
if (typeof newValue == "string") {
newValue = newValue.trim();
}
//If there is no project model
if (!this.model.get("project")) {
var model = new EMLProject({ parentModel: this.model });
this.model.set("project", model);
} else var model = this.model.get("project");
var currentFundingValues = model.get("funding");
//If the new value is an empty string, then remove that index in the array
if (typeof newValue == "string" && newValue.trim().length == 0) {
currentFundingValues = currentFundingValues.splice(rowNum, 1);
} else {
currentFundingValues[rowNum] = newValue;
}
if (isNew && newValue != "") {
$(row).removeClass("new");
// Add in a remove button
$(e.target)
.parent()
.append(
this.createRemoveButton(
"project",
"funding",
".funding-row",
"div.funding-container",
),
);
this.addFunding();
}
this.model.trickleUpChange();
},
//TODO: Comma and semi-colon separate keywords
updateKeywords: function (e) {
var keywordSets = this.model.get("keywordSets"),
newKeywordSets = [];
//Get all the keywords in the view
_.each(
this.$(".keyword-row"),
function (thisRow) {
var thesaurus = this.model.cleanXMLText(
$(thisRow).find("select").val(),
),
keyword = this.model.cleanXMLText($(thisRow).find("input").val());
if (!keyword) return;
var keywordSet = _.find(newKeywordSets, function (keywordSet) {
return keywordSet.get("thesaurus") == thesaurus;
});
if (typeof keywordSet != "undefined") {
keywordSet.get("keywords").push(keyword);
} else {
newKeywordSets.push(
new EMLKeywordSet({
parentModel: this.model,
keywords: [keyword],
thesaurus: thesaurus,
}),
);
}
},
this,
);
//Update the EML model
this.model.set("keywordSets", newKeywordSets);
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();
}
}
},
/*
* Update the EML Geo Coverage models and views when the user interacts with the locations section
*/
updateLocations: function (e) {
if (!e) return;
e.preventDefault();
var viewEl = $(e.target).parents(".eml-geocoverage"),
geoCovModel = viewEl.data("model");
//If the EMLGeoCoverage is new
if (viewEl.is(".new")) {
if (this.$(".eml-geocoverage.new").length > 1) return;
//Render the new geo coverage view
var newGeo = new EMLGeoCoverageView({
edit: this.edit,
model: new EMLGeoCoverage({ parentModel: this.model, isNew: true }),
isNew: true,
});
this.$(".locations-table").append(newGeo.render().el);
newGeo.$el
.find(".remove-container")
.append(
this.createRemoveButton(
null,
"geoCoverage",
".eml-geocoverage",
".locations-table",
),
);
//Unmark the view as new
viewEl.data("view").notNew();
//Get the EMLGeoCoverage model attached to this EMlGeoCoverageView
var geoModel = viewEl.data("model"),
//Get the current EMLGeoCoverage models set on the parent EML model
currentCoverages = this.model.get("geoCoverage");
//Add this new geo coverage model to the parent EML model
if (Array.isArray(currentCoverages)) {
if (!_.contains(currentCoverages, geoModel)) {
currentCoverages.push(geoModel);
this.model.trigger("change:geoCoverage");
}
} else {
currentCoverages = [currentCoverages, geoModel];
this.model.set("geoCoverage", currentCoverages);
}
}
},
/*
* If all the EMLGeoCoverage models are valid, remove the error messages for the Locations section
*/
updateLocationsError: function () {
var allValid = _.every(
this.model.get("geoCoverage"),
function (geoCoverageModel) {
return geoCoverageModel.isValid();
},
);
if (allValid) {
this.$(".side-nav-item.error[data-category='geoCoverage']")
.removeClass("error")
.find(".icon.error")
.hide();
this.$(".section[data-section='locations'] .notification.error")
.removeClass("error")
.text("");
}
},
/*
* Creates the text elements
*/
createEMLText: function (textModel, edit, category) {
if (!textModel && edit) {
return $(document.createElement("textarea"))
.attr("data-category", category)
.addClass("xlarge text");
} else if (!textModel && !edit) {
return $(document.createElement("div")).attr(
"data-category",
category,
);
}
//Get the EMLText from the EML model
var finishedEl;
//Get the text attribute from the EMLText model
var paragraphs = textModel.get("text"),
paragraphsString = "";
//If the text should be editable,
if (edit) {
//Format the paragraphs with carriage returns between paragraphs
paragraphsString = paragraphs.join(String.fromCharCode(13));
//Create the textarea element
finishedEl = $(document.createElement("textarea"))
.addClass("xlarge text")
.attr("data-category", category)
.html(paragraphsString);
} else {
//Format the paragraphs with HTML
_.each(paragraphs, function (p) {
paragraphsString += "<p>" + p + "</p>";
});
//Create a div
finishedEl = $(document.createElement("div"))
.attr("data-category", category)
.append(paragraphsString);
}
$(finishedEl).data({ model: textModel });
//Return the finished DOM element
return finishedEl;
},
/*
* Updates a basic text field in the EML after the user changes the value
*/
updateText: function (e) {
if (!e) return false;
var category = $(e.target).attr("data-category"),
currentValue = this.model.get(category),
textModel = $(e.target).data("model"),
value = this.model.cleanXMLText($(e.target).val());
//We can't update anything without a category
if (!category) return false;
//Get the list of paragraphs - checking for carriage returns and line feeds
var paragraphsCR = value.split(String.fromCharCode(13));
var paragraphsLF = value.split(String.fromCharCode(10));
//Use the paragraph list that has the most
var paragraphs =
paragraphsCR > paragraphsLF ? paragraphsCR : paragraphsLF;
//If this category isn't set yet, then create a new EMLText model
if (!textModel) {
//Get the current value for this category and create a new EMLText model
var newTextModel = new EMLText({
text: paragraphs,
parentModel: this.model,
});
// Save the new model onto the underlying DOM node
$(e.target).data({ model: newTextModel });
//Set the new EMLText model on the EML model
if (Array.isArray(currentValue)) {
currentValue.push(newTextModel);
this.model.trigger("change:" + category);
this.model.trigger("change");
} else {
this.model.set(category, newTextModel);
}
}
//Update the existing EMLText model
else {
//If there are no paragraphs or all the paragraphs are empty...
if (
!paragraphs.length ||
_.every(paragraphs, function (p) {
return p.trim() == "";
})
) {
//Remove this text model from the array of text models since it is empty
var newValue = _.without(currentValue, textModel);
this.model.set(category, newValue);
} else {
textModel.set("text", paragraphs);
textModel.trigger("change:text");
//Is this text model set on the EML model?
if (
Array.isArray(currentValue) &&
!_.contains(currentValue, textModel)
) {
//Push this text model into the array of EMLText models
currentValue.push(textModel);
this.model.trigger("change:" + category);
this.model.trigger("change");
}
}
}
},
/*
* Creates and returns an array of basic text input field for editing
*/
createBasicTextFields: function (category, placeholder) {
var textContainer = $(document.createElement("div")).addClass(
"text-container",
),
modelValues = this.model.get(category),
textRow; // Holds the DOM for each field
//Format as an array
if (!Array.isArray(modelValues) && modelValues)
modelValues = [modelValues];
//For each value in this category, create an HTML element with the value inserted
_.each(
modelValues,
function (value, i, allModelValues) {
if (this.edit) {
var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");
textRow.append(input.clone().val(value));
if (category !== "title" && category !== "canonicalDataset")
textRow.append(
this.createRemoveButton(
null,
category,
"div.basic-text-row",
"div.text-container",
),
);
textContainer.append(textRow);
//At the end, append an empty input for the user to add a new one
if (
i + 1 == allModelValues.length &&
category !== "title" &&
category !== "canonicalDataset"
) {
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);
}
} else {
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.attr("data-category", category)
.text(value),
);
}
},
this,
);
if ((!modelValues || !modelValues.length) && this.edit) {
var input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text new")
.attr("placeholder", placeholder || "Add a new " + category);
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.append(input),
);
}
return textContainer;
},
updateBasicText: function (e) {
if (!e) return false;
//Get the category, new value, and model
var category = $(e.target).attr("data-category"),
value = this.model.cleanXMLText($(e.target).val()),
model = $(e.target).data("model") || this.model;
//We can't update anything without a category
if (!category) return false;
//Get the current value
var currentValue = model.get(category);
//Insert the new value into the array
if (Array.isArray(currentValue)) {
//Find the position this text input is in
var position = $(e.target)
.parents("div.text-container")
.first()
.children("div")
.index($(e.target).parent());
//Set the value in that position in the array
currentValue[position] = value;
//Set the changed array on this model
model.set(category, currentValue);
model.trigger("change:" + category);
}
//Update the model if the current value is a string
else if (typeof currentValue == "string") {
model.set(category, [value]);
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 != "" &&
category != "title" &&
category !== "canonicalDataset"
) {
$(e.target).removeClass("new");
this.addBasicText(e);
}
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/* One-off handler for updating pubDate on the model when the form
input changes. Fairly similar but just a pared down version of
updateBasicText. */
updatePubDate: function (e) {
if (!e) return false;
this.model.set("pubDate", $(e.target).val().trim());
this.model.trigger("change");
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},
/*
* Adds a basic text input
*/
addBasicText: function (e) {
var category = $(e.target).attr("data-category"),
allBasicTexts = $(
".basic-text.new[data-category='" + category + "']",
);
//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" || category === "canonicalDataset")
return;
//Add another blank text input
var newRow = $(document.createElement("div")).addClass(
"basic-text-row",
);
newRow.append(
$(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.attr("placeholder", $(e.target).attr("placeholder"))
.addClass("new basic-text"),
);
$(e.target).parent().after(newRow);
$(e.target).after(
this.createRemoveButton(
null,
category,
".basic-text-row",
"div.text-container",
),
);
},
previewTextRemove: function (e) {
$(e.target).parents(".basic-text-row").toggleClass("remove-preview");
},
// publication date validation.
isDateFormatValid: function (dateString) {
//Date strings that are four characters should be a full year. Make sure all characters are numbers
if (dateString.length == 4) {
var digits = dateString.match(/[0-9]/g);
return digits.length == 4;
}
//Date strings that are 10 characters long should be a valid date
else {
var dateParts = dateString.split("-");
if (
dateParts.length != 3 ||
dateParts[0].length != 4 ||
dateParts[1].length != 2 ||
dateParts[2].length != 2
)
return false;
dateYear = dateParts[0];
dateMonth = dateParts[1];
dateDay = dateParts[2];
// Validating the values for the date and month if in YYYY-MM-DD format.
if (dateMonth < 1 || dateMonth > 12) return false;
else if (dateDay < 1 || dateDay > 31) return false;
else if (
(dateMonth == 4 ||
dateMonth == 6 ||
dateMonth == 9 ||
dateMonth == 11) &&
dateDay == 31
)
return false;
else if (dateMonth == 2) {
// Validation for leap year dates.
var isleap =
dateYear % 4 == 0 && (dateYear % 100 != 0 || dateYear % 400 == 0);
if (dateDay > 29 || (dateDay == 29 && !isleap)) return false;
}
var digits = _.filter(dateParts, function (part) {
return part.match(/[0-9]/g).length == part.length;
});
return digits.length == 3;
}
},
/* Event handler for showing validation messaging for the pubDate input
which has to conform to the EML yearDate type (YYYY or YYYY-MM-DD) */
showPubDateValidation: function (e) {
var container = $(e.target).parents(".pubDate").first(),
input = $(e.target),
messageEl = $(container).find(".notification"),
value = input.val(),
errors = [];
// Remove existing error borders and notifications
input.removeClass("error");
messageEl.text("");
messageEl.removeClass("error");
if (value != "" && value.length > 0) {
if (!this.isDateFormatValid(value)) {
errors.push(
"The value entered for publication date, '" +
value +
"' is not a valid value for this field. Enter either a year (e.g. 2017) or a date in the format YYYY-MM-DD.",
);
input.addClass("error");
}
}
if (errors.length > 0) {
messageEl.text(errors[0]).addClass("error");
}
},
// Creates a table to hold a single EMLTaxonCoverage element (table) for
// each root-level taxonomicClassification
createTaxonomicCoverage: function (coverage) {
var finishedEls = $(
this.taxonomicCoverageTemplate({
generalTaxonomicCoverage:
coverage.get("generalTaxonomicCoverage") || "",
}),
),
coverageEl = finishedEls.filter(".taxonomic-coverage");
coverageEl.data({ model: coverage });
var classifications = coverage.get("taxonomicClassification");
// Makes a table... for the root level
for (var i = 0; i < classifications.length; i++) {
coverageEl.append(
this.createTaxonomicClassificationTable(classifications[i]),
);
}
// Create a new, blank table for another taxonomicClassification
var newTableEl = this.createTaxonomicClassificationTable();
coverageEl.append(newTableEl);
return finishedEls;
},
createTaxonomicClassificationTable: function (classification) {
// updating the taxonomic table indexes before adding a new table to the page.
var taxaNums = this.$(".editor-header-index");
for (var i = 0; i < taxaNums.length; i++) {
$(taxaNums[i]).text(i + 1);
}
// Adding the taxoSpeciesCounter to the table header for enhancement of the view
var finishedEl = $(
'<div class="row-striped root-taxonomic-classification-container"></div>',
);
$(finishedEl).append(
'<h6>Species <span class="editor-header-index">' +
(taxaNums.length + 1) +
"</span> </h6>",
);
// Add a remove button if this is not a new table
if (!(typeof classification === "undefined")) {
$(finishedEl).append(
this.createRemoveButton(
"taxonCoverage",
"taxonomicClassification",
".root-taxonomic-classification-container",
".taxonomic-coverage",
),
);
}
var tableEl = $(this.taxonomicClassificationTableTemplate());
var tableBodyEl = $(document.createElement("tbody"));
var queue = [classification],
rows = [],
cur;
while (queue.length > 0) {
cur = queue.pop();
// I threw this in here so I can this function without an
// argument to generate a new table from scratch
if (typeof cur === "undefined") {
continue;
}
cur.taxonRankName = cur.taxonRankName?.toLowerCase();
rows.push(cur);
if (cur.taxonomicClassification) {
for (var i = 0; i < cur.taxonomicClassification.length; i++) {
queue.push(cur.taxonomicClassification[i]);
}
}
}
for (var j = 0; j < rows.length; j++) {
tableBodyEl.append(this.makeTaxonomicClassificationRow(rows[j]));
}
var newRowEl = this.makeNewTaxonomicClassificationRow();
$(tableBodyEl).append(newRowEl);
$(tableEl).append(tableBodyEl);
// Add the new class to the entire table if it's a new one
if (typeof classification === "undefined") {
$(tableEl).addClass("new");
}
$(finishedEl).append(tableEl);
return finishedEl;
},
/**
* Create the HTML for a single row in a taxonomicClassification table
* @param {EMLTaxonCoverage#taxonomicClassification} classification A
* classification object from an EMLTaxonCoverage model, may include
* a taxonRank, taxonValue, taxonId, commonName, and nested
* taxonomicClassification objects
* @returns {jQuery} A jQuery object containing the HTML for a single
* row in a taxonomicClassification table
* @since 2.24.0
*/
makeTaxonomicClassificationRow: function (classification) {
try {
if (!classification) classification = {};
var finishedEl = $(
this.taxonomicClassificationRowTemplate({
taxonRankName: classification.taxonRankName || "",
taxonRankValue: classification.taxonRankValue || "",
}),
);
// Save a reference to other taxon attributes that we need to keep
// when serializing the model
if (classification.taxonId) {
$(finishedEl).data("taxonId", classification.taxonId);
}
if (classification.commonName) {
$(finishedEl).data("commonName", classification.commonName);
}
return finishedEl;
} catch (e) {
console.log("Error making taxonomic classification row: ", e);
}
},
/**
* Create the HTML for a new row in a taxonomicClassification table
* @returns {jQuery} A jQuery object containing the HTML for a new row
* in a taxonomicClassification table
* @since 2.24.0
*/
makeNewTaxonomicClassificationRow: function () {
const row = this.makeTaxonomicClassificationRow({});
$(row).addClass("new");
return row;
},
/* Update the underlying model and DOM for an EML TaxonomicCoverage
section. This method handles updating the underlying TaxonomicCoverage
models when the user changes form fields as well as inserting new
form fields automatically when the user needs them.
Since a dataset has multiple TaxonomicCoverage elements at the dataset
level, each Taxonomic Coverage is represented by a table element and
all taxonomicClassifications within are rows in that table.
TODO: Finish this function
TODO: Link this function into the DOM
*/
updateTaxonCoverage: function (options) {
if (options.target) {
// Ignore the event if the target is a quick add taxon UI element.
const quickAddEl = $(this.taxonQuickAddEl);
if (quickAddEl && quickAddEl.has(options.target).length) {
return;
}
var e = options;
/* Getting `model` here is different than in other places because
the thing being updated is an `input` or `select` element which
is part of a `taxonomicClassification`. The model is
`TaxonCoverage` which has one or more
`taxonomicClassifications`. So we have to walk up to the
hierarchy from input < td < tr < tbody < table < div to get at
the underlying TaxonCoverage model.
*/
var coverage = $(e.target).parents(".taxonomic-coverage"),
classificationEl = $(e.target).parents(
".root-taxonomic-classification",
),
model = $(coverage).data("model") || this.model,
category = $(e.target).attr("data-category"),
value = this.model.cleanXMLText($(e.target).val());
//We can't update anything without a coverage, or
//classification
if (!coverage) return false;
if (!classificationEl) return false;
// Use `category` to determine if we're updating the generalTaxonomicCoverage or
// the taxonomicClassification
if (category && category === "generalTaxonomicCoverage") {
model.set("generalTaxonomicCoverage", value);
return;
}
} else {
var coverage = options.coverage,
model = $(coverage).data("model");
}
// Find all of the root-level taxonomicClassifications
var classificationTables = $(coverage).find(
".root-taxonomic-classification",
);
if (!classificationTables) return false;
//TODO :This should probably (at least) be in its own View and
//definitely refactored into tidy functions.*/
var rows,
collectedClassifications = [];
for (var i = 0; i < classificationTables.length; i++) {
rows = $(classificationTables[i]).find("tbody tr");
if (!rows) continue;
var topLevelClassification = {},
classification = topLevelClassification,
currentRank,
currentValue;
for (var j = 0; j < rows.length; j++) {
const thisRow = rows[j];
currentRank =
this.model.cleanXMLText($(thisRow).find("select").val()) || "";
currentValue =
this.model.cleanXMLText($(thisRow).find("input").val()) || "";
// Maintain classification attributes that exist in the EML but are not visible in the editor
const taxonId = $(thisRow).data("taxonId");
const commonName = $(thisRow).data("commonName");
// Skip over rows with empty Rank or Value
if (!currentRank.length || !currentValue.length) {
continue;
}
//After the first row, start nesting taxonomicClassification objects
if (j > 0) {
classification.taxonomicClassification = [{}];
classification = classification.taxonomicClassification[0];
}
// Add it to the classification object
classification.taxonRankName = currentRank;
classification.taxonRankValue = currentValue;
classification.taxonId = taxonId;
classification.commonName = commonName;
}
//Add the top level classification to the array
if (Object.keys(topLevelClassification).length)
collectedClassifications.push(topLevelClassification);
}
if (
!_.isEqual(
collectedClassifications,
model.get("taxonomicClassification"),
)
) {
model.set("taxonomicClassification", collectedClassifications);
this.model.trigger("change");
}
// Handle adding new tables and rows
// Do nothing if the value isn't set
if (value) {
// Add a new row if this is itself a new row
if ($(e.target).parents("tr").first().is(".new")) {
var newRowEl = this.makeNewTaxonomicClassificationRow();
$(e.target).parents("tbody").first().append(newRowEl);
$(e.target).parents("tr").first().removeClass("new");
}
// Add a new classification table if this is itself a new table
if ($(classificationEl).is(".new")) {
$(classificationEl).removeClass("new");
$(classificationEl).append(
this.createRemoveButton(
"taxonCoverage",
"taxonomicClassification",
".root-taxonomic-classification-container",
".taxonomic-coverage",
),
);
$(coverage).append(this.createTaxonomicClassificationTable());
}
}
// update the quick add interface
this.updateQuickAddTaxa();
},
/**
* Update the options for the quick add taxon select interface. This
* ensures that only taxonomic classifications that are not already
* included in the taxonomic coverage are available for selection.
* @since 2.24.0
*/
updateQuickAddTaxa: function () {
const selects = this.taxonSelects;
if (!selects || !selects.length) return;
const taxa = this.getTaxonQuickAddOptions();
if (!taxa || !taxa.length) return;
selects.forEach((select, i) => {
select.updateOptions(taxa[i].options);
});
},
/*
* Adds a new row and/or table to the taxonomic coverage section
*/
addNewTaxon: function (e) {
// Don't do anything if the current classification doesn't have new content
if ($(e.target).val().trim() === "") return;
// If the row is new, add a new row to the table
if ($(e.target).parents("tr").is(".new")) {
var newRow = this.makeNewTaxonomicClassificationRow();
//Append the new row and remove the new class from the old row
$(e.target).parents("tr").removeClass("new").after(newRow);
}
},
/**
* Insert the "quick add" interface for adding common taxa to the
* taxonomic coverage section. Only renders if there is a list of taxa
* configured in the appModel.
*/
renderTaxaQuickAdd: function () {
try {
const view = this;
// To render the taxon select, the view must be in editor mode and we
// need a list of taxa configured for the theme
if (!view.edit) return;
// remove any existing quick add interface:
if (view.taxonQuickAddEl) view.taxonQuickAddEl.remove();
const quickAddTaxa = view.getTaxonQuickAddOptions();
if (!quickAddTaxa || !quickAddTaxa.length) {
// If the taxa are configured as SID for a dataObject, then wait
// for the dataObject to be loaded
this.listenToOnce(
MetacatUI.appModel,
"change:quickAddTaxa",
this.renderTaxaQuickAdd,
);
return;
}
// Create & insert the basic HTML for the taxon select interface
const template = `<div class="taxa-quick-add">
<p class="taxa-quick-add__text">
<b>⭐️ Quick Add Taxa:</b> Select one or more common taxa. Click "Add" to add them to the list.
</p>
<div class="taxa-quick-add__controls">
<div class="taxa-quick-add__selects"></div>
<button class="btn btn-primary taxa-quick-add__button">Add Taxa</button>
</div>
</div>`;
const parser = new DOMParser();
const doc = parser.parseFromString(template, "text/html");
const quickAddEl = doc.body.firstChild;
const button = quickAddEl.querySelector("button");
const container = quickAddEl.querySelector(
".taxa-quick-add__selects",
);
const rowSelector = ".root-taxonomic-classification-container";
const firstRow = document.querySelector(rowSelector);
firstRow.parentNode.insertBefore(quickAddEl, firstRow);
view.taxonQuickAddEl = quickAddEl;
// Update the taxon coverage when the button is clicked
const onButtonClick = () => {
const taxonSelects = view.taxonSelects;
if (!taxonSelects || !taxonSelects.length) return;
const selectedItems = taxonSelects
.map((select) => select.model.get("selected"))
.flat();
if (!selectedItems || !selectedItems.length) return;
const selectedItemObjs = selectedItems.map((item) => {
try {
// It will be encoded JSON if it's a pre-defined taxon
return JSON.parse(decodeURIComponent(item));
} catch (e) {
// Otherwise it will be a string a user typed in
return {
taxonRankName: "",
taxonRankValue: item,
};
}
});
view.addTaxa(selectedItemObjs);
taxonSelects.forEach((select) =>
select.model.setSelected([], { silent: true }),
);
};
button.removeEventListener("click", onButtonClick);
button.addEventListener("click", onButtonClick);
// Create the search selects
view.taxonSelects = [];
const componentPath = "views/searchSelect/SearchSelectView";
require([componentPath], function (SearchSelect) {
quickAddTaxa.forEach((taxaList, i) => {
try {
const taxaInput = new SearchSelect({
options: taxaList.options,
placeholderText: taxaList.placeholder,
inputLabel: taxaList.label,
allowMulti: true,
allowAdditions: true,
separatorTextOptions: false,
selected: [],
});
container.appendChild(taxaInput.el);
taxaInput.render();
view.taxonSelects.push(taxaInput);
} catch (e) {
console.log("Failed to create taxon select: ", e);
}
});
});
} catch (e) {
console.log("Failed to render taxon select: ", e);
}
},
/**
* Get the list of options for the taxon quick add interface. Filter
* out any that have already been added to the taxonomic coverage.
* @returns {Object[]} An array of search select options
* @since 2.24.0
*/
getTaxonQuickAddOptions: function () {
const quickAddTaxa = MetacatUI.appModel.getQuickAddTaxa();
if (!quickAddTaxa || !quickAddTaxa.length) return;
const coverages = this.model.get("taxonCoverage");
for (const taxaList of quickAddTaxa) {
const opts = [];
for (const taxon of taxaList.taxa) {
// check that it is not a duplicate in any coverages
let isDuplicate = false;
for (cov of coverages) {
if (cov.isDuplicate(taxon)) {
isDuplicate = true;
break;
}
}
if (!isDuplicate) {
opts.push(this.taxonOptionToSearchSelectItem(taxon));
}
}
taxaList.options = opts;
}
return quickAddTaxa;
},
/**
* Reformats a taxon option, as provided in the appModel
* {@link AppModel#quickAddTaxa}, as a search select item.
* @param {Object} option A single taxon classification with at least a
* taxonRankValue and taxonRankName. It may also have a taxonId (object
* with provider and value) and a commonName.
* @returns {Object} A search select item with label, value, and
* description properties.
*/
taxonOptionToSearchSelectItem: function (option) {
try {
// option must have a taxonRankValue and taxonRankName or it is invalid
if (!option.taxonRankValue || !option.taxonRankName) {
console.log("Invalid taxon option: ", option);
return null;
}
// Create a description
let description = option.taxonRankName + ": " + option.taxonRankValue;
if (option.taxonId) {
description +=
" (" +
option.taxonId.provider +
": " +
option.taxonId.value +
")";
}
// search select doesn't work with some of the json characters
const val = encodeURIComponent(JSON.stringify(option));
return {
label: option.commonName || option.taxonRankValue,
value: val,
description: description,
};
} catch (e) {
console.log(
"Failed to reformat taxon option as search select item: ",
e,
);
return null;
}
},
/**
* Add new taxa to the EML model and re-render the taxa section. The new
* taxa will be added to the first <taxonomicCoverage> element in the EML
* model. If there is no <taxonomicCoverage> element, one will be created.
* @param {Object[]} newClassifications - An array of objects with any of
* the following properties:
* - taxonRankName: (sting) The name of the taxonomic rank, e.g.
* "Kingdom"
* - taxonRankValue: (string) The value of the taxonomic rank, e.g.
* "Animalia"
* - commonName: (string) The common name of the taxon, e.g. "Animals"
* - taxonId: (object) The official ID of the taxon, including "provider"
* and "value".
* - taxonomicClassification: (array) An array of nested taxonomic
* classifications
* @since 2.24.0
* @example
* this.addTaxon([{
* taxonRankName: "Kingdom",
* taxonRankValue: "Animalia",
* commonName: "Animals",
* taxonId: {
* provider: "https://www.itis.gov/",
* value: "202423"
* }]);
*/
addTaxa: function (newClassifications) {
try {
// TODO: validate the new taxon before adding it to the model?
const taxonCoverages = this.model.get("taxonCoverage");
// We expect that there is already a taxonCoverage array on the model.
// If the EML was made in the editor, there can only be one
// <taxonomicCoverage> element. Add the new taxon to its
// <taxonomicClassification> array. If there is more than one, then the
// new taxon will be added to the first <taxonomicCoverage> element.
if (taxonCoverages && taxonCoverages.length >= 1) {
const taxonCoverage = taxonCoverages[0];
const classifications = taxonCoverage.get(
"taxonomicClassification",
);
const allClass = classifications.concat(newClassifications);
taxonCoverage.set("taxonomicClassification", allClass);
} else {
// If there is no <taxonomicCoverage> element for some reason,
// create one and add the new taxon to its <taxonomicClassification>
// array.
const newCov = new EMLTaxonCoverage({
taxonomicClassification: newClassifications,
parentModel: this.model,
});
this.model.set("taxonCoverage", [newCov]);
}
// Re-render the taxa section
this.renderTaxa();
} catch (e) {
console.log("Error adding taxon to EML model: ", e);
}
},
removeTaxonRank: function (e) {
var row = $(e.target).parents(".taxonomic-coverage-row"),
coverageEl = $(row).parents(".taxonomic-coverage"),
view = this;
//Animate the row away and then remove it
row.slideUp("fast", function () {
row.remove();
view.updateTaxonCoverage({ coverage: coverageEl });
});
},
/*
* After the user focuses out, show validation help, if needed
*/
showTaxonValidation: function (e) {
//Get the text inputs and select menus
var row = $(e.target).parents("tr"),
allInputs = row.find("input, select"),
tableContainer = $(e.target).parents("table"),
errorInputs = [];
//If none of the inputs have a value and this is a new row, then do nothing
if (
_.every(allInputs, function (i) {
return !i.value;
}) &&
row.is(".new")
)
return;
//Add the error styling to any input with no value
_.each(allInputs, function (input) {
// Keep track of the number of clicks of each input element so we only show the
// error message after the user has focused on both input elements
if (!input.value) errorInputs.push(input);
});
if (errorInputs.length) {
//Show the error message after a brief delay
setTimeout(function () {
//If the user focused on another element in the same row, don't do anything
if (_.contains(allInputs, document.activeElement)) return;
//Add the error styling
$(errorInputs).addClass("error");
//Add the error message
if (!tableContainer.prev(".notification").length) {
tableContainer.before(
$(document.createElement("p"))
.addClass("error notification")
.text("Enter a rank name AND value in each row."),
);
}
}, 200);
} else {
allInputs.removeClass("error");
if (!tableContainer.find(".error").length)
tableContainer.prev(".notification").remove();
}
},
previewTaxonRemove: function (e) {
var removeBtn = $(e.target);
if (removeBtn.parent().is(".root-taxonomic-classification")) {
removeBtn.parent().toggleClass("remove-preview");
} else {
removeBtn
.parents(".taxonomic-coverage-row")
.toggleClass("remove-preview");
}
},
updateRadioButtons: function (e) {
//Get the element of this radio button set that is checked
var choice = this.$(
"[name='" + $(e.target).attr("name") + "']:checked",
).val();
if (typeof choice == "undefined" || !choice)
this.model.set($(e.target).attr("data-category"), "");
else this.model.set($(e.target).attr("data-category"), choice);
this.model.trickleUpChange();
},
/*
* Switch to the given section
*/
switchSection: function (e) {
if (!e) return;
e.preventDefault();
var clickedEl = $(e.target),
section =
clickedEl.attr("data-section") ||
clickedEl.children("[data-section]").attr("data-section") ||
clickedEl.parents("[data-section]").attr("data-section");
if (this.visibleSection == "all") this.scrollToSection(section);
else {
this.$(".section." + this.activeSection).hide();
this.$(".section." + section).show();
this.highlightTOC(section);
this.activeSection = section;
this.visibleSection = section;
$("body").scrollTop(
this.$(".section." + section).offset().top - $("#Navbar").height(),
);
}
},
/*
* When a user clicks on the section names in the side tabs, jump to the section
*/
scrollToSection: function (e) {
if (!e) return false;
//Stop navigation
e.preventDefault();
var section = $(e.target).attr("data-section"),
sectionEl = this.$(".section." + section);
if (!sectionEl) return false;
//Temporarily unbind the scroll listener while we scroll to the clicked section
$(document).unbind("scroll");
var view = this;
setTimeout(function () {
$(document).scroll(view.highlightTOC.call(view));
}, 1500);
//Scroll to the section
if (sectionEl == section[0]) MetacatUI.appView.scrollToTop();
else MetacatUI.appView.scrollTo(sectionEl, $("#Navbar").outerHeight());
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
//Set the clicked item to active
$(".side-nav-item a[data-section='" + section + "']").addClass(
"active",
);
//Set the active section on this view
this.activeSection = section;
},
/*
* Highlight the given menu item.
* The first argument is either an event object or the section name
*/
highlightTOC: function (section) {
this.resizeTOC();
//Now change sections
if (typeof section == "string") {
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
$(".side-nav-item a[data-section='" + section + "']").addClass(
"active",
);
this.activeSection = section;
this.visibleSection = section;
return;
} else if (this.visibleSection == "all") {
//Remove the active class from all the menu items
$(".side-nav-item a.active").removeClass("active");
//Get the section
var top = $(window).scrollTop() + $("#Navbar").outerHeight() + 70,
sections = $(".metadata-container .section");
//If we're somewhere in the middle, find the right section
for (var i = 0; i < sections.length; i++) {
if (
top > $(sections[i]).offset().top &&
top < $(sections[i + 1]).offset().top
) {
$($(".side-nav-item a")[i]).addClass("active");
this.activeSection = $(sections[i]).attr("data-section");
this.visibleSection = $(sections[i]).attr("data-section");
break;
}
}
}
},
/*
* Resizes the vertical table of contents so it's always the same height as the editor body
*/
resizeTOC: function () {
var tableBottomHandle = $("#editor-body .ui-resizable-handle");
if (!tableBottomHandle.length) return;
var tableBottom = tableBottomHandle[0].getBoundingClientRect().bottom,
navTop = tableBottom;
if (tableBottom < $("#Navbar").outerHeight()) {
if ($("#Navbar").css("position") == "fixed")
navTop = $("#Navbar").outerHeight();
else navTop = 0;
}
$(".metadata-toc").css("top", navTop);
},
/*
* -- This function is for development/testing purposes only --
* Trigger a change on all the form elements
* so that when values are changed by Javascript, we make sure the change event
* is fired. This is good for capturing changes by Javascript, or
* browser plugins that fill-in forms, etc.
*/
triggerChanges: function () {
$("#metadata-container input").change();
$("#metadata-container textarea").change();
$("#metadata-container select").change();
},
/* Creates "Remove" buttons for removing non-required sections
of the EML from the DOM */
createRemoveButton: function (submodel, attribute, selector, container) {
return $(document.createElement("span"))
.addClass("icon icon-remove remove pointer")
.attr("title", "Remove")
.data({
submodel: submodel,
attribute: attribute,
selector: selector,
container: container,
});
},
/* Generic event handler for removing sections of the EML (both
the DOM and inside the EML211Model) */
handleRemove: function (e) {
var submodel = $(e.target).data("submodel"), // Optional sub-model to remove attribute from
attribute = $(e.target).data("attribute"), // Attribute on the EML211 model we're removing from
selector = $(e.target).data("selector"), // Selector to find the parent DOM elemente we'll remove
container = $(e.target).data("container"), // Selector to find the parent container so we can remove by index
parentEl, // Element we'll remove
model; // Specific sub-model we're removing
if (!attribute) return;
if (!container) return;
// Find the element we'll remove from the DOM
if (selector) {
parentEl = $(e.target).parents(selector).first();
} else {
parentEl = $(e.target).parents().first();
}
if (parentEl.length == 0) return;
// Handle remove on a EML model / sub-model
if (submodel) {
model = this.model.get(submodel);
if (!model) return;
// Get the current value of the attribute so we can remove from it
var currentValue, submodelIndex;
if (Array.isArray(this.model.get(submodel))) {
// Stop now if there's nothing to remove in the first place
if (this.model.get(submodel).length == 0) return;
// For multi-valued submodels, find *which* submodel we are removing or
// removingn from
submodelIndex = $(container).index(
$(e.target).parents(container).first(),
);
if (submodelIndex === -1) return;
currentValue = this.model
.get(submodel)
[submodelIndex].get(attribute);
} else {
currentValue = this.model.get(submodel).get(attribute);
}
//FInd the position of this field in the list of fields
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index($(e.target).parents(selector));
// Remove from the EML Model
if (position >= 0) {
if (Array.isArray(this.model.get(submodel))) {
currentValue.splice(position, 1); // Splice returns the removed members
this.model
.get(submodel)
[submodelIndex].set(attribute, currentValue);
} else {
currentValue.splice(position, 1); // Splice returns the removed members
this.model.get(submodel).set(attribute, currentValue);
}
}
} else if (selector) {
// Find the index this attribute is in the DOM
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index($(e.target).parents(selector));
//Remove this index of the array
var currentValue = this.model.get(attribute);
if (Array.isArray(currentValue)) currentValue.splice(position, 1);
//Set the array on the model so the 'set' function is executed
this.model.set(attribute, currentValue);
}
// Handle remove on a basic text field
else {
// The DOM order matches the EML model attribute order so we can remove
// by that
var position = $(e.target)
.parents(container)
.first()
.children(selector)
.index(selector);
var currentValue = this.model.get(attribute);
// Remove from the EML Model
if (position >= 0) {
currentValue.splice(position, 1);
this.model.set(attribute, currentValue);
}
}
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
// Remove the DOM
$(parentEl).remove();
//updating the tablesIndex once the element has been removed
var tableNums = this.$(".editor-header-index");
for (var i = 0; i < tableNums.length; i++) {
$(tableNums[i]).text(i + 1);
}
// If this was a taxon, update the quickAdd interface
if (submodel === "taxonCoverage") {
this.updateQuickAddTaxa();
}
},
/**
* Adds an {@link EMLAnnotation} to the {@link EML211} model currently being edited.
* Attributes for the annotation are retreived from the HTML attributes from the HTML element
* that was interacted with.
* @param {Event} e - An Event on an Element that contains {@link EMLAnnotation} data
*/
addAnnotation: function (e) {
try {
if (!e || !e.target) {
return;
}
let annotationData = _.clone(e.target.dataset);
//If this is a radio button, we only want one annotation of this type.
if (e.target.getAttribute("type") == "radio") {
annotationData.allowDuplicates = false;
}
//Set the valueURI from the input value
annotationData.valueURI = $(e.target).val();
//Reformat the propertyURI property
if (annotationData.propertyUri) {
annotationData.propertyURI = annotationData.propertyUri;
delete annotationData.propertyUri;
}
this.model.addAnnotation(annotationData);
} catch (error) {
console.error("Couldn't add annotation: ", e);
}
},
/* Close the view and its sub views */
onClose: function () {
this.remove(); // remove for the DOM, stop listening
this.off(); // remove callbacks, prevent zombies
this.model.off();
//Remove the scroll event listeners
$(document).unbind("scroll");
this.model = null;
this.subviews = [];
window.onbeforeunload = null;
},
},
);

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

renderOverview: function () {
//Get the overall view mode
var edit = this.edit;
var view = this;
//Append the empty layout
var overviewEl = this.$container.find(".overview");
$(overviewEl).html(this.overviewTemplate());
//Title
this.renderTitle();
this.listenTo(this.model, "change:title", this.renderTitle);
//Data Sensitivity
this.renderDataSensitivity();
//Abstract
_.each(
this.model.get("abstract"),
function (abs) {
var abstractEl = this.createEMLText(abs, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
},
this,
);
if (!this.model.get("abstract").length) {
var abstractEl = this.createEMLText(null, edit, "abstract");
//Add the abstract element to the view
$(overviewEl).find(".abstract").append(abstractEl);
}
//Keywords
//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.get("thesaurus"));
},
this,
);
},
this,
);
//Add a new keyword row
this.addKeyword();
//Alternate Ids
var altIdsEls = this.createBasicTextFields(
"alternateIdentifier",
"Add a new alternate identifier",
);
$(overviewEl).find(".altids").append(altIdsEls);
// Canonical Identifier
const canonicalIdEl = this.createBasicTextFields(
"canonicalDataset",
"Add a new canonical identifier",
);
$(overviewEl).find(".canonical-id").append(canonicalIdEl);
//Usage
//Find the model value that matches a radio button and check it
// Note the replace() call removing newlines and replacing them with a single space
// character. This is a temporary hack to fix https://github.com/NCEAS/metacatui/issues/128
if (this.model.get("intellectualRights"))
this.$(
".checkbox .usage[value='" +
this.model.get("intellectualRights").replace(/\r?\n|\r/g, " ") +
"']",
).prop("checked", true);
//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();
},

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🚫 [eslint] <vars-on-top> reported by reviewdog 🐶
All 'var' declarations must be at the top of the function scope.

var altIdsEls = this.createBasicTextFields(
"alternateIdentifier",
"Add a new alternate identifier",
);

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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

var altIdsEls = this.createBasicTextFields(
"alternateIdentifier",
"Add a new alternate identifier",
);

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

createBasicTextFields: function (category, placeholder) {
var textContainer = $(document.createElement("div")).addClass(
"text-container",
),
modelValues = this.model.get(category),
textRow; // Holds the DOM for each field
//Format as an array
if (!Array.isArray(modelValues) && modelValues)
modelValues = [modelValues];
//For each value in this category, create an HTML element with the value inserted
_.each(
modelValues,
function (value, i, allModelValues) {
if (this.edit) {
var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");
textRow.append(input.clone().val(value));
if (category !== "title" && category !== "canonicalDataset")
textRow.append(
this.createRemoveButton(
null,
category,
"div.basic-text-row",
"div.text-container",
),
);
textContainer.append(textRow);
//At the end, append an empty input for the user to add a new one
if (
i + 1 == allModelValues.length &&
category !== "title" &&
category !== "canonicalDataset"
) {
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);
}
} else {
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.attr("data-category", category)
.text(value),
);
}
},
this,
);
if ((!modelValues || !modelValues.length) && this.edit) {
var input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text new")
.attr("placeholder", placeholder || "Add a new " + category);
textContainer.append(
$(document.createElement("div"))
.addClass("basic-text-row")
.append(input),
);
}
return textContainer;
},

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🚫 [eslint] <one-var> reported by reviewdog 🐶
Split 'var' declarations into multiple statements.

var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");

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🚫 [eslint] <vars-on-top> reported by reviewdog 🐶
All 'var' declarations must be at the top of the function scope.

var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");

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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

var textRow = $(document.createElement("div")).addClass(
"basic-text-row",
),
input = $(document.createElement("input"))
.attr("type", "text")
.attr("data-category", category)
.addClass("basic-text");

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🚫 [eslint] <object-shorthand> reported by reviewdog 🐶
Expected method shorthand.

updateBasicText: function (e) {
if (!e) return false;
//Get the category, new value, and model
var category = $(e.target).attr("data-category"),
value = this.model.cleanXMLText($(e.target).val()),
model = $(e.target).data("model") || this.model;
//We can't update anything without a category
if (!category) return false;
//Get the current value
var currentValue = model.get(category);
//Insert the new value into the array
if (Array.isArray(currentValue)) {
//Find the position this text input is in
var position = $(e.target)
.parents("div.text-container")
.first()
.children("div")
.index($(e.target).parent());
//Set the value in that position in the array
currentValue[position] = value;
//Set the changed array on this model
model.set(category, currentValue);
model.trigger("change:" + category);
}
//Update the model if the current value is a string
else if (typeof currentValue == "string") {
model.set(category, [value]);
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 != "" &&
category != "title" &&
category !== "canonicalDataset"
) {
$(e.target).removeClass("new");
this.addBasicText(e);
}
// Trigger a change on the entire package
MetacatUI.rootDataPackage.packageModel.set("changed", true);
},

Original file line number Diff line number Diff line change
Expand Up @@ -302,6 +302,13 @@ define([
);
$(overviewEl).find(".altids").append(altIdsEls);

// Canonical Identifier
const canonicalIdEl = this.createBasicTextFields(
"canonicalDataset",
"Add a new canonical identifier",
);
$(overviewEl).find(".canonical-id").append(canonicalIdEl);

//Usage
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Usage
// Usage

//Find the model value that matches a radio button and check it
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Find the model value that matches a radio button and check it
// Find the model value that matches a radio button and check it

// Note the replace() call removing newlines and replacing them with a single space
Expand Down Expand Up @@ -1909,7 +1916,7 @@ define([
.addClass("basic-text");
textRow.append(input.clone().val(value));

if (category != "title")
if (category !== "title" && category !== "canonicalDataset")
textRow.append(
this.createRemoveButton(
null,
Expand All @@ -1922,7 +1929,11 @@ define([
textContainer.append(textRow);

//At the end, append an empty input for the user to add a new one
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//At the end, append an empty input for the user to add a new one
// At the end, append an empty input for the user to add a new one

if (i + 1 == allModelValues.length && category != "title") {
if (
i + 1 == allModelValues.length &&
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🚫 [eslint] <eqeqeq> reported by reviewdog 🐶
Expected '===' and instead saw '=='.

category !== "title" &&
category !== "canonicalDataset"
) {
var newRow = $(
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🚫 [eslint] <no-var> reported by reviewdog 🐶
Unexpected var, use let or const instead.

Suggested change
var newRow = $(
let newRow = $(

$(document.createElement("div")).addClass("basic-text-row"),
);
Comment on lines 1937 to 1939
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🚫 [eslint] <vars-on-top> reported by reviewdog 🐶
All 'var' declarations must be at the top of the function scope.

Expand Down Expand Up @@ -2006,7 +2017,12 @@ define([
}

//Add another blank text input
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Add another blank text input
// Add another blank text input

if ($(e.target).is(".new") && value != "" && category != "title") {
if (
$(e.target).is(".new") &&
value != "" &&
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🚫 [eslint] <eqeqeq> reported by reviewdog 🐶
Expected '!==' and instead saw '!='.

category != "title" &&
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🚫 [eslint] <eqeqeq> reported by reviewdog 🐶
Expected '!==' and instead saw '!='.

category !== "canonicalDataset"
) {
$(e.target).removeClass("new");
this.addBasicText(e);
}
Expand Down Expand Up @@ -2036,12 +2052,12 @@ define([
allBasicTexts = $(
".basic-text.new[data-category='" + category + "']",
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🚫 [eslint] <prefer-template> reported by reviewdog 🐶
Unexpected string concatenation.

Suggested change
".basic-text.new[data-category='" + category + "']",
`.basic-text.new[data-category='${ category }']`,

);

//Only show one new row at a time
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Only show one new row at a time
// Only show one new row at a time

if (allBasicTexts.length == 1 && !allBasicTexts.val()) return;
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🚫 [eslint] <eqeqeq> reported by reviewdog 🐶
Expected '===' and instead saw '=='.

else if (allBasicTexts.length > 1) return;
//We are only supporting one title right now
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//We are only supporting one title right now
// We are only supporting one title right now

else if (category == "title") return;
else if (category === "title" || category === "canonicalDataset")
return;
Comment on lines 2057 to +2060
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🚫 [eslint] <no-else-return> reported by reviewdog 🐶
Unnecessary 'else' after 'return'.

reviewdog suggestion errorGitHub comment range and suggestion line range must be same. L2057-L2060 v.s. L2050-L2057


//Add another blank text input
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🚫 [eslint] <spaced-comment> reported by reviewdog 🐶
Expected exception block, space or tab after '//' in comment.

Suggested change
//Add another blank text input
// Add another blank text input

var newRow = $(document.createElement("div")).addClass(
Expand Down
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