From fd275aa0a8a7e124b90ff999ed4f929e98c47497 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Thu, 2 Apr 2020 17:19:41 +0300 Subject: [PATCH 01/14] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 124735cb1..05d6a4957 100644 --- a/package.json +++ b/package.json @@ -22,7 +22,7 @@ "bootstrap": "3.3.7", "chise": "^2.0.0", "chroma-js": "^1.3.4", - "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#master", + "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#unstable", "cytoscape-autopan-on-drag": "^2.2.0", "cytoscape-clipboard": "^2.2.1", "cytoscape-context-menus": "^3.0.7", From d9293c68ef275e84899689115b7327324132e183 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Wed, 8 Apr 2020 18:31:38 +0300 Subject: [PATCH 02/14] Update package.json --- package.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/package.json b/package.json index 05d6a4957..6eb56598d 100644 --- a/package.json +++ b/package.json @@ -20,13 +20,13 @@ "backbone": "1.3.3", "body-parser": "^1.19.0", "bootstrap": "3.3.7", - "chise": "^2.0.0", + "chise": "github:iVis-at-Bilkent/chise.js#unstable", "chroma-js": "^1.3.4", "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#unstable", - "cytoscape-autopan-on-drag": "^2.2.0", - "cytoscape-clipboard": "^2.2.1", - "cytoscape-context-menus": "^3.0.7", - "cytoscape-edge-editing": "^2.0.0", + "cytoscape-autopan-on-drag": "github:iVis-at-Bilkent/cytoscape.js-autopan-on-drag#unstable", + "cytoscape-clipboard": "github:iVis-at-Bilkent/cytoscape.js-clipboard#unstable", + "cytoscape-context-menus": "github:iVis-at-Bilkent/cytoscape.js-context-menus#unstable", + "cytoscape-edge-editing": "github:iVis-at-Bilkent/cytoscape.js-edge-editing#unstable", "cytoscape-edgehandles": "~2.13.1", "cytoscape-expand-collapse": "github:iVis-at-Bilkent/cytoscape.js-expand-collapse#unstable", "cytoscape-fcose": "github:iVis-at-Bilkent/cytoscape.js-fcose#unstable", @@ -49,7 +49,7 @@ "multer": "^1.4.2", "natives": "^1.1.6", "request": "^2.81.0", - "sbgnviz": "^5.0.0", + "sbgnviz": "github:iVis-at-Bilkent/sbgnviz.js#unstable", "tippy.js": "^3.4.0", "nodemailer": "6.4.5" }, From b46e540cd05508213494502e1a4bc4c39b314d69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Sun, 10 May 2020 06:38:19 +0300 Subject: [PATCH 03/14] Fix #584 Prevent unnecessary operations on layoutstop --- app/js/app-cy.js | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/app/js/app-cy.js b/app/js/app-cy.js index a031e6fc4..b69ba1526 100644 --- a/app/js/app-cy.js +++ b/app/js/app-cy.js @@ -585,7 +585,7 @@ module.exports = function (chiseInstance) { result = true; }); - return !node.data()["expanding"] && result && !chiseInstance.elementUtilities.isResizedToContent(node) && (cy.zoom() > 0.5); + return !node.data("onLayout") && result && !chiseInstance.elementUtilities.isResizedToContent(node) && (cy.zoom() > 0.5); }, resizeToContentFunction: appUtilities.resizeNodesToContent, resizeToContentCuePosition: 'bottom-right', @@ -751,18 +751,21 @@ module.exports = function (chiseInstance) { }); cy.on("expandcollapse.beforeexpand",function(event){ - var node = event.target; - node.data("expanding", true); - - }); + var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties'); + if(currentGeneralProperties.recalculateLayoutOnComplexityManagement){ + var node = cy.nodes(":selected"); + if(node.length == 1 && event.target.selected()) + node[0].data("onLayout", true); + } + }); /* cy.on("expandcollapse.afterexpand",function(event){ var node = event.target; node.data("expanding", false); }); */ //Updates arrow-scale of edges after expand cy.on("expandcollapse.afterexpand", function(event) { - var currentArrowScale = Number($('#arrow-scale').val()); - cy.edges().style('arrow-scale', currentArrowScale); + var currentArrowScale = Number($('#arrow-scale').val()); + cy.edges().style('arrow-scale', currentArrowScale); }); //Changes arrow-scale of pasted edges @@ -1271,6 +1274,12 @@ module.exports = function (chiseInstance) { updateInfoBox(node); } }); */ + + cy.on("layoutstart",function(event){ + var node = cy.nodes(":selected"); + if(node.length == 1 && node.data("collapsedChildren") == null) + node[0].data("onLayout", true); + }); cy.on('layoutstop', function (event) { /* @@ -1298,7 +1307,7 @@ module.exports = function (chiseInstance) { chiseInstance.elementUtilities.fitUnits(ele, locations); //Force fit }); */ - cy.nodes().forEach(function(node){node.data("expanding", false); }); + cy.nodes("[?onLayout]").forEach(function(node){node.removeData("onLayout"); }); }); // if the position of compound changes by repositioning its children From ed8f7ec7c45755c2d327981fda6352fbffb9cc8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Sun, 10 May 2020 11:57:01 +0300 Subject: [PATCH 04/14] Fix #584 Consider only selected parent nodes --- app/js/app-cy.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/js/app-cy.js b/app/js/app-cy.js index b69ba1526..8b2295ddd 100644 --- a/app/js/app-cy.js +++ b/app/js/app-cy.js @@ -1276,8 +1276,8 @@ module.exports = function (chiseInstance) { }); */ cy.on("layoutstart",function(event){ - var node = cy.nodes(":selected"); - if(node.length == 1 && node.data("collapsedChildren") == null) + var node = cy.nodes(":selected").nodes(":parent"); + if(node.length == 1) node[0].data("onLayout", true); }); From a9d78c818323e13055ef08ecf7c6f1dca7ce0e77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Wed, 13 May 2020 17:30:11 +0300 Subject: [PATCH 05/14] Resolve #586 --- app/js/app-menu.js | 41 +++++++++++++++++++++++++++++++++++++---- app/js/app-utilities.js | 17 +++-------------- 2 files changed, 40 insertions(+), 18 deletions(-) diff --git a/app/js/app-menu.js b/app/js/app-menu.js index 5f6525995..e40038b6f 100644 --- a/app/js/app-menu.js +++ b/app/js/app-menu.js @@ -97,7 +97,7 @@ module.exports = function() { topologyGrouping.clearAppliedFlag(); // unlock graph topology in case it is locked - chiseInstance.elementUtilities.unlockGraphTopology(); + chiseInstance.elementUtilities.unlockGraphTopology(); // if the event is triggered for the active instance do the followings if ( isActiveInstance ) { @@ -109,13 +109,46 @@ module.exports = function() { $('#inspector-map-tab a').tab('show'); } - if ( $('#inspector-console-tab')[0].style.display == "block") { - $('#inspector-console-tab')[0].style.display = "none"; - + if ($('#inspector-console-tab')[0].style.display == "block") { + $('#inspector-console-tab')[0].style.display = "none"; } + } + }); + + // Event triggered before file loaded by URL/URI + $(document).on('sbgnvizLoadFromURL sbgnvizLoadFromURI', function(event, filename, cy) { + + var chiseInstance = appUtilities.getChiseInstance(cy); + + var urlParams = appUtilities.getScratch(cy, 'urlParams'); + + // get current general properties for cy + var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties'); + // inferNestingOnLoad and compoundPadding must be set before file loaded + if (urlParams) { + // filter map properties from the url parameters + var mapPropsFromUrl = appUtilities.filterMapProperties(urlParams); + + if("inferNestingOnLoad" in mapPropsFromUrl){ + currentGeneralProperties.inferNestingOnLoad = (mapPropsFromUrl.inferNestingOnLoad == 'true'); + } + else if(event.type == 'sbgnvizLoadFromURL'){ + currentGeneralProperties.inferNestingOnLoad = true; + } + else if(event.type == 'sbgnvizLoadFromURI'){ + currentGeneralProperties.inferNestingOnLoad = false; + } + + if("compoundPadding" in mapPropsFromUrl){ + currentGeneralProperties.compoundPadding = Number(mapPropsFromUrl.compoundPadding); + chiseInstance.setCompoundPadding(Number(mapPropsFromUrl.compoundPadding)); + } } + // set 'currentGeneralProperties' on scratchpad of cy + appUtilities.setScratch(cy, 'currentGeneralProperties', currentGeneralProperties); + }); $(document).on('updateGraphEnd', function(event, cy) { diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index e846cfcac..28703c0f2 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -2416,7 +2416,7 @@ appUtilities.setMapProperties = function(mapProperties, _chiseInstance) { // refresh map with new settings chiseInstance.setShowComplexName(currentGeneralProperties.showComplexName); chiseInstance.refreshPaddings(); // Refresh/recalculate paddings - + if (currentGeneralProperties.enablePorts) { chiseInstance.enablePorts(); } @@ -2489,9 +2489,6 @@ appUtilities.launchWithModelFile = function() { tutorial.introduction(true); function loadFromURL(filepath, chiseInstance, promptInvalidURLWarning){ - // get current general properties - var currentGeneralProperties = appUtilities.getScratch(cyInstance, 'currentGeneralProperties'); - var currentInferNestingOnLoad = currentGeneralProperties.inferNestingOnLoad; var loadCallbackSBGNMLValidity = function (text) { $.ajax({ @@ -2540,12 +2537,12 @@ appUtilities.launchWithModelFile = function() { success: function(data){ // here we can get 404 as well, for example, so there are still error cases to handle if (!data.error && data.response.statusCode == 200 && data.response.body) { + $(document).trigger('sbgnvizLoadFromURL', [filename, cyInstance]); var fileToLoad = new File([data.response.body], filename, { type: 'text/' + fileExtension, lastModified: Date.now() }); - currentGeneralProperties.inferNestingOnLoad = true; chiseInstance.loadNwtFile(fileToLoad, loadCallbackSBGNMLValidity, loadCallbackInvalidityWarning); } else { @@ -2557,11 +2554,6 @@ appUtilities.launchWithModelFile = function() { } }); - $(document).one("sbgnvizLoadFileEnd", function(){ - currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad; - appUtilities.mapTabGeneralPanel.render(); - }); - } function loadFromURI(uri, chiseInstance, promptInvalidURIWarning){ @@ -2574,8 +2566,6 @@ appUtilities.launchWithModelFile = function() { chiseInstance.startSpinner('paths-byURI-spinner'); - var currentGeneralProperties = appUtilities.getScratch(cyInstance, 'currentGeneralProperties'); - var currentInferNestingOnLoad = currentGeneralProperties.inferNestingOnLoad; var currentLayoutProperties = appUtilities.getScratch(cyInstance, 'currentLayoutProperties'); $.ajax({ @@ -2587,9 +2577,8 @@ appUtilities.launchWithModelFile = function() { if (data.response.statusCode == 200 && data.response.body) { var xml = $.parseXML(data.response.body); $(document).trigger('sbgnvizLoadFile', [filename, cyInstance]); - currentGeneralProperties.inferNestingOnLoad = false; + $(document).trigger('sbgnvizLoadFromURI', [filename, cyInstance]); chiseInstance.updateGraph(chiseInstance.convertSbgnmlToJson(xml), undefined, currentLayoutProperties); - currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad; chiseInstance.endSpinner('paths-byURI-spinner'); $(document).trigger('sbgnvizLoadFileEnd', [filename, cyInstance]); } From 33d5bdfa0740d30ee6f8aaaf0629667b43bf8658 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Wed, 13 May 2020 18:24:17 +0300 Subject: [PATCH 06/14] Resolve #586 inferNestingOnLoad is false by default for both URL and URI --- app/js/app-menu.js | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/app/js/app-menu.js b/app/js/app-menu.js index e40038b6f..08cfd2a4b 100644 --- a/app/js/app-menu.js +++ b/app/js/app-menu.js @@ -130,13 +130,10 @@ module.exports = function() { // filter map properties from the url parameters var mapPropsFromUrl = appUtilities.filterMapProperties(urlParams); - if("inferNestingOnLoad" in mapPropsFromUrl){ + if("inferNestingOnLoad" in mapPropsFromUrl) { currentGeneralProperties.inferNestingOnLoad = (mapPropsFromUrl.inferNestingOnLoad == 'true'); } - else if(event.type == 'sbgnvizLoadFromURL'){ - currentGeneralProperties.inferNestingOnLoad = true; - } - else if(event.type == 'sbgnvizLoadFromURI'){ + else { currentGeneralProperties.inferNestingOnLoad = false; } From edfbcc712d9c5822640bf3fb1c2df4f4bc49af67 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Wed, 13 May 2020 18:35:16 +0300 Subject: [PATCH 07/14] Small performance improvement while setting map properties --- app/js/app-utilities.js | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index 28703c0f2..89902c838 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -2416,6 +2416,8 @@ appUtilities.setMapProperties = function(mapProperties, _chiseInstance) { // refresh map with new settings chiseInstance.setShowComplexName(currentGeneralProperties.showComplexName); chiseInstance.refreshPaddings(); // Refresh/recalculate paddings + + cy.edges().css('arrow-scale', currentGeneralProperties.arrowScale); if (currentGeneralProperties.enablePorts) { chiseInstance.enablePorts(); @@ -2439,9 +2441,6 @@ appUtilities.setMapProperties = function(mapProperties, _chiseInstance) { chiseInstance.omitCompoundSizes(); } - cy.edges().css('arrow-scale', currentGeneralProperties.arrowScale); - cy.style().update(); - // reset 'currentGeneralProperties' on scratchpad of cy appUtilities.setScratch(cy, 'currentGeneralProperties', currentGeneralProperties); From 77b78e9e04a5dc2955692a836e3d7e5abb762d57 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Thu, 14 May 2020 20:02:27 +0300 Subject: [PATCH 08/14] Disable unused triggers after expand-collapse --- app/js/app-utilities.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index 89902c838..3ece548f8 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -839,11 +839,11 @@ appUtilities.getExpandCollapseOptions = function (_cy) { var cy = _cy || self.getActiveCy(); if ( !self.getScratch(cy, 'currentGeneralProperties').recalculateLayoutOnComplexityManagement ) { - cy.trigger('fit-units-after-expandcollapse'); +// cy.trigger('fit-units-after-expandcollapse'); return; } self.triggerLayout(cy, false); - cy.trigger('fit-units-after-expandcollapse'); +// cy.trigger('fit-units-after-expandcollapse'); }, expandCollapseCueSize: 12, expandCollapseCuePosition: function (node) { From 560a2b34daf4a2b9fa07195135193c9487053c0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Fri, 15 May 2020 13:11:45 +0300 Subject: [PATCH 09/14] Resolve #586 --- app/js/app-menu.js | 16 ++++++++++++++-- app/js/app-utilities.js | 12 ++++++++---- 2 files changed, 22 insertions(+), 6 deletions(-) diff --git a/app/js/app-menu.js b/app/js/app-menu.js index 08cfd2a4b..a461e7afe 100644 --- a/app/js/app-menu.js +++ b/app/js/app-menu.js @@ -135,12 +135,16 @@ module.exports = function() { } else { currentGeneralProperties.inferNestingOnLoad = false; - } + } if("compoundPadding" in mapPropsFromUrl){ currentGeneralProperties.compoundPadding = Number(mapPropsFromUrl.compoundPadding); chiseInstance.setCompoundPadding(Number(mapPropsFromUrl.compoundPadding)); - } + } + else { + currentGeneralProperties.compoundPadding = 0; + chiseInstance.setCompoundPadding(currentGeneralProperties.compoundPadding); + } } // set 'currentGeneralProperties' on scratchpad of cy @@ -595,6 +599,14 @@ module.exports = function() { // filter map properties from the url parameters var mapPropsFromUrl = appUtilities.filterMapProperties(urlParams); + + if(!("inferNestingOnLoad" in mapPropsFromUrl)) { + mapPropsFromUrl.inferNestingOnLoad = false; + } + + if(!("compoundPadding" in mapPropsFromUrl)){ + mapPropsFromUrl.compoundPadding = 0; + } // merge the map properties coming from url into // the map properties read from file diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index 3ece548f8..3182400ea 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -751,11 +751,10 @@ appUtilities.defaultGeneralProperties = { allowCompoundNodeResize: true, mapColorScheme: 'black_white', mapColorSchemeStyle: 'solid', - mapType: function() {return appUtilities.getActiveChiseInstance().getMapType() || "Unknown"}, + mapType: function() {return (appUtilities.getActiveChiseInstance().getMapType() || "Unknown");}, mapName: "", mapDescription: "", - enableSIFTopologyGrouping: false, - experimentDescription: "", + experimentDescription: "" }; appUtilities.setFileContent = function (fileName) { @@ -2475,7 +2474,12 @@ appUtilities.launchWithModelFile = function() { // attach url params to the object to be used on sbgnvizLoadFileEnd event // it will be cleared immediately after usage - appUtilities.setScratch(cyInstance, 'urlParams', paramObj); + if(url_path || uri_path) { + appUtilities.setScratch(cyInstance, 'urlParams', paramObj); + } + else { + appUtilities.setScratch(cyInstance, 'urlParams', undefined); + } var promptInvalidURIWarning = this.promptInvalidURIWarning; var promptInvalidURLWarning = this.promptInvalidURLWarning; From d44f9bb563d6885a3c0cb5b7c02760c2f36f9959 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Mon, 18 May 2020 13:45:04 +0300 Subject: [PATCH 10/14] Adapt changes in expand/collapse Small additions to redraw expand/collapse cue after resize --- app/js/app-cy.js | 9 ++++++++- app/js/app-utilities.js | 30 +++++++++++++++++------------- 2 files changed, 25 insertions(+), 14 deletions(-) diff --git a/app/js/app-cy.js b/app/js/app-cy.js index 8b2295ddd..e5c9b89d5 100644 --- a/app/js/app-cy.js +++ b/app/js/app-cy.js @@ -757,7 +757,14 @@ module.exports = function (chiseInstance) { if(node.length == 1 && event.target.selected()) node[0].data("onLayout", true); } - }); + }); + + // To redraw expand/collapse cue after resize + cy.on("noderesize.resizeend", function (e, type, node) { + if(node.isParent() && node.selected()) + node.trigger("select"); + }); + /* cy.on("expandcollapse.afterexpand",function(event){ var node = event.target; node.data("expanding", false); diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index 3182400ea..d199c31ed 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -3002,19 +3002,23 @@ appUtilities.resizeNodesToContent = function(nodes){ var chiseInstance = appUtilities.getActiveChiseInstance(); var cy = appUtilities.getActiveCy(); var collection; - if(nodes.length == 1){ - collection = cy.collection(); - collection = collection.add(nodes[0]); - }else{ - collection = nodes; - } - - if(!chiseInstance.areCompoundSizesConsidered()){ - collection = collection.difference(":parent,[class*='compartment'],[class*='submap']"); - } - chiseInstance.resizeNodesToContent(collection, false); - cy.nodeResize('get').refreshGrapples(); - cy.expandCollapse('get').clearVisualCue(); + if(nodes.length == 1){ + collection = cy.collection(); + collection = collection.add(nodes[0]); + }else{ + collection = nodes; + } + + if(!chiseInstance.areCompoundSizesConsidered()){ + collection = collection.difference(":parent,[class*='compartment'],[class*='submap']"); + } + chiseInstance.resizeNodesToContent(collection, false); + cy.nodeResize('get').refreshGrapples(); + cy.expandCollapse('get').clearVisualCue(); + // To redraw expand/collapse cue after resize to content + if(collection.length == 1 && (collection[0].isParent() || collection[0].data('collapsedChildren')) && collection[0].selected()) { + cy.$(':selected').trigger('select'); + }; }; From 38b387d0affc24dca2a0e5f82fab6faa5969ce58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Mon, 18 May 2020 15:11:34 +0300 Subject: [PATCH 11/14] Fix #590 --- app/samples/drosophila_cell_cycle.nwt | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/app/samples/drosophila_cell_cycle.nwt b/app/samples/drosophila_cell_cycle.nwt index 59f1844eb..fecb8c87f 100644 --- a/app/samples/drosophila_cell_cycle.nwt +++ b/app/samples/drosophila_cell_cycle.nwt @@ -562,7 +562,7 @@ - + @@ -617,13 +617,13 @@ - + - + @@ -653,12 +653,12 @@ - + - + @@ -679,7 +679,7 @@ - + @@ -699,7 +699,7 @@ - + @@ -743,7 +743,7 @@ - + @@ -751,7 +751,7 @@ - + @@ -767,7 +767,7 @@ - + @@ -788,7 +788,7 @@ - + From a490aa8cf4ea027c07e5d2b95dda09cebcb7e996 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Tue, 19 May 2020 18:47:57 +0300 Subject: [PATCH 12/14] Change version number to 3.0.1 --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index b1a2658d9..005564b89 100644 --- a/index.html +++ b/index.html @@ -914,7 +914,7 @@

About

-

Newt Editor version 3.0

+

Newt Editor version 3.0.1

From f875ab91f55405a3ff90a86252d8a4341d7909e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Tue, 19 May 2020 19:52:55 +0300 Subject: [PATCH 13/14] Update package.json --- package.json | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/package.json b/package.json index dd224ef2c..8c39c36f6 100644 --- a/package.json +++ b/package.json @@ -20,23 +20,23 @@ "backbone": "1.3.3", "body-parser": "^1.19.0", "bootstrap": "3.3.7", - "chise": "github:iVis-at-Bilkent/chise.js#unstable", + "chise": "^3.0.0", "chroma-js": "^1.3.4", - "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#unstable", - "cytoscape-autopan-on-drag": "github:iVis-at-Bilkent/cytoscape.js-autopan-on-drag#unstable", - "cytoscape-clipboard": "github:iVis-at-Bilkent/cytoscape.js-clipboard#unstable", - "cytoscape-context-menus": "github:iVis-at-Bilkent/cytoscape.js-context-menus#unstable", - "cytoscape-edge-editing": "github:iVis-at-Bilkent/cytoscape.js-edge-editing#unstable", + "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#master", + "cytoscape-autopan-on-drag": "2.2.1", + "cytoscape-clipboard": "2.2.1", + "cytoscape-context-menus": "3.1.0", + "cytoscape-edge-editing": "2.0.1", "cytoscape-edgehandles": "~2.13.1", - "cytoscape-expand-collapse": "^3.2.1", - "cytoscape-fcose": "^1.2.1", - "cytoscape-grid-guide": "^2.3.1", - "cytoscape-layout-utilities": "^1.0.1", + "cytoscape-expand-collapse": "4.0.0", + "cytoscape-fcose": "1.2.2", + "cytoscape-grid-guide": "2.3.2", + "cytoscape-layout-utilities": "1.0.2", "cytoscape-node-resize": "3.2.1", "cytoscape-panzoom": "~2.5.2", "cytoscape-popper": "^1.0.2", - "cytoscape-undo-redo": "^1.3.3", - "cytoscape-view-utilities": "^4.0.0", + "cytoscape-undo-redo": "1.3.3", + "cytoscape-view-utilities": "4.1.0", "file-saver": "^2.0.2", "intro.js": "2.9.3", "jquery": "~3.3.1", @@ -49,7 +49,7 @@ "multer": "^1.4.2", "natives": "^1.1.6", "request": "^2.81.0", - "sbgnviz": "github:iVis-at-Bilkent/sbgnviz.js#unstable", + "sbgnviz": "^6.0.1", "tippy.js": "^3.4.0", "nodemailer": "6.4.5" }, From 376e37055cb17899f312260d18d8cd34dd800492 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hasan=20Balc=C4=B1?= Date: Wed, 20 May 2020 16:12:38 +0300 Subject: [PATCH 14/14] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 8c39c36f6..5d836205f 100644 --- a/package.json +++ b/package.json @@ -29,7 +29,7 @@ "cytoscape-edge-editing": "2.0.1", "cytoscape-edgehandles": "~2.13.1", "cytoscape-expand-collapse": "4.0.0", - "cytoscape-fcose": "1.2.2", + "cytoscape-fcose": "1.2.3", "cytoscape-grid-guide": "2.3.2", "cytoscape-layout-utilities": "1.0.2", "cytoscape-node-resize": "3.2.1",