From 34da6cbd148658814a4c6300e517a3f4e0a9e062 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Umut=20Utku=20ER=C5=9EAH=C4=B0NCE?= Date: Mon, 1 Jul 2024 12:10:16 +0300 Subject: [PATCH] query view refactoring + disconnected node removal #717 #719 --- app/css/chise.css | 7 + app/js/app-utilities.js | 35 ++ app/js/backbone-views.js | 1004 ++++++++++++-------------------------- index.html | 160 ++++-- 4 files changed, 471 insertions(+), 735 deletions(-) diff --git a/app/css/chise.css b/app/css/chise.css index 0158d955..95ef2801 100644 --- a/app/css/chise.css +++ b/app/css/chise.css @@ -711,6 +711,13 @@ hr.inspector-divider { margin: 1px; } +.caption-style-text { + padding-top: 8px; + padding-bottom: 8px; + color: #777; + text-align: left; +} + .chise-tab a { color: #555; padding-left: 5px !important; diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js index 295e7334..6193ee7f 100644 --- a/app/js/app-utilities.js +++ b/app/js/app-utilities.js @@ -3791,4 +3791,39 @@ appUtilities.selectAllElementsOfSameType = function(ele) { cy.elements('[class="' + sbgnclass + '"]').select(); }; +appUtilities.removeDisconnectedNodesAfterQuery = function( querySeedGenes ){ + var isAggregateNode = function (node) { + return node.data("class") == "compartment" || node.data("class") == "submap" + || node.data("class") == "complex"; + } + + var lowerCaseQuerySeedGenes = querySeedGenes.map( (gene) => { + return gene.toLowerCase(); + }); + + var cy = appUtilities.getActiveCy(); + var nodesToDelete = cy.collection(); + cy.nodes().forEach( (node, idx) => { + if(isAggregateNode(node) && node.children().connectedEdges().length != 0){ + node.children().forEach( (node, idx) => { + if(node.connectedEdges().length == 0 && !isAggregateNode(node)){ + var querySeedNode = false; + if(node.data("label")){ + var lowerCaseNodeLabel = node.data("label").toLowerCase(); + lowerCaseQuerySeedGenes.forEach( (gene) => { + if(lowerCaseNodeLabel.indexOf(gene) >= 0){ + querySeedNode = true; + } + }); + } + if(!querySeedNode) + nodesToDelete.merge(node); + } + }) + } + }); + cy.remove(nodesToDelete); + // cy.viewUtilities("get").highlight(nodesToDelete); +} + module.exports = appUtilities; diff --git a/app/js/backbone-views.js b/app/js/backbone-views.js index ae9817c5..5dee1c8d 100644 --- a/app/js/backbone-views.js +++ b/app/js/backbone-views.js @@ -2048,16 +2048,17 @@ var NeighborhoodQueryView = Backbone.View.extend({ // use the associated cy instance var cy = chiseInstance.getCy(); - - $(self.el).modal("toggle"); - + self.currentQueryParameters.geneSymbols = document.getElementById( "query-neighborhood-gene-symbols" ).value; self.currentQueryParameters.lengthLimit = Number( document.getElementById("query-neighborhood-length-limit").value ); - + var removeDisconnected = document.getElementById( + "query-neighborhood-checkbox" + ).checked; + var geneSymbols = self.currentQueryParameters.geneSymbols.trim(); if (geneSymbols.length === 0) { document.getElementById("query-neighborhood-gene-symbols").focus(); @@ -2080,27 +2081,20 @@ var NeighborhoodQueryView = Backbone.View.extend({ document.getElementById("query-neighborhood-length-limit").focus(); return; } - + var geneSymbolsArray = geneSymbols - .replaceAll("\n", " ") - .replaceAll("\t", " ") - .split(" "); + .replaceAll("\n", " ") + .replaceAll("\t", " ") + .split(" "); // Check if duplicate symbols are given or not if (handleDuplicateGenes(geneSymbolsArray)) { return; } - - chiseInstance.startSpinner("neighborhood-spinner"); - // Check if the gene symbols that are added even exist in the database or not - if (await handleGeneDoesNotExist(geneSymbolsArray)) { - chiseInstance.endSpinner("neighborhood-spinner"); - return; - } - + var queryURL = - "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=NEIGHBORHOOD&limit=" + - self.currentQueryParameters.lengthLimit; - + "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=NEIGHBORHOOD&limit=" + + self.currentQueryParameters.lengthLimit; + var filename = ""; var sources = ""; for (var i = 0; i < geneSymbolsArray.length; i++) { @@ -2114,7 +2108,7 @@ var NeighborhoodQueryView = Backbone.View.extend({ continue; } sources = sources + "&source=" + currentGeneSymbol; - + if (filename == "") { filename = currentGeneSymbol; } else { @@ -2123,18 +2117,51 @@ var NeighborhoodQueryView = Backbone.View.extend({ } filename = filename + "_NEIGHBORHOOD.nwt"; queryURL = queryURL + sources; + + + var neighborhoodQueryHighlighting = function () { + eles = cy.collection(); + geneSymbolsArray.forEach(function (gene) { + eles.merge( + cy.nodes().filter(function (ele) { + if ( + ele.data("label") && + ele + .data("label") + .toLowerCase() + .indexOf(gene.toLowerCase()) >= 0 + ) { + return true; + } + return false; + }) + ); + }); + var x = cy + .elements() + .kNeighborhood( + eles, + self.currentQueryParameters.lengthLimit, + "BOTHSTREAM" + ); + cy.viewUtilities("get").highlight(x.neighborNodes, 2); + cy.viewUtilities("get").highlight(x.neighborEdges, 2); + cy.viewUtilities("get").highlight(eles, 3); + } - if (cy.nodes().length == 0) { + // Define this after the queryURL to make sure. + var sendNeighborhoodQuery = function () { var currentGeneralProperties = appUtilities.getScratch( cy, "currentGeneralProperties" - ); + ); var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; + currentGeneralProperties.inferNestingOnLoad; var currentLayoutProperties = appUtilities.getScratch( cy, "currentLayoutProperties" ); + $.ajax({ type: "get", url: "/utilities/testURL", @@ -2145,40 +2172,22 @@ var NeighborhoodQueryView = Backbone.View.extend({ data.response.statusCode == 200 && data.response.body ) { - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; + var xml = $.parseXML(data.response.body); + $(document).trigger("sbgnvizLoadFile", [filename, cy]); + currentGeneralProperties.inferNestingOnLoad = false; + chiseInstance.updateGraph( + chiseInstance.convertSbgnmlToJson(xml), + undefined, + currentLayoutProperties + ); + currentGeneralProperties.inferNestingOnLoad = + currentInferNestingOnLoad; - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge(cy.nodes().filter(function (ele) { - if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){ - return true; - } - return false; - })) - }) - var x = cy.elements().kNeighborhood(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM'); - cy.viewUtilities('get').highlight(x.neighborNodes, 2); - cy.viewUtilities('get').highlight(x.neighborEdges, 2); - cy.viewUtilities('get').highlight(eles, 3); - // Highlighting feature end + if(removeDisconnected) + appUtilities.removeDisconnectedNodesAfterQuery(geneSymbolsArray); + neighborhoodQueryHighlighting(); - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - } + $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); } else if (data.error) { let { code } = data.error; if (code === "ESOCKETTIMEDOUT") { @@ -2186,11 +2195,15 @@ var NeighborhoodQueryView = Backbone.View.extend({ el: "#prompt-requestTimedOut-table", }).render(); } + } else if (data.response.body === "") { + new PromptEmptyQueryResultView({ + el: "#prompt-emptyQueryResult-table", + }).render(); } else { new PromptInvalidQueryView({ el: "#prompt-invalidQuery-table", }).render(); - } + } chiseInstance.endSpinner("neighborhood-spinner"); }, error: function (xhr, options, err) { @@ -2200,101 +2213,27 @@ var NeighborhoodQueryView = Backbone.View.extend({ chiseInstance.endSpinner("neighborhood-spinner"); }, }); + } + + var sendQueries = async function () { + $(self.el).modal("toggle"); + chiseInstance.startSpinner("neighborhood-spinner"); + // Check if the gene symbols that are added even exist in the database or not + if (await handleGeneDoesNotExist(geneSymbolsArray)) { + chiseInstance.endSpinner("neighborhood-spinner"); + return; + } + sendNeighborhoodQuery(); + } - } - else { + // Ask for permission + if(cy.nodes().length != 0){ new PromptConfirmationView({ el: "#prompt-confirmation-table", - }).render(function () { - var currentGeneralProperties = appUtilities.getScratch( - cy, - "currentGeneralProperties" - ); - var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( - cy, - "currentLayoutProperties" - ); - - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if ( - !data.error && - data.response.statusCode == 200 && - data.response.body - ) { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - var x = cy - .elements() - .kNeighborhood( - eles, - self.currentQueryParameters.lengthLimit, - "BOTHSTREAM" - ); - cy.viewUtilities("get").highlight(x.neighborNodes, 2); - cy.viewUtilities("get").highlight(x.neighborEdges, 2); - cy.viewUtilities("get").highlight(eles, 3); - // Highlighting feature end - - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - } - } else if (data.response.body === "") { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - } else { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - } - chiseInstance.endSpinner("neighborhood-spinner"); - }, - error: function (xhr, options, err) { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - chiseInstance.endSpinner("neighborhood-spinner"); - }, - }); - },()=>chiseInstance.endSpinner("neighborhood-spinner")); + }).render(sendQueries, ()=>{return;}); + } + else{ + sendQueries(); } }); @@ -2344,14 +2283,15 @@ var PathsBetweenQueryView = Backbone.View.extend({ // use the associated cy instance var cy = chiseInstance.getCy(); - $(self.el).modal("toggle"); - self.currentQueryParameters.geneSymbols = document.getElementById( "query-pathsbetween-gene-symbols" ).value; self.currentQueryParameters.lengthLimit = Number( document.getElementById("query-pathsbetween-length-limit").value ); + var removeDisconnected = document.getElementById( + "query-pathsbetween-checkbox" + ).checked; var geneSymbols = self.currentQueryParameters.geneSymbols.trim(); if (geneSymbols.length === 0) { @@ -2382,16 +2322,7 @@ var PathsBetweenQueryView = Backbone.View.extend({ .split(" "); // Check if duplicate symbols are given or not - if (handleDuplicateGenes(geneSymbolsArray)) { - - return; - } - - - chiseInstance.startSpinner("paths-between-spinner"); - // Check if the gene symbols that are added even exist in the database or not - if (await handleGeneDoesNotExist(geneSymbolsArray)) { - chiseInstance.endSpinner("paths-between-spinner"); + if (handleDuplicateGenes(geneSymbolsArray)) { return; } @@ -2424,88 +2355,89 @@ var PathsBetweenQueryView = Backbone.View.extend({ } filename = filename + "_PATHSBETWEEN.nwt"; queryURL = queryURL + sources; - - if (cy.nodes().length == 0) { + + var pathsBetweenQueryHighlighting = function () { + eles = cy.collection(); + geneSymbolsArray.forEach(function (gene) { + eles.merge( + cy.nodes().filter(function (ele) { + if ( + ele.data("label") && + ele + .data("label") + .toLowerCase() + .indexOf(gene.toLowerCase()) >= 0 + ) { + return true; + } + return false; + }) + ); + }); + var x = cy + .elements() + .pathsBetween( + eles, + self.currentQueryParameters.lengthLimit, + "UNDIRECTED" + ); + cy.viewUtilities("get").highlight(x.resultEdges, 2); + cy.viewUtilities("get").highlight(x.resultNodes, 2); + cy.viewUtilities("get").highlight(eles, 3); + } + + var sendPathsBetweenQuery = function () { var currentGeneralProperties = appUtilities.getScratch( cy, "currentGeneralProperties" ); - var currentInferNestingOnLoad = + var currentInferNestingOnLoad = currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( + var currentLayoutProperties = appUtilities.getScratch( cy, "currentLayoutProperties" ); - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if (!data.error && data.response.statusCode == 200) { - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - // chiseInstance.endSpinner("paths-between-spinner"); - - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - var x = cy - .elements() - .pathsBetween( - eles, - self.currentQueryParameters.lengthLimit, - "UNDIRECTED" - ); - cy.viewUtilities("get").highlight(x.resultEdges, 2); - cy.viewUtilities("get").highlight(x.resultNodes, 2); - cy.viewUtilities("get").highlight(eles, 3); - // Highlighting feature end + $.ajax({ + type: "get", + url: "/utilities/testURL", + data: { url: queryURL }, + success: function (data) { + if (!data.error && data.response.statusCode == 200) { + if (data.response.body !== "") { + var xml = $.parseXML(data.response.body); + $(document).trigger("sbgnvizLoadFile", [filename, cy]); + currentGeneralProperties.inferNestingOnLoad = false; + chiseInstance.updateGraph( + chiseInstance.convertSbgnmlToJson(xml), + undefined, + currentLayoutProperties + ); + currentGeneralProperties.inferNestingOnLoad = + currentInferNestingOnLoad; + + if(removeDisconnected) + appUtilities.removeDisconnectedNodesAfterQuery(geneSymbolsArray); + pathsBetweenQueryHighlighting(); - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-requestTimedOut-table", - }).render(); - // chiseInstance.endSpinner("paths-between-spinner"); - } - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - // chiseInstance.endSpinner("paths-between-spinner"); - } + $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); } else { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", + new PromptEmptyQueryResultView({ + el: "#prompt-requestTimedOut-table", }).render(); - } + } + } else if (data.error) { + let { code } = data.error; + if (code === "ESOCKETTIMEDOUT") { + new PromptRequestTimedOutView({ + el: "#prompt-requestTimedOut-table", + }).render(); + } + } else { + new PromptInvalidQueryView({ + el: "#prompt-invalidQuery-table", + }).render(); + } chiseInstance.endSpinner("paths-between-spinner"); }, error: function (xhr, options, err) { @@ -2515,104 +2447,27 @@ var PathsBetweenQueryView = Backbone.View.extend({ chiseInstance.endSpinner("paths-between-spinner"); }, }); - // $(self.el).modal("toggle"); - } else { - // console.log("Came here where there are nodes in cy"); + } + + var sendQueries = async function() { + $(self.el).modal("toggle"); + chiseInstance.startSpinner("paths-between-spinner"); + // Check if the gene symbols that are added even exist in the database or not + if (await handleGeneDoesNotExist(geneSymbolsArray)) { + chiseInstance.endSpinner("paths-between-spinner"); + return; + } + + sendPathsBetweenQuery(); + } + + if (cy.nodes().length != 0) { new PromptConfirmationView({ el: "#prompt-confirmation-table", - }).render(function () { - var currentGeneralProperties = appUtilities.getScratch( - cy, - "currentGeneralProperties" - ); - var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( - cy, - "currentLayoutProperties" - ); - - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if (!data.error && data.response.statusCode == 200) { - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - // chiseInstance.endSpinner("paths-between-spinner"); - - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - var x = cy - .elements() - .pathsBetween( - eles, - self.currentQueryParameters.lengthLimit, - "UNDIRECTED" - ); - cy.viewUtilities("get").highlight(x.resultEdges, 2); - cy.viewUtilities("get").highlight(x.resultNodes, 2); - cy.viewUtilities("get").highlight(eles, 3); - // Highlighting feature end - - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - // chiseInstance.endSpinner("paths-between-spinner"); - } - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - // chiseInstance.endSpinner("paths-between-spinner"); - } - } else { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - } - chiseInstance.endSpinner("paths-between-spinner"); - }, - error: function (xhr, options, err) { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - chiseInstance.endSpinner("paths-between-spinner"); - }, - }) - },()=>chiseInstance.endSpinner("paths-between-spinner")); + }).render(sendQueries, ()=>{return;}); + } else { + sendQueries(); } - }); $(document) @@ -2662,8 +2517,6 @@ var PathsFromToQueryView = Backbone.View.extend({ // use the associated cy instance var cy = chiseInstance.getCy(); - $(self.el).modal("toggle"); - self.currentQueryParameters.sourceSymbols = document.getElementById( "query-pathsfromto-source-symbols" ).value; @@ -2673,6 +2526,9 @@ var PathsFromToQueryView = Backbone.View.extend({ self.currentQueryParameters.lengthLimit = Number( document.getElementById("query-pathsfromto-length-limit").value ); + var removeDisconnected = document.getElementById( + "query-pathsfromto-checkbox" + ).checked; var sourceSymbols = self.currentQueryParameters.sourceSymbols.trim(); if (sourceSymbols.length === 0) { @@ -2703,7 +2559,7 @@ var PathsFromToQueryView = Backbone.View.extend({ }).render(); return; } - + if (self.currentQueryParameters.lengthLimit > 3) { $(self.el).modal("toggle"); new PromptInvalidLengthLimitView({ @@ -2712,10 +2568,7 @@ var PathsFromToQueryView = Backbone.View.extend({ document.getElementById("query-pathsfromto-length-limit").focus(); return; } - - var queryURL = - "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=PATHSFROMTO&limit=" + - self.currentQueryParameters.lengthLimit; + var sourceSymbolsArray = sourceSymbols .replaceAll("\n", " ") .replaceAll("\t", " ") @@ -2725,29 +2578,15 @@ var PathsFromToQueryView = Backbone.View.extend({ .replaceAll("\t", " ") .split(" "); - - chiseInstance.startSpinner("paths-fromto-spinner"); // Check if duplicate symbols are given or not if (handleDuplicateGenes(sourceSymbolsArray)) { chiseInstance.endSpinner("paths-fromto-spinner"); return; } - // Check if the gene symbols that are added even exist in the database or not - if (await handleGeneDoesNotExist(sourceSymbolsArray)) { - chiseInstance.endSpinner("paths-fromto-spinner"); - return; - } - // Check if duplicate symbols are given or not - if (handleDuplicateGenes(targetSymbolsArray)) { - chiseInstance.endSpinner("paths-fromto-spinner"); - return; - } - // Check if the gene symbols that are added even exist in the database or not - if (await handleGeneDoesNotExist(targetSymbolsArray)) { - chiseInstance.endSpinner("paths-fromto-spinner"); - return; - } + var queryURL = + "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=PATHSFROMTO&limit=" + + self.currentQueryParameters.lengthLimit; var filename = ""; var sources = ""; @@ -2762,8 +2601,8 @@ var PathsFromToQueryView = Backbone.View.extend({ ) { continue; } - sources = sources + "&source=" + currentGeneSymbol; - + sources = sources + "&source=" + currentGeneSymbol; + if (filename == "") { filename = currentGeneSymbol; } else { @@ -2781,7 +2620,6 @@ var PathsFromToQueryView = Backbone.View.extend({ continue; } targets = targets + "&target=" + currentGeneSymbol; - if (filename == "") { filename = currentGeneSymbol; } else { @@ -2791,8 +2629,57 @@ var PathsFromToQueryView = Backbone.View.extend({ filename = filename + "_PATHSFROMTO.nwt"; queryURL = queryURL + sources + targets; - if (cy.nodes().length == 0) { - + var pathsFromToQueryHighlighting = function () { + source_eles = cy.collection(); + sourceSymbolsArray.forEach(function (gene) { + source_eles.merge( + cy.nodes().filter(function (ele) { + if ( + ele.data("label") && + ele + .data("label") + .toLowerCase() + .indexOf(gene.toLowerCase()) >= 0 + ) { + return true; + } + return false; + }) + ); + }); + target_eles = cy.collection(); + targetSymbolsArray.forEach(function (gene) { + target_eles.merge( + cy.nodes().filter(function (ele) { + if ( + ele.data("label") && + ele + .data("label") + .toLowerCase() + .indexOf(gene.toLowerCase()) >= 0 + ) { + return true; + } + return false; + }) + ); + }); + var x = cy + .elements() + .pathsFromTo( + source_eles, + target_eles, + self.currentQueryParameters.lengthLimit, + self.currentQueryParameters.lengthLimit, + "UNDIRECTED" + ); + cy.viewUtilities("get").highlight(x.edgesOnThePaths, 2); + // cy.viewUtilities('get').highlight(x.nodesOnThePaths, 2); + cy.viewUtilities('get').highlight(source_eles, 3); + cy.viewUtilities('get').highlight(target_eles, 1); + } + + var sendPathsFromToQuery = function () { var currentGeneralProperties = appUtilities.getScratch( cy, "currentGeneralProperties" @@ -2803,8 +2690,7 @@ var PathsFromToQueryView = Backbone.View.extend({ cy, "currentLayoutProperties" ); - - + $.ajax({ type: "get", url: "/utilities/testURL", @@ -2822,63 +2708,16 @@ var PathsFromToQueryView = Backbone.View.extend({ ); currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad; - - // Highlighting feature - source_eles = cy.collection(); - sourceSymbolsArray.forEach(function (gene) { - source_eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - target_eles = cy.collection(); - targetSymbolsArray.forEach(function (gene) { - target_eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - var x = cy - .elements() - .pathsFromTo( - source_eles, - target_eles, - self.currentQueryParameters.lengthLimit, - self.currentQueryParameters.lengthLimit, - "UNDIRECTED" - ); - cy.viewUtilities("get").highlight(x.edgesOnThePaths, 2); - // cy.viewUtilities('get').highlight(x.nodesOnThePaths, 2); - cy.viewUtilities('get').highlight(source_eles, 3); - cy.viewUtilities('get').highlight(target_eles, 1); - // Highlighting feature end + + if(removeDisconnected) + appUtilities.removeDisconnectedNodesAfterQuery(sourceSymbolsArray.concat(targetSymbolsArray)); + pathsFromToQueryHighlighting(); $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); } else { new PromptEmptyQueryResultView({ el: "#prompt-emptyQueryResult-table", }).render(); - // chiseInstance.endSpinner("paths-fromto-spinner"); } } else if (data.error) { let { code } = data.error; @@ -2886,7 +2725,6 @@ var PathsFromToQueryView = Backbone.View.extend({ new PromptRequestTimedOutView({ el: "#prompt-requestTimedOut-table", }).render(); - // chiseInstance.endSpinner("paths-fromto-spinner"); } } else { @@ -2903,103 +2741,25 @@ var PathsFromToQueryView = Backbone.View.extend({ chiseInstance.endSpinner("paths-fromto-spinner"); }, }); + } - // $(self.el).modal("toggle"); - } else { + var sendQueries = async function () { + $(self.el).modal("toggle"); + // Check if the gene symbols that are added even exist in the database or not + chiseInstance.startSpinner("paths-fromto-spinner"); + if (await handleGeneDoesNotExist(sourceSymbolsArray)) { + chiseInstance.endSpinner("paths-fromto-spinner"); + return; + } + sendPathsFromToQuery(); + } + + if (cy.nodes().length != 0) { new PromptConfirmationView({ el: "#prompt-confirmation-table", - }).render(function () { - var currentGeneralProperties = appUtilities.getScratch( - cy, - "currentGeneralProperties" - ); - var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( - cy, - "currentLayoutProperties" - ); - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if (!data.error && data.response.statusCode == 200) { - - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - - // Highlighting feature - source_eles = cy.collection(); - sourceSymbolsArray.forEach(function (gene) { - source_eles.merge( - cy.nodes().filter(function (ele) { - if ( - ele.data("label") && - ele - .data("label") - .toLowerCase() - .indexOf(gene.toLowerCase()) >= 0 - ) { - return true; - } - return false; - }) - ); - }); - target_eles = cy.collection(); - targetSymbolsArray.forEach(function (gene) { - target_eles.merge(cy.nodes().filter(function (ele) { - if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){ - return true; - } - return false; - })) - }) - var x = cy.elements().pathsFromTo(source_eles, target_eles, self.currentQueryParameters.lengthLimit, self.currentQueryParameters.lengthLimit, 'UNDIRECTED'); - cy.viewUtilities('get').highlight(x.edgesOnThePaths, 2); - // cy.viewUtilities('get').highlight(x.nodesOnThePaths, 2); - cy.viewUtilities('get').highlight(source_eles, 3); - cy.viewUtilities('get').highlight(target_eles, 1); - // Highlighting feature end - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - } - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - } - } else { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - } - chiseInstance.endSpinner("paths-fromto-spinner"); - }, - error: function (xhr, options, err) { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - chiseInstance.endSpinner("paths-fromto-spinner"); - }, - }); - - },()=>chiseInstance.endSpinner("paths-fromto-spinner")); + }).render(sendQueries, ()=>{return;}); + } else { + sendQueries(); } }); @@ -3049,14 +2809,15 @@ var CommonStreamQueryView = Backbone.View.extend({ // use the associated cy instance var cy = chiseInstance.getCy(); - $(self.el).modal("toggle"); - self.currentQueryParameters.geneSymbols = document.getElementById( "query-commonstream-gene-symbols" ).value; self.currentQueryParameters.lengthLimit = Number( document.getElementById("query-commonstream-length-limit").value ); + var removeDisconnected = document.getElementById( + "query-commonstream-checkbox" + ).checked; var geneSymbols = self.currentQueryParameters.geneSymbols.trim(); if (geneSymbols.length === 0) { @@ -3081,26 +2842,19 @@ var CommonStreamQueryView = Backbone.View.extend({ return; } - var queryURL = - "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=COMMONSTREAM&limit=" + - self.currentQueryParameters.lengthLimit; var geneSymbolsArray = geneSymbols - .replaceAll("\n", " ") - .replaceAll("\t", " ") - .split(" "); - + .replaceAll("\n", " ") + .replaceAll("\t", " ") + .split(" "); + // Check if duplicate symbols are given or not if (handleDuplicateGenes(geneSymbolsArray)) { return; } - - chiseInstance.startSpinner("common-stream-spinner"); - // Check if the gene symbols that are added even exist in the database or not - if (await handleGeneDoesNotExist(geneSymbolsArray)) { - chiseInstance.endSpinner("common-stream-spinner"); - return; - } - + + var queryURL = + "http://www.pathwaycommons.org/pc2/graph?format=SBGN&kind=COMMONSTREAM&limit=" + + self.currentQueryParameters.lengthLimit; var filename = ""; var sources = ""; for (var i = 0; i < geneSymbolsArray.length; i++) { @@ -3124,8 +2878,24 @@ var CommonStreamQueryView = Backbone.View.extend({ filename = filename + "_COMMONSTREAM.nwt"; queryURL = queryURL + sources; - if (cy.nodes().length == 0) { - + var commonStreamHighlighting = function () { + eles = cy.collection(); + geneSymbolsArray.forEach(function (gene) { + eles.merge(cy.nodes().filter(function (ele) { + if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){ + return true; + } + return false; + })) + }) + var x = cy.elements().commonStream(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM'); + cy.viewUtilities('get').highlight(x.nodesOnPath, 2); + cy.viewUtilities('get').highlight(x.edgesOnPath, 2); + cy.viewUtilities('get').highlight(x.commonNodes, 1); + cy.viewUtilities('get').highlight(eles, 3); + } + + var sendCommonStreamQuery = function () { var currentGeneralProperties = appUtilities.getScratch( cy, "currentGeneralProperties" @@ -3154,23 +2924,10 @@ var CommonStreamQueryView = Backbone.View.extend({ ); currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad; - - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge(cy.nodes().filter(function (ele) { - if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){ - return true; - } - return false; - })) - }) - var x = cy.elements().commonStream(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM'); - cy.viewUtilities('get').highlight(x.nodesOnPath, 2); - cy.viewUtilities('get').highlight(x.edgesOnPath, 2); - cy.viewUtilities('get').highlight(x.commonNodes, 1); - cy.viewUtilities('get').highlight(eles, 3); - // Highlighting feature end + + if(removeDisconnected) + appUtilities.removeDisconnectedNodesAfterQuery(geneSymbolsArray); + commonStreamHighlighting(); $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); } else { @@ -3199,87 +2956,25 @@ var CommonStreamQueryView = Backbone.View.extend({ chiseInstance.endSpinner("common-stream-spinner"); }, }); + } - } else { + var sendQueries = async function () { + $(self.el).modal("toggle"); + chiseInstance.startSpinner("common-stream-spinner"); + // Check if the gene symbols that are added even exist in the database or not + if (await handleGeneDoesNotExist(geneSymbolsArray)) { + chiseInstance.endSpinner("common-stream-spinner"); + return; + } + sendCommonStreamQuery(); + } + + if (cy.nodes().length != 0) { new PromptConfirmationView({ el: "#prompt-confirmation-table", - }).render(function () { - - var currentGeneralProperties = appUtilities.getScratch( - cy, - "currentGeneralProperties" - ); - var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( - cy, - "currentLayoutProperties" - ); - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if (!data.error && data.response.statusCode == 200) { - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - - // Highlighting feature - eles = cy.collection(); - geneSymbolsArray.forEach(function (gene) { - eles.merge(cy.nodes().filter(function (ele) { - if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){ - return true; - } - return false; - })) - }) - var x = cy.elements().commonStream(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM'); - cy.viewUtilities('get').highlight(x.nodesOnPath, 2); - cy.viewUtilities('get').highlight(x.edgesOnPath, 2); - cy.viewUtilities('get').highlight(x.commonNodes, 1); - cy.viewUtilities('get').highlight(eles, 3); - // Highlighting feature end - - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - } - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - } - } else { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - } - chiseInstance.endSpinner("common-stream-spinner"); - }, - error: function (xhr, options, err) { - new PromptInvalidQueryView({ - el: "#prompt-invalidQuery-table", - }).render(); - chiseInstance.endSpinner("common-stream-spinner"); - }, - }); - - - },()=>chiseInstance.endSpinner("common-stream-spinner")); + }).render(sendQueries, ()=>{return;}); + } else { + sendQueries(); } }); @@ -3292,6 +2987,7 @@ var CommonStreamQueryView = Backbone.View.extend({ return this; }, }); + /** * Paths By URI Query view for the Sample Application. */ @@ -3326,8 +3022,6 @@ var PathsByURIQueryView = Backbone.View.extend({ // use the associated cy instance var cy = chiseInstance.getCy(); - $(self.el).modal("toggle"); - self.currentQueryParameters.URI = document.getElementById( "query-pathsbyURI-URI" ).value; @@ -3355,11 +3049,9 @@ var PathsByURIQueryView = Backbone.View.extend({ } else { filename = filename + "_" + uri; } - filename = filename + "_URI.nwt"; - if (cy.nodes().length == 0) { - + var sendPathsByURIQuery = function () { var currentGeneralProperties = appUtilities.getScratch( cy, "currentGeneralProperties" @@ -3389,6 +3081,7 @@ var PathsByURIQueryView = Backbone.View.extend({ ); currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad; + appUtilities.removeDisconnectedNodesAfterQuery([]); $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); } else { new PromptEmptyQueryResultView({ @@ -3418,70 +3111,15 @@ var PathsByURIQueryView = Backbone.View.extend({ }, }); - } else { + $(self.el).modal("toggle"); + } + + if (cy.nodes().length != 0) { new PromptConfirmationView({ el: "#prompt-confirmation-table", - }).render(function () { - - var currentGeneralProperties = appUtilities.getScratch( - cy, - "currentGeneralProperties" - ); - var currentInferNestingOnLoad = - currentGeneralProperties.inferNestingOnLoad; - var currentLayoutProperties = appUtilities.getScratch( - cy, - "currentLayoutProperties" - ); - chiseInstance.startSpinner("paths-byURI-spinner"); - $.ajax({ - type: "get", - url: "/utilities/testURL", - data: { url: queryURL }, - success: function (data) { - if (!data.error && data.response.statusCode == 200) { - if (data.response.body !== "") { - var xml = $.parseXML(data.response.body); - $(document).trigger("sbgnvizLoadFile", [filename, cy]); - currentGeneralProperties.inferNestingOnLoad = false; - chiseInstance.updateGraph( - chiseInstance.convertSbgnmlToJson(xml), - undefined, - currentLayoutProperties - ); - currentGeneralProperties.inferNestingOnLoad = - currentInferNestingOnLoad; - $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]); - } else { - new PromptEmptyQueryResultView({ - el: "#prompt-emptyQueryResult-table", - }).render(); - } - } else if (data.error) { - let { code } = data.error; - if (code === "ESOCKETTIMEDOUT") { - new PromptRequestTimedOutView({ - el: "#prompt-requestTimedOut-table", - }).render(); - } - } else { - new PromptInvalidURIView({ - el: "#prompt-invalidURI-table", - }).render(); - - } - chiseInstance.endSpinner("paths-byURI-spinner"); - }, - error: function (xhr, options, err) { - new PromptInvalidURIView({ - el: "#prompt-invalidURI-table", - }).render(); - chiseInstance.endSpinner("paths-byURI-spinner"); - }, - }); - - - },()=>chiseInstance.endSpinner("paths-byURI-spinner")); + }).render(sendPathsByURIQuery ,()=>{return;}); + } else { + sendPathsByURIQuery(); } }); diff --git a/index.html b/index.html index e46d0db1..477e03e3 100644 --- a/index.html +++ b/index.html @@ -3532,44 +3532,55 @@

Layout Properties

- -

Neighborhood Query

+ +

Neighborhood Query

- - - - - +
- - Find the neighbors of an entity within a certain distance               -
+ + + + - - + - + - - -
+ + Find the neighbors of an entity within a certain distance               +
- Gene Symbols:
- - 		+ + + + + + +
Gene Symbols
+ + +
+ 		- - - - - - - - -
Stop Distance
Length limit >
- 		+ + + + + + + + +
Stop Distance
Length limit >
+
+
Remove Disconnected Nodes:
+ +
+
+ + +
- - + +
@@ -3592,22 +3603,34 @@

Paths Between Query

- - Gene Symbols:
- - - - - - - - - - - - -
Stop Distance
Length limit >
- + + + + + + + +
Gene Symbols
+ + +
+ + + + + + + + + + + +
Stop Distance
Length limit >
+
+
Remove Disconnected Nodes:
+ +
+ @@ -3622,7 +3645,7 @@

Paths Between Query