Merge pull request #555 from jjgao/master

release v0.1.2

.codeclimate.yml

@@ -0,0 +1,27 @@
+languages:
+    JavaScript: true
+    Python: true
+
+exclude_paths:
+- "test/*"
+
+engines:
+  rubocop:
+    enabled: true
+  golint:
+    enabled: true
+  gofmt:
+    enabled: true
+  csslint:
+    enabled: true
+
+ratings:
+   paths:
+   - app/**
+   - lib/**
+   - "**.rb"
+   - "**.go"
+
+exclude_paths:
+- spec/**/*
+- vendor/**/*

business/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>0.1.1</version>
+    <version>0.1.2</version>
   </parent>
 
   <!-- module metadata -->

core/pom.xml

@@ -5,7 +5,7 @@
   <parent>
 	<artifactId>master</artifactId>
 	<groupId>org.mskcc.cbio</groupId>
-	<version>0.1.1</version>
+	<version>0.1.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>

core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

@@ -1228,6 +1228,7 @@ public static Collection<Map<String, Object>> countSamplesWithProteinPosStarts(
 				String hugo = gene.getHugoGeneSymbolAllCaps();
 
 				d.put("protein_pos_start", proteinPosStart);
+				d.put("protein_start_with_hugo", hugo+"_"+proteinPosStart);
 				d.put("hugo", hugo);
 				d.put("cancer_study", name);
 				d.put("cancer_type", cancerType);

core/src/main/java/org/mskcc/cbio/portal/servlet/MutationsJSON.java

@@ -536,6 +536,8 @@ private Map<String,List> initMap() {
         map.put("end", new ArrayList());
         map.put("entrez", new ArrayList());
         map.put("gene", new ArrayList());
+        map.put("protein-start", new ArrayList());
+        map.put("protein-end", new ArrayList());
         map.put("aa", new ArrayList());
 	map.put("aa-orig", new ArrayList());
         map.put("ref", new ArrayList());
@@ -599,6 +601,8 @@ private void exportMutation(Map<String,List> data, Map<Long, Integer> mapMutatio
         String symbol = mutation.getGeneSymbol();
         data.get("entrez").add(mutation.getEntrezGeneId());
         data.get("gene").add(symbol);
+        data.get("protein-start").add(mutation.getOncotatorProteinPosStart());
+        data.get("protein-end").add(mutation.getOncotatorProteinPosEnd());
         data.get("aa").add(mutation.getProteinChange());
 	data.get("aa-orig").add(mutation.getAminoAcidChange());
         data.get("ref").add(mutation.getReferenceAllele());

core/src/main/java/org/mskcc/cbio/portal/servlet/PancancerMutationsJSON.java

@@ -53,6 +53,9 @@
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import org.mskcc.cbio.portal.model.CanonicalGene;
 
 /**
  * @author Gideon Dresdner <dresdnerg@cbio.mskcc.org>
@@ -136,19 +139,31 @@ public Collection<Map<String, Object>> byProteinPosStarts(List<String> proteinPo
 	{
 		List<String> posWithEntrez = new ArrayList<String>();
 
+                DaoGeneOptimized daoGeneOptimized = DaoGeneOptimized.getInstance();
+
+                // assuming that protein position start string is in a format <GENE>_<POSITION>
+                Pattern p = Pattern.compile("(.+)_([0-9]+)");
 		for (String proteinPos: proteinPosStarts)
 		{
+                        Matcher m = p.matcher(proteinPos);
+                        if (m.find()) {
+                            String symbol = m.group(1);
+                            String position = m.group(2);
+                            CanonicalGene gene = daoGeneOptimized.getGene(symbol);
+                            if (gene!=null) {
+                                long entrezId = gene.getEntrezGeneId();
+
+                                // create the query string: (<ENTREZ ID>,<POSITION>)
+                                posWithEntrez.add("(" + entrezId + "," + position + ")");
+                            }
+                        }
+
 			String[] parts = proteinPos.split("_");
-
-			// assuming that protein position start string is in a format <GENE>_<POSITION>
-			if (parts.length > 1)
-			{
-				// get entrez gene id corresponding to the gene symbol
-				long entrezId = DaoGeneOptimized.getInstance().getGene(parts[0]).getEntrezGeneId();
-				// create the query string: (<ENTREZ ID>,<POSITION>)
-				posWithEntrez.add("(" + entrezId + "," + parts[1] + ")");
-			}
 		}
+
+                if (posWithEntrez.isEmpty()) {
+                    return Collections.emptySet();
+                }
 
 		return DaoMutation.countSamplesWithProteinPosStarts(posWithEntrez, internalGeneticProfileIds());
 	}

pom.xml

@@ -6,7 +6,7 @@
     <artifactId>master</artifactId>
     <packaging>pom</packaging>
     <name>Portal Master</name>
-    <version>0.1.1</version>
+    <version>0.1.2</version>
     <description>master maven module</description>
     <scm>
         <developerConnection>scm:git:https://github.com/cBioPortal/cbioportal.git</developerConnection>

portal/pom.xml

@@ -4,7 +4,7 @@
   <parent>
 	<artifactId>master</artifactId>
 	<groupId>org.mskcc.cbio</groupId>
-	<version>0.1.1</version>
+	<version>0.1.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>cbioportal</artifactId>

portal/src/main/webapp/WEB-INF/jsp/cross_cancer_results.jsp

@@ -123,9 +123,8 @@
     var showHotspot = <%=showHotspot%>;
     var enableMyCancerGenome = myCancerGenomeUrl?true:false;
 
-    OncoKB.setUrl('<%=oncokbUrl%>');
-
     $(document).ready(function() {
+        OncoKB.setUrl('<%=oncokbUrl%>');
         //Set Event listener for the modify query button (expand the hidden form)
         $("#modify_query_btn").click(function () {
             $("#query_form_on_results_page").toggle();

portal/src/main/webapp/WEB-INF/jsp/mutation_details.jsp

@@ -86,10 +86,9 @@
     _mut3dVis = new Mutation3dVis("default3dView");
     _mut3dVis.init();
 
-    OncoKB.setUrl('<%=oncokbUrl%>');
-
     // Set up Mutation View
     $(document).ready(function () {
+        OncoKB.setUrl('<%=oncokbUrl%>');
         var sampleArray = _.keys(PortalGlobals.getPatientSampleIdMap());
         var mutationProxy = DataProxyFactory.getDefaultMutationDataProxy();
 
@@ -168,7 +167,7 @@
                             }
 
                             if(showHotspot && mutation['isHotspot']) {
-                                vars.changHotspotAlt = "<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on Chang, M. et al. Nature Biotech. 2015).";
+                                vars.changHotspotAlt = "<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on <a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/26619011&quot; target=&quot;_blank&quot;>Chang, M. et al. Nature Biotech. 2015</a>).";
                             }
 
                             var templateFn = BackboneTemplateCache.getTemplateFn("mutation_table_protein_change_oncokb_template");
@@ -254,7 +253,7 @@
                             }
 
                             if(showHotspot && mutation['isHotspot']) {
-                                vars.changHotspotAlt = "<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on Chang, M. et al. Nature Biotech. 2015).";
+                                vars.changHotspotAlt = "<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on <a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/26619011&quot; target=&quot;_blank&quot;>Chang, M. et al. Nature Biotech. 2015</a>).";
                             }
 
                             var templateFn = BackboneTemplateCache.getTemplateFn("mutation_table_protein_change_oncokb_template");

portal/src/main/webapp/WEB-INF/jsp/networks.jsp

@@ -70,7 +70,7 @@
 <script type="text/javascript" src="js/lib/json2.js?<%=GlobalProperties.getAppVersion()%>"></script>
 <script type="text/javascript" src="js/lib/cytoscape_js/cytoscape.js?<%=GlobalProperties.getAppVersion()%>"></script>
 <script type="text/javascript" src="js/lib/cytoscape_js/cytoscape.js-panzoom.js?<%=GlobalProperties.getAppVersion()%>"></script>
-<script type="text/javascript" src="js/lib/cytoscape_js/layout.cose2.js?<%=GlobalProperties.getAppVersion()%>"></script>
+<script type="text/javascript" src="js/lib/cytoscape_js/layout.cose-bilkent.js?<%=GlobalProperties.getAppVersion()%>"></script>
 
 <!-- <script type="text/javascript" src="js/src/network/network-ui.js?<%=GlobalProperties.getAppVersion()%>"></script> -->
 <script type="text/javascript" src="js/src/network/network-visualization.js?<%=GlobalProperties.getAppVersion()%>"></script>

portal/src/main/webapp/WEB-INF/jsp/step3_json.jsp

@@ -50,14 +50,20 @@
 	 				Build Case Set
 	 			</a>
 	 			-->
-                <div style="padding-left: 10px">
+	 		</td>
+		</tr>
+        <tr>
+            <td></td>
+            <td>
+                <div>
                     <!-- add new link for the new functionality which links to the study view -->
                     <a id="build_case_set" onclick="openStudyView()" title="Build a Case Set via Study View">
                         <%= GlobalProperties.getStudyviewLinkText()%>
                     </a>
                 </div>
-	 		</td>
-		</tr>
+            </td>
+            <td></td>
+        </tr>
 	</table>
 
 	<div id="custom_case_set_dialog" title="Build a Case Set">

portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/mutations.jsp

@@ -57,17 +57,19 @@
             $(oTable).find('.pancan_mutations_histogram_count').each(function() {
                 if ($(this).hasClass("initialized")) return;
                 $(this).addClass("initialized");
+                var proteinPos = $(this).attr('protein_pos');
                 var keyword = $(this).attr('keyword');
                 var gene = $(this).attr('gene');
-                $(this).html(genomicEventObs.pancan_mutation_frequencies.countByKey(keyword));
+                $(this).html(genomicEventObs.pancan_mutation_frequencies.countByKey(proteinPos));
                 $(this).qtip({
                     content: {text: 'pancancer mutation bar chart is broken'},
                     events: {
                         render: function(event, api) {
+                            var byPositionData = genomicEventObs.pancan_mutation_frequencies.data[proteinPos];
                             var byKeywordData = genomicEventObs.pancan_mutation_frequencies.data[keyword];
                             var byHugoData = genomicEventObs.pancan_mutation_frequencies.data[gene];
                             var invisible_container = document.getElementById("pancan_mutations_histogram_container");
-                            var histogram = PancanMutationHistogram(byKeywordData, byHugoData, window.cancer_study_meta_data, invisible_container, {this_cancer_study: window.cancerStudyName});
+                            var histogram = PancanMutationHistogram(byPositionData, byKeywordData, byHugoData, window.cancer_study_meta_data, invisible_container, {this_cancer_study: window.cancerStudyName});
 
                             var title = "<div><div><h3>"+gene+" mutations across all cancer studies</h3></div>" +
                                         "<div style='float:right;'><button class='cross-cancer-download' file-type='pdf'>PDF</button>"+
@@ -704,10 +706,11 @@
                             if (type === 'display') {
                                 var keyword = mutations.getValue(source[0], "key");
                                 var hugo = mutations.getValue(source[0], "gene");
+                                var proteinPos = hugo+"_"+mutations.getValue(source[0], "protein-start");
 
-                                var ret = "<div class='pancan_mutations_histogram_thumbnail' gene='"+hugo+"' keyword='"+keyword+"'></div>";
+                                var ret = "<div class='pancan_mutations_histogram_thumbnail' protein_pos='"+proteinPos+"' gene='"+hugo+"' keyword='"+keyword+"'></div>";
                                     ret += "<img width='15' height='15' class='pancan_mutations_histogram_wait' src='images/ajax-loader.gif'/>";
-                                    ret += "<div class='pancan_mutations_histogram_count' style='float:right' gene='"+hugo+"' keyword='"+keyword+"'></div>";
+                                    ret += "<div class='pancan_mutations_histogram_count' style='float:right' protein_pos='"+proteinPos+"' gene='"+hugo+"' keyword='"+keyword+"'></div>";
 
                                 return ret;
                             }
@@ -897,7 +900,7 @@
                     addNoteTooltip("."+table_id+"-tip");
                     addNoteTooltip("."+table_id+"-ma-tip",null,{my:'top right',at:'bottom center',viewport: $(window)});
                     if(showHotspot) {
-                        addNoteTooltip('.'+table_id+'-hotspot', '<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on Chang, M. et al. Nature Biotech. 2015).');
+                        addNoteTooltip('.'+table_id+'-hotspot', "<b>Recurrent Hotspot</b><br/>This mutated amino acid was identified as a recurrent hotspot (statistical significance, q-value < 0.01) in a set of 11,119 tumor samples of various cancer types (based on <a href='http://www.ncbi.nlm.nih.gov/pubmed/26619011' target='_blank'>Chang, M. et al. Nature Biotech. 2015</a>).");
                     }
                     addDrugsTooltip("."+table_id+"-drug-tip", 'top right', 'bottom center');
                     addCosmicTooltip(table_id);
@@ -1155,6 +1158,7 @@
                     var pancanMutationsUrl = "pancancerMutations.json";
                     var byKeywordResponse = [];
                     var byHugoResponse = [];
+                    var byProteinPosResponse = [];
 
                     function munge(response, key) {
                         // munge data to get it into the format: keyword -> corresponding datum
@@ -1179,10 +1183,12 @@
                                                 cmd: cmd,
                                                 q: accData
                                             }, function(batchData) {
-                                                if(cmd == "byKeywords") {
+                                                if(cmd === "byKeywords") {
                                                     byKeywordResponse = byKeywordResponse.concat(batchData);
-                                                } else if( cmd == "byHugos") {
+                                                } else if( cmd === "byHugos") {
                                                     byHugoResponse = byHugoResponse.concat(batchData);
+                                                } else if (cmd === "byProteinPos") {
+                                                    byProteinPosResponse = byProteinPosResponse.concat(batchData);
                                                 } else {
                                                     console.trace("Ooops! Something is wrong!");
                                                 }
@@ -1195,11 +1201,17 @@
                         return jobs;
                     };
 
-                    var jobs = splitJobs("byKeywords", genomicEventObs.mutations.data.key)
-                            .concat(splitJobs("byHugos", genomicEventObs.mutations.data.gene));
+                    var keys = genomicEventObs.mutations.data.key;
+                    var genes = genomicEventObs.mutations.data.gene;
+                    var positions = _.map(_.zip.apply(_, [genes, genomicEventObs.mutations.data['protein-start']]), function(pieces) {
+                                    return pieces[0]+"_"+pieces[1];
+                               });
+                    var jobs = splitJobs("byKeywords", keys)
+                            .concat(splitJobs("byHugos", genes))
+                            .concat(splitJobs("byProteinPos", positions));
                     $.when.apply($, jobs).done(function() {
                         genomicEventObs.pancan_mutation_frequencies.setData(
-                                _.extend(munge(byKeywordResponse, "keyword"), munge(byHugoResponse, "hugo")));
+                                _.extend(munge(byProteinPosResponse, "protein_start_with_hugo"), munge(byKeywordResponse, "keyword"), munge(byHugoResponse, "hugo")));
                         genomicEventObs.fire("pancan-mutation-frequency-built");
                     });
 

portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp

@@ -419,10 +419,8 @@ var caseMetaData = {
 var oncokbGeneStatus = <%=oncokbGeneStatus%>;
 var showHotspot = <%=showHotspot%>;
 
-OncoKB.setUrl('<%=oncokbUrl%>');
-
-
 $(document).ready(function(){
+    OncoKB.setUrl('<%=oncokbUrl%>');
     if (print) $('#page_wrapper_table').css('width', '900px');
     tweaksStyles();
     outputClinicalData();
@@ -1190,6 +1188,11 @@ function outputClinicalData() {
             diseaseInfo.push("Serum PSA: "+serumPsa);
         }
 
+        var driverMutations = guessClinicalData(clinicalData,["DRIVER_MUTATIONS"]);
+        if (driverMutations!==null) {
+            diseaseInfo.push(driverMutations);
+        }
+
         return diseaseInfo;
     }
 

portal/src/main/webapp/WEB-INF/jsp/visualize.jsp

@@ -288,6 +288,7 @@
 			        clearInterval(interval);
 			        if (firstTime)
 			        {
+                $(window).resize();
 				        send2cytoscapeweb(window.networkGraphJSON, "cytoscapeweb", "network");
 				        firstTime = false;
 			        }
@@ -297,19 +298,27 @@
 
         $("a.result-tab").click(function(){
 
-            if($(this).attr("href")=="#network") {
-                if(firstTime)
-                {
-                  send2cytoscapeweb(window.networkGraphJSON, "cytoscapeweb", "network");
-                  firstTime = false;
-                }
-	            else
+            if($(this).attr("href")=="#network")
+            {
+              var interval = setInterval(function() {
+                if (window.networkGraphJSON != null)
                 {
-	                // TODO this is a workaround to adjust cytoscape canvas
-	                // and probably not the best way to do it...
-	                $(window).resize();
-                }
+                  clearInterval(interval);
+                  if(firstTime)
+                  {
+                    $(window).resize();
+                    send2cytoscapeweb(window.networkGraphJSON, "cytoscapeweb", "network");
+                    firstTime = false;
+                  }
+                else
+                  {
+                    // TODO this is a workaround to adjust cytoscape canvas
+                    // and probably not the best way to do it...
+                    $(window).resize();
+                  }
 
+                }
+              }, 50);
             } else {
                 if($(this).attr("href")=="#bookmark_email") {
                     $("#bookmark-link").attr("href",window.location.href);