switching to specific servers

.travis.yml

@@ -37,31 +37,30 @@ jobs:
         - export VFB_REPO=$(echo ${TRAVIS_REPO_SLUG##*/} | awk '{gsub(/\-/,"_",$0);gsub(/\./,"_",$0);print toupper($0)}')
         - export REPO=$(echo ${TRAVIS_REPO_SLUG} | awk '{gsub(/\./,"_",$0);print tolower($0)}')
         - export TAG=`if [ "$TRAVIS_BRANCH" == "master" ]; then echo "latest"; else echo ${TRAVIS_BRANCH/\//-}; fi`
-        - if [ "$BUILD_TYPE" == "development" ]; then
-            export VFB_TREE_PDB_SERVER=https://pdb-dev.virtualflybrain.org;
-            export VFB_PDB_SERVER=http://pdb-dev.virtualflybrain.org;
-            export VFB_OWL_SERVER=http://owl-dev.virtualflybrain.org/kbs/vfb/;
-            export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
-            export SOLR_SERVER=https://solr-dev.virtualflybrain.org/solr/ontology/select;
-            export TAG=$TAG-development;
-          elif [ "$BUILD_TYPE" == "staging" ]; then
+        - export VFB_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
+        - export VFB_OWL_SERVER=http://owl.p2.virtualflybrain.org/kbs/vfb/;
+        - export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
+        - export VFB_TREE_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
+        - export SOLR_SERVER=https://solr.p2.virtualflybrain.org/solr/ontology/select;
+        - if [ "$TRAVIS_BRANCH" == "master" ]; then
             export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
             export VFB_PDB_SERVER=http://pdb.virtualflybrain.org;
             export VFB_OWL_SERVER=http://owl.virtualflybrain.org/kbs/vfb/;
             export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
             export SOLR_SERVER=https://solr.virtualflybrain.org/solr/ontology/select;
-          else
-            export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
-            export VFB_PDB_SERVER=http://pdb.virtualflybrain.org;
-            export VFB_OWL_SERVER=http://owl.virtualflybrain.org/kbs/vfb/;
+          elif [ "$BUILD_TYPE" == "staging" ] || [ "$BUILD_TYPE" == "development" ]; then
+            export VFB_PDB_SERVER=https://pdb-dev.virtualflybrain.org;
+            export VFB_OWL_SERVER=http://owl-dev.virtualflybrain.org/kbs/vfb/;
             export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
-            export SOLR_SERVER=https://solr.virtualflybrain.org/solr/ontology/select;
+            export VFB_TREE_PDB_SERVER=https://pdb-dev.virtualflybrain.org;
+            export SOLR_SERVER=https://solr-dev.virtualflybrain.org/solr/ontology/select;
+          elif [ "$TRAVIS_BRANCH" == "alpha" ]; then
+            export VFB_PDB_SERVER=https://pdb-alpha.virtualflybrain.org;
+            export VFB_OWL_SERVER=http://owl-alpha.virtualflybrain.org/kbs/vfb/;
+            export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
+            export VFB_TREE_PDB_SERVER=https://pdb-alpha.virtualflybrain.org;
+            export SOLR_SERVER=https://solr-alpha.virtualflybrain.org/solr/ontology/select;
           fi;
-          export VFB_TREE_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
-          export VFB_PDB_SERVER=http://pdb.p2.virtualflybrain.org;
-          export VFB_OWL_SERVER=http://owl.p2.virtualflybrain.org/kbs/vfb/;
-          export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
-          export SOLR_SERVER=https://solr.p2.virtualflybrain.org/solr/ontology/select;
         - export TAG="$TAG-TEST"
       before_script:
         - docker login -u $DOCKER_USER -p $DOCKER_PASS;
@@ -210,21 +209,22 @@ jobs:
             export VFB_PDB_SERVER=http://pdb:7474;
             export VFB_OWL_SERVER=http://owl:8080/kbs/vfb/;
             export VFB_R_SERVER=http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast;
-            if [ "$BUILD_TYPE" == "development" ]; then
-              export VFB_TREE_PDB_SERVER=https://pdb-dev.virtualflybrain.org;
-              export SOLR_SERVER=https://solr-dev.virtualflybrain.org/solr/ontology/select;
-            elif [ "$BUILD_TYPE" == "staging" ]; then
+            if [ "$TRAVIS_BRANCH" == "master" ]; then
               export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
+              export VFB_PDB_SERVER=http://pdb.virtualflybrain.org;
+              export VFB_OWL_SERVER=http://owl.virtualflybrain.org/kbs/vfb/;
+              export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
               export SOLR_SERVER=https://solr.virtualflybrain.org/solr/ontology/select;
+            elif [ "$BUILD_TYPE" == "staging" ] || [ "$BUILD_TYPE" == "development" ]; then
+              export VFB_TREE_PDB_SERVER=https://pdb-dev.virtualflybrain.org;
+              export SOLR_SERVER=https://solr-dev.virtualflybrain.org/solr/ontology/select;
+            elif [ "$TRAVIS_BRANCH" == "alpha" ]; then
+              export VFB_TREE_PDB_SERVER=https://pdb-alpha.virtualflybrain.org;
+              export SOLR_SERVER=https://solr-alpha.virtualflybrain.org/solr/ontology/select;
             else
               export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
               export SOLR_SERVER=https://solr.virtualflybrain.org/solr/ontology/select;
             fi;
-            export VFB_TREE_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
-            export VFB_PDB_SERVER=http://pdb.p2.virtualflybrain.org;
-            export VFB_OWL_SERVER=http://owl.p2.virtualflybrain.org/kbs/vfb/;
-            export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
-            export SOLR_SERVER=https://solr.p2.virtualflybrain.org/solr/ontology/select;
             docker build --cache-from metacell/java-virgo-maven:development -t=$REPO:$TAG.wss --build-arg VFB_TREE_PDB_SERVER_ARG=$VFB_TREE_PDB_SERVER --build-arg SOLR_SERVER_ARG=$SOLR_SERVER --build-arg VFB_R_SERVER_ARG=$VFB_R_SERVER --build-arg VFB_OWL_SERVER_ARG=$VFB_OWL_SERVER --build-arg VFB_PDB_SERVER_ARG=$VFB_PDB_SERVER --build-arg build_type=$BUILD_TYPE --build-arg targetBranch=$TRAVIS_BRANCH --build-arg originBranch=$BRANCH --build-arg defaultBranch=$DEFAULT_BRANCH --build-arg finalBuild=true $DOCKER_FOLDER && docker push $REPO:$TAG.wss;
           fi;
 

components/VFBMain.js

@@ -165,7 +165,7 @@ class VFBMain extends React.Component {
           if ($.inArray(idsList[singleId], this.vfbLoadBuffer) == -1) {
             this.vfbLoadBuffer.push(idsList[singleId]);
           }
-          if (window[idsList[singleId]] != undefined) {
+          if (Instances.getInstance(idsList[singleId]) !== undefined) {
             this.handleSceneAndTermInfoCallback(idsList[singleId]);
             idsList.splice($.inArray(idsList[singleId], idsList), 1);
             this.vfbLoadBuffer.splice($.inArray(idsList[singleId], this.vfbLoadBuffer), 1);
@@ -250,6 +250,7 @@ class VFBMain extends React.Component {
         }.bind(this));
       } else {
         this.handlerInstanceUpdate(meta);
+        this.setActiveTab("termInfo");
       }
       // if the element is not invalid (try-catch) or it is part of the scene then remove it from the buffer
       if (window[variableIds[singleId]] != undefined) {

components/configuration/VFBListViewer/listViewerConfiguration.js

@@ -1,7 +1,6 @@
 import React from 'react';
-import ListViewerControlsMenu from '../../interface/VFBListViewer/ListViewerControlsMenu';
-import { MultiStatusComponent, GroupComponent, ImageComponent, IconComponent, ColorComponent } from "@geppettoengine/geppetto-ui/list-viewer/ListViewer";
 import Tooltip from '@material-ui/core/Tooltip';
+import ListViewerControlsMenu from '../../interface/VFBListViewer/ListViewerControlsMenu';
 
 /**
  * Create component to display controls
@@ -36,10 +35,10 @@ const conf = [
   {
     id: "name",
     title: "Name",
-    customComponent: component => { 
+    customComponent: component => {
       // Retrieve instance path
       let path = component.value.get("path").split(".")[0];
-        
+
       let instance = Instances.getInstance(path);
       var self = this;
 
@@ -48,8 +47,11 @@ const conf = [
         window.setTermInfo(Instances.getInstance(path)[path + "_meta"], path);
       };
       // Create new HTML string with the Type name and tags only
-      let typeHTML = '<a id="' + instance.id + '" style="color:white;text-decoration: none;">' + instance.getName() + "</a>" ;
-
+      let typeHTML = '<a id="' + instance.id + '" style="color:white;text-decoration: none;cursor:pointer">' + instance.getName() + "</a>" ;
+      if (instance.isSelected()) {
+        typeHTML = '<a id="' + instance.id + '" style="color:yellow;text-decoration: none;cursor:pointer">' + instance.getName() + "</a>" ;
+      }
+
       // Set HTML string inside div ready for React
       return <div onClick={e => click(e)} dangerouslySetInnerHTML={{ __html: typeHTML }} />
     },
@@ -58,36 +60,53 @@ const conf = [
   {
     id: "type",
     title: "Type",
-    customComponent: component => { 
+    customComponent: component => {
       // Retrieve instance path
       let path = component.value.get("path").split(".")[0];
-      
+
       let instance = Instances.getInstance(path)[path + "_meta"];
-      
+
       if ( instance === undefined ) {
         return null;
       }
-      
+
       // Retrieve the HTML type from the Instance, it's in the form of an HTML element saved as a string
       let html = instance.getTypes().map(function (t) {
         return t.type.getInitialValue().value
       })[0].html;
-      
+
       // Extract HTML element anchor from html string
       var matchAnchor = /<a[^>]*>([\s\S]*?)<\/a>/g
         , type = html.match(matchAnchor);
-      
+
       // Extract HTML element anchor from html string
       var matchSpan = /<span[^>]*>([\s\S]*?)<\/span>/g
         , tags = html.match(matchSpan);
-
-      // Make anchor open in new tab, and fix path by adding 'geppetto?' to href
-      let textContent = type.join().replace('href="?', 'target="_blank" href="geppetto?');
+
+      var matchID = /data-instancepath\=\"([A-Za-z0-9 _]*)\"/
+        , classID = type[0].match(matchID)[1];
+
+      var matchText = /<a [^>]+>(.*?)<\/a>/
+        , newText = type[0].match(matchText)[1]
+
+      let textClass = '<a id="' + classID + '" style="color:#428bca;text-decoration: none;cursor:pointer">' + newText + "</a>"
       // Create new HTML string with the Type name and tags only
-      let typeHTML = "<div>" + textContent + tags.join('') + "</div>" ;
-
+      let typeHTML = tags.join('') ;
+
+      let click = value => {
+        let id = value.target.id;
+        if (Instances.getInstance(id) === undefined) {
+          window.addVfbId(id);
+        } else {
+          window.setTermInfo(Instances.getInstance(id)[id + "_meta"], id);
+        }
+      };
+
       // Set HTML string inside div ready for React
-      return <div dangerouslySetInnerHTML={{ __html: typeHTML }} />
+      return <div>
+        <div style={{ width: "40%", textAlign: "left", float: "left" }} onClick={e => click(e)} dangerouslySetInnerHTML={{ __html: textClass }} />
+        <div style={{ textAlign: "right", width: "60%", float: "right" }} dangerouslySetInnerHTML={{ __html: typeHTML }} />
+      </div>
     },
     source : entity => entity
   },
@@ -118,4 +137,4 @@ const conf = [
   }
 ];
 
-export default conf;
+export default conf;

components/interface/VFBFocusTerm/VFBFocusTerm.js

@@ -373,16 +373,20 @@ class VFBFocusTerm extends React.Component {
         if (window[classId] === undefined) {
           window.fetchVariableThenRun(classId, () => {
             var variable = GEPPETTO.ModelFactory.getTopLevelVariablesById([classId])[0]
-            var allQueries = GEPPETTO.ModelFactory.getMatchingQueries(variable.getType(), undefined);
-            if (allQueries.length > 0) {
-              this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
+            if (variable !== undefined) {
+              var allQueries = GEPPETTO.ModelFactory.getMatchingQueries(variable.getType(), undefined);
+              if (allQueries.length > 0) {
+                this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
+              }
             }
           });
         } else {
           var variable = GEPPETTO.ModelFactory.getTopLevelVariablesById([classId])[0]
-          var allQueries = GEPPETTO.ModelFactory.getMatchingQueries(variable.getType(), undefined);
-          if (allQueries.length > 0) {
-            this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
+          if (variable !== undefined) {
+            var allQueries = GEPPETTO.ModelFactory.getMatchingQueries(variable.getType(), undefined);
+            if (allQueries.length > 0) {
+              this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
+            }
           }
         }
       }

components/interface/VFBTree/VFBTree.js

@@ -569,4 +569,4 @@ function mapDispatchToProps (dispatch) {
   return { setTermInfo: (instance, visible) => dispatch(setTermInfo(instance, visible )) }
 }
 
-export default connect(mapStateToProps, mapDispatchToProps)(VFBTree);
+export default connect(mapStateToProps, mapDispatchToProps, null, { forwardRef : true } )(VFBTree);

model/vfb.xmi

@@ -171,7 +171,7 @@
           name="anatomy_query"
           description="fetch Individual instances from Class ID list"
           runForCount="false"
-          query=""statement": "MATCH (primary:Class:Anatomy) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)<-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {primary:primary}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, '58214d4' AS version, 'anatomy_query' AS query, anatomy_channel_image", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS }"
+          query=""statement": "MATCH (primary:Class) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)<-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {primary:primary}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, '58214d4' AS version, 'anatomy_query' AS query, anatomy_channel_image", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS }"
           countQuery=""statement": "MATCH (n:Class) WHERE n.short_form IN {ARRAY_ID_RESULTS} RETURN count(n) AS count", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS }"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"