Merge pull request #463 from VirtualFlyBrain/vfb_geppetto_application

Updating latest changes from Vfb geppetto application
VirtualFlyBrain · Dec 6, 2019 · 6a65949 · 6a65949
2 parents 27604b1 + a8bbba4
commit 6a65949
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Showing 11 changed files with 520 additions and 289 deletions.
diff --git a/components/VFBMain.js b/components/VFBMain.js
@@ -788,7 +788,7 @@ export default class VFBMain extends React.Component {
           instance={this.instanceOnFocus}
           size={{ height: _height, width: _width }}
           ref={ref => this.treeBrowserReference = ref}
-          selectionHandler={this.addVfbId}/>
+          selectionHandler={this.addVfbId} />
       </div>);
     }
   }

diff --git a/components/configuration/buttonBarConfiguration.js b/components/configuration/buttonBarConfiguration.js
@@ -7,7 +7,7 @@ var buttonBarConfig = {
   "queryBuilderVisible": {
     "icon": "fa fa-quora",
     "label": "",
-    "tooltip": "Open Query"
+    "tooltip": "Query Results"
   },
   "controlPanelVisible": {
     "icon": "fa fa-list",

diff --git a/components/configuration/queryBuilderConfiguration.js b/components/configuration/queryBuilderConfiguration.js
@@ -76,12 +76,26 @@ var queryResultsColMeta = [
     "locked": false,
     "visible": true,
     "displayName": "Stage",
-    "cssClassName": "query-results-stage-column"
+    "cssClassName": "query-results-stage-column",
+    "sortDirectionCycle": ['asc', 'desc', null]
   },
   {
-    "columnName": "controls",
+    "columnName": "license",
     "order": 8,
     "locked": false,
+    "visible": true,
+    "customComponent": QueryLinkComponent,
+    "actions": "window.addVfbId('$entity$');",
+    "entityIndex": 1,
+    "entityDelimiter": "----",
+    "displayName": "License",
+    "cssClassName": "query-results-license-column",
+    "sortDirectionCycle": ['asc', 'desc', null]
+  },
+  {
+    "columnName": "controls",
+    "order": 9,
+    "locked": false,
     "visible": false,
     "customComponent": QueryResultsControlsComponent,
     "displayName": "Controls",
@@ -91,7 +105,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "images",
-    "order": 9,
+    "order": 10,
     "locked": false,
     "visible": true,
     "customComponent": SlideshowImageComponent,
@@ -102,17 +116,26 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "score",
-    "order": 10,
+    "order": 11,
     "locked": false,
     "visible": true,
     "displayName": "Score",
     "cssClassName": "query-results-score-column",
     "sortDirectionCycle": ['desc', 'asc', null]
+  },
+  {
+    "columnName": "image_count",
+    "order": 12,
+    "locked": false,
+    "visible": true,
+    "displayName": "Image_count",
+    "cssClassName": "query-results-image_count-column",
+    "sortDirectionCycle": ['desc', 'asc', null]
   }
 ];
 
 // which columns to display in the results
-var queryResultsColumns = ['name', 'expressed_in', 'description', 'reference', 'type', 'stage', 'images', 'score'];
+var queryResultsColumns = ['name', 'expressed_in', 'description', 'reference', 'type', 'stage', 'license', 'images', 'score','image_count'];
 
 var queryResultsControlConfig = {
   "Common": {
@@ -140,7 +163,7 @@ var queryResultsControlConfig = {
 
 var queryBuilderDatasourceConfig = {
   VFB: {
-    url: "https://solr.virtualflybrain.org/solr/ontology/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(vfb)&fq=shortform_autosuggest:VFB*%20OR%20shortform_autosuggest:FB*%20OR%20is_defining_ontology:true&rows=100&bq=is_obsolete:false%5E100.0%20shortform_autosuggest:VFB*%5E110.0%20shortform_autosuggest:FBbt*%5E100.0%20is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=$SEARCH_TERM$%20OR%20$SEARCH_TERM$*%20OR%20*$SEARCH_TERM$*&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true", 
+    url: "https://solr.virtualflybrain.org/solr/ontology/select?fl=short_form,label,synonym,id,type,has_narrow_synonym_annotation,has_broad_synonym_annotation&start=0&fq=ontology_name:(vfb)&fq=shortform_autosuggest:VFB*%20OR%20shortform_autosuggest:FB*%20OR%20is_defining_ontology:true&rows=100&bq=is_obsolete:false%5E100.0%20shortform_autosuggest:VFB*%5E110.0%20shortform_autosuggest:FBbt*%5E100.0%20is_defining_ontology:true%5E100.0%20label_s:%22%22%5E2%20synonym_s:%22%22%20in_subset_annotation:BRAINNAME%5E3%20short_form:FBbt_00003982%5E2&q=$SEARCH_TERM$%20OR%20$SEARCH_TERM$*%20OR%20*$SEARCH_TERM$*&defType=edismax&qf=label%20synonym%20label_autosuggest_ws%20label_autosuggest_e%20label_autosuggest%20synonym_autosuggest_ws%20synonym_autosuggest_e%20synonym_autosuggest%20shortform_autosuggest%20has_narrow_synonym_annotation%20has_broad_synonym_annotation&wt=json&indent=true",
     crossDomain: true,
     id: "short_form",
     label: { field: "label", formatting: "$VALUE$" },
@@ -280,6 +303,10 @@ var sorterColumns = [
     column: "score",
     order: "DESC"
   },
+  {
+    column: "image_count",
+    order: "DESC"
+  },
   {
     column: "images",
     order: "DESC"

diff --git a/components/configuration/treeWidgetConfiguration.js b/components/configuration/treeWidgetConfiguration.js
@@ -3,14 +3,30 @@ var restPostConfig = {
   contentType: "application/json"
 };
 
+/*
+ * var treeCypherQuery = instance => ({
+ *   "statements": [
+ *     {
+ *       "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'" + instance + "'})"
+ *       + "<-[:depicts]-(tc:Individual)<-[ie:in_register_with]-(c:Individual)-[:depicts]->(image:"
+ *       + "Individual)-[r:INSTANCEOF]->(anat:Class) WHERE has(ie.index) WITH root, anat,r,image"
+ *       + " MATCH p=allShortestPaths((root)<-[:SUBCLASSOF|part_of*..]-(anat:Class)) RETURN p,r,image",
+ *       "resultDataContents": ["graph"]
+ *     }
+ *   ]
+ * });
+ */
+
 var treeCypherQuery = instance => ({
   "statements": [
     {
       "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'" + instance + "'})"
       + "<-[:depicts]-(tc:Individual)<-[ie:in_register_with]-(c:Individual)-[:depicts]->(image:"
       + "Individual)-[r:INSTANCEOF]->(anat:Class) WHERE has(ie.index) WITH root, anat,r,image"
-      + " MATCH p=allShortestPaths((root)<-[:SUBCLASSOF|part_of*..]-(anat:Class)) RETURN p,r,image",
-      "resultDataContents": ["graph"]
+      + " MATCH p=allShortestPaths((root)<-[:SUBCLASSOF|part_of*..]-(anat)) "
+      + "RETURN collect(distinct { node_id: id(anat), short_form: anat.short_form, image: image.short_form })"
+      + " AS image_nodes, id(root) AS root, collect(p)",
+      "resultDataContents": ["row", "graph"]
     }
   ]
 });
@@ -19,4 +35,4 @@ var treeCypherQuery = instance => ({
 module.exports = {
   restPostConfig,
   treeCypherQuery
-};
+};
diff --git a/components/interface/ErrorCatcher.js b/components/interface/ErrorCatcher.js
@@ -47,7 +47,7 @@ class ErrorCatcher extends React.Component {
 
     handleClose = () => {
       var customMessage = "Steps to reproduce the problem: \n\nPlease fill the below with the necessary steps to reproduce the problem\n\n\n\nError Information:\n\n"
-      var url = "https://github.com/VirtualFlyBrain/VFB2/issues/new?body=" + customMessage + this.state.error.message + "\n\n" + this.state.error.stack.replace("#",escape("#")) + "\n\n```diff\n" + window.console.logs.slice(-10).join('\n').replace("#",escape("#")) + "\n```\n";
+      var url = "https://github.com/VirtualFlyBrain/VFB2/issues/new?body=" + customMessage + this.state.error.message + "\n\n" + this.state.error.stack.replace("#",escape("#")) + "\n\n```diff\n" + window.console.logs.slice(-8).join('\n').replace("#",escape("#")) + "\n```\n";
       var win = window.open(encodeURI(url), '_blank');
       win.focus();
     };

diff --git a/components/interface/FocusTerm.js b/components/interface/FocusTerm.js
@@ -498,14 +498,14 @@ export default class FocusTerm extends React.Component {
                     }} />
                 </Tooltip>
                 <Tooltip placement="top-end"
-                  title="Open query results">
+                  title="Query results">
                   <i className="fa fa-quora arrowsStyle"
                     onClick={() => {
                       this.props.UIUpdateManager("queryBuilderVisible");
                     }} />
                 </Tooltip>
                 <Tooltip placement="top-end"
-                  title="Open the control panel">
+                  title="Layers">
                   <i className="fa fa-list arrowsStyle"
                     onClick={() => {
                       this.props.UIUpdateManager("controlPanelVisible");