Merge branch 'vfb_geppetto_application' into Feature_333

VirtualFlyBrain · Jul 3, 2019 · 51c1a69 · 51c1a69
2 parents 3fa1d68 + fc5685d
commit 51c1a69
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Showing 5 changed files with 61 additions and 47 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -80,4 +80,5 @@ RUN cd $HOME/workspace/org.geppetto/utilities/source_setup && python update_serv
 
 
 EXPOSE 8080
+EXPOSE 8443
 CMD [ "/bin/bash", "-c", "/startup.sh" ]
diff --git a/components/VFBMain.js b/components/VFBMain.js
@@ -840,6 +840,7 @@ export default class VFBMain extends React.Component {
         <VFBTermInfoWidget
           termInfoHandler={this.termInfoHandler}
           ref={ref => this.termInfoReference = ref}
+          queryBuilder={this.refs.querybuilderRef}
           showButtonBar={true}
           termInfoName={this.termInfoName}
           termInfoId={this.termInfoId}
@@ -996,12 +997,6 @@ export default class VFBMain extends React.Component {
       });
     }
 
-    // Query builder initialization
-    this.refs.querybuilderRef.setResultsColumnMeta(this.queryResultsColMeta);
-    this.refs.querybuilderRef.setResultsColumns(this.queryResultsColumns);
-    this.refs.querybuilderRef.setResultsControlsConfig(this.queryResultsControlConfig);
-    this.refs.querybuilderRef.addDataSource(this.queryBuilderDatasourceConfig);
-
     // Loading ids passed through the browser's url
     if ((this.props.location.search.indexOf("id=") == -1) && (this.props.location.search.indexOf("i=") == -1)) {
       var that = this;
@@ -1127,11 +1122,11 @@ export default class VFBMain extends React.Component {
         enableResizing={{
           top: false, right: false, bottom: false,
           left: false, topRight: false, bottomRight: false,
-          bottomLeft: false, topLeft: false 
+          bottomLeft: false, topLeft: false
         }}
         default={{
           x: this.modalX, y: this.modalY,
-          height: 150, width: 150 
+          height: 150, width: 150
         }}
         className="historyModal"
         disableDragging={true}
@@ -1205,19 +1200,18 @@ export default class VFBMain extends React.Component {
     this.htmlToolbarRender = (this.state.htmlFromToolbar !== undefined)
       ? <Rnd enableResizing={{
         top: false, right: false, bottom: false, left: false,
-        topRight: false, bottomRight: false, bottomLeft: false,
-        topLeft: false
+        topRight: false, bottomRight: false, bottomLeft: false, topLeft: false
       }}
       default={{
         x: 50, y: 50,
         height: window.innerHeight - 100,
-        width: window.innerWidth - 100 
+        width: window.innerWidth - 100
       }}className="htmlViewerVFB"
       disableDragging={true}
       maxHeight={window.innerHeight - 100} minHeight={100}
       maxWidth={window.innerWidth - 100} minWidth={100}
       ref={d => {
-        this.rnd2 = d; 
+        this.rnd2 = d;
       }} >
         <div><i onClick={this.closeHtmlViewer} className='close-slider fa fa-times'/></div>
         <div ref={this.htmlToolbarRef}>
@@ -1229,27 +1223,27 @@ export default class VFBMain extends React.Component {
             style={{
               width: '100%',
               height: '100%',
-              float: 'center' 
+              float: 'center'
             }}
             ref="htmlViewer" />
         </div>
       </Rnd> : undefined;
 
     return (
       <div style={{ height: '100%', width: '100%' }}>
-        <VFBToolBar 
+        <VFBToolBar
           htmlOutputHandler={this.renderHTMLViewer}
           menuHandler={this.menuHandler}/>
 
         <Rnd
           enableResizing={{
-            top: false, right: false, bottom: false,
-            left: false, topRight: false, bottomRight: false,
-            bottomLeft: false, topLeft: false 
+            top: false, right: false, bottom: false, left: false,
+            topRight: false, bottomRight: false, bottomLeft: false, topLeft: false
           }}
           default={{
-            x: this.getButtonBarDefaultX(), y: this.getButtonBarDefaultY(),
-            height: 28, width: 340 
+            x: this.getButtonBarDefaultX(),
+            y: this.getButtonBarDefaultY(),
+            height: 28, width: 340
           }}
           className="new-widget"
           disableDragging={true}
@@ -1275,19 +1269,32 @@ export default class VFBMain extends React.Component {
           clickOnBordersAction={clickOnBordersAction}/>
 
         <div id="spotlight" style={{ top: 0 }}>
-          <SpotLight ref="spotlightRef" indexInstances={false} spotlightConfig={this.spotlightConfig}
-            spotlightDataSourceConfig={this.spotlightDataSourceConfig} icon={"styles.Modal"}
+          <SpotLight ref="spotlightRef"
+            indexInstances={false}
+            spotlightConfig={this.spotlightConfig}
+            spotlightDataSourceConfig={this.spotlightDataSourceConfig}
+            icon={"styles.Modal"}
             useBuiltInFilter={false} />
         </div>
 
         <div id="controlpanel" style={{ top: 0 }}>
-          <ControlPanel ref="controlpanelRef" icon={"styles.Modal"} enableInfiniteScroll={true}
-            useBuiltInFilter={false} controlPanelColMeta={this.controlPanelColMeta}
-            controlPanelConfig={this.controlPanelConfig} columns={this.controlPanelColumns}
+          <ControlPanel ref="controlpanelRef"
+            icon={"styles.Modal"}
+            enableInfiniteScroll={true}
+            useBuiltInFilter={false}
+            controlPanelColMeta={this.controlPanelColMeta}
+            controlPanelConfig={this.controlPanelConfig}
+            columns={this.controlPanelColumns}
             controlPanelControlConfigs={this.controlPanelControlConfigs}/>
         </div>
 
-        <QueryBuilder ref="querybuilderRef" icon={"styles.Modal"} useBuiltInFilter={false} />
+        <QueryBuilder ref="querybuilderRef"
+          icon={"styles.Modal"}
+          useBuiltInFilter={false}
+          resultsColMeta={this.queryResultsColMeta}
+          resultsColumns={this.queryResultsColumns}
+          resultsControlConfig={this.queryResultsControlConfig}
+          datasourceConfig={this.queryBuilderDatasourceConfig} />
 
         <div id="tutorialDiv">
           {this.tutorialRender}

diff --git a/components/interface/VFBTermInfo.js b/components/interface/VFBTermInfo.js
@@ -570,6 +570,7 @@ export default class VFBTermInfoWidget extends React.Component {
     var otherId;
     var otherName;
     var target = widget;
+    var that = this;
     var meta = path + "." + path + "_meta";
     if (n != undefined) {
       var metanode = Instances.getInstance(meta);
@@ -599,38 +600,38 @@ export default class VFBTermInfoWidget extends React.Component {
       var entity = Model[path];
       if (typeof (entity) != 'undefined' && entity instanceof Query) {
         // clear query builder unless ctrl pressed them add to compound.
-        GEPPETTO.QueryBuilder.open();
+        this.props.queryBuilder.open();
         if (!GEPPETTO.isKeyPressed("shift")) {
-          GEPPETTO.QueryBuilder.switchView(false, false);
-          GEPPETTO.QueryBuilder.clearAllQueryItems();
+          this.props.queryBuilder.switchView(false, false);
+          this.props.queryBuilder.clearAllQueryItems();
         } else {
-          GEPPETTO.QueryBuilder.switchView(false, false);
+          this.props.queryBuilder.switchView(false, false);
         }
 
         GEPPETTO.trigger('spin_logo');
         $("body").css("cursor", "progress");
 
         var callback = function () {
           // check if any results with count flag
-          if (GEPPETTO.QueryBuilder.props.model.count > 0) {
+          if (that.props.queryBuilder.props.model.count > 0) {
             // runQuery if any results
-            GEPPETTO.QueryBuilder.runQuery();
+            that.props.queryBuilder.runQuery();
           } else {
-            GEPPETTO.QueryBuilder.switchView(false);
+            that.props.queryBuilder.switchView(false);
           }
           // show query component
-          GEPPETTO.QueryBuilder.open();
+          that.props.queryBuilder.open();
           $("body").css("cursor", "default");
           GEPPETTO.trigger('stop_spin_logo');
         };
         // add query item + selection
         if (window[otherId] == undefined) {
           window.fetchVariableThenRun(otherId, function () {
-            GEPPETTO.QueryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity }, callback) 
+            that.props.queryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity }, callback) 
           });
         } else {
           setTimeout(function () {
-            GEPPETTO.QueryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity }, callback); 
+            that.props.queryBuilder.addQueryItem({ term: otherName, id: otherId, queryObj: entity }, callback); 
           }, 100);
         }
       } else {
@@ -725,8 +726,6 @@ export default class VFBTermInfoWidget extends React.Component {
   }
 
   render () {
-    // var VFBTermInfoWidget = WidgetCapability.createWidget(VFBTermInfo);
-
     return (
       <VFBTermInfo
         id={this.idWidget}

diff --git a/dockerFiles/startup.sh b/dockerFiles/startup.sh
@@ -5,12 +5,19 @@ grep -rls pdb.virtualflybrain.org $HOME/ | xargs sed -i "s@pdb.virtualflybrain.o
 grep -rls owl.virtualflybrain.org $HOME/workspace/ | xargs sed -iv "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g"	grep -rls owl.virtualflybrain.org /home/ | xargs sed -i "s@owl.virtualflybrain.org@$VFB_OWL_SERVER@g" &
 grep -rls solr.virtualflybrain.org $HOME/workspace/ | xargs sed -iv "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g"	grep -rls solr.virtualflybrain.org /home/ | xargs sed -i "s@http://solr.virtualflybrain.org/solr/ontology/select@$SOLR_SERVER@g" &
 
+#Start a logfile
+mkdir -p $SERVER_HOME/serviceability/logs
+echo 'Start of log...' > $SERVER_HOME/serviceability/logs/log.log
+
 # re-deploy Geppetto
 cd $HOME/workspace/org.geppetto/utilities/source_setup && python update_server.py
 
 # set java memory maximum 
 sed 's/XX:MaxPermSize=512m/XX:MaxPermSize=$MAXSIZE/g' -i $SERVER_HOME/bin/dmk.sh
 sed 's/Xmx512m/Xmx$MAXSIZE/' -i $SERVER_HOME/bin/dmk.sh
 
+# output log
+tail -F --retry $SERVER_HOME/serviceability/logs/log.log & 
+
 # start virgo server
 $SERVER_HOME/bin/startup.sh
Original file line number	Diff line number	Diff line change
Expand Up		@@ -80,4 +80,5 @@ RUN cd $HOME/workspace/org.geppetto/utilities/source_setup && python update_serv


		EXPOSE 8080
		EXPOSE 8443
		CMD [ "/bin/bash", "-c", "/startup.sh" ]