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Dockerfile

@@ -16,7 +16,7 @@ ARG geppettoSimulationRelease=vfb_20200604_a
 ARG geppettoDatasourceRelease=vfb_20200604_a
 ARG geppettoModelSwcRelease=v1.0.1
 ARG geppettoFrontendRelease=development
-ARG geppettoClientRelease=VFBv2.2.0.7
+ARG geppettoClientRelease=VFBv2.2.0.7-feature/1238
 ARG ukAcVfbGeppettoRelease=download
 
 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster"
@@ -38,6 +38,7 @@ ENV VFB_OWL_SERVER=${VFB_OWL_SERVER_ARG}
 ENV VFB_R_SERVER=${VFB_R_SERVER_ARG}
 ENV SOLR_SERVER=${SOLR_SERVER_ARG}
 ENV googleAnalyticsSiteCode=${googleAnalyticsSiteCode_ARG}
+ENV LOG4J_FORMAT_MSG_NO_LOOKUPS=true
 
 RUN /bin/echo -e "\e[1;35mORIGIN BRANCH ------------ $originBranch\e[0m" &&\
   /bin/echo -e "\e[1;35mTARGET BRANCH ------------ $targetBranch\e[0m" &&\

components/VFBMain.js

@@ -9,6 +9,7 @@ import VFBTermInfoWidget from './interface/VFBTermInfo/VFBTermInfo';
 import Logo from '@geppettoengine/geppetto-client/components/interface/logo/Logo';
 import Canvas from '@geppettoengine/geppetto-client/components/interface/3dCanvas/Canvas';
 import QueryBuilder from '@geppettoengine/geppetto-client/components/interface/query/queryBuilder';
+import VFBDownloadContents from './interface/VFBDownloadContents/VFBDownloadContents';
 import VFBUploader from './interface/VFBUploader/VFBUploader';
 import HTMLViewer from '@geppettoengine/geppetto-ui/html-viewer/HTMLViewer';
 import VFBListViewer from './interface/VFBListViewer/VFBListViewer';
@@ -52,6 +53,7 @@ class VFBMain extends React.Component {
       quickHelpVisible: undefined,
       UIUpdated: true,
       wireframeVisible: false,
+      downloadContentsVisible : true,
       uploaderContentsVisible : true
     };
 
@@ -488,6 +490,12 @@ class VFBMain extends React.Component {
         [buttonState]: !this.state[buttonState]
       });
       break;
+    case 'downloadContentsVisible':
+      this.refs.downloadContentsRef?.openDialog();
+      break;
+    case 'uploaderContentsVisible':
+      this.refs.uploaderContentsRef?.openDialog();
+      break;
     case 'quickHelpVisible':
       if (this.state[buttonState] === undefined) {
         this.setState({
@@ -527,6 +535,9 @@ class VFBMain extends React.Component {
     case 'triggerSetTermInfo':
       this.handlerInstanceUpdate(click.value[0]);
       break;
+    case 'downloadContentsVisible':
+      this.refs.downloadContentsRef?.openDialog();
+      break;
     case 'uploaderContentsVisible':
       this.refs.uploaderContentsRef?.openDialog();
       break;
@@ -1752,7 +1763,10 @@ class VFBMain extends React.Component {
           searchConfiguration={this.searchConfiguration}
           datasourceConfiguration={this.datasourceConfiguration} />
 
+        <VFBDownloadContents ref="downloadContentsRef" open={false} />
+
         <VFBUploader ref="uploaderContentsRef" open={false} />
+
         {this.htmlToolbarRender}
       </div>
     );

components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js

@@ -19,11 +19,20 @@ var locationCypherQuery = ( instances, paths, weight ) => ({
       + " WITH * ORDER BY index DESC"
       + " UNWIND relationships(path) as sr"
       + " OPTIONAL MATCH cp=(x:Neuron:has_neuron_connectivity)-[:synapsed_to]-(y:Neuron:has_neuron_connectivity) WHERE x=apoc.rel.startNode(sr) AND y=apoc.rel.endNode(sr) OPTIONAL MATCH fp=(x)-[r:synapsed_to]->(y) WHERE r.weight[0] >= " + weight?.toString()
-      + " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY ",
+      + " OPTIONAL MATCH (x)-[xio:INSTANCEOF]->(xpc:Class) OPTIONAL MATCH (y)-[yio:INSTANCEOF]->(ypc:Class) WITH *,'\"'+ x.short_form+'\":{\"'+xpc.short_form+'\":\"' + xpc.label + '\"},\"'+ y.short_form+'\":{\"'+ypc.short_form+'\":\"' + ypc.label + '\"}' as Class"
+      + " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY, "
+      + " apoc.convert.fromJsonMap('{' + apoc.text.join(collect(Class),',') + '}') as class ",
       "resultDataContents": ["row", "graph"]
     }
   ]
 });
+
+var Neo4jLabels = {
+  FAFB : "FAFB",
+  L1EM : "L1EM",
+  FlyEM_HB : "FlyEM_HB"
+}
+
 // See query explanation on https://github.com/VirtualFlyBrain/graph_queries/blob/main/weighted_path.md 
 
 var configuration = {
@@ -120,5 +129,6 @@ module.exports = {
   configuration,
   styling,
   restPostConfig,
-  locationCypherQuery
+  locationCypherQuery,
+  Neo4jLabels
 };

components/configuration/VFBDownloadContents/configuration.json

@@ -0,0 +1,34 @@
+{
+	"postURL":"https://zip.virtualflybrain.org/download",
+	"contentType": "application/json",
+	"zipName" : "VFB Files.zip",
+	"options" :{
+		"obj": { 
+		  "label" : "OBJ",
+		  "tooltip" : "Download OBJ"
+		},
+		"swc": { 
+		  "label" : "SWC",
+		  "tooltip" : "Download SWC"
+		},
+		"nrrd": { 
+		  "label" : "NRRD",
+		  "tooltip" : "Download NRRD"
+		},
+		"reference": { 
+		  "label" : "References",
+		  "tooltip" : "Download References"
+		}
+	},
+	"text" : {
+		"title" : "Download Data",
+		"typesSubtitle" : "Please select the desired types",
+		"variablesSubtitle" : "Please select Variables:",
+		"noVariablesSubtitle" : "No loaded variables",
+		"errorMessage" : "Something went wrong...  We were not able to download the data.  Please try again.",
+		"noEntriesFound" : "No entries found for the types and variables selected.",
+		"cancelButton" : "Cancel",
+		"downloadButton" : "Download",
+		"tryAgainButton" : "Try Again"
+	}
+}

components/configuration/VFBMain/searchConfiguration.js

@@ -60,7 +60,7 @@ var searchStyle = {
   singleResult: {
     "color": "white",
     "fontSize": "18px",
-
+    "whiteSpace" : "normal",
     ":hover": {
       "color": "#11bffe",
       "background-color": "#252323",
@@ -99,17 +99,21 @@ var datasourceConfiguration = {
       ],
       "rows": "100",
       "wt": "json",
-      "bq": "shortform_autosuggest:VFB*^110.0 shortform_autosuggest:FBbt*^100.0 label_s:\"\"^2 synonym_s:\"\" short_form:FBbt_00003982^2 facets_annotation:Deprecated^0.001"
+      "bq": "shortform_autosuggest:VFBexp*^10.0 shortform_autosuggest:VFB*^100.0 shortform_autosuggest:FBbt*^100.0 label_s:\"\"^2 synonym_s:\"\" short_form:FBbt_00003982^2 facets_annotation:Deprecated^0.001"
     }
 };
 
 var searchConfiguration = {
   "resultsMapping":
     {
       "name": "label",
-      "id": "short_form"
+      "id": "short_form",
+      "labels" : "facets_annotation"
     },
+  "label_manipulation" : label => label,
   "filters_expanded": true,
+  "filter_positive" : "^100",
+  "filter_negative" : "^0.001",
   "filters": [
     {
       "key": "facets_annotation",
@@ -305,6 +309,13 @@ var searchConfiguration = {
     if (b.label.toLowerCase().indexOf(InputString.toLowerCase()) > -1 && b.label.toLowerCase().indexOf(InputString.toLowerCase()) < a.label.toLowerCase().indexOf(InputString.toLowerCase())) {
       return 1;
     }
+    // move up expression (VFBexp) terms
+    if (a.id.indexOf("VFBexp") > -1 && b.id.indexOf("VFBexp") < 0) {
+      return -1;
+    }
+    if (b.id.indexOf("VFBexp") > -1 && a.id.indexOf("VFBexp") < 0) {
+      return 1;
+    }
     // if the match in the id is closer to start then move up
     if (a.id.toLowerCase().indexOf(InputString.toLowerCase()) > -1 && a.id.toLowerCase().indexOf(InputString.toLowerCase()) < b.id.toLowerCase().indexOf(InputString.toLowerCase())) {
       return -1;
@@ -323,11 +334,16 @@ var searchConfiguration = {
   },
   "clickHandler": function (id) {
     window.addVfbId(id);
+  },
+  "Neo4jLabels" : {
+    "FAFB" : "FAFB",
+    "L1EM" : "L1EM",
+    "FlyEM_HB" : "FlyEM_HB"
   }
 };
 
 module.exports = {
   searchStyle,
   searchConfiguration,
-  datasourceConfiguration,
+  datasourceConfiguration
 };

components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js

@@ -253,6 +253,14 @@ var toolbarMenu = {
             parameters: ["circuitBrowserVisible"]
           }
         },
+        {
+          label: "Download Contents",
+          icon: "fa fa-download",
+          action: {
+            handlerAction: "downloadContentsVisible",
+            parameters: []
+          }
+        },
         {
           label: "NBLAST Uploader",
           icon: "fa fa-upload",

components/configuration/VFBTree/VFBTreeConfiguration.js

@@ -8,7 +8,7 @@ var treeCypherQuery = instance => ({
     {
       "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Template {short_form:'" + instance + "'})"
       + "<-[:depicts]-(tc:Template)<-[ie:in_register_with]-(c:Individual)-[:depicts]->(image:"
-      + "Individual)-[r:INSTANCEOF]->(anat:Class:Nervous_system) WHERE exists(ie.index) WITH root, anat,r,image"
+      + "Individual)-[r:INSTANCEOF]->(anat:Class:Anatomy) WHERE exists(ie.index) WITH root, anat,r,image"
       + " MATCH p=allshortestpaths((root)<-[:SUBCLASSOF|part_of*..]-(anat)) "
       + "UNWIND nodes(p) as n UNWIND nodes(p) as m WITH * WHERE id(n) < id(m) "
       + "MATCH path = allShortestPaths( (n)-[:SUBCLASSOF|part_of*..1]-(m) ) "

components/configuration/VFBUploader/configuration.json

@@ -1,12 +1,27 @@
 {
-	"nblastURL" : "https://zip.virtualflybrain.org/download",
-	"contentType" : "",
-	"templates" : [
-	  { "VFB_00101567" : "VFB_00101567 Template" },
-	  { "VFB_00000001" : "VFB_00000001 Template" }
-	],
-	"acceptedFiles" : [".swc"],
-	"filesLimit" : 10,
+	"nblastURL" : "http://upload.virtualflybrain.org/files/UNIQUE_ID?token=bec3a40f0ab377c39103",
+	"contentType" : "multipart/form-data",
+	"templates" : [{"short_form":"VFB_00101567","label":"JRC2018Unisex"},{"short_form":"VFB_00200000","label":"JRC2018UnisexVNC"}] ,
+	"acceptedFiles" : [".swc", ".nrrd"],
+	"filesLimit" : 1,
 	"maxFileSize" : 3000000,
-	"dropZoneMessage" : "Drag and drop a SWC file here or click"
+	"queryType": "uploaderQuery",
+	"cookieStorageDays" : 100,
+	"cookiesLearnLink" : "https://en.wikipedia.org/wiki/HTTP_cookie",
+	"text" : {
+		"dialogTitle" : "Upload Data File",
+		"dialogSubtitle" : "Generate a nblast query from your own data.",
+		"selectTemplate" : "1. Select a Template",
+		"select" : "Select",
+		"addYourFile" : "2. Add your file (Please use a .swc)",
+		"dropZoneMessage" : "Click or Drag & Drop your file here",
+		"agreeTerms" : "I agree to the use of cookies to store the NBLAST QUERY URL. ",
+		"learnMore" : "Learn More",
+		"blastButtonText" : "Generate a nblast query link",
+		"restartButtonText" : "Restart",
+		"copyButtonText" : "Copy",
+		"infoMessage" : "Generating a nblast query can take up to 30 min. Save this link to find the result of your query.",
+		"errorDialog" : "Something went wrong... We were not able to generate a nblast query link from your data. Please try again.",
+		"errorButtonText" : "Try Again"
+	}
 }

components/interface/ErrorCatcher.js

@@ -38,22 +38,44 @@ const styles = {
 class ErrorCatcher extends React.Component {
   constructor (props) {
     super(props);
-    this.state = { 
-      hasError: false, 
+    this.state = {
+      hasError: false,
       open: true,
       error: undefined
     };
   }
-
     handleClose = () => {
       var url = "https://github.com/VirtualFlyBrain/VFB2/issues/new";
       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 body = customMessage + this.state.error.message + "\n\n" + this.state.error.stack.replace("#",escape("#")) + "\n\n```diff\n" + window.console.logs.slice(-50).join('\n').replace("#",escape("#")) + "\n```\n";
+      // return as much of the log up to the last 10 events < 1000 characters:
+      var logLength = -1;
+      var limitedLog = window.console.logs.slice(logLength).join('%0A').replace(
+        /\&/g,escape('&')
+      ).replace(
+        /\#/g,escape('#')
+      ).replace(
+        /\-/g,'%2D'
+      ).replace(
+        /\+/g,'%2B'
+      );
+      while (limitedLog.length < 1000 && logLength > -50) {
+        logLength -= 1;
+        limitedLog = window.console.logs.slice(logLength).join('%0A').replace(
+          /\&/g,escape('&')
+        ).replace(
+          /\#/g,escape('#')
+        ).replace(
+          /\-/g,'%2D'
+        ).replace(
+          /\+/g,'%2B'
+        );
+      }
+      var body = customMessage + this.state.error.message + "\n\n" + this.state.error.stack.replace("#",escape("#")) + "\n\n```diff\n" + limitedLog + "\n```\n";
       var form = document.createElement("form");
       form.setAttribute("method", "get");
       form.setAttribute("action", url);
       form.setAttribute("target", "view");
-      var hiddenField = document.createElement("input"); 
+      var hiddenField = document.createElement("input");
       hiddenField.setAttribute("type", "hidden");
       hiddenField.setAttribute("name", "body");
       hiddenField.setAttribute("value", body);
@@ -62,7 +84,7 @@ class ErrorCatcher extends React.Component {
       window.open('', 'view');
       form.submit();
     };
-  
+
     componentDidCatch (error, info) {
       // Report error to GA
       window.ga('vfb.send', 'event', 'error', 'react', error.message + " - " + error.stack.replace("#",escape("#")));