Merge pull request #1318 from VirtualFlyBrain/debug-sync-0806

sync: debug with debug-sync-0806
VirtualFlyBrain · Mar 14, 2022 · 0b82bf5 · 0b82bf5
2 parents b234092 + 8d7fd0e
commit 0b82bf5
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Showing 45 changed files with 1,857 additions and 519 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -31,15 +31,15 @@ jobs:
       - name: Setup local servers
         id: local-servers
         shell: bash
-        run: if [ "${GITHUB_REF#refs/heads/}" == master ] ; then
+        run: if [ "${GITHUB_REF#refs/heads/}" == master ] || [[ "${GITHUB_REF#refs/heads/}" == v* ]]; then
             echo "::debug::Set to master setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.v4.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
             echo "::set-output name=BUILD_TYPE::release";
-          elif [ "${GITHUB_REF#refs/heads/}" == debug ] || [ "${GITHUB_REF#refs/heads/}" == pipeline2 ] || [ "${GITHUB_REF#refs/heads/}" == vfb_geppetto_application ] || [ "${GITHUB_REF#refs/heads/}" == development ] ; then
+          elif [ "${GITHUB_REF#refs/heads/}" == debug ] || [ "${GITHUB_REF#refs/heads/}" == pipeline2 ] || [ "${GITHUB_REF#refs/heads/}" == vfb_geppetto_application ] || [ "${GITHUB_REF#refs/heads/}" == development ] || [[ "${GITHUB_REF#refs/heads/}" == f* ]]; then
             echo "::debug::Set to dev setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
@@ -67,15 +67,15 @@ jobs:
       - name: Setup remote servers
         id: remote-servers
         shell: bash
-        run: if [ "${GITHUB_REF#refs/heads/}" == master ] ; then
+        run: if [ "${GITHUB_REF#refs/heads/}" == master ] || [[ "${GITHUB_REF#refs/heads/}" == v* ]]; then
             echo "::debug::Set to master setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb.v4.virtualflybrain.org";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.v4.virtualflybrain.org";
             echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
             echo "::set-output name=BUILD_TYPE::release";
-          elif [ "${GITHUB_REF#refs/heads/}" == debug ] || [ "${GITHUB_REF#refs/heads/}" == pipeline2 ] || [ "${GITHUB_REF#refs/heads/}" == vfb_geppetto_application ] || [ "${GITHUB_REF#refs/heads/}" == development ] ; then
+          elif [ "${GITHUB_REF#refs/heads/}" == debug ] || [ "${GITHUB_REF#refs/heads/}" == pipeline2 ] || [ "${GITHUB_REF#refs/heads/}" == vfb_geppetto_application ] || [ "${GITHUB_REF#refs/heads/}" == development ] || [[ "${GITHUB_REF#refs/heads/}" == f* ]]; then
             echo "::debug::Set to dev setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb-dev.virtualflybrain.org";
             echo "::set-output name=VFB_OWL_SERVER::http://owl-dev.virtualflybrain.org/kbs/vfb/";

diff --git a/Dockerfile b/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=VFBv2.2.2
 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" &&\

diff --git a/components/VFBMain.js b/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;
@@ -1286,63 +1297,6 @@ class VFBMain extends React.Component {
           idsList += ",";
         }
         idsList += this.idFromURL;
-        // populate page meta for this term for indexing
-        try {
-          window.ga('vfb.send', 'pageview', window.location.href );
-          if ( window.XMLHttpRequest ) {
-            var xhr = new XMLHttpRequest();
-            xhr.onload = function () {
-              try {
-                if (this.responseXML.title.indexOf("404 Not Found") < 0) {
-                  document.title = 'Virtual Fly Brain (' + this.responseXML.title + ')';
-                  document.body.style.font = "x-large";
-                  document.querySelector('meta[property="og:title"]').setAttribute("content",this.responseXML.title);
-                  document.querySelector('meta[name="description"]').setAttribute("content",this.responseXML.getElementById('json').innerText.substring(0, 4900));
-                  document.querySelector('meta[property="og:description"]').setAttribute("content",this.responseXML.getElementById('json').innerText.substring(0, 4900));
-                  if (document.getElementById('metaDesc') != null) {
-                    if (this.responseXML.head != undefined && this.responseXML.head.getElementsByTagName('script') != undefined && this.responseXML.head.getElementsByTagName('script') != null && this.responseXML.head.getElementsByTagName('script')[1] != undefined) {
-                      document.getElementById('metaDesc').innerHTML = this.responseXML.head.getElementsByTagName('script')[1].innerHTML;
-                    }
-                  } else {
-                    if (this.responseXML.head != undefined && this.responseXML.head.getElementsByTagName('script') != undefined && this.responseXML.head.getElementsByTagName('script') != null && this.responseXML.head.getElementsByTagName('script')[1] != undefined) {
-                      var script = document.createElement('script');
-                      script.type = 'application/ld+json';
-                      script.id = 'metaDesc';
-                      script.innerHTML = this.responseXML.head.getElementsByTagName('script')[1].innerHTML;
-                      document.getElementsByTagName('head')[0].appendChild(script);
-                    }
-                  }
-                  var viewport = !!document.querySelector("meta[name='viewport']");
-                  viewport = viewport ? document.querySelector("meta[name='viewport']") : document.createElement('meta');
-                  viewport.setAttribute('name', 'viewport');
-                  viewport.setAttribute('content', 'width=device-width, initial-scale=1');
-                  document.head.appendChild(viewport);
-                }
-              } catch (err) {
-                console.log(err);
-              }
-            }
-            xhr.open( 'GET', 'https://virtualflybrain.org/data/VFB/json/' + this.idFromURL + '.html')
-            xhr.responseType = 'document';
-            xhr.send();
-          }
-        } catch (err) {
-          console.error(err);
-        }
-        try {
-          var link = !!document.querySelector("link[rel='amphtml']");
-          link = link ? document.querySelector("link[rel='amphtml']") : document.createElement('link');
-          link.setAttribute('rel', 'amphtml');
-          link.setAttribute('href', 'https://virtualflybrain.org/data/VFB/json/' + this.idFromURL + '.html');
-          document.head.appendChild(link);
-          var conlink = !!document.querySelector("link[rel='canonical']");
-          conlink = conlink ? document.querySelector("link[rel='canonical']") : document.createElement('link');
-          conlink.setAttribute('rel', 'canonical');
-          conlink.setAttribute('href', 'https://virtualflybrain.org/reports/' + this.idFromURL);
-          document.head.appendChild(conlink);
-        } catch (err) {
-          console.error(err);
-        }
       } else if (idList[list].indexOf("i=") > -1) {
         if (idsList.length > 0) {
           idsList = "," + idsList;
@@ -1351,7 +1305,7 @@ class VFBMain extends React.Component {
       } else if (idList[list].indexOf("q=") > -1) {
         const multipleQueries = idList[list].replace("q=","").replace("%20", " ").split(";");
         let that = this;
-        multipleQueries?.forEach( query => { 
+        multipleQueries?.forEach( query => {
           const querySplit = query.split(",");
           that.urlQueryLoader.push({ id : querySplit[0].trim(), selection : querySplit[1].trim() });
         });
@@ -1392,7 +1346,7 @@ class VFBMain extends React.Component {
     GEPPETTO.on(GEPPETTO.Events.Instance_added, function (instance) {
       that.props.instanceAdded(instance);
     });
-    
+
     GEPPETTO.on(GEPPETTO.Events.Instances_created, function (instances) {
       // Set template Instance to be not clickable in 3D viewer
       if ( instances[0]?.id?.includes(window.templateID) ) {
@@ -1529,6 +1483,10 @@ class VFBMain extends React.Component {
 
     GEPPETTO.on(GEPPETTO.Events.Websocket_disconnected, function () {
       window.ga('vfb.send', 'event', 'disconnected', 'websocket-disconnect', (window.location.pathname + window.location.search));
+      if (GEPPETTO.MessageSocket.protocol == 'wss://' && location.protocol !== 'https:') {
+        console.log("%c Unsecure connection used reloading with HTTPS connection... ", 'background: #444; color: #bada55');
+        location.replace(`https:${location.href.substring(location.protocol.length)}`);
+      }
       if (GEPPETTO.MessageSocket.socketStatus == GEPPETTO.Resources.SocketStatus.CLOSE) {
         if (GEPPETTO.MessageSocket.attempts < 10) {
           window.ga('vfb.send', 'event', 'reconnect-attempt:' + GEPPETTO.MessageSocket.attempts, 'websocket-disconnect', (window.location.pathname + window.location.search));
@@ -1752,7 +1710,10 @@ class VFBMain extends React.Component {
           searchConfiguration={this.searchConfiguration}
           datasourceConfiguration={this.datasourceConfiguration} />
 
+        <VFBDownloadContents ref="downloadContentsRef" open={false} />
+
         <VFBUploader ref="uploaderContentsRef" open={false} />
+
         {this.htmlToolbarRender}
       </div>
     );

diff --git a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js b/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 = {
@@ -63,46 +72,43 @@ var styling = {
   // Color apply to target and source nodes when hovering over a link or a node.
   defaultNeighborNodesHoverColor : "orange",
   // Font used for text in nodes
-  defaultNodeFont : "5px sans-serif",
+  defaultNodeFont : "8px sans-serif",
   // Color of font in node's text
   defaultNodeFontColor : "black",
   // Node border color
   defaultBorderColor : "black",
   // When hovering over a node, the node's border color changes to create a halo effect
   defaultNodeHoverBoderColor : "red",
   // Title bar (in node) background color
-  defaultNodeTitleBackgroundColor : "#11bffe",
+  defaultNodeTitleBackgroundColor : "grey",
   // Description area (in node) background color
   defaultNodeDescriptionBackgroundColor : "white",
   nodeColorsByLabel : {
-    "Template" : "#ff6cc8",
-    "GABAergic" : "#9551ff",
-    "Dopaminergic" : "#3551ff",
-    "Cholinergic" : "#95515f",
-    "Glutamatergic" : "#95f1ff",
-    "Octopaminergic" : "#f3511f",
-    "Serotonergic" : "#9501f0",
-    "Motor_neuron" : "#fffa30",
-    "Sensory_neuron" : "#ff3a3a",
-    "Peptidergic_neuron" : "#5f6a3a",
-    "Glial_cell" : "#ff3a6a",
-    "Clone" : "#d6007d",
-    "Synaptic_neuropil" : "#00a2aa",
-    "License" : "#0164d8",
-    "Person" : "#023f00",
-    "Neuron" : "#7f2100",
-    "Neuron_projection_bundle" : "#d6327d",
-    "Resource" : "#005f1d",
-    "Site" : "#005f1d",
-    "Expression_pattern" : "#534700",
-    "Split" : "#e012e3",
-    "DataSet" : "#b700b5",
-    "Ganglion" : "#d6007d",
-    "Neuromere" : "#d6507d",
-    "Cell" : "#ff6a3a",
-    "Property" : "#005f1d",
-    "Anatomy" : "#00a2aa",
-    "_Class" : "#0164d8"
+    "Adult" : "#ffffb3",
+    "Anatomy" : "#33a02c",
+    "Cholinergic" : "#bebada",
+    "Clone" : "#cab2d6",
+    "Cluster" : "#ffed6f",
+    "Dopaminergic" : "#fdbf6f",
+    "Expression_pattern" : "#b3de69",
+    "Expression_pattern_fragment" : "#6a3d9a",
+    "GABAergic" : "#1f78b4",
+    "Ganglion" : "#ff7f00",
+    "Glutamatergic" : "#b2df8a",
+    "Larva" : "#ccebc5",
+    "Motor_neuron" : "#e31a1c",
+    "Muscle" : "#a6cee3",
+    "Nervous_system" : "#fdb462",
+    "Neuromere" : "#8dd3c7",
+    "Neuron" : "#b15928",
+    "Neuron_projection_bundle" : "#bc80bd",
+    "Octopaminergic" : "#ffff99",
+    "Peptidergic_neuron" : "#80b1d3",
+    "Sensory_neuron" : "#fb9a99",
+    "Serotonergic" : "#d9d9d9",
+    "Synaptic_neuropil_block" : "#fccde5",
+    "Synaptic_neuropil_domain" : "#fb8072",
+    "Synaptic_neuropil_subdomain" : "#88ffb3"
   },
   controlIcons : {
     home : "fa fa-home",
@@ -112,13 +118,14 @@ var styling = {
 }
 
 var restPostConfig = {
-  url: "https://pdb-dev.virtualflybrain.org/db/neo4j/tx/commit",
+  url: "https://pdb.v4.virtualflybrain.org/db/neo4j/tx/commit",
   contentType: "application/json"
 };
 
 module.exports = { 
   configuration,
   styling,
   restPostConfig,
-  locationCypherQuery
+  locationCypherQuery,
+  Neo4jLabels
 };
diff --git a/components/configuration/VFBCircuitBrowser/datasources/SOLRclient.tsx b/components/configuration/VFBCircuitBrowser/datasources/SOLRclient.tsx
@@ -1,7 +1,7 @@
 import axios from 'axios';
 
 const globalConfiguration:any = {
-    "url": "https://solr-dev.virtualflybrain.org/solr/ontology/select",
+    "url": "https://solr.virtualflybrain.org/solr/ontology/select",
     "query_settings":
     {
         "q": "$SEARCH_TERM$ OR $SEARCH_TERM$* OR *$SEARCH_TERM$*",
@@ -197,7 +197,7 @@ function refineResults(e) {
 }
 
 export const datasourceConfiguration = {
-  "url": "https://solr-dev.virtualflybrain.org/solr/ontology/select",
+  "url": "https://solr.virtualflybrain.org/solr/ontology/select",
   "query_settings":
     {
       "q": "$SEARCH_TERM$ OR $SEARCH_TERM$* OR *$SEARCH_TERM$*",

diff --git a/components/configuration/VFBDownloadContents/configuration.json b/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"
+	}
+}
diff --git a/components/configuration/VFBDownloadContents/nrrd.png b/components/configuration/VFBDownloadContents/nrrd.png
diff --git a/components/configuration/VFBDownloadContents/obj.png b/components/configuration/VFBDownloadContents/obj.png
diff --git a/components/configuration/VFBDownloadContents/reference.png b/components/configuration/VFBDownloadContents/reference.png
diff --git a/components/configuration/VFBDownloadContents/swc.png b/components/configuration/VFBDownloadContents/swc.png