sync: pipeline2 with pipeline2-sync-f89b

.github/workflows/main.yml

@@ -6,6 +6,7 @@ name: CI
 on:
   push:
     branches: '*'
+  release:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

.github/workflows/sync.yml

@@ -0,0 +1,23 @@
+name: Sync
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  sync-branches:
+    runs-on: ubuntu-latest
+    name: Syncing branches
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Node
+        uses: actions/setup-node@v1
+        with:
+          node-version: 12
+      - name: Create Sync PR
+        uses: sudoStatus200/create-sync-pr@0.3.1
+        with:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          SOURCE_BRANCH: "master"
+          TARGET_BRANCH: "development,debug,alpha,vfb_geppetto_application,pipeline2"

Dockerfile

@@ -14,7 +14,7 @@ ARG geppettoSimulationRelease=vfb_20200604_a
 ARG geppettoDatasourceRelease=vfb_20200604_a
 ARG geppettoModelSwcRelease=v1.0.1
 ARG geppettoFrontendRelease=development
-ARG geppettoClientRelease=VFBv2.2.0.5
+ARG geppettoClientRelease=VFBv2.2.0.6
 ARG ukAcVfbGeppettoRelease=pipeline2
 
 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster"

NoLongerUsed.travis.yml

@@ -37,10 +37,10 @@ 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 ${TRAVIS_BRANCH/\//-}; fi`
-        - export VFB_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
+        - export VFB_PDB_SERVER=https://pdb.virtualflybrain.org;
         - export VFB_OWL_SERVER=http://owl.p2.virtualflybrain.org/kbs/vfb/;
         - export VFB_R_SERVER=http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast;
-        - export VFB_TREE_PDB_SERVER=https://pdb.p2.virtualflybrain.org;
+        - export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
         - export SOLR_SERVER=https://solr.p2.virtualflybrain.org/solr/ontology/select;
         - if [ "$TRAVIS_BRANCH" == "master" ]; then
             export VFB_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
@@ -249,8 +249,8 @@ jobs:
         #     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_TREE_PDB_SERVER=https://pdb.virtualflybrain.org;
+        - export VFB_PDB_SERVER=http://pdb.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;

components/VFBMain.js

@@ -37,7 +37,7 @@ class VFBMain extends React.Component {
       canvasVisible: true,
       listViewerVisible: true,
       graphVisible : true,
-      circuitBrowserVisible : true,
+      circuitBrowserVisible : false,
       htmlFromToolbar: undefined,
       idSelected: undefined,
       instanceOnFocus: undefined,
@@ -531,9 +531,12 @@ class VFBMain extends React.Component {
       var otherName = click.parameters[0].split(',')[2];
       var path = click.parameters[0].split(',')[0];
       var entity = Model[path];
+
+      $("body").css("cursor", "progress");
       this.refs.querybuilderRef.open();
       this.refs.querybuilderRef.switchView(false, false);
       this.refs.querybuilderRef.clearAllQueryItems();
+      // $('#add-new-query-container')[0].hidden = true; $('#query-builder-items-container')[0].hidden = true;
 
       var callback = function () {
         // check if any results with count flag
@@ -545,6 +548,7 @@ class VFBMain extends React.Component {
         }
         // show query component
         that.refs.querybuilderRef.open();
+        $("body").css("cursor", "default");
         GEPPETTO.trigger('stop_spin_logo');
       };
       // add query item + selection

components/configuration/VFBGraph/graphConfiguration.js

@@ -1,7 +1,7 @@
 var locationCypherQuery = instance => ({
   "statements": [
     {
-      "statement": "MATCH p=(n:Entity {short_form:'" + instance + "'})-[r:INSTANCEOF|part_of|has_synaptic_terminal_in|has_presynaptic_terminal_in|"
+      "statement": "MATCH (n:Entity {short_form:'" + instance + "'}) OPTIONAL MATCH p=(n)-[r:INSTANCEOF|part_of|has_synaptic_terminal_in|has_presynaptic_terminal_in|"
       + "has_postsynaptic_terminal_in|overlaps*..]->(x) "
       + "RETURN distinct n,r,x,n.short_form as root",
       "resultDataContents": ["graph"]
@@ -13,7 +13,7 @@ var whatCypherQuery = instance => ({
   "statements": [
     {
       "statement": "MATCH (n:Entity {short_form:'" + instance + "'}) OPTIONAL MATCH p=(n)-[:INSTANCEOF|:SUBCLASSOF*..]->(x) "
-      + "WHERE (('Anatomy' IN  labels(x)) AND ('Class' IN  labels(n))) OR (('Cell' IN  labels(x)) OR ('synaptic neuropil' IN labels(x))) "
+      + "WHERE ('Anatomy' IN  labels(x)) OR (('Cell' IN  labels(x)) OR ('synaptic neuropil' IN labels(x))) "
       + " OR (('Ganglion' IN  labels(x)) OR ('Neuron_projection_bundle' IN labels(x))) "
       + "RETURN  n,p, n.short_form as root",
       "resultDataContents": ["graph"]
@@ -84,7 +84,7 @@ var styling = {
 }
 
 var restPostConfig = {
-  url: "https://pdb.p2.virtualflybrain.org/db/data/transaction/commit",
+  url: "https://pdb.virtualflybrain.org/db/data/transaction/commit",
   contentType: "application/json"
 };
 

components/configuration/VFBMain/layoutModel.js

@@ -71,11 +71,6 @@ var modelJson = {
             "type": "tab",
             "name": "Layers",
             "component": "vfbListViewer"
-          },
-          {
-            "type": "tab",
-            "name": "Circuit Browser",
-            "component": "vfbCircuitBrowser"
           }
         ]
       },

components/configuration/VFBMain/searchConfiguration.js

@@ -124,8 +124,8 @@ var searchConfiguration = {
           "enabled": "disabled",
         },
         {
-          "key": "Larval",
-          "filter_name": "Larval",
+          "key": "Larva",
+          "filter_name": "Larva",
           "enabled": "disabled",
         },
         {
@@ -157,6 +157,11 @@ var searchConfiguration = {
           "key": "Neuron",
           "filter_name": "Neuron",
           "enabled": "disabled",
+        },
+        {
+          "key": "Deprecated",
+          "filter_name": "Deprecated",
+          "enabled": "negative",
         }
       ]
     },
@@ -191,6 +196,26 @@ var searchConfiguration = {
     if (InputString.toLowerCase() == b.label.toLowerCase()) {
       return 1;
     }
+    if (InputString.toLowerCase().indexOf(' ') > -1) {
+      var lcInputStingFac = InputString.toLowerCase().split(' ');
+      var compare = (a1, a2) => a1.filter(v => a2.includes(v)).length;
+      var cA = compare(lcInputStingFac, a.label.toLowerCase().split(' '));
+      var cB = compare(lcInputStingFac, b.label.toLowerCase().split(' '));
+      if (cA > 0 || cB > 0) {
+        if (cA > cB) {
+          return -1;
+        }
+        if (cA < cB) {
+          return 1;
+        }
+        if (a.label.length < b.label.length) {
+          return -1;
+        }
+        if (a.label.length > b.label.length) {
+          return 1;
+        }
+      }
+    }
     // close match without case matching ['xx ('ID/Label)]
     if (a.label.toLowerCase().indexOf(InputString.toLowerCase()) == 0) {
       return -1;

components/configuration/VFBTermInfo/VFBTermInfoConfiguration.js

@@ -144,7 +144,7 @@ const linksConfiguration = {
   "CircuitBrowser": {
     "title": "Circuit browser For",
     "visibility": true,
-    "superType": "Neuron"
+    "superType": "hasSynapses"
   }
 }
 

components/configuration/VFBToolbar/vfbtoolbarHTML.js

@@ -13,7 +13,7 @@ var feedback
   + "[<a href='https://github.com/VirtualFlyBrain/VFB2' target='_blank'>VirtualFlyBrain/VFB2</a>].</p>"
   + "<p>If you have a GitHub account you can easily raise a new issue: "
   + "<form id='GitHubIssue' method='get' action='https://github.com/VirtualFlyBrain/VFB2/issues/new' target='_blank'>"
-  + "<input type='hidden' name='body' value='%0A%0A%0A%0A%0A%0ASupport%20info%3A%0A$DATE$%0A$BROWSER$%20$VERSION$%20%5B$SCREEN$%5D%0A$URL$%0A%0A%60%60%60diff%0A$LOG$%0A%60%60%60%0A' />"
+  + "<input type='hidden' name='body' value='Please give details of the issue:\n\n\n\n\nSupport info:\n$DATE$\n$BROWSER$\n$VERSION$ [$SCREEN$]\n$URL$\n\n\n\'\'\'diff\n$LOG$\n\'\'\'\n' />"
   + "<input type='submit' value='Create GitHub Issue' style='color: black; border-color: darkcyan;'></form>"
   + "</p>"
   + "<p> This could simply be a question or a new feature request, but if you have found a bug we missed please copy in "

components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js

@@ -245,14 +245,6 @@ var toolbarMenu = {
             parameters: ["graphVisible"]
           }
         },
-        {
-          label: "Circuit Browser",
-          icon: "fa fa-cogs",
-          action: {
-            handlerAction: "UIElementHandler",
-            parameters: ["circuitBrowserVisible"]
-          }
-        },
         {
           label: "NBLAST",
           icon: "",

components/configuration/VFBTree/VFBTreeConfiguration.js

@@ -1,5 +1,5 @@
 var restPostConfig = {
-  url: "https://pdb.p2.virtualflybrain.org/db/data/transaction/commit",
+  url: "https://pdb.virtualflybrain.org/db/data/transaction/commit",
   contentType: "application/json"
 };
 

components/interface/VFBGraph/VFBGraph.js

@@ -226,7 +226,15 @@ class VFBGraph extends Component {
 
   resetCamera () {
     if ( this.graphRef.current !== null ) {
-      this.graphRef.current.ggv.current.zoomToFit();
+      // If more than one graph node, use library's 'zoomToFit' method to center camera
+      if ( this.state.graph.nodes.length > 1 ) {
+        this.graphRef.current.ggv.current.zoomToFit();
+      } else if ( this.state.graph.nodes.length == 1 ) {
+        // Only one graph node, center camera around it
+        let x = this.state.graph.nodes[0].x;
+        let y = this.state.graph.nodes[0].y;
+        this.graphRef.current.ggv.current.centerAt(x,y);
+      }
       this.focused = true;
     }
   }
@@ -474,7 +482,7 @@ class VFBGraph extends Component {
     // No graph to display, message is shown instead of graph
     if (Object.keys(this.props.instanceOnFocus).length === 0 && this.props.instanceOnFocus.constructor === Object) {
       return (
-        <p>No graph available for {this.state.currentQuery.name} , where {this.state.currentQuery.name} is either 'show classification for $Instance' or 'show location for $instance'</p>
+        <p>Model not loaded, graph not available yet</p>
       );
     }
 

components/interface/VFBToolbar/VFBToolBar.js

@@ -174,11 +174,7 @@ export default class VFBToolBar extends React.Component {
     }
     this.props.htmlOutputHandler(
       htmlContent.replace(
-        /\$URL\$/g,window.location.href.replace(
-          /\&/g,escape('&')
-        ).replace(
-          /\#/g,escape('#')
-        )
+        /\$URL\$/g,window.location.href
       ).replace(
         /\$BROWSER\$/g, browserName
       ).replace(

css/VFBMain.less

@@ -1663,3 +1663,10 @@
   user-select: text;
 }
 
+img[class^="VFBQuickHelp-image-"] {
+  object-fit: contain !important;
+}
+
+#querybuilder .query-item-option {
+  padding: 0px 8px !important;
+}

css/VFBTermInfo.less

@@ -385,6 +385,10 @@
     background-color:#e012e3 !important;
 }
 
+.label.types>.label.label-Deprecated {
+    background-color:#ff0000 !important;
+}
+
 .button-bar-vfbHistoryLinks-back {
     position:absolute;
     left:10px;