Merge pull request #1369 from VirtualFlyBrain/development

Fix for show 3D volume issue
VirtualFlyBrain · Sep 1, 2022 · fa18b6d · fa18b6d
2 parents 88a8d14 + 144df85
commit fa18b6d
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Showing 5 changed files with 94 additions and 30 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@ ARG geppettoCoreRelease=vfb_20200604_a
 ARG geppettoSimulationRelease=vfb_20200604_a
 ARG geppettoDatasourceRelease=vfb_20200604_a
 ARG geppettoModelSwcRelease=v1.0.1
-ARG geppettoFrontendRelease=development
+ARG geppettoFrontendRelease=VFBv2.1.0.3
 ARG geppettoClientRelease=VFBv2.2.2
 ARG ukAcVfbGeppettoRelease=download
 

diff --git a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js
@@ -97,31 +97,54 @@ var styling = {
   // Description area (in node) background color
   defaultNodeDescriptionBackgroundColor : "white",
   nodeColorsByLabel : {
-    "Adult" : "#ffffb3",
-    "Anatomy" : "#33a02c",
-    "Cholinergic" : "#bebada",
-    "Clone" : "#cab2d6",
-    "Cluster" : "#ffed6f",
-    "Dopaminergic" : "#fdbf6f",
-    "Expression_pattern" : "#b3de69",
+    "API": "#000000",
+    "Neuron" : "#b15928",
     "Expression_pattern_fragment" : "#6a3d9a",
+    "Visual_system" : "#0000aa",
     "GABAergic" : "#1f78b4",
-    "Ganglion" : "#ff7f00",
+    "Cholinergic" : "#bebada",
+    "Olfactory_system" : "#00aa00",
     "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",
+    "Synaptic_neuropil_subdomain" : "#88ffb3",
     "Sensory_neuron" : "#fb9a99",
+    "Mechanosensory_system": "#00aaaa",
+    "Peptidergic_neuron" : "#80b1d3",
+    "Thermosensory_system" : "#aa0000",
+    "Muscle" : "#a6cee3",
     "Serotonergic" : "#d9d9d9",
-    "Synaptic_neuropil_block" : "#fccde5",
+    "Dopaminergic" : "#fdbf6f",
+    "Auditory_system" : "#aa00aa",
+    "Gustatory_system" : "#aaaa00",
+    "Proprioceptive_system" : "#00aaaa",
+    "Octopaminergic" : "#ffff99",
+    "Motor_neuron" : "#e31a1c",
+    "Chemosensory_system" : "#ea9e24",
     "Synaptic_neuropil_domain" : "#fb8072",
-    "Synaptic_neuropil_subdomain" : "#88ffb3"
+    "Glial_cell" : "#ff6a3a",
+    "Hygrosensory_system" : "#0000ff",
+    "Clone" : "#cab2d6",
+    "Ganglion" : "#ff7f00",
+    "Neuromere" : "#8dd3c7",
+    "Expression_pattern" : "#b3de69",
+    "Split" : "#e012e3",
+    "Synaptic_neuropil_block" : "#fccde5",
+    "Deprecated" : "#ff0000",
+    "Larva" : "#ccebc5",
+    "Nociceptive_system" : "#ffa500",
+    "Neuroblast" : "#8df8f9",
+    "Synaptic_neuropil" : "#00a2aa",
+    "GMC" : "#ecf7f7",
+    "Transgenic_Construct" : "#F8BBD0",
+    "Gene" : "#ffcdd2",
+    "Insertion" : "#D1C4E9",
+    "Allele" : "#DCEDC8",
+    "DataSet" : "#b700b5",
+    "Site" : "#005f1d",
+    "Person" : "#023f00",
+    "pub" : "#0164d8",
+    "License" : "#0164d8",
+    "Cluster" : "#ffed6f"
   },
   controlIcons : {
     home : "fa fa-home",

diff --git a/components/configuration/VFBTermInfo/VFBTermInfoConfiguration.js b/components/configuration/VFBTermInfo/VFBTermInfoConfiguration.js
@@ -62,7 +62,7 @@ const buttonBarConfiguration = {
       "condition": "(function() { var visible = false; if ($instance$.getType().$instance$_obj != undefined && $instance$.getType().$instance$_obj.getType().getMetaType() != GEPPETTO.Resources.IMPORT_TYPE && $instance$.$instance$_obj != undefined) { visible = GEPPETTO.SceneController.isVisible([$instance$.$instance$_obj]); } return visible; })()",
       "false": {
         "id": "visibility_obj",
-        "actions": ["(function(){var color = $instance$.getColor(); var instance = Instances.getInstance('$instance$.$instance$_obj'); if (instance.getType().getMetaType() == GEPPETTO.Resources.IMPORT_TYPE) { var col = instance.getParent().getColor(); instance.getType().resolve(function() { instance.setColor(col); GEPPETTO.trigger('experiment:visibility_changed', instance); GEPPETTO.ControlPanel.refresh(); }); } else { if(GEPPETTO.SceneController.isInstancePresent(instance)) { GEPPETTO.SceneController.show([instance]); } else { GEPPETTO.SceneController.display(instance); instance.setColor(color);}}})()"],
+        "actions": ["(function(){var color = $instance$.getColor();var instance = $instance$.$instance$_obj; if ($instance$.$instance$_obj == undefined || $instance$.getType().$instance$_obj.getType().getMetaType() == GEPPETTO.Resources.IMPORT_TYPE) { var col = $instance$.getColor(); $instance$.getType().$instance$_obj.getType().resolve(function() { var instance = Instances.getInstance('$instance$.$instance$_obj'); instance.setColor(col); GEPPETTO.trigger('experiment:visibility_changed', instance); GEPPETTO.ControlPanel.refresh(); }); } else { var instance = Instances.getInstance('$instance$.$instance$_obj'); if(GEPPETTO.SceneController.isInstancePresent(instance)) { GEPPETTO.SceneController.show([instance]); } else { GEPPETTO.SceneController.display(instance); instance.setColor(color);}}})()"],
         "icon": "gpt-shapehide",
         "label": "Hidden",
         "tooltip": "Enable 3D Volume"

diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less
@@ -428,7 +428,7 @@
 }
 
  .label.types>.label.label-Cell {
-    background-color:#ff6a3a !important;
+    background-color:#fbcf1d !important;
     color: #3a3939;
 }
 
@@ -547,6 +547,54 @@
     background-color: #fe8 !important;
     color: black;
 }
+.label.types>.label.label-Thermosensory_system {
+    background-color: #AA0000 !important;
+    color: white;
+}
+.label.types>.label.label-Neuroblast {
+    background-color: #8df8f9 !important;
+    color: black;
+}
+.label.types>.label.label-GMC {
+    background-color: #ecf7f7 !important;
+    color: black;
+}
+.label.types>.label.label-Mechanosensory_system {
+    background-color: #00aaaa !important;
+    color: black;
+}
+.label.types>.label.label-Visual_system {
+    background-color: #0000aa !important;
+    color: white;
+}
+.label.types>.label.label-Olfactory_system {
+    background-color: #00aa00 !important;
+    color: black;
+}
+.label.types>.label.label-Auditory_system {
+    background-color: #aa00aa !important;
+    color: white;
+}
+.label.types>.label.label-Gustatory__system {
+    background-color: #aaaa00 !important;
+    color: black;
+}
+.label.types>.label.label-Proprioceptive_system {
+    background-color: #00aaaa !important;
+    color: black;
+}
+.label.types>.label.label-Chemosensory_system {
+    background-color: #ea9e24 !important;
+    color: black;
+}
+.label.types>.label.label-Hygrosensory_system {
+    background-color: #0000ff !important;
+    color: white;
+}
+.label.types>.label.label-Nociceptive_system {
+    background-color: #ffa500 !important;
+    color: black;
+}
 
 .button-bar-vfbHistoryLinks-back {
     position:absolute;

diff --git a/model/vfb.xmi b/model/vfb.xmi
@@ -1166,6 +1166,8 @@
       queryChain="//@dataSources.0/@queries.19">
     <matchingCriteria
         type="//@libraries.3/@types.0 //@libraries.3/@types.27 //@libraries.3/@types.44"/>
+    <matchingCriteria
+        type="//@libraries.3/@types.0 //@libraries.3/@types.46 //@libraries.3/@types.44"/>
   </queries>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="SimilarMorphologyToNB"
@@ -1187,13 +1189,4 @@
     <matchingCriteria
         type="//@libraries.3/@types.45 //@libraries.3/@types.0 //@libraries.3/@types.2"/>
   </queries>
-  <queries xsi:type="gep_2:CompoundRefQuery"
-      id="SimilarMorphologyToPartOfexp"
-      name="has_similar_morphology_to_part_of_exp_frag"
-      description="Neurons with similar morphology to part of $NAME  [NBLAST mean score]"
-      returnType="//@libraries.3/@types.0"
-      queryChain="//@dataSources.0/@queries.19">
-    <matchingCriteria
-        type="//@libraries.3/@types.0 //@libraries.3/@types.46 //@libraries.3/@types.44"/>
-  </queries>
 </gep:GeppettoModel>