Merge pull request #1458 from VirtualFlyBrain/development

Development
VirtualFlyBrain · Jan 21, 2024 · d0721b0 · d0721b0
2 parents 9508264 + 98dd628
commit d0721b0
Show file tree

Hide file tree

Showing 8 changed files with 23 additions and 9 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1 @@
+{}
diff --git a/Dockerfile b/Dockerfile
@@ -12,7 +12,7 @@ VOLUME /tmp/error
 ARG geppettoRelease=vfb_20200604_a
 ARG geppettoModelRelease=vfb_20200604_a
 ARG geppettoCoreRelease=VFBv2.2.0
-ARG geppettoSimulationRelease=vfb_20200604_a
+ARG geppettoSimulationRelease=VFBv2.1.0.2
 ARG geppettoDatasourceRelease=passingSOLR
 ARG geppettoModelSwcRelease=v1.0.1
 ARG geppettoFrontendRelease=VFBv2.1.0.3

diff --git a/components/configuration/VFBMain/searchConfiguration.js b/components/configuration/VFBMain/searchConfiguration.js
@@ -149,6 +149,11 @@ var searchConfiguration = {
           "filter_name": "Neuron",
           "enabled": "disabled",
         },
+        {
+          "key": "Class",
+          "filter_name": "Type",
+          "enabled": "disabled",
+        },
         {
           "key": "has_image",
           "filter_name": "Image",

diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js
@@ -270,11 +270,10 @@ var toolbarMenu = {
             },
             {
               label: "NBLAST against your own data",
-              icon: "",
-              trailerIcon: "fa fa-external-link",
+              icon: "fa fa-upload",
               action: {
-                handlerAction: "openNewTab",
-                parameters: ["http://nblast.virtualflybrain.org:8080/NBLAST_on-the-fly/?gal4_n=10&all_use_mean=F&all_query=&tab=One%20against%20all&gal4_query="]
+                handlerAction: "uploaderContentsVisible",
+                parameters: []
               }
             }
           ]

diff --git a/components/configuration/VFBUploader/configuration.json b/components/configuration/VFBUploader/configuration.json
@@ -1,10 +1,10 @@
 {
-	"nblastURL" : "http://upload.virtualflybrain.org/files/UNIQUE_ID?token=bec3a40f0ab377c39103",
+	"nblastURL" : "https://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,
+	"maxFileSize" : 5242880,
 	"queryType": "uploaderQuery",
 	"cookieStorageDays" : 100,
 	"cookiesLearnLink" : "https://en.wikipedia.org/wiki/HTTP_cookie",

diff --git a/components/interface/VFBFocusTerm/VFBFocusTerm.js b/components/interface/VFBFocusTerm/VFBFocusTerm.js
@@ -363,6 +363,8 @@ class VFBFocusTerm extends React.Component {
                                                                               { variable: variable2, allQueries: allQueries2 }];
             }
           });
+        } else {
+          this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
         }
       } else {
         this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];
@@ -568,6 +570,13 @@ class VFBFocusTerm extends React.Component {
                   </Tooltip>
                   : <i className="fa fa-chevron-right arrowsStyle isDisabled" /> 
                 }
+                <Tooltip placement="top-end"
+                  title="NBLAS Uploader">
+                  <i id="fa-upload" className="fa fa-upload arrowsStyle"
+                    onClick={() => {
+                      this.props.UIUpdateManager("uploaderContentsVisible");
+                    }} />
+                </Tooltip>
                 <Tooltip placement="top-end"
                   title="Download Contents">
                   <i className="fa fa-download arrowsStyle"

diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less
@@ -848,7 +848,7 @@
 	color: white;
 	clear: both;
 	max-width: 100%;
-    max-width: 260px;
+    max-height: 260px;
     margin-left: 25px;
 }
 

diff --git a/model/vfb.xmi b/model/vfb.xmi
@@ -600,7 +600,7 @@
           id="cluster_expression_query"
           name="Get JSON for cluster expression query"
           description="Get JSON for cluster expression query"
-          query="&quot;statement&quot;: &quot;MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) WITH e.expression_level[0] as expression_level, e.expression_extent[0] as expression_extent, { short_form: g.short_form, label: coalesce(g.label,''), iri: g.iri, types: labels(g), unique_facets: apoc.coll.sort(coalesce(g.uniqueFacets, [])), symbol: coalesce(([]+g.symbol)[0], '')}  AS gene,primary MATCH (a:Anatomy)&lt;-[:composed_primarily_of]-(primary) WITH { short_form: a.short_form, label: coalesce(a.label,''), iri: a.iri, types: labels(a), unique_facets: apoc.coll.sort(coalesce(a.uniqueFacets, [])), symbol: coalesce(([]+a.symbol)[0], '')}  AS anatomy,primary,expression_level,expression_extent,gene  RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(([]+primary.symbol)[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for cluster expression query' AS query, 'a3c0d68' AS version , expression_level, expression_extent, gene, anatomy&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"
+          query="&quot;statement&quot;: &quot;MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) WITH coalesce(e.expression_level_padded[0], e.expression_level[0]) as expression_level, e.expression_extent[0] as expression_extent, { short_form: g.short_form, label: coalesce(g.label,''), iri: g.iri, types: labels(g), unique_facets: apoc.coll.sort(coalesce(g.uniqueFacets, [])), symbol: coalesce(([]+g.symbol)[0], '')}  AS gene,primary MATCH (a:Anatomy)&lt;-[:composed_primarily_of]-(primary) WITH { short_form: a.short_form, label: coalesce(a.label,''), iri: a.iri, types: labels(a), unique_facets: apoc.coll.sort(coalesce(a.uniqueFacets, [])), symbol: coalesce(([]+a.symbol)[0], '')}  AS anatomy,primary,expression_level,expression_extent,gene  RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(([]+primary.symbol)[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for cluster expression query' AS query, 'a3c0d68' AS version , expression_level, expression_extent, gene, anatomy&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"
           countQuery="&quot;statement&quot;: &quot;MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) RETURN count(g) as count&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"