Merge pull request #340 from VirtualFlyBrain/vfb_geppetto_application

changes from Vfb geppetto application

.travis.yml

@@ -22,7 +22,8 @@ install:
   - npm install jest@24.8.0 puppeteer@1.17.0 jest-puppeteer@3.9.0 babel-preset-env@1.6.0 url-join@4.0.0
 script:
   - echo -e "travis_fold:start:Docker_Build" || true
-  - travis_retry docker build -t=$REPO:$TAG --build-arg targetBranch=$TRAVIS_BRANCH --build-arg originBranch=$TRAVIS_PULL_REQUEST_BRANCH --build-arg defaultBranch=$DEFAULT_BRANCH $DOCKER_FOLDER || travis_terminate 1 
+  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
+  - travis_retry docker build -t=$REPO:$TAG --build-arg targetBranch=$TRAVIS_BRANCH --build-arg originBranch=$BRANCH --build-arg defaultBranch=$DEFAULT_BRANCH $DOCKER_FOLDER || travis_terminate 1 
   - echo -e "travis_fold:end:Docker_Build" || true
   - echo -e "travis_fold:start:Docker_Run" || true
   - travis_retry docker run  -t -dit --name=$CONTAINER_NAME -p 8080:8080 $REPO:$TAG || travis_terminate 1 

components/configuration/queryBuilderConfiguration.js

@@ -22,24 +22,48 @@ var queryResultsColMeta = [
     "cssClassName": "query-results-name-column",
   },
   {
-    "columnName": "description",
+    "columnName": "expressed_in",
     "order": 3,
     "locked": false,
     "visible": true,
+    "displayName": "Expressed_in",
+    "cssClassName": "query-results-expressed_in-column"
+  },
+  {
+    "columnName": "description",
+    "order": 4,
+    "locked": false,
+    "visible": true,
     "displayName": "Definition",
     "cssClassName": "query-results-description-column"
   },
+  {
+    "columnName": "reference",
+    "order": 5,
+    "locked": false,
+    "visible": true,
+    "displayName": "Reference",
+    "cssClassName": "query-results-reference-column"
+  },
   {
     "columnName": "type",
-    "order": 4,
+    "order": 6,
     "locked": false,
     "visible": true,
     "displayName": "Type",
     "cssClassName": "query-results-type-column"
   },
+  {
+    "columnName": "stage",
+    "order": 7,
+    "locked": false,
+    "visible": true,
+    "displayName": "Stage",
+    "cssClassName": "query-results-stage-column"
+  },
   {
     "columnName": "controls",
-    "order": 5,
+    "order": 8,
     "locked": false,
     "visible": false,
     "customComponent": QueryResultsControlsComponent,
@@ -49,7 +73,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "images",
-    "order": 6,
+    "order": 9,
     "locked": false,
     "visible": true,
     "customComponent": SlideshowImageComponent,
@@ -59,7 +83,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "score",
-    "order": 7,
+    "order": 10,
     "locked": false,
     "visible": true,
     "displayName": "Score",
@@ -68,7 +92,7 @@ var queryResultsColMeta = [
 ];
 
 // which columns to display in the results
-var queryResultsColumns = ['name', 'description', 'type', 'images', 'score'];
+var queryResultsColumns = ['name', 'expressed_in', 'description', 'reference', 'type', 'stage', 'images', 'score'];
 
 var queryResultsControlConfig = {
   "Common": {

css/VFBMain.less

@@ -222,3 +222,14 @@
 .griddle-body {
 	font-size: 14px !important;
 }
+
+.query-results-slick-image img {
+	margin-left: auto;
+    	margin-right: auto;	
+}
+
+#querybuilder .griddle td {
+	min-width: 14VW;
+}
+
+

model/vfb.xmi

@@ -299,57 +299,63 @@
     </queries>
     <queries
         xsi:type="gep_2:CompoundQuery"
-        name="Test Query for exp from anatomy with warning"
+        name="Query for exp from anatomy with warning"
         description="">
       <queryChain
           xsi:type="gep_2:SimpleQuery"
           name="Test Query for Exp from Anatomy"
           description="Test Query for Exp from Anatomy"
           returnType="//@libraries.3/@types.0"
-          query="MATCH (anat:Class) WHERE anat.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat) WITH DISTINCT collect(ar.pub) as pubs, anat, ep UNWIND pubs as p MATCH (pub:Individual:pub { short_form: p}) WITH anat, ep, collect({ core: { short_form: pub.short_form, label: coalesce(pub.label,''), iri: pub.iri, types: labels(pub) } , PubMed: coalesce(pub.PMID, ''), FlyBase: coalesce(pub.FlyBase, ''), DOI: coalesce(pub.DOI, '') }) as pubs OPTIONAL MATCH (anat)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, anat, ep, pubs , i limit 5 OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN null ELSE { anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} } END AS anatomy_channel_image ,anat,ep,pubs UNWIND pubs as p with anatomy_channel_image ,anat,ep,COLLECT(p.core.label) as refs RETURN ep.short_form as class_Id, ep.label as class_Name, 'Expressed in ' + coalesce(anat.label,'') + '&lt;br>&lt;small>Note: expression in this cell may be localised to regions of the cell that do not overlap the queried structure&lt;/small>' as class_Desc, refs as class_Type, CASE WHEN anatomy_channel_image IS NULL THEN [] ELSE COLLECT (DISTINCT { image_name: anatomy_channel_image.anatomy.label, image_id: anatomy_channel_image.anatomy.short_form, image_thumb: replace(anatomy_channel_image.image.image_folder,'http:','https:') + '/thumbnailT.png', template_id: anatomy_channel_image.image.template_anatomy.short_form}) END AS inds"
-          countQuery="MATCH (anat:Class) WHERE anat.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat) RETURN count(ep) as count"/>
+          query="MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat:Class) WHERE anat.short_form in $ARRAY_ID_RESULTS WITH DISTINCT collect(ar.pub) as pubs, anat, ep UNWIND pubs as p MATCH (pub:pub { short_form: p}) WITH anat, ep, collect({ core: { short_form: pub.short_form, label: coalesce(pub.label,''), iri: pub.iri, types: labels(pub) } , PubMed: coalesce(pub.PMID, ''), FlyBase: coalesce(pub.FlyBase, ''), DOI: coalesce(pub.DOI, '') }) as pubs OPTIONAL MATCH (ep)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, anat, ep, pubs , i  OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} }) END AS anatomy_channel_image ,anat,ep,pubs RETURN { short_form: anat.short_form, label: coalesce(anat.label + ' Note: expression in this cell may be localised to regions of the cell that do not overlap the queried structure.',''), iri: anat.iri, types: labels(anat) }  as anatomy, { short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep) }  AS expression_pattern, 'Get JSON for anat_2_ep query' AS query, '6959794' AS version , pubs, anatomy_channel_image"
+          countQuery="MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat:Class) WHERE anat.short_form in $ARRAY_ID_RESULTS WITH DISTINCT RETURN count(ep) as count"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"
-          name="Process Images"
+          id="vfb_query_schema_processor"
+          name="vfb_query schema processor"
+          description="vfb_query schema processor"
           runForCount="false"
           returnType="//@libraries.3/@types.1"
-          queryProcessorId="vfbCreateImagesForQueryResultsQueryProcessor"/>
+          queryProcessorId="neo4jQueryProcessor"/>
     </queries>
     <queries
         xsi:type="gep_2:CompoundQuery"
-        name="Test Query for exp from anatomy without warning"
+        name="Query for exp from anatomy without warning"
         description="">
       <queryChain
           xsi:type="gep_2:SimpleQuery"
           name="Test Query for Exp from Anatomy"
           description="Test Query for Exp from Anatomy"
           returnType="//@libraries.3/@types.0"
-          query="MATCH (anat:Class) WHERE anat.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat) WITH DISTINCT COLLECT(ar.pub) as pubs, anat, ep UNWIND pubs as p MATCH (pub:Individual:pub { short_form: p}) WITH anat, ep, collect({ core: { short_form: pub.short_form, label: coalesce(pub.label,''), iri: pub.iri, types: labels(pub) } , PubMed: coalesce(pub.PMID, ''), FlyBase: coalesce(pub.FlyBase, ''), DOI: coalesce(pub.DOI, '') }) as pubs OPTIONAL MATCH (anat)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, anat, ep, pubs , i limit 5 OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN null ELSE { anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} } END AS anatomy_channel_image ,anat,ep,pubs UNWIND pubs as p with anatomy_channel_image ,anat,ep,COLLECT(p.core.label) as refs RETURN ep.short_form as class_Id, ep.label as class_Name, 'Expressed in ' + coalesce(anat.label,'') as class_Desc, refs as class_Type, CASE WHEN anatomy_channel_image IS NULL THEN [] ELSE COLLECT (DISTINCT { image_name: anatomy_channel_image.anatomy.label, image_id: anatomy_channel_image.anatomy.short_form, image_thumb: replace(anatomy_channel_image.image.image_folder,'http:','https:') + '/thumbnailT.png', template_id: anatomy_channel_image.image.template_anatomy.short_form}) END AS inds"
-          countQuery="MATCH (anat:Class) WHERE anat.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat) RETURN count(ep) as count"/>
+          query="MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat:Class) WHERE anat.short_form in $ARRAY_ID_RESULTS WITH DISTINCT collect(ar.pub) as pubs, anat, ep UNWIND pubs as p MATCH (pub:pub { short_form: p}) WITH anat, ep, collect({ core: { short_form: pub.short_form, label: coalesce(pub.label,''), iri: pub.iri, types: labels(pub) } , PubMed: coalesce(pub.PMID, ''), FlyBase: coalesce(pub.FlyBase, ''), DOI: coalesce(pub.DOI, '') }) as pubs OPTIONAL MATCH (ep)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, anat, ep, pubs , i  OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} }) END AS anatomy_channel_image ,anat,ep,pubs RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat) }  as anatomy, { short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep) }  AS expression_pattern, 'Get JSON for anat_2_ep query' AS query, '6959794' AS version , pubs, anatomy_channel_image"
+          countQuery="MATCH (ep:Class)&lt;-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat:Class) WHERE anat.short_form in $ARRAY_ID_RESULTS WITH DISTINCT RETURN count(ep) as count"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"
-          name="Process Images"
+          id="vfb_query_schema_processor"
+          name="vfb_query schema processor"
+          description="vfb_query schema processor"
           runForCount="false"
           returnType="//@libraries.3/@types.1"
-          queryProcessorId="vfbCreateImagesForQueryResultsQueryProcessor"/>
+          queryProcessorId="neo4jQueryProcessor"/>
     </queries>
     <queries
         xsi:type="gep_2:CompoundQuery"
-        name="Test Query for anatomy from expression "
+        name="Query for anatomy from expression "
         description="">
       <queryChain
           xsi:type="gep_2:SimpleQuery"
           name="Test Query for Anatomy from Exp"
           description="Test Query for Anatomy from Exp"
           returnType="//@libraries.3/@types.0"
-          query="MATCH (ep:Expression_pattern:Class)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in ['$ID'] WITH  anoni, anat, ar, ep OPTIONAL MATCH (p:pub:Individual { short_form: ar.pub}) WITH ep, anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p) } , PubMed: coalesce(p.PMID, ''), FlyBase: coalesce(p.FlyBase, ''), DOI: coalesce(p.DOI, '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.uri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o) }  }) END AS stages ,anoni,anat,pub,ep OPTIONAL MATCH (ep)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH ep, template, channel, template_anat, irw, anoni, anat, pub, stages , i OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages,ep UNWIND anatomy_channel_image as images WITH images as anatomy_channel_image,anat,ep,pub.core.label as refs RETURN ep.short_form as class_Id, ep.label as class_Name, 'Expressed in ' + coalesce(anat.label,'') as class_Desc, COLLECT(DISTINCT refs) as class_Type, CASE WHEN anatomy_channel_image IS NULL THEN [] ELSE COLLECT (DISTINCT { image_name: anatomy_channel_image.anatomy.label, image_id: anatomy_channel_image.anatomy.short_form, image_thumb: replace(anatomy_channel_image.image.image_folder,'http:','https:') + '/thumbnailT.png', template_id: anatomy_channel_image.image.template_anatomy.short_form}) END AS inds"
+          query="MATCH (ep:Expression_pattern:Class)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in ['$ID'] WITH  anoni, anat, ar OPTIONAL MATCH (p:pub { short_form: ar.pub}) WITH anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p) } , PubMed: coalesce(p.PMID, ''), FlyBase: coalesce(p.FlyBase, ''), DOI: coalesce(p.DOI, '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.uri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o) }  }) END AS stages ,anoni,anat,pub OPTIONAL MATCH (anat:Synaptic_neuropil)&lt;-[:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, anoni, anat, pub, stages , i  OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i) } , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel) } , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique) } ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template) } , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat) } ,image_folder: irw.folder, index: coalesce(irw.index, []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat) }  AS anatomy, 'Get JSON for ep_2_anat query' AS query, '6959794' AS version , pub, stages, anatomy_channel_image"
           countQuery="MATCH (ep:Expression_pattern:Class)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in ['$ID'] RETURN count(anat) as count"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"
-          name="Process Images"
+          id="vfb_query_schema_processor"
+          name="vfb_query schema processor"
+          description="vfb_query schema processor"
           runForCount="false"
           returnType="//@libraries.3/@types.1"
-          queryProcessorId="vfbCreateImagesForQueryResultsQueryProcessor"/>
+          queryProcessorId="neo4jQueryProcessor"/>
     </queries>
     <fetchVariableQuery
         xsi:type="gep_2:CompoundQuery"