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changes from Vfb geppetto application #340

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merged 9 commits into from
Jul 8, 2019
Merged

changes from Vfb geppetto application #340

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ae8c948
fixing non pull builds
Robbie1977 Jul 4, 2019
e747900
adding new headers
Robbie1977 Jul 5, 2019
bf2a421
Merge branch 'vfb_geppetto_application' of https://github.com/Virtual…
Robbie1977 Jul 5, 2019
7326600
swapping to vfb_query schema queries
Robbie1977 Jul 5, 2019
0aa113c
correcting note position
Robbie1977 Jul 6, 2019
8cebed4
correcting location of warning
Robbie1977 Jul 7, 2019
37f98bd
centering images
Robbie1977 Jul 7, 2019
be1b689
tweaking column min width
Robbie1977 Jul 7, 2019
5d20248
typo fix
Robbie1977 Jul 7, 2019
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3 changes: 2 additions & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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36 changes: 30 additions & 6 deletions components/configuration/queryBuilderConfiguration.js
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Expand Up @@ -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,
Expand All @@ -49,7 +73,7 @@ var queryResultsColMeta = [
},
{
"columnName": "images",
"order": 6,
"order": 9,
"locked": false,
"visible": true,
"customComponent": SlideshowImageComponent,
Expand All @@ -59,7 +83,7 @@ var queryResultsColMeta = [
},
{
"columnName": "score",
"order": 7,
"order": 10,
"locked": false,
"visible": true,
"displayName": "Score",
Expand All @@ -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": {
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11 changes: 11 additions & 0 deletions css/VFBMain.less
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}


34 changes: 20 additions & 14 deletions model/vfb.xmi
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Expand Up @@ -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"
Expand Down