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Fixes for NBLAST queries #745

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merged 11 commits into from
Nov 4, 2020
Merged

Fixes for NBLAST queries #745

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ad1030c
fixing graph so always focus term returned
Robbie1977 Oct 30, 2020
929f285
Merge pull request #736 from VirtualFlyBrain/debug
Robbie1977 Nov 2, 2020
cfbf795
Merge pull request #742 from VirtualFlyBrain/debug
Robbie1977 Nov 3, 2020
0bdc9d1
expanding timeout to allow for system delays
Robbie1977 Nov 3, 2020
c6e4c77
passing score outside table
Robbie1977 Nov 4, 2020
fc64008
Merge branch 'debug' of https://github.com/VirtualFlyBrain/geppetto-v…
Robbie1977 Nov 4, 2020
ae38f6b
Merge pull request #744 from VirtualFlyBrain/development
Robbie1977 Nov 4, 2020
ecb0ff5
cypher fix
Robbie1977 Nov 4, 2020
4bd541f
Merge branch 'debug' of https://github.com/VirtualFlyBrain/geppetto-v…
Robbie1977 Nov 4, 2020
bb9d65b
removing new NBLAST query
Robbie1977 Nov 4, 2020
92ac58c
Merge pull request #746 from VirtualFlyBrain/debug
Robbie1977 Nov 4, 2020
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6 changes: 3 additions & 3 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
# The type of runner that the job will run on
runs-on: ubuntu-latest
# total job timeout:
timeout-minutes: 45
timeout-minutes: 60

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
Expand Down Expand Up @@ -122,7 +122,7 @@ jobs:

- name: Build and push local wss
id: docker_build_local
timeout-minutes: 10
timeout-minutes: 15
uses: docker/build-push-action@v2
with:
push: true
Expand All @@ -141,7 +141,7 @@ jobs:

- name: Build and push remote
id: docker_build_remote
timeout-minutes: 10
timeout-minutes: 15
uses: docker/build-push-action@v2
with:
push: true
Expand Down
6 changes: 3 additions & 3 deletions components/configuration/VFBGraph/graphConfiguration.js
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Expand Up @@ -12,10 +12,10 @@ var locationCypherQuery = instance => ({
var whatCypherQuery = instance => ({
"statements": [
{
"statement": "MATCH p=(n:Entity {short_form:'" + instance + "'})-[:INSTANCEOF|:SUBCLASSOF*..]->(x) "
+ "WHERE ('Anatomy' IN labels(x)) OR (('Cell' IN labels(x)) OR ('synaptic neuropil' IN labels(x))) "
"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))) "
+ " OR (('Ganglion' IN labels(x)) OR ('Neuron_projection_bundle' IN labels(x))) "
+ "RETURN p, n.short_form as root",
+ "RETURN n,p, n.short_form as root",
"resultDataContents": ["graph"]
}
]
Expand Down
7 changes: 5 additions & 2 deletions model/vfb.xmi
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Expand Up @@ -138,6 +138,9 @@
<types xsi:type="gep_1:SimpleType"
id="VFB_00200000"
name="JRC2018VU template"/>
<types xsi:type="gep_1:SimpleType"
id="NBLAST2"
name="NEW NBLAST"/>
</libraries>
<libraries
id="vfbLibrary"
Expand Down Expand Up @@ -189,7 +192,7 @@
name="anat_image_query"
description="Get images for individual list"
runForCount="false"
query="&quot;statement&quot;: &quot;MATCH (primary:Individual) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, '58214d4' AS version, 'anat_image_query' AS query, channel_image, types&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"
query="&quot;statement&quot;: &quot;MATCH (primary:Individual) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, '58214d4' AS version, 'anat_image_query' AS query, channel_image, types $EXTRA_RESULT_COLUMNS&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"
countQuery="&quot;statement&quot;: &quot;MATCH(i:Individual) WHERE i.short_form IN {ARRAY_ID_RESULTS} RETURN count(i) as count&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
Expand Down Expand Up @@ -1036,6 +1039,6 @@
returnType="//@libraries.3/@types.2"
queryChain="//@dataSources.5/@queries.0 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.2"/>
type="//@libraries.3/@types.40 //@libraries.3/@types.0 //@libraries.3/@types.2"/>
</queries>
</gep:GeppettoModel>