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Merge pull request #697 from VirtualFlyBrain/debug
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typo fix
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@Robbie1977
Robbie1977 authored Oct 14, 2020
2 parents 8f2e9da + fdfc9a7 commit d9364e1
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6 changes: 3 additions & 3 deletions model/vfb.xmi
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description="Get JSON for ep_2_anat query"
returnType="//@libraries.3/@types.0"
query=""statement": "MATCH (ep:Class:Expression_pattern)<-[ar:overlaps|part_of]-(:Individual)-[:INSTANCEOF]->(anat:Class) WHERE anat.short_form in {ARRAY_ID_RESULTS} WITH DISTINCT collect(DISTINCT ar.pub) as pubs, anat, ep UNWIND pubs as p MATCH (pub:pub { short_form: p}) WITH DISTINCT collect(DISTINCT 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), symbol: coalesce(pub.`IAO_0000028`[0], '')} , PubMed: coalesce(pub.PMID[0], ''), FlyBase: coalesce(pub.FlyBase[0], ''), DOI: coalesce(pub.DOI[0], '') }) as pubs CALL apoc.cypher.run('WITH ep OPTIONAL MATCH (ep)<- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)<-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {ep:ep}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, anat, ep, pubs 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), symbol: coalesce(i.`IAO_0000028`[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.`IAO_0000028`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`IAO_0000028`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`IAO_0000028`[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.`IAO_0000028`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,anat,ep,pubs RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat), symbol: coalesce(anat.`IAO_0000028`[0], '')} as anatomy, { short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep), symbol: coalesce(ep.`IAO_0000028`[0], '')} AS expression_pattern, 'Get JSON for anat_2_ep query' AS query, '58214d4' AS version , pubs, anatomy_channel_image", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS}"
countQuery=""statement": "MATCH (ep:Class:Expression_pattern)<-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in [{ID}] RETURN count(anat) as count", "parameters" : { "ID" : "$ID" }"/>
countQuery=""statement": "MATCH (ep:Class:Expression_pattern)<-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in {ARRAY_ID_RESULTS} RETURN count(anat) as count", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS}" />
<queryChain
xsi:type="gep_2:ProcessQuery"
id="vfb_query_schema_processor"
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name="template_2_datasets_query"
description="Get JSON for template_2_datasets query"
returnType="//@libraries.3/@types.24"
query="&quot;statement&quot;: &quot;MATCH (t:Template) &lt;-[depicts]-(tc:Template)-[:in_register_with]-(c:Individual)-[:depicts]->(ai:Individual)-[:has_source]->(ds:DataSet) WHERE t.short_form in ['VFB_00050000'] WITH distinct ds CALL apoc.cypher.run('WITH ds OPTIONAL MATCH (ds) &lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual) &lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {ds:ds}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, ds 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), symbol: coalesce(i.`IAO_0000028`[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.`IAO_0000028`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`IAO_0000028`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`IAO_0000028`[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.`IAO_0000028`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,ds OPTIONAL MATCH (ds)-[rp:has_reference]->(p:pub) WITH CASE WHEN p is null THEN [] ELSE collect({ core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`IAO_0000028`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,ds,anatomy_channel_image OPTIONAL MATCH (ds)-[:has_license]->(l:License) WITH collect ({ icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), symbol: coalesce(l.`IAO_0000028`[0], '')} }) as license,ds,anatomy_channel_image,pubs OPTIONAL MATCH (ds) &lt;-[:has_source]-(i:Individual) WITH i, ds, anatomy_channel_image, pubs, license OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,ds,anatomy_channel_image,pubs,license RETURN { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.`IAO_0000028`[0], '')} as dataset, '58214d4' AS version, 'template_2_datasets_query' AS query, anatomy_channel_image, pubs, license, dataset_counts&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
query="&quot;statement&quot;: &quot;MATCH (t:Template) &lt;-[depicts]-(tc:Template)-[:in_register_with]-(c:Individual)-[:depicts]->(ai:Individual)-[:has_source]->(ds:DataSet) WHERE t.short_form in [{ID}] WITH distinct ds CALL apoc.cypher.run('WITH ds OPTIONAL MATCH (ds) &lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual) &lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {ds:ds}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, ds 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), symbol: coalesce(i.`IAO_0000028`[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.`IAO_0000028`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`IAO_0000028`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`IAO_0000028`[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.`IAO_0000028`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,ds OPTIONAL MATCH (ds)-[rp:has_reference]->(p:pub) WITH CASE WHEN p is null THEN [] ELSE collect({ core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`IAO_0000028`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,ds,anatomy_channel_image OPTIONAL MATCH (ds)-[:has_license]->(l:License) WITH collect ({ icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), symbol: coalesce(l.`IAO_0000028`[0], '')} }) as license,ds,anatomy_channel_image,pubs OPTIONAL MATCH (ds) &lt;-[:has_source]-(i:Individual) WITH i, ds, anatomy_channel_image, pubs, license OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,ds,anatomy_channel_image,pubs,license RETURN { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.`IAO_0000028`[0], '')} as dataset, '58214d4' AS version, 'template_2_datasets_query' AS query, anatomy_channel_image, pubs, license, dataset_counts&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
countQuery="&quot;statement&quot;: &quot;MATCH (t:Template)&lt;-[depicts]-(tc:Template)-[:in_register_with]-(c:Individual)-[:depicts]->(ai:Individual)-[:has_source]->(ds:DataSet) WHERE t.short_form in [{ID}] WITH distinct ds RETURN count(ds) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
Expand All @@ -418,7 +418,7 @@
name="test_all_datasets_query"
description="Get JSON for template_2_datasets query"
returnType="//@libraries.3/@types.24"
query="&quot;statement&quot;: &quot;MATCH (t:Template) &lt;-[depicts]-(tc:Template)-[:in_register_with]-(c:Individual)-[:depicts]->(ai:Individual)-[:has_source]->(ds:DataSet) WHERE t.short_form in ['VFB_00050000'] WITH distinct ds CALL apoc.cypher.run('WITH ds OPTIONAL MATCH (ds) &lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual) &lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {ds:ds}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, ds 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), symbol: coalesce(i.`IAO_0000028`[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.`IAO_0000028`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`IAO_0000028`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`IAO_0000028`[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.`IAO_0000028`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,ds OPTIONAL MATCH (ds)-[rp:has_reference]->(p:pub) WITH CASE WHEN p is null THEN [] ELSE collect({ core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`IAO_0000028`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,ds,anatomy_channel_image OPTIONAL MATCH (ds)-[:has_license]->(l:License) WITH collect ({ icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), symbol: coalesce(l.`IAO_0000028`[0], '')} }) as license,ds,anatomy_channel_image,pubs OPTIONAL MATCH (ds) &lt;-[:has_source]-(i:Individual) WITH i, ds, anatomy_channel_image, pubs, license OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,ds,anatomy_channel_image,pubs,license RETURN { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.`IAO_0000028`[0], '')} as dataset, '58214d4' AS version, 'template_2_datasets_query' AS query, anatomy_channel_image, pubs, license, dataset_counts&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
query="&quot;statement&quot;: &quot;MATCH (t:Template) &lt;-[depicts]-(tc:Template)-[:in_register_with]-(c:Individual)-[:depicts]->(ai:Individual)-[:has_source]->(ds:DataSet) WHERE t.short_form in [{ID}] WITH distinct ds CALL apoc.cypher.run('WITH ds OPTIONAL MATCH (ds) &lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual) &lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {ds:ds}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, ds 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), symbol: coalesce(i.`IAO_0000028`[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.`IAO_0000028`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`IAO_0000028`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`IAO_0000028`[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.`IAO_0000028`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,ds OPTIONAL MATCH (ds)-[rp:has_reference]->(p:pub) WITH CASE WHEN p is null THEN [] ELSE collect({ core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`IAO_0000028`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,ds,anatomy_channel_image OPTIONAL MATCH (ds)-[:has_license]->(l:License) WITH collect ({ icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), symbol: coalesce(l.`IAO_0000028`[0], '')} }) as license,ds,anatomy_channel_image,pubs OPTIONAL MATCH (ds) &lt;-[:has_source]-(i:Individual) WITH i, ds, anatomy_channel_image, pubs, license OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,ds,anatomy_channel_image,pubs,license RETURN { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.`IAO_0000028`[0], '')} as dataset, '58214d4' AS version, 'template_2_datasets_query' AS query, anatomy_channel_image, pubs, license, dataset_counts&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
countQuery="&quot;statement&quot;: &quot;MATCH (ds:DataSet) WITH distinct ds RETURN count(ds) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
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