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Cluster fixes from Debug #750

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merged 2 commits into from
Nov 5, 2020
Merged

Cluster fixes from Debug #750

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ef28ca8
fix for cluster dataset link
Robbie1977 Nov 5, 2020
6357270
fixing priority order
Robbie1977 Nov 5, 2020
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20 changes: 10 additions & 10 deletions model/vfb.xmi
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Original file line number Diff line number Diff line change
Expand Up @@ -513,6 +513,16 @@
<matchingCriteria
type="//@libraries.3/@types.0"/>
</queryChain>
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Get JSON for Cluster"
description="Get JSON for Cluster"
runForCount="false"
query="&quot;statement&quot;: &quot;MATCH (primary:Cluster) WHERE primary.short_form in [{ID}] WITH primary OPTIONAL MATCH (primary)-[:has_source]->(ds:DataSet)-[:has_license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link, ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds) } }, license: { 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) } }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)&lt;-[r:SUBCLASSOF|INSTANCEOF]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o) } ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)&lt;-[r {type:'Related'}]-(primary) 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 relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: primary.self_xref }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: s.link_base[0], accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s) } , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix, '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)&lt;-[dbx:hasDbXref]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: s.link_base[0], accession: coalesce(dbx.accession, ''), link_text: primary.label + ' on ' + s.label, site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s) } , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix, '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary, dataset_license, parents, relationships, xrefs 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) } , 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[0], index: coalesce(irw.index[0], []) + [] }}) END AS channel_image,primary,dataset_license,parents,relationships,xrefs OPTIONAL MATCH (o:Individual)&lt;-[r {type:'Related'}]-(primary) 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 related_individuals ,primary,dataset_license,parents,relationships,xrefs,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary) } , description : coalesce(primary.description, []), comment : coalesce(primary.`annotation-comment`, []) } AS term, 'Get JSON for Individual:Anatomy' AS query, 'ca9ab19' AS version , dataset_license, parents, relationships, xrefs, channel_image, related_individuals&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
countQuery="&quot;statement&quot;: &quot;MATCH (primary:Cluster {short_form: {ID}} ) RETURN count(primary) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }">
<matchingCriteria
type="//@libraries.3/@types.22"/>
</queryChain>
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Get JSON for Template"
Expand Down Expand Up @@ -553,16 +563,6 @@
<matchingCriteria
type="//@libraries.3/@types.30"/>
</queryChain>
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Get JSON for Cluster"
description="Get JSON for Cluster"
runForCount="false"
query="&quot;statement&quot;: &quot;MATCH (primary:Cluster) WHERE primary.short_form in [{ID}] WITH primary OPTIONAL MATCH (primary)-[:has_source]->(ds:DataSet)-[:has_license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link, ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds) } }, license: { 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) } }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)&lt;-[r:SUBCLASSOF|INSTANCEOF]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o) } ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)&lt;-[r {type:'Related'}]-(primary) 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 relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: primary.self_xref }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: s.link_base[0], accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s) } , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix, '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)&lt;-[dbx:hasDbXref]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: s.link_base[0], accession: coalesce(dbx.accession, ''), link_text: primary.label + ' on ' + s.label, site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s) } , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix, '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary, dataset_license, parents, relationships, xrefs 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) } , 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[0], index: coalesce(irw.index[0], []) + [] }}) END AS channel_image,primary,dataset_license,parents,relationships,xrefs OPTIONAL MATCH (o:Individual)&lt;-[r {type:'Related'}]-(primary) 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 related_individuals ,primary,dataset_license,parents,relationships,xrefs,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary) } , description : coalesce(primary.description, []), comment : coalesce(primary.`annotation-comment`, []) } AS term, 'Get JSON for Individual:Anatomy' AS query, 'ca9ab19' AS version , dataset_license, parents, relationships, xrefs, channel_image, related_individuals&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
countQuery="&quot;statement&quot;: &quot;MATCH (primary:Cluster {short_form: {ID}} ) RETURN count(primary) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }">
<matchingCriteria
type="//@libraries.3/@types.22"/>
</queryChain>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Term JSON"
Expand Down