From 62e66af3241d2e600ed598fae59c92e0ae205f3c Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 28 May 2021 18:01:34 +0100 Subject: [PATCH 01/10] reverting to paths --- .../VFBCircuitBrowser/circuitBrowserConfiguration.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js index 07a11f2cb..30a1c60a0 100644 --- a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js +++ b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js @@ -10,7 +10,7 @@ var locationCypherQuery = ( instances, paths, weight ) => ({ + weight.toString() + " RETURN id(a) AS source, id(b) AS target, type(r) as type, 5000-r.weight[0] as weight_p'," + " sourceNode: id(source)," + " targetNode: id(target)," - + " k: " + hops.toString() + "," + + " k: " + paths.toString() + "," + " relationshipWeightProperty: 'weight_p'," + " relationshipTypes: ['*']," + " path: true" From aa08f1ae6ab8ac3b696681d2feb37cc0fd4ffdd9 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 28 Mar 2022 13:01:19 +0100 Subject: [PATCH 02/10] defaulting to symbol vs label if available --- .../VFBCircuitBrowser/circuitBrowserConfiguration.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js index 2f71224f6..7ef45e896 100644 --- a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js +++ b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js @@ -19,7 +19,7 @@ var locationCypherQuery = ( instances, paths, weight ) => ({ + " WITH * ORDER BY index DESC" + " UNWIND relationships(path) as sr" + " OPTIONAL MATCH cp=(x:Neuron:has_neuron_connectivity)-[:synapsed_to]-(y:Neuron:has_neuron_connectivity) WHERE x=apoc.rel.startNode(sr) AND y=apoc.rel.endNode(sr) OPTIONAL MATCH fp=(x)-[r:synapsed_to]->(y) WHERE r.weight[0] >= " + weight?.toString() - + " OPTIONAL MATCH (x)-[xio:INSTANCEOF]->(xpc:Class) OPTIONAL MATCH (y)-[yio:INSTANCEOF]->(ypc:Class) WITH *,'\"'+ x.short_form+'\":{\"'+xpc.short_form+'\":\"' + xpc.label + '\"},\"'+ y.short_form+'\":{\"'+ypc.short_form+'\":\"' + ypc.label + '\"}' as Class" + + " OPTIONAL MATCH (x)-[xio:INSTANCEOF]->(xpc:Class) OPTIONAL MATCH (y)-[yio:INSTANCEOF]->(ypc:Class) WITH *,'\"'+ x.short_form+'\":{\"'+xpc.short_form+'\":\"' + coalesce(xpc.symbol[0], xpc.label) + '\"},\"'+ y.short_form+'\":{\"'+ypc.short_form+'\":\"' + coalesce(ypc.symbol[0], ypc.label) + '\"}' as Class" + " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY, " + " apoc.convert.fromJsonMap('{' + apoc.text.join(collect(Class),',') + '}') as class ", "resultDataContents": ["row", "graph"] From f9d6ce80707e83cdb64269c3936d11f984417588 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Thu, 31 Mar 2022 17:47:36 +0100 Subject: [PATCH 03/10] updating cluster report to latest Individual + related_individuals from Template query --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 22e054d64..531e5b635 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -627,7 +627,7 @@ name="Get JSON for Cluster" description="Get JSON for Cluster" runForCount="false" - query=""statement": "MATCH (primary:Cluster) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]->(ds:DataSet)-[:has_license|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)<-[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)<-[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: apoc.convert.toList(primary.self_xref)[0]}) 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[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[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[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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)<-[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", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Cluster) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), 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,dataset_license,parents,relationships,xrefs OPTIONAL MATCH (o:Individual)<-[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, unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], ''), 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) , unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')}, description: coalesce(primary.description, []), comment : coalesce(primary.comment, primary.`annotation-comment`, []) } AS term, 'Get JSON for Cluster using modified Individual:Anatomy' AS query, 'ca9ab19' AS version , dataset_license, parents, relationships, xrefs, channel_image, related_individuals", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Cluster {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From 747bd08b6461e44f54c18645835134eb15d97ce6 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Thu, 31 Mar 2022 21:38:34 +0100 Subject: [PATCH 04/10] update from https://github.com/VirtualFlyBrain/VFB_json_schema/runs/5777898977?check_suite_focus=true --- model/vfb.xmi | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 531e5b635..eaee45040 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -587,7 +587,7 @@ name="Get JSON for Class" description="Get JSON for Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<-[: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), 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 anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Class' AS query, '4025897' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -597,7 +597,7 @@ name="Get JSON for Neuron Class" description="Get JSON for Neuron Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<-[: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), 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 anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(ep:Class)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(primary) WITH CASE WHEN ep IS NULL THEN [] ELSE COLLECT({ short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep), symbol: coalesce(ep.symbol[0], '')} ) END AS targeting_splits,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Neuron Class' AS query, '4025897' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, targeting_splits", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(ep:Class)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(primary) WITH CASE WHEN ep IS NULL THEN [] ELSE COLLECT({ short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep), unique_facets: apoc.coll.sort(coalesce(ep.uniqueFacets, [])), symbol: coalesce(ep.symbol[0], '')} ) END AS targeting_splits,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Neuron Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, targeting_splits", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -607,7 +607,7 @@ name="Get JSON for Split Class" description="Get JSON for Split Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<-[: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), 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 anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(primary)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(n:Neuron) WITH CASE WHEN n IS NULL THEN [] ELSE COLLECT({ short_form: n.short_form, label: coalesce(n.label,''), iri: n.iri, types: labels(n), symbol: coalesce(n.symbol[0], '')} ) END AS target_neurons,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Split Class' AS query, '4025897' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, target_neurons", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(primary)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(n:Neuron) WITH CASE WHEN n IS NULL THEN [] ELSE COLLECT({ short_form: n.short_form, label: coalesce(n.label,''), iri: n.iri, types: labels(n), unique_facets: apoc.coll.sort(coalesce(n.uniqueFacets, [])), symbol: coalesce(n.symbol[0], '')} ) END AS target_neurons,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Split Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, target_neurons", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -617,7 +617,7 @@ name="Get JSON for Individual" description="Get JSON for Individual:Anatomy" runForCount="false" - query=""statement": "MATCH (primary:Individual) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), 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,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Individual:Anatomy' AS query, '4025897' AS version , dataset_license, parents, relationships, xrefs, channel_image", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:Anatomy) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), 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,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Individual:Anatomy' AS query, 'e9ce0b8' AS version , dataset_license, parents, relationships, xrefs, channel_image", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -637,7 +637,7 @@ name="Get JSON for Template" description="Get JSON for Template" runForCount="false" - query=""statement": "MATCH (primary:Template) WHERE primary.short_form in [$id] WITH primary MATCH (channel:Individual)<-[irw:in_register_with]-(channel:Individual)-[:depicts]->(primary) WITH { index: coalesce(apoc.convert.toInteger(irw.index), []) + [], extent: irw.extent[0], center: irw.center[0], voxel: irw.voxel[0], orientation: coalesce(irw.orientation[0], ''), image_folder: coalesce(irw.folder[0],''), channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} } as template_channel,primary OPTIONAL MATCH (technique:Class)<-[:is_specified_output_of]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(primary) WHERE technique.short_form IN ['FBbi_00000224','FBbi_00000251'] AND exists(irw.index) WITH primary, template_channel, collect ({ channel: channel, irw: irw}) AS painted_domains UNWIND painted_domains AS pd OPTIONAL MATCH (channel:Individual { short_form: pd.channel.short_form})-[:depicts]-(ai:Individual)-[:INSTANCEOF]->(c:Class) WITH collect({ anatomical_type: { short_form: c.short_form, label: coalesce(c.label,''), iri: c.iri, types: labels(c), symbol: coalesce(c.symbol[0], '')} , anatomical_individual: { short_form: ai.short_form, label: coalesce(ai.label,''), iri: ai.iri, types: labels(ai), symbol: coalesce(ai.symbol[0], '')} , folder: pd.irw.folder[0], center: coalesce (pd.irw.center, []), index: [] + coalesce (pd.irw.index, []) }) AS template_domains,primary,template_channel OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary,template_channel,template_domains OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,template_channel,template_domains,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,template_channel,template_domains,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, template_channel, template_domains, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,template_channel,template_domains,dataset_license,parents,relationships OPTIONAL MATCH (o:Individual)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets,[])), symbol: coalesce(o.symbol[0], '')} }) END AS related_individuals ,primary,template_channel,template_domains,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Template with expanded domain techniques' AS query, 'm20211015' AS version , template_channel, template_domains, dataset_license, parents, relationships, xrefs, related_individuals", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Template) WHERE primary.short_form in [$id] WITH primary MATCH (channel:Individual)<-[irw:in_register_with]-(channel:Individual)-[:depicts]->(primary) WITH { index: coalesce(apoc.convert.toInteger(irw.index), []) + [], extent: irw.extent[0], center: irw.center[0], voxel: irw.voxel[0], orientation: coalesce(irw.orientation[0], ''), image_folder: coalesce(irw.folder[0],''), channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} } as template_channel,primary OPTIONAL MATCH (technique:Class)<-[:is_specified_output_of]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(primary) WHERE technique.short_form IN ['FBbi_00000224','FBbi_00000251'] AND exists(irw.index) WITH primary, template_channel, collect ({ channel: channel, irw: irw}) AS painted_domains UNWIND painted_domains AS pd OPTIONAL MATCH (channel:Individual { short_form: pd.channel.short_form})-[:depicts]-(ai:Individual)-[:INSTANCEOF]->(c:Class) WITH collect({ anatomical_type: { short_form: c.short_form, label: coalesce(c.label,''), iri: c.iri, types: labels(c), unique_facets: apoc.coll.sort(coalesce(c.uniqueFacets, [])), symbol: coalesce(c.symbol[0], '')} , anatomical_individual: { short_form: ai.short_form, label: coalesce(ai.label,''), iri: ai.iri, types: labels(ai), unique_facets: apoc.coll.sort(coalesce(ai.uniqueFacets, [])), symbol: coalesce(ai.symbol[0], '')} , folder: pd.irw.folder[0], center: coalesce (pd.irw.center, []), index: [] + coalesce (pd.irw.index, []) }) AS template_domains,primary,template_channel OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary,template_channel,template_domains OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,template_channel,template_domains,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,template_channel,template_domains,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, template_channel, template_domains, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,template_channel,template_domains,dataset_license,parents,relationships OPTIONAL MATCH (o:Individual)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS related_individuals ,primary,template_channel,template_domains,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Template' AS query, 'e9ce0b8' AS version , template_channel, template_domains, dataset_license, parents, relationships, xrefs, related_individuals", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Template {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -657,7 +657,7 @@ name="Get JSON for DataSet" description="Get JSON for DataSet" runForCount="false" - query=""statement": "MATCH (primary:DataSet) WHERE primary.short_form in [$id] WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<-[: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 10', {primary:primary}) 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, primary 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.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), 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 anatomy_channel_image ,primary OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0]}) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, anatomy_channel_image OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets,[])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,anatomy_channel_image OPTIONAL MATCH (primary)-[:has_license|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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }) as license,primary,anatomy_channel_image,xrefs OPTIONAL MATCH (primary)-[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.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,primary,anatomy_channel_image,xrefs,license OPTIONAL MATCH (primary)<-[:has_source]-(i:Individual) WITH i, primary, anatomy_channel_image, xrefs, license, pubs OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,primary,anatomy_channel_image,xrefs,license,pubs RETURN { link : coalesce(primary.dataset_link[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for DataSet' AS query, 'bac066c' AS version , anatomy_channel_image, xrefs, license, pubs, dataset_counts", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:DataSet) WHERE primary.short_form in [$id] WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, anatomy_channel_image OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,anatomy_channel_image OPTIONAL MATCH (primary)-[:has_license|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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }) as license,primary,anatomy_channel_image,xrefs OPTIONAL MATCH (primary)-[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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,primary,anatomy_channel_image,xrefs,license OPTIONAL MATCH (primary)<-[:has_source]-(i:Individual) WITH i, primary, anatomy_channel_image, xrefs, license, pubs OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,primary,anatomy_channel_image,xrefs,license,pubs RETURN { link : coalesce(primary.dataset_link[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for DataSet' AS query, 'e9ce0b8' AS version , anatomy_channel_image, xrefs, license, pubs, dataset_counts", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:DataSet {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -667,7 +667,7 @@ name="Get JSON for License" description="Get JSON for License" runForCount="false" - query=""statement": "MATCH (primary:License) WHERE primary.short_form in [$id] WITH primary RETURN { icon : coalesce(primary.license_logo[0], ''), link : coalesce(primary.license_url[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for License' AS query, 'bac066c' AS version", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:License) WHERE primary.short_form in [$id] WITH primary RETURN { icon : coalesce(primary.license_logo[0], ''), link : coalesce(primary.license_url[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for License' AS query, 'e9ce0b8' AS version ", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:License {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From 339826579a4878a54b2d3841e09c5a82ba19f2fe Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 10:38:43 +0100 Subject: [PATCH 05/10] naming pub query for comparison --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index eaee45040..80322d8bf 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -647,7 +647,7 @@ name="Get JSON for pub" description="Fetches JSON for pub." runForCount="false" - query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'bac066c' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for pub' AS query, 'manual' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:pub:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From e58b3257d3db8d8abb1f7e53b6e1220eb481abd8 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 11:28:18 +0100 Subject: [PATCH 06/10] updating xmi from https://github.com/VirtualFlyBrain/VFB_json_schema/runs/5785585304?check_suite_focus=true --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 80322d8bf..5831b2539 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -647,7 +647,7 @@ name="Get JSON for pub" description="Fetches JSON for pub." runForCount="false" - query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for pub' AS query, 'manual' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'e9ce0b8' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:pub:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From f2cdd8daea58fdf90b1e953cbfe4107a328f089f Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 11:51:46 +0100 Subject: [PATCH 07/10] removing any channels shouldn't be in solr but just incase --- components/configuration/VFBMain/searchConfiguration.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/configuration/VFBMain/searchConfiguration.js b/components/configuration/VFBMain/searchConfiguration.js index 993b3952e..447d26ef6 100644 --- a/components/configuration/VFBMain/searchConfiguration.js +++ b/components/configuration/VFBMain/searchConfiguration.js @@ -95,7 +95,7 @@ var datasourceConfiguration = { "start": "0", "pf":"true", "fq": [ - "short_form:VFB* OR short_form:FB* OR facets_annotation:DataSet OR facets_annotation:pub" + "(short_form:VFB* OR short_form:FB* OR facets_annotation:DataSet OR facets_annotation:pub) AND NOT short_form:VFBc_*" ], "rows": "100", "wt": "json", From 7ecdadd6d90ed6481b2d280a73f1039b1b40c5ac Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 13:18:44 +0100 Subject: [PATCH 08/10] Revert "updating xmi from https://github.com/VirtualFlyBrain/VFB_json_schema/runs/5785585304?check_suite_focus=true" This reverts commit e58b3257d3db8d8abb1f7e53b6e1220eb481abd8. --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 5831b2539..80322d8bf 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -647,7 +647,7 @@ name="Get JSON for pub" description="Fetches JSON for pub." runForCount="false" - query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'e9ce0b8' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for pub' AS query, 'manual' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:pub:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From 87620852718756d118588c60b483e3a151a15517 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 13:27:08 +0100 Subject: [PATCH 09/10] updating pub query with name --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 80322d8bf..1d7d71ae2 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -647,7 +647,7 @@ name="Get JSON for pub" description="Fetches JSON for pub." runForCount="false" - query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets,[])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for pub' AS query, 'manual' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:pub) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_reference]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, license: { icon : coalesce(l.license_logo[0], ''), link : coalesce(l.license_url[0], ''), core : { short_form: l.short_form, label: coalesce(l.label,''), iri: l.iri, types: labels(l), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for pub' AS query, 'c6643e1' AS version , dataset_license, {title: coalesce(primary.title[0], '') ,PubMed: coalesce(primary.PMID[0], ''), FlyBase: coalesce(primary.FlyBase[0], ''), DOI: coalesce(primary.DOI[0], '') }AS pub_specific_content", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:pub:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> From 99c68eab789efd6905749b310e41f01e7f16cbff Mon Sep 17 00:00:00 2001 From: Rob Court Date: Fri, 1 Apr 2022 14:43:24 +0100 Subject: [PATCH 10/10] update to match https://github.com/VirtualFlyBrain/VFB_json_schema/runs/5787754443?check_suite_focus=true --- model/vfb.xmi | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 1d7d71ae2..5783f2f86 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -587,7 +587,7 @@ name="Get JSON for Class" description="Get JSON for Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Class' AS query, 'c6643e1' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -597,7 +597,7 @@ name="Get JSON for Neuron Class" description="Get JSON for Neuron Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(ep:Class)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(primary) WITH CASE WHEN ep IS NULL THEN [] ELSE COLLECT({ short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep), unique_facets: apoc.coll.sort(coalesce(ep.uniqueFacets, [])), symbol: coalesce(ep.symbol[0], '')} ) END AS targeting_splits,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Neuron Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, targeting_splits", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(ep:Class)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(primary) WITH CASE WHEN ep IS NULL THEN [] ELSE COLLECT({ short_form: ep.short_form, label: coalesce(ep.label,''), iri: ep.iri, types: labels(ep), unique_facets: apoc.coll.sort(coalesce(ep.uniqueFacets, [])), symbol: coalesce(ep.symbol[0], '')} ) END AS targeting_splits,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Neuron Class' AS query, 'c6643e1' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, targeting_splits", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -607,7 +607,7 @@ name="Get JSON for Split Class" description="Get JSON for Split Class" runForCount="false" - query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(primary)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(n:Neuron) WITH CASE WHEN n IS NULL THEN [] ELSE COLLECT({ short_form: n.short_form, label: coalesce(n.label,''), iri: n.iri, types: labels(n), unique_facets: apoc.coll.sort(coalesce(n.uniqueFacets, [])), symbol: coalesce(n.symbol[0], '')} ) END AS target_neurons,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Split Class' AS query, 'e9ce0b8' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, target_neurons", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Class) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,parents,relationships CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary, parents, relationships, xrefs 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary,parents,relationships,xrefs OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) where rp.typ = 'syn' WITH CASE WHEN p is null THEN [] ELSE collect({ pub: { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } , synonym: { label: coalesce(rp.value[0], ''), scope: coalesce(rp.scope, ''), type: coalesce(rp.has_synonym_type[0],'') } }) END AS pub_syn,primary,parents,relationships,xrefs,anatomy_channel_image OPTIONAL MATCH (primary)-[rp:has_reference]->(p:pub) WHERE rp.typ = 'def' 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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS def_pubs,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn OPTIONAL MATCH (:Class { label: 'intersectional expression pattern'})<-[:SUBCLASSOF]-(primary)<-[ar:part_of]-(anoni:Individual)-[:INSTANCEOF]->(n:Neuron) WITH CASE WHEN n IS NULL THEN [] ELSE COLLECT({ short_form: n.short_form, label: coalesce(n.label,''), iri: n.iri, types: labels(n), unique_facets: apoc.coll.sort(coalesce(n.uniqueFacets, [])), symbol: coalesce(n.symbol[0], '')} ) END AS target_neurons,primary,parents,relationships,xrefs,anatomy_channel_image,pub_syn,def_pubs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Split Class' AS query, 'c6643e1' AS version , parents, relationships, xrefs, anatomy_channel_image, pub_syn, def_pubs, target_neurons", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Class {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -617,7 +617,7 @@ name="Get JSON for Individual" description="Get JSON for Individual:Anatomy" runForCount="false" - query=""statement": "MATCH (primary:Individual:Anatomy) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), 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,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Individual:Anatomy' AS query, 'e9ce0b8' AS version , dataset_license, parents, relationships, xrefs, channel_image", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual) WHERE primary.short_form in [$id] WITH primary OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,dataset_license,parents,relationships OPTIONAL MATCH (primary)<-[: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), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), 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,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Individual' AS query, 'c6643e1' AS version , dataset_license, parents, relationships, xrefs, channel_image", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Individual {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -637,7 +637,7 @@ name="Get JSON for Template" description="Get JSON for Template" runForCount="false" - query=""statement": "MATCH (primary:Template) WHERE primary.short_form in [$id] WITH primary MATCH (channel:Individual)<-[irw:in_register_with]-(channel:Individual)-[:depicts]->(primary) WITH { index: coalesce(apoc.convert.toInteger(irw.index), []) + [], extent: irw.extent[0], center: irw.center[0], voxel: irw.voxel[0], orientation: coalesce(irw.orientation[0], ''), image_folder: coalesce(irw.folder[0],''), channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} } as template_channel,primary OPTIONAL MATCH (technique:Class)<-[:is_specified_output_of]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(primary) WHERE technique.short_form IN ['FBbi_00000224','FBbi_00000251'] AND exists(irw.index) WITH primary, template_channel, collect ({ channel: channel, irw: irw}) AS painted_domains UNWIND painted_domains AS pd OPTIONAL MATCH (channel:Individual { short_form: pd.channel.short_form})-[:depicts]-(ai:Individual)-[:INSTANCEOF]->(c:Class) WITH collect({ anatomical_type: { short_form: c.short_form, label: coalesce(c.label,''), iri: c.iri, types: labels(c), unique_facets: apoc.coll.sort(coalesce(c.uniqueFacets, [])), symbol: coalesce(c.symbol[0], '')} , anatomical_individual: { short_form: ai.short_form, label: coalesce(ai.label,''), iri: ai.iri, types: labels(ai), unique_facets: apoc.coll.sort(coalesce(ai.uniqueFacets, [])), symbol: coalesce(ai.symbol[0], '')} , folder: pd.irw.folder[0], center: coalesce (pd.irw.center, []), index: [] + coalesce (pd.irw.index, []) }) AS template_domains,primary,template_channel OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary,template_channel,template_domains OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,template_channel,template_domains,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,template_channel,template_domains,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, template_channel, template_domains, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,template_channel,template_domains,dataset_license,parents,relationships OPTIONAL MATCH (o:Individual)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS related_individuals ,primary,template_channel,template_domains,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Template' AS query, 'e9ce0b8' AS version , template_channel, template_domains, dataset_license, parents, relationships, xrefs, related_individuals", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Template) WHERE primary.short_form in [$id] WITH primary MATCH (channel:Individual)<-[irw:in_register_with]-(channel:Individual)-[:depicts]->(primary) WITH { index: coalesce(apoc.convert.toInteger(irw.index), []) + [], extent: irw.extent[0], center: irw.center[0], voxel: irw.voxel[0], orientation: coalesce(irw.orientation[0], ''), image_folder: coalesce(irw.folder[0],''), channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} } as template_channel,primary OPTIONAL MATCH (technique:Class)<-[:is_specified_output_of]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(primary) WHERE technique.short_form IN ['FBbi_00000224','FBbi_00000251'] AND exists(irw.index) WITH primary, template_channel, collect ({ channel: channel, irw: irw}) AS painted_domains UNWIND painted_domains AS pd OPTIONAL MATCH (channel:Individual { short_form: pd.channel.short_form})-[:depicts]-(ai:Individual)-[:INSTANCEOF]->(c:Class) WITH collect({ anatomical_type: { short_form: c.short_form, label: coalesce(c.label,''), iri: c.iri, types: labels(c), unique_facets: apoc.coll.sort(coalesce(c.uniqueFacets, [])), symbol: coalesce(c.symbol[0], '')} , anatomical_individual: { short_form: ai.short_form, label: coalesce(ai.label,''), iri: ai.iri, types: labels(ai), unique_facets: apoc.coll.sort(coalesce(ai.uniqueFacets, [])), symbol: coalesce(ai.symbol[0], '')} , folder: pd.irw.folder[0], center: coalesce (pd.irw.center, []), index: [] + coalesce (pd.irw.index, []) }) AS template_domains,primary,template_channel OPTIONAL MATCH (primary)-[:has_source]-(ds:DataSet)-[:has_license|license]->(l:License) WITH COLLECT ({ dataset: { link : coalesce(ds.dataset_link[0], ''), core : { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(ds.symbol[0], '')} }, 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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }}) AS dataset_license,primary,template_channel,template_domains OPTIONAL MATCH (o:Class)<-[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), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} ) END AS parents ,primary,template_channel,template_domains,dataset_license OPTIONAL MATCH (o:Class)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS relationships ,primary,template_channel,template_domains,dataset_license,parents OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, template_channel, template_domains, dataset_license, parents, relationships OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,template_channel,template_domains,dataset_license,parents,relationships OPTIONAL MATCH (o:Individual)<-[r {type:'Related'}]-(primary) WITH CASE WHEN o IS NULL THEN [] ELSE COLLECT ({ relation: { label: r.label, iri: r.iri, type: type(r) } , object: { short_form: o.short_form, label: coalesce(o.label,''), iri: o.iri, types: labels(o), unique_facets: apoc.coll.sort(coalesce(o.uniqueFacets, [])), symbol: coalesce(o.symbol[0], '')} }) END AS related_individuals ,primary,template_channel,template_domains,dataset_license,parents,relationships,xrefs RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Template' AS query, 'c6643e1' AS version , template_channel, template_domains, dataset_license, parents, relationships, xrefs, related_individuals", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Template {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -657,7 +657,7 @@ name="Get JSON for DataSet" description="Get JSON for DataSet" runForCount="false" - query=""statement": "MATCH (primary:DataSet) WHERE primary.short_form in [$id] WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, anatomy_channel_image OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,anatomy_channel_image OPTIONAL MATCH (primary)-[:has_license|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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }) as license,primary,anatomy_channel_image,xrefs OPTIONAL MATCH (primary)-[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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,primary,anatomy_channel_image,xrefs,license OPTIONAL MATCH (primary)<-[:has_source]-(i:Individual) WITH i, primary, anatomy_channel_image, xrefs, license, pubs OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,primary,anatomy_channel_image,xrefs,license,pubs RETURN { link : coalesce(primary.dataset_link[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for DataSet' AS query, 'e9ce0b8' AS version , anatomy_channel_image, xrefs, license, pubs, dataset_counts", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:DataSet) WHERE primary.short_form in [$id] WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [: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 10', {primary:primary}) 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, primary 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), unique_facets: apoc.coll.sort(coalesce(i.uniqueFacets, [])), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets, [])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets, [])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets, [])), 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), unique_facets: apoc.coll.sort(coalesce(template_anat.uniqueFacets, [])), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary OPTIONAL MATCH (s:Site { short_form: apoc.convert.toList(primary.self_xref)[0] }) WITH CASE WHEN s IS NULL THEN [] ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(primary.short_form, ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) END AS self_xref, primary, anatomy_channel_image OPTIONAL MATCH (s:Site)<-[dbx:database_cross_reference]-(primary) WITH CASE WHEN s IS NULL THEN self_xref ELSE COLLECT({ link_base: coalesce(s.link_base[0], ''), accession: coalesce(dbx.accession[0], ''), link_text: primary.label + ' on ' + s.label, homepage: coalesce(s.homepage[0], ''), site: { short_form: s.short_form, label: coalesce(s.label,''), iri: s.iri, types: labels(s), unique_facets: apoc.coll.sort(coalesce(s.uniqueFacets, [])), symbol: coalesce(s.symbol[0], '')} , icon: coalesce(s.link_icon_url[0], ''), link_postfix: coalesce(s.link_postfix[0], '')}) + self_xref END AS xrefs,primary,anatomy_channel_image OPTIONAL MATCH (primary)-[:has_license|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), unique_facets: apoc.coll.sort(coalesce(l.uniqueFacets, [])), symbol: coalesce(l.symbol[0], '')} }) as license,primary,anatomy_channel_image,xrefs OPTIONAL MATCH (primary)-[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), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } ) END AS pubs,primary,anatomy_channel_image,xrefs,license OPTIONAL MATCH (primary)<-[:has_source]-(i:Individual) WITH i, primary, anatomy_channel_image, xrefs, license, pubs OPTIONAL MATCH (i)-[:INSTANCEOF]-(c:Class) WITH DISTINCT { images: count(distinct i),types: count(distinct c) } as dataset_counts,primary,anatomy_channel_image,xrefs,license,pubs RETURN { link : coalesce(primary.dataset_link[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for DataSet' AS query, 'c6643e1' AS version , anatomy_channel_image, xrefs, license, pubs, dataset_counts", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:DataSet {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> @@ -667,7 +667,7 @@ name="Get JSON for License" description="Get JSON for License" runForCount="false" - query=""statement": "MATCH (primary:License) WHERE primary.short_form in [$id] WITH primary RETURN { icon : coalesce(primary.license_logo[0], ''), link : coalesce(primary.license_url[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for License' AS query, 'e9ce0b8' AS version ", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:License) WHERE primary.short_form in [$id] WITH primary RETURN { icon : coalesce(primary.license_logo[0], ''), link : coalesce(primary.license_url[0], ''), core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for License' AS query, 'c6643e1' AS version ", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:License {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }">