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Merge pull request #959 from VirtualFlyBrain/pipeline2-sync-a239
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sync: pipeline2  with pipeline2-sync-a239
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@Robbie1977
Robbie1977 authored Jan 7, 2021
2 parents 618950e + 983adf3 commit f56f05d
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9 changes: 5 additions & 4 deletions components/VFBMain.js
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Original file line number Diff line number Diff line change
Expand Up @@ -1197,6 +1197,7 @@ class VFBMain extends React.Component {
script.id = 'metaDesc';
script.innerHTML = '{"@context": "https://schema.org","@type": "Organization","url": "https://virtualflybrain.org","logo": "https://v2.virtualflybrain.org/images/vfbbrain_icon.png","name":"Virtual Fly Brain",'
+ '"description":"VFB integrates data curated from the literature with image data from many bulk sources. The search system allows you to search for neurons and neuroanatomical structures using almost any name found in the literature. The query system can identify neurons innervating any specified neuropil or fasciculating with any specified tract. It also allows queries for genes, transgenes and phenotypes expressed in any brain region or neuron. Search and query results combine referenced textual descriptions with 3D images and links to originating data sources. VFB features tens of thousands of 3D images of neurons, clones and expression patterns, registered to standard template brains. Any combination of these images can be viewed together. A BLAST-type query system (NBLAST) allows you to find similar neurons and drivers starting from a registered neuron.",'
+ '"headline":"A hub for fruit fly (Drosophila melanogaster) neuronal anatomy, connectivity & imaging data",'
+ '"affiliation":['
+ '{"@type": "Organization","name":"Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh","logo":"https://v2.virtualflybrain.org/images/vfb/project/logos/InformaticsLogo.gif","url":"https://web.inf.ed.ac.uk/anc"},'
+ '{"@type": "Organization","name":"Department of Genetics, University of Cambridge","logo":"https://v2.virtualflybrain.org/images/vfb/project/logos/CUnibig.png","url":"http://www.gen.cam.ac.uk/"},'
Expand All @@ -1207,8 +1208,8 @@ class VFBMain extends React.Component {
+ '],"funder":{"@type": "Organization","name":"Wellcome Trust","logo":"https://v2.virtualflybrain.org/images/vfb/project/logos/wtvm050446.png","url":"https://wellcome.org/"},'
+ '"sameAs":"https://en.wikipedia.org/wiki/Virtual_Fly_Brain","alternateName":"VFB",'
+ '"subjectOf":['
+ '{"@type": "ScholarlyArticle","citation":"http://dx.doi.org/10.1093/bioinformatics/btr677","sameAs":"http://dx.doi.org/10.1093/bioinformatics/btr677","name":"The Virtual Fly Brain browser and query interface","datePublished":"2012","author":[{"@type":"person","name":"Milyaev, N."},{"@type":"person","name":"Osumi-Sutherland, D."},{"@type":"person","name":"Reeve, S."},{"@type":"person","name":"Burton, N."},{"@type":"person","name":"Baldock, R. A."},{"@type":"person","name":"Armstrong, J. D."}],"publisher":"Bioinformatics"},'
+ '{"@type": "ScholarlyArticle","citation":"http://dx.doi.org/10.1098/rstb.2017.0380","sameAs":"http://dx.doi.org/10.1098/rstb.2017.0380","name":"Geppetto: a reusable modular open platform for exploring neuroscience data and models","author":"Cantarelli, Matteo and Marin, Boris and Quintana, Adrian and Earnshaw, Matt and Court, Robert and Gleeson, Padraig and Dura-Bernal, Salvador and Silver, R. Angus and Idili, Giovanni","publisher": "Philosophical Transactions of the Royal Society B: Biological Sciences","datePublished": "2018"}'
+ '{"@type": "ScholarlyArticle","citation":"http://dx.doi.org/10.1093/bioinformatics/btr677","sameAs":"http://dx.doi.org/10.1093/bioinformatics/btr677","headline":"The Virtual Fly Brain browser and query interface","name":"The Virtual Fly Brain browser and query interface","datePublished":"2012","author":[{"@type":"person","name":"Milyaev, N."},{"@type":"person","name":"Osumi-Sutherland, D."},{"@type":"person","name":"Reeve, S."},{"@type":"person","name":"Burton, N."},{"@type":"person","name":"Baldock, R. A."},{"@type":"person","name":"Armstrong, J. D."}],"publisher":"Bioinformatics"},'
+ '{"@type": "ScholarlyArticle","citation":"http://dx.doi.org/10.1098/rstb.2017.0380","sameAs":"http://dx.doi.org/10.1098/rstb.2017.0380","headline":"Geppetto: a reusable modular open platform for exploring neuroscience data and models","name":"Geppetto: a reusable modular open platform for exploring neuroscience data and models","author":"Cantarelli, Matteo and Marin, Boris and Quintana, Adrian and Earnshaw, Matt and Court, Robert and Gleeson, Padraig and Dura-Bernal, Salvador and Silver, R. Angus and Idili, Giovanni","publisher": "Philosophical Transactions of the Royal Society B: Biological Sciences","datePublished": "2018"}'
+ ']}';
document.getElementsByTagName('head')[0].appendChild(script);
setTimeout(function () {
Expand Down Expand Up @@ -1288,8 +1289,8 @@ class VFBMain extends React.Component {
document.title = 'Virtual Fly Brain (' + this.responseXML.title + ')';
document.body.style.font = "x-large";
document.querySelector('meta[property="og:title"]').setAttribute("content",this.responseXML.title);
document.querySelector('meta[name="description"]').setAttribute("content",this.responseXML.body.innerText);
document.querySelector('meta[property="og:description"]').setAttribute("content",this.responseXML.body.innerText);
document.querySelector('meta[name="description"]').setAttribute("content",this.responseXML.body.getElementById('json').innerText.substring(0, 4900));
document.querySelector('meta[property="og:description"]').setAttribute("content",this.responseXML.body.getElementById('json').innerText.substring(0, 4900));
if (document.getElementById('metaDesc') != null) {
if (this.responseXML.head != undefined && this.responseXML.head.getElementsByTagName('script') != undefined && this.responseXML.head.getElementsByTagName('script') != null && this.responseXML.head.getElementsByTagName('script')[1] != undefined) {
document.getElementById('metaDesc').innerHTML = this.responseXML.head.getElementsByTagName('script')[1].innerHTML;
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7 changes: 4 additions & 3 deletions model/vfb.xmi
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Original file line number Diff line number Diff line change
Expand Up @@ -350,7 +350,7 @@
name="Query for Anatomy from Exp"
description="Get JSON for ep_2_anat query"
returnType="//@libraries.3/@types.1"
query=""statement": "MATCH (ep:Expression_pattern:Class)<-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in {ARRAY_ID_RESULTS} WITH anoni, anat, ar OPTIONAL MATCH (p:pub { short_form: ar.pub}) WITH anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) 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), symbol: coalesce(o.symbol[0], '')} }) END AS stages ,anoni,anat,pub CALL apoc.cypher.run('WITH anat OPTIONAL MATCH (anat:Synaptic_neuropil)<- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)<-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {anat:anat}) 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, anoni, anat, pub, stages 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), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat), symbol: coalesce(anat.symbol[0], '')} AS anatomy, 'Get JSON for ep_2_anat query' AS query, 'bac066c' AS version , pub, stages, anatomy_channel_image", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS}"
query=""statement": "MATCH (ep:Expression_pattern:Class)<-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in {ARRAY_ID_RESULTS} WITH anoni, anat, ar OPTIONAL MATCH (p:pub { short_form: ar.pub}) WITH anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.symbol[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) 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), symbol: coalesce(o.symbol[0], '')} }) END AS stages ,anoni,anat,pub CALL apoc.cypher.run('WITH anat OPTIONAL MATCH (anat)<- [: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', {anat:anat}) 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, anoni, anat, pub, stages 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), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat), symbol: coalesce(anat.symbol[0], '')} AS anatomy, 'Get JSON for ep_2_anat query' AS query, 'bac066c' AS version , pub, stages, anatomy_channel_image", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS}"
countQuery=""statement": "MATCH (ep:Expression_pattern:Class)<-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in {ARRAY_ID_RESULTS} RETURN count(anat) as count", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS}"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
Expand All @@ -367,11 +367,12 @@
description="Get JSON for anat_2_ep query">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="ep_2_anat_query"
name="Test Query for Anatomy from Exp"
description="Get JSON for ep_2_anat query"
returnType="//@libraries.3/@types.1"
query="&quot;statement&quot;: &quot;MATCH (ep:Expression_pattern:Class)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in [{ID}] WITH anoni, anat, ar OPTIONAL MATCH (p:pub { short_form: ar.pub}) WITH anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`symbol`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) 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), symbol: coalesce(o.`symbol`[0], '')} }) END AS stages ,anoni,anat,pub CALL apoc.cypher.run('WITH anat OPTIONAL MATCH (anat:Synaptic_neuropil)&lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {anat:anat}) 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, anoni, anat, pub, stages 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), symbol: coalesce(channel.`symbol`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`symbol`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`symbol`[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.`symbol`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat), symbol: coalesce(anat.`symbol`[0], '')} AS anatomy, 'Get JSON for ep_2_anat query' AS query, '3f881fe' AS version , pub, stages, anatomy_channel_image&quot;, &quot;parameters&quot; : { &quot;ID&quot; : $ID}"
countQuery="&quot;statement&quot;: &quot;MATCH (ep:Class:Expression_pattern)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in {ARRAY_ID_RESULTS} RETURN count(anat) as count&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"/>
query="&quot;statement&quot;: &quot;MATCH (ep:Expression_pattern:Class)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in [{ID}] WITH anoni, anat, ar OPTIONAL MATCH (p:pub { short_form: ar.pub}) WITH anat, anoni, { core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), symbol: coalesce(p.`symbol`[0], '')} , PubMed: coalesce(p.PMID[0], ''), FlyBase: coalesce(p.FlyBase[0], ''), DOI: coalesce(p.DOI[0], '') } AS pub OPTIONAL MATCH (anoni)-[r:Related]->(o:FBdv) 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), symbol: coalesce(o.`symbol`[0], '')} }) END AS stages ,anoni,anat,pub CALL apoc.cypher.run('WITH anat OPTIONAL MATCH (anat)&lt;- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)&lt;-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 10', {anat:anat}) 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, anoni, anat, pub, stages 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), symbol: coalesce(channel.`symbol`[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.`symbol`[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.`symbol`[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.`symbol`[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,anoni,anat,pub,stages RETURN { short_form: anat.short_form, label: coalesce(anat.label,''), iri: anat.iri, types: labels(anat), symbol: coalesce(anat.`symbol`[0], '')} AS anatomy, 'Get JSON for ep_2_anat query' AS query, '3f881fe' AS version , pub, stages, anatomy_channel_image&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot;}"
countQuery="&quot;statement&quot;: &quot;MATCH (ep:Class:Expression_pattern)&lt;-[ar:overlaps|part_of]-(anoni:Individual)-[:INSTANCEOF]->(anat:Class) WHERE ep.short_form in [{ID}] RETURN count(anat) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot;}"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
id="vfb_query_schema_processor"
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