diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 33da97746..d97a77926 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -26,8 +26,8 @@ jobs: # Decide based on branch which servers to use - name: Pass branch id: branch - run: echo "::set-output name=value::${GITHUB_REF#refs/heads/}"; - echo "::set-output name=clean::$(echo ${GITHUB_REF#refs/heads/} | sed 's@[/\\]@-@g')"; + run: echo "::set-output name=value::$(echo ${GITHUB_REF} | sed 's@refs/heads/@@g' | sed 's@refs/tags/@@g' )"; + echo "::set-output name=clean::$(echo ${GITHUB_REF} | sed 's@refs/heads/@@g' | sed 's@refs/tags/@@g' | sed 's@[/\\]@-@g')"; - name: Setup local servers id: local-servers shell: bash diff --git a/README.md b/README.md index 69ac2a8a8..f4023640e 100755 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://github.com/VirtualFlyBrain/geppetto-vfb/workflows/CI/badge.svg)](https://github.com/Robbie1977/geppetto-vfb/actions?query=workflow%3ACI)[![Docker Hub](https://www.shippable.com/assets/images/logos/docker-hub.jpg)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/) +[![Build Status](https://github.com/VirtualFlyBrain/geppetto-vfb/workflows/CI/badge.svg)](https://github.com/Robbie1977/geppetto-vfb/actions?query=workflow%3ACI)[![Docker Hub](https://d1q6f0aelx0por.cloudfront.net/product-logos/644d2f15-c5db-4731-a353-ace6235841fa-registry.png)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/) # geppetto-vfb Virtual Fly Brain project customised Geppetto build diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js index 42d1711c6..f6a1f6774 100644 --- a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js +++ b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js @@ -253,14 +253,6 @@ var toolbarMenu = { parameters: ["circuitBrowserVisible"] } }, - { - label: "NBLAST Uploader", - icon: "fa fa-upload", - action: { - handlerAction: "uploaderContentsVisible", - parameters: [] - } - }, { label: "NBLAST", icon: "", diff --git a/model/vfb.xmi b/model/vfb.xmi index 474473989..4590f5d37 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -637,7 +637,7 @@ name="Get JSON for Template" description="Get JSON for Template" runForCount="false" - query=""statement": "MATCH (primary:Template) WHERE primary.short_form in [$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), 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 = 'FBbi_00000224' 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), 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), 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), 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), 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), 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), 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), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for Template' AS query, 'bac066c' 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), 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), 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), 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), 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), 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), 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), 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), 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" }" countQuery=""statement": "MATCH (primary:Template {short_form: $id} ) RETURN count(primary) as count", "parameters" : { "id" : "$ID" }"> diff --git a/tests/jest/vfb/batch1/.Rhistory b/tests/jest/vfb/batch1/.Rhistory deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/jest/vfb/batch2/tree-browser-tests.js b/tests/jest/vfb/batch2/tree-browser-tests.js index 980543317..51fe67ea5 100644 --- a/tests/jest/vfb/batch2/tree-browser-tests.js +++ b/tests/jest/vfb/batch2/tree-browser-tests.js @@ -62,7 +62,7 @@ const clickNodeIcon = async (page, text, icon) => page.evaluate(async (text, ico describe('VFB Tree Browser Component Tests', () => { beforeAll(async () => { //increases timeout to ~8 minutes - jest.setTimeout(500000); + jest.setTimeout(800000); await page.goto(projectURL); }); diff --git a/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png b/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png index 3ba5c2496..41a04136b 100644 Binary files a/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png and b/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png differ