From 1e10e42507921427480802de4fd5a5c25f9d3bb0 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 11:49:04 +0100 Subject: [PATCH 01/11] testing for meta rather than parent on selection. --- components/interface/VFBTermInfo/VFBTermInfo.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/interface/VFBTermInfo/VFBTermInfo.js b/components/interface/VFBTermInfo/VFBTermInfo.js index 98c35936c..9e07d4405 100644 --- a/components/interface/VFBTermInfo/VFBTermInfo.js +++ b/components/interface/VFBTermInfo/VFBTermInfo.js @@ -732,12 +732,12 @@ class VFBTermInfoWidget extends React.Component { return; } var Query = require('@geppettoengine/geppetto-core/model/Query'); - var n = window[path]; var otherId; var otherName; var target = widget; var that = this; var meta = path + "." + path + "_meta"; + var n = window[meta]; if (n != undefined) { var metanode = Instances.getInstance(meta); if ((this.data.length > 0) && (this.data[0] == metanode)) { From 0ba856da3ef7a9ec25d26f5b1c42350a043f4dab Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 13:08:55 +0100 Subject: [PATCH 02/11] Revert "updating help menu size" This reverts commit 04083920cb10c50f51dfc6fd8e97562ca74693d5. --- tests/jest/vfb/batch1/menu-component-tests.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/jest/vfb/batch1/menu-component-tests.js b/tests/jest/vfb/batch1/menu-component-tests.js index 0c256e321..9f65e6a63 100644 --- a/tests/jest/vfb/batch1/menu-component-tests.js +++ b/tests/jest/vfb/batch1/menu-component-tests.js @@ -105,7 +105,7 @@ describe('VFB Menu Component Tests', () => { await wait4selector(page, "ul.MuiList-root", { visible: true, timeout : 120000 }) // Check there's four elements in the drop down menu of 'Help' const dropDownMenuItems = await page.evaluate(async () => document.getElementsByClassName("MuiListItem-root").length); - expect(dropDownMenuItems).toEqual(5); + expect(dropDownMenuItems).toEqual(4); }) it('Help Modal FAQ Tab Opened', async () => { From f5dd7a85c9ed4b5bf1f01c757304c69126fcdf7f Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 13:09:06 +0100 Subject: [PATCH 03/11] Revert "changing image" This reverts commit de696518d8c0da02bc24c4dc6427833050f62e61. --- components/configuration/VFBOverview/quickHelp.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json index 189bf6731..57b2aeafc 100644 --- a/components/configuration/VFBOverview/quickHelp.json +++ b/components/configuration/VFBOverview/quickHelp.json @@ -4,7 +4,7 @@ "width": "900", "steps": [{ "title": "Welcome to Virtual Fly Brain", - "image" : "https://VirtualFlyBrain.org/data/VFB/screencaps/VFB_3D_400x400.jpg", + "image" : "geppetto/build/VFBqHelpMain.jpg", "instructions": [{ "icon" : "fa fa-question-circle-o", "label" : "Hi, we are currently running a VFB User Survey, once you have used the site please consider completing this survey to help us improve it by clicking User Survey in the Help menu above." From ffff90e74361afceb6b43f166566ba5f812d4611 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 13:09:11 +0100 Subject: [PATCH 04/11] Revert "adding user survey" This reverts commit 9a1c2df4f221eca3d8ead8d48e55c7157c2f79af. --- .../VFBToolbar/vfbtoolbarMenuConfiguration.js | 8 -------- 1 file changed, 8 deletions(-) diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js index 052786ed2..0412122a8 100644 --- a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js +++ b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js @@ -624,14 +624,6 @@ var toolbarMenu = { position: "bottom-start", list: [ { - label: "User Survey", - icon: "", - trailerIcon: "fa fa-external-link", - action: { - handlerAction: "openNewTab", - parameters: ["https://www.surveymonkey.co.uk/r/5HDZZRR"] - } - },{ label: "F.A.Q.", icon: "", trailerIcon: "fa fa-external-link", From a19d93684862e9a089382da18e97a48092adfbd7 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 13:10:31 +0100 Subject: [PATCH 05/11] Revert "typo fix" This reverts commit 50db76e40d63ca32b8e6e849fbd08c56c5bf0862. --- components/configuration/VFBOverview/quickHelp.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json index 57b2aeafc..b79594539 100644 --- a/components/configuration/VFBOverview/quickHelp.json +++ b/components/configuration/VFBOverview/quickHelp.json @@ -10,7 +10,7 @@ "label" : "Hi, we are currently running a VFB User Survey, once you have used the site please consider completing this survey to help us improve it by clicking User Survey in the Help menu above." },{ "icon" : "fa fa-fast-forward", - "label" : "Just click NEXT below for handy tips on using VFB or SKIP INTRO to close this and jump right into VFB." + "label" : "Just click NEXT for handy tips on using VFB or SKIP INTO to close this and jump right into VFB." }] },{ "title": "Welcome to Virtual Fly Brain", From 394d7bca72aa0827bc4ef51599d4d7ee7f0b3c1a Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 13:10:36 +0100 Subject: [PATCH 06/11] Revert "adding survey text" This reverts commit ebe39aefc9b7326c0ee86e00afb1f282269535cb. --- components/configuration/VFBOverview/quickHelp.json | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json index b79594539..75d0ade4d 100644 --- a/components/configuration/VFBOverview/quickHelp.json +++ b/components/configuration/VFBOverview/quickHelp.json @@ -3,16 +3,6 @@ "height": "575", "width": "900", "steps": [{ - "title": "Welcome to Virtual Fly Brain", - "image" : "geppetto/build/VFBqHelpMain.jpg", - "instructions": [{ - "icon" : "fa fa-question-circle-o", - "label" : "Hi, we are currently running a VFB User Survey, once you have used the site please consider completing this survey to help us improve it by clicking User Survey in the Help menu above." - },{ - "icon" : "fa fa-fast-forward", - "label" : "Just click NEXT for handy tips on using VFB or SKIP INTO to close this and jump right into VFB." - }] - },{ "title": "Welcome to Virtual Fly Brain", "image" : "geppetto/build/VFBqHelpMain.jpg", "instructions": [{ From 8509162b645addbbb41b4b90cb5e57480b1b2cff Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 2 May 2021 20:32:20 +0100 Subject: [PATCH 07/11] reverting to fixed query menus --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ab9df7a4e..aadfe94ae 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ ARG geppettoDatasourceRelease=vfb_20200604_a ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=development ARG geppettoClientRelease=VFBv2.2.0.7 -ARG ukAcVfbGeppettoRelease=pipeline2 +ARG ukAcVfbGeppettoRelease=2021-03-06 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster" From af3b56f6e4858b24bc38f1845365d203a68e4c53 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 3 May 2021 08:36:40 +0100 Subject: [PATCH 08/11] swapping to neo NBLAST to GAL4 --- model/vfb.xmi | 41 ++++++++++++++++++++++++++++++++--------- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 2b95dbe72..423bd962d 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -150,6 +150,9 @@ + + + + + - - - + + + From 63e26396efcb6303ca939eea3dd20359352a4484 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 3 May 2021 11:11:56 +0100 Subject: [PATCH 09/11] enabling collapsable queries --- Dockerfile | 2 +- css/VFBTermInfo.less | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index aadfe94ae..81868d22f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ ARG geppettoDatasourceRelease=vfb_20200604_a ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=development ARG geppettoClientRelease=VFBv2.2.0.7 -ARG ukAcVfbGeppettoRelease=2021-03-06 +ARG ukAcVfbGeppettoRelease=2021-05-03 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster" diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less index 0d7e199ce..cf2356afb 100644 --- a/css/VFBTermInfo.less +++ b/css/VFBTermInfo.less @@ -934,3 +934,19 @@ transition: all 0.50s; } } + +details > summary > i.fa-chevron-circle-right { + display: inline-block; +} + +details > summary > i.fa-chevron-circle-down { + display: none; +} + +details[open] > summary > i.fa-chevron-circle-down { + display: inline-block; +} + +details[open] > summary > i.fa-chevron-circle-right { + display: none; +} \ No newline at end of file From 9515c964386609a615e28c7a2d094b91b3b80a01 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 3 May 2021 11:34:01 +0100 Subject: [PATCH 10/11] update query for links to Ind Exp --- model/vfb.xmi | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index 423bd962d..f61b7ac31 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -553,8 +553,8 @@ name="NBLAST_anat_image_query" description="find has_similar_morphology_to relationships" returnType="//@libraries.3/@types.1" - query=""statement": "MATCH (n:Individual)-[nblast:has_similar_morphology_to_part_of]-(c:Class) WHERE n.short_form in [$id] WITH c, nblast OPTIONAL MATCH (c:Class)<-[:INSTANCEOF|SUBCLASSOF*..]-(primary:Individual)<-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary, nblast OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary, nblast OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image, nblast RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, nblast.NBLAST_score[0] as score, 'm20210406' AS version, 'NBLASTexp_anat_image_query' AS query, channel_image, types", "parameters" : { "id" : "$ID" }" - countQuery=""statement": "MATCH (n:Individual)-[nblast:has_similar_morphology_to_part_of]-(primary:Class) WHERE n.short_form in [$id] RETURN count(primary) AS count", "parameters" : { "id" : "$ID" }"/> + query=""statement": "MATCH (n:Neuron)-[nblast:has_similar_morphology_to_part_of]->(primary:Expression_pattern) WHERE n.short_form in [$id] WITH primary, nblast OPTIONAL MATCH (c:Class)<-[:INSTANCEOF]-(primary) OPTIONAL MATCH (primary)<-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary, nblast OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary, nblast OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image, nblast RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, nblast.NBLAST_score[0] as score, 'm20210503' AS version, 'NBLASTexp_anat_image_query' AS query, channel_image, types", "parameters" : { "id" : "$ID" }" + countQuery=""statement": "MATCH (n:Individual)-[nblast:has_similar_morphology_to_part_of]->(primary:Individual) WHERE n.short_form in [$id] RETURN count(primary) AS count", "parameters" : { "id" : "$ID" }"/> Date: Mon, 3 May 2021 15:13:51 +0100 Subject: [PATCH 11/11] swapping to latest --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 81868d22f..ab9df7a4e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ ARG geppettoDatasourceRelease=vfb_20200604_a ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=development ARG geppettoClientRelease=VFBv2.2.0.7 -ARG ukAcVfbGeppettoRelease=2021-05-03 +ARG ukAcVfbGeppettoRelease=pipeline2 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster"