From f7b947d53572b5efbd049b6721574e4025466e56 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 30 May 2023 16:38:14 +0100 Subject: [PATCH 1/9] typo fix --- css/VFBTermInfo.less | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less index 48bc2dfd5..0bc192a21 100644 --- a/css/VFBTermInfo.less +++ b/css/VFBTermInfo.less @@ -848,7 +848,7 @@ color: white; clear: both; max-width: 100%; - max-width: 260px; + max-height: 260px; margin-left: 25px; } From 87f359976e156d39d69cd2188056cd3d0be69520 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 6 Jun 2023 08:40:36 +0100 Subject: [PATCH 2/9] Handling null pointer error --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 20cc2ca41..c6ea1d760 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,7 @@ VOLUME /tmp/error ARG geppettoRelease=vfb_20200604_a ARG geppettoModelRelease=vfb_20200604_a ARG geppettoCoreRelease=VFBv2.2.0 -ARG geppettoSimulationRelease=vfb_20200604_a +ARG geppettoSimulationRelease=VFBv2.1.0.2 ARG geppettoDatasourceRelease=passingSOLR ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=VFBv2.1.0.3 From 9501e333c2c9b6c5ae8207d48e545d065cc7c0b1 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 12 Jun 2023 11:46:29 +0100 Subject: [PATCH 3/9] Create settings.json --- .vscode/settings.json | 1 + 1 file changed, 1 insertion(+) create mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 000000000..9e26dfeeb --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1 @@ +{} \ No newline at end of file From 32990d0d540b468f6c2d0996966d3d6b32620492 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Wed, 28 Jun 2023 17:52:34 +0100 Subject: [PATCH 4/9] Adding NBLAST upload --- .../VFBToolbar/vfbtoolbarMenuConfiguration.js | 7 +++---- components/interface/VFBFocusTerm/VFBFocusTerm.js | 7 +++++++ 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js index 9e4a99ddd..8600770f6 100644 --- a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js +++ b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js @@ -270,11 +270,10 @@ var toolbarMenu = { }, { label: "NBLAST against your own data", - icon: "", - trailerIcon: "fa fa-external-link", + icon: "fa fa-upload", action: { - handlerAction: "openNewTab", - parameters: ["http://nblast.virtualflybrain.org:8080/NBLAST_on-the-fly/?gal4_n=10&all_use_mean=F&all_query=&tab=One%20against%20all&gal4_query="] + handlerAction: "uploaderContentsVisible", + parameters: [] } } ] diff --git a/components/interface/VFBFocusTerm/VFBFocusTerm.js b/components/interface/VFBFocusTerm/VFBFocusTerm.js index dd8a10262..28d41946b 100644 --- a/components/interface/VFBFocusTerm/VFBFocusTerm.js +++ b/components/interface/VFBFocusTerm/VFBFocusTerm.js @@ -568,6 +568,13 @@ class VFBFocusTerm extends React.Component { : } + + { + this.props.UIUpdateManager("uploaderContentsVisible"); + }} /> + Date: Thu, 29 Jun 2023 15:59:11 +0100 Subject: [PATCH 5/9] https req --- components/configuration/VFBUploader/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/components/configuration/VFBUploader/configuration.json b/components/configuration/VFBUploader/configuration.json index 45126dc53..85f1df101 100644 --- a/components/configuration/VFBUploader/configuration.json +++ b/components/configuration/VFBUploader/configuration.json @@ -1,10 +1,10 @@ { - "nblastURL" : "http://upload.virtualflybrain.org/files/UNIQUE_ID?token=bec3a40f0ab377c39103", + "nblastURL" : "https://upload.virtualflybrain.org/files/UNIQUE_ID?token=bec3a40f0ab377c39103", "contentType" : "multipart/form-data", "templates" : [{"short_form":"VFB_00101567","label":"JRC2018Unisex"},{"short_form":"VFB_00200000","label":"JRC2018UnisexVNC"}] , "acceptedFiles" : [".swc", ".nrrd"], "filesLimit" : 1, - "maxFileSize" : 3000000, + "maxFileSize" : 5242880, "queryType": "uploaderQuery", "cookieStorageDays" : 100, "cookiesLearnLink" : "https://en.wikipedia.org/wiki/HTTP_cookie", From 262ab182e377c261f1e875f3c3a1e0058705530b Mon Sep 17 00:00:00 2001 From: jrmartin Date: Wed, 12 Jul 2023 15:58:32 -0700 Subject: [PATCH 6/9] #360 Fix Focus Term menu not showing up on page load. --- components/interface/VFBFocusTerm/VFBFocusTerm.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/components/interface/VFBFocusTerm/VFBFocusTerm.js b/components/interface/VFBFocusTerm/VFBFocusTerm.js index 28d41946b..72f1182d3 100644 --- a/components/interface/VFBFocusTerm/VFBFocusTerm.js +++ b/components/interface/VFBFocusTerm/VFBFocusTerm.js @@ -363,6 +363,8 @@ class VFBFocusTerm extends React.Component { { variable: variable2, allQueries: allQueries2 }]; } }); + } else { + this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }]; } } else { this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }]; From 17b2fd8aebcef1ccf3d1484a2ec1cf4bee910d03 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 4 Sep 2023 11:12:25 +0100 Subject: [PATCH 7/9] fix to use _padded expression level version if exists --- model/vfb.xmi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/vfb.xmi b/model/vfb.xmi index cc8faf7df..51340b1e4 100644 --- a/model/vfb.xmi +++ b/model/vfb.xmi @@ -597,7 +597,7 @@ id="cluster_expression_query" name="Get JSON for cluster expression query" description="Get JSON for cluster expression query" - query=""statement": "MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) WITH e.expression_level[0] as expression_level, e.expression_extent[0] as expression_extent, { short_form: g.short_form, label: coalesce(g.label,''), iri: g.iri, types: labels(g), unique_facets: apoc.coll.sort(coalesce(g.uniqueFacets, [])), symbol: coalesce(([]+g.symbol)[0], '')} AS gene,primary MATCH (a:Anatomy)<-[:composed_primarily_of]-(primary) WITH { short_form: a.short_form, label: coalesce(a.label,''), iri: a.iri, types: labels(a), unique_facets: apoc.coll.sort(coalesce(a.uniqueFacets, [])), symbol: coalesce(([]+a.symbol)[0], '')} AS anatomy,primary,expression_level,expression_extent,gene RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(([]+primary.symbol)[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for cluster expression query' AS query, 'a3c0d68' AS version , expression_level, expression_extent, gene, anatomy", "parameters" : { "id" : "$ID" }" + query=""statement": "MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) WITH coalesce(e.expression_level_padded[0], e.expression_level[0]) as expression_level, e.expression_extent[0] as expression_extent, { short_form: g.short_form, label: coalesce(g.label,''), iri: g.iri, types: labels(g), unique_facets: apoc.coll.sort(coalesce(g.uniqueFacets, [])), symbol: coalesce(([]+g.symbol)[0], '')} AS gene,primary MATCH (a:Anatomy)<-[:composed_primarily_of]-(primary) WITH { short_form: a.short_form, label: coalesce(a.label,''), iri: a.iri, types: labels(a), unique_facets: apoc.coll.sort(coalesce(a.uniqueFacets, [])), symbol: coalesce(([]+a.symbol)[0], '')} AS anatomy,primary,expression_level,expression_extent,gene RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(([]+primary.symbol)[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for cluster expression query' AS query, 'a3c0d68' AS version , expression_level, expression_extent, gene, anatomy", "parameters" : { "id" : "$ID" }" countQuery=""statement": "MATCH (primary:Individual:Cluster) WHERE primary.short_form in [$id] WITH primary MATCH (primary)-[e:expresses]->(g:Gene:Class) RETURN count(g) as count", "parameters" : { "id" : "$ID" }"/> Date: Mon, 4 Sep 2023 11:46:23 +0100 Subject: [PATCH 8/9] Adding Class/Type filter to search --- components/configuration/VFBMain/searchConfiguration.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/components/configuration/VFBMain/searchConfiguration.js b/components/configuration/VFBMain/searchConfiguration.js index 91c2eb23a..bb3168ea0 100644 --- a/components/configuration/VFBMain/searchConfiguration.js +++ b/components/configuration/VFBMain/searchConfiguration.js @@ -149,6 +149,11 @@ var searchConfiguration = { "filter_name": "Neuron", "enabled": "disabled", }, + { + "key": "Class", + "filter_name": "Type", + "enabled": "disabled", + }, { "key": "has_image", "filter_name": "Image", From 98dd6286b3d79f40ad4e024d855e1c50e7156f0f Mon Sep 17 00:00:00 2001 From: Rob Court Date: Sun, 21 Jan 2024 14:44:14 +0000 Subject: [PATCH 9/9] indent fix --- components/interface/VFBFocusTerm/VFBFocusTerm.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/interface/VFBFocusTerm/VFBFocusTerm.js b/components/interface/VFBFocusTerm/VFBFocusTerm.js index 72f1182d3..12d6e78d8 100644 --- a/components/interface/VFBFocusTerm/VFBFocusTerm.js +++ b/components/interface/VFBFocusTerm/VFBFocusTerm.js @@ -364,7 +364,7 @@ class VFBFocusTerm extends React.Component { } }); } else { - this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }]; + this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }]; } } else { this.configuration.buttons[0].dynamicListInjector.parameters = [{ variable: variable, allQueries: allQueries }];