From e6c44d2d6cfc166718690e44560e95e28b20951c Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 09:36:57 -0400 Subject: [PATCH 01/17] latest header --- public/schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/schema.json b/public/schema.json index 0b61dddc..42d9b1af 100644 --- a/public/schema.json +++ b/public/schema.json @@ -9467,7 +9467,7 @@ "type": "page", "component": "KnowledgeGraph", "props": { - "title": "Term & Gene Search: Find connections between genes and terms from the datasets of Harmonizome.", + "title": "Term & Gene Search: Visualize connections between genes and terms from the 200+ datasets of Harmonizome.", "description": "Search one or two genes or terms to see related entities.", "init_function": "initialize_kg", "initial_query": { From 4d76b0db8cc02ff803047ab5577403528784ebae Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 11:54:20 -0400 Subject: [PATCH 02/17] building again --- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index b57ed85a..734a833c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.1 + image: nlingam05/harmonizome-kg:2.4.2 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 7a714041..62ec0605 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.1", + "version": "2.4.2", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.1", + "version": "2.4.2", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index c00b2001..fd4b6c52 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.1", + "version": "2.4.2", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From d1ba3fcd974de71537f264294b672ee6febff4bb Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 12:18:50 -0400 Subject: [PATCH 03/17] fixed footer issue --- components/misc/index.tsx | 4 ++-- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/components/misc/index.tsx b/components/misc/index.tsx index 9f3dd7a3..16f2238d 100644 --- a/components/misc/index.tsx +++ b/components/misc/index.tsx @@ -194,7 +194,7 @@ const HarmonizomeFooter = () => {
  • - Ma'ayan Laboratory of Computational Systems Biology + Ma'ayan Laboratory of Computational Systems Biology
    • @@ -221,7 +221,7 @@ const HarmonizomeFooter = () => { - Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. + Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100. diff --git a/docker-compose.yml b/docker-compose.yml index 734a833c..17b6e07c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.2 + image: nlingam05/harmonizome-kg:2.4.3 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 62ec0605..3ae74bec 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.2", + "version": "2.4.3", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.2", + "version": "2.4.3", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index fd4b6c52..c2340607 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.2", + "version": "2.4.3", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From 9db74dc79245692984790d60070844c6da966149 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 12:29:00 -0400 Subject: [PATCH 04/17] trying to fix compilation error --- components/Download/edge_only.tsx | 4 ++-- components/misc/index.tsx | 4 ++-- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/components/Download/edge_only.tsx b/components/Download/edge_only.tsx index efa4fa0e..dfdace4d 100644 --- a/components/Download/edge_only.tsx +++ b/components/Download/edge_only.tsx @@ -19,8 +19,8 @@ const EdgeOnly = ({download}: {download: Array<{ Each dataset below contains a link to `[source].new_archive.zip` file. - This zip file contains 1. a '[source].nodes.csv' file containing the terms' information; 2. edges files containing - the triple source, relation, and target signifying an edge in the network, and 3. a '[genes].nodes.csv' file containing the genes that are covered in the dataset. + This zip file contains 1. a `[source].nodes.csv` file containing the terms` information; 2. edges files containing + the triple source, relation, and target signifying an edge in the network, and 3. a `[genes].nodes.csv` file containing the genes that are covered in the dataset. Additionally these files may also include associated metadata for the source and target nodes as well as the edges. diff --git a/components/misc/index.tsx b/components/misc/index.tsx index 16f2238d..8342c8a9 100644 --- a/components/misc/index.tsx +++ b/components/misc/index.tsx @@ -194,7 +194,7 @@ const HarmonizomeFooter = () => {
  • - Ma'ayan Laboratory of Computational Systems Biology + Ma`ayan Laboratory of Computational Systems Biology
    • @@ -221,7 +221,7 @@ const HarmonizomeFooter = () => { - Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. + Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma`ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100. diff --git a/docker-compose.yml b/docker-compose.yml index 17b6e07c..81699736 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.3 + image: nlingam05/harmonizome-kg:2.4.4 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 3ae74bec..c1a1e126 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.3", + "version": "2.4.4", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.3", + "version": "2.4.4", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index c2340607..32e5a67a 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.3", + "version": "2.4.4", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From 467c7262fa5ed2bab2edf8e3380797a180e50f34 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 12:54:11 -0400 Subject: [PATCH 05/17] trying to rebuild again --- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 81699736..93ffb88b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.4 + image: nlingam05/harmonizome-kg:2.4.5 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index c1a1e126..4d45884c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.4", + "version": "2.4.5", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.4", + "version": "2.4.5", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index 32e5a67a..198547b7 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.4", + "version": "2.4.5", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From 649851cc4ab0ad850c827bc37c229849972a8554 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 13:41:17 -0400 Subject: [PATCH 06/17] cleaning... --- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 93ffb88b..cf03bcac 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.5 + image: nlingam05/harmonizome-kg:2.4.6 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 4d45884c..9cc49571 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.5", + "version": "2.4.6", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.5", + "version": "2.4.6", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index 198547b7..a2fdb971 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.5", + "version": "2.4.6", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From f0c09acc91a575cbb6fb29357767e86e8b32a31a Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 14:06:03 -0400 Subject: [PATCH 07/17] cleaning --- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index cf03bcac..a9c6e9a2 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.6 + image: nlingam05/harmonizome-kg:2.4.7 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 8f98f432..e60cd56d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.6", + "version": "2.4.7", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.6", + "version": "2.4.7", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index a48ffac3..c4e9d2a0 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.6", + "version": "2.4.7", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From a6fbe170f19fcd1a3c9b340bcd1e23cb1de91856 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 14:50:07 -0400 Subject: [PATCH 08/17] 2.4.8 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index e60cd56d..fbf14285 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.7", + "version": "2.4.8", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.7", + "version": "2.4.8", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index c4e9d2a0..552df724 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.7", + "version": "2.4.8", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From b06a30851b041017a145831d1187e5f7f555c4c9 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 14:58:42 -0400 Subject: [PATCH 09/17] cleaning --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index a9c6e9a2..2a071c72 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.7 + image: nlingam05/harmonizome-kg:2.4.8 x-kubernetes: strategy: type: Recreate From faae157dde3c841b3e0f0254dc70ca869b260813 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 15:17:35 -0400 Subject: [PATCH 10/17] 2.4.9 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index fbf14285..9dc50ff2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.8", + "version": "2.4.9", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.8", + "version": "2.4.9", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index 552df724..703f14d6 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.8", + "version": "2.4.9", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From 1206b28a6d00166c8980635dad14ba570ea6f49d Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 15:56:01 -0400 Subject: [PATCH 11/17] cleaning --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 2a071c72..23830b32 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.8 + image: nlingam05/harmonizome-kg:2.4.9 x-kubernetes: strategy: type: Recreate From 12ecee5908c58a91a545c755be287c27cbbc1e31 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 15:57:21 -0400 Subject: [PATCH 12/17] changed margin --- themes/harmonizome-kg.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/themes/harmonizome-kg.ts b/themes/harmonizome-kg.ts index bf19657a..ca7bac0d 100644 --- a/themes/harmonizome-kg.ts +++ b/themes/harmonizome-kg.ts @@ -154,7 +154,7 @@ export const harmonizome_kg_theme = createTheme({ height: 50, background: "#132457", boxShadow: "0 2px 5px 0 rgba(0, 0, 0, 0.26)", - marginBottom: 10, + marginBottom: 35, }, }, }, From 7e107ef5846947300a6774470db92b180a15521d Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 16:18:21 -0400 Subject: [PATCH 13/17] 2.4.10 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 9dc50ff2..182c5261 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.9", + "version": "2.4.10", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.9", + "version": "2.4.10", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index 703f14d6..fc66a0ba 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.9", + "version": "2.4.10", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From 066e0e04987887b20c8382d1330b634b75470f8a Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 16:36:27 -0400 Subject: [PATCH 14/17] deleted KG tab's text --- docker-compose.yml | 2 +- public/schema.json | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 23830b32..259aea83 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.9 + image: nlingam05/harmonizome-kg:2.4.10 x-kubernetes: strategy: type: Recreate diff --git a/public/schema.json b/public/schema.json index 36d134c6..a350c72b 100644 --- a/public/schema.json +++ b/public/schema.json @@ -9467,8 +9467,6 @@ "type": "page", "component": "KnowledgeGraph", "props": { - "title": "Term & Gene Search: Visualize connections between genes and terms from the 200+ datasets of Harmonizome.", - "description": "Search one or two genes or terms to see related entities.", "init_function": "initialize_kg", "initial_query": { "start": "gene", From 09a7d77c8f20b4330a960ed3cbbd172ea1967d07 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 16:40:41 -0400 Subject: [PATCH 15/17] rebuilding --- docker-compose.yml | 2 +- package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 259aea83..c0f22a43 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.10 + image: nlingam05/harmonizome-kg:2.4.11 x-kubernetes: strategy: type: Recreate diff --git a/package-lock.json b/package-lock.json index 182c5261..8b023f45 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.10", + "version": "2.4.11", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.10", + "version": "2.4.11", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index fc66a0ba..213cbc66 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.10", + "version": "2.4.11", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From bec65a3e333a54d6cc7ec8f97cf3edc9e8a4e365 Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 16:54:45 -0400 Subject: [PATCH 16/17] 2.4.12 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 8b023f45..c72892d3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.11", + "version": "2.4.12", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "cfde-knowledge-exchange", - "version": "2.4.11", + "version": "2.4.12", "dependencies": { "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", diff --git a/package.json b/package.json index 213cbc66..29ffec6b 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "cfde-knowledge-exchange", - "version": "2.4.11", + "version": "2.4.12", "private": true, "scripts": { "dev": "NODE_ENV=development next dev", From f9b1575a289c35a0cfbccaeea11126ea02f73eec Mon Sep 17 00:00:00 2001 From: Nia Lingam Date: Fri, 9 Aug 2024 17:09:57 -0400 Subject: [PATCH 17/17] final commit --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index c0f22a43..46bd91c8 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: context: . dockerfile: ./Dockerfile.next platform: linux/amd64 - image: nlingam05/harmonizome-kg:2.4.11 + image: nlingam05/harmonizome-kg:2.4.12 x-kubernetes: strategy: type: Recreate