From 99453b52c7d219e77ef9cc666879bf4364ed2740 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 17:24:30 +0200
Subject: [PATCH 1/8] cleaned environments and deploymenet options; updated to
new production server
---
angular.json | 76 ++-----------------
package.json | 11 +--
src/environments/environment.dev.ts | 7 +-
...nment.prod.dock1.ts => environment.old.ts} | 1 +
src/environments/environment.prod.stage.ts | 4 -
src/environments/environment.prod.ts | 4 -
src/environments/environment.prod.uhh.ts | 4 -
src/environments/environment.ts | 17 +----
src/index.html | 2 +-
9 files changed, 16 insertions(+), 110 deletions(-)
rename src/environments/{environment.prod.dock1.ts => environment.old.ts} (99%)
delete mode 100644 src/environments/environment.prod.stage.ts
delete mode 100644 src/environments/environment.prod.ts
delete mode 100644 src/environments/environment.prod.uhh.ts
diff --git a/angular.json b/angular.json
index c12cc93d..cca7fddf 100644
--- a/angular.json
+++ b/angular.json
@@ -49,69 +49,13 @@
"namedChunks": true
},
"configurations": {
- "local": {
+ "old": {
"fileReplacements": [
{
"replace": "src/environments/environment.ts",
- "with": "src/environments/environment.dev.ts"
- }
- ]
- },
- "uhh-production": {
- "fileReplacements": [
- {
- "replace": "src/environments/environment.ts",
- "with": "src/environments/environment.prod.uhh.ts"
+ "with": "src/environments/environment.old.ts"
}
],
- "optimization": true,
- "outputHashing": "all",
- "sourceMap": false,
- "namedChunks": false,
- "extractLicenses": true,
- "vendorChunk": false,
- "buildOptimizer": true,
- "budgets": [
- {
- "type": "initial",
- "maximumWarning": "2mb",
- "maximumError": "5mb"
- },
- {
- "type": "anyComponentStyle",
- "maximumWarning": "6kb",
- "maximumError": "500kb"
- }
- ]
- },
- "dock1-production": {
- "fileReplacements": [
- {
- "replace": "src/environments/environment.ts",
- "with": "src/environments/environment.prod.dock1.ts"
- }
- ],
- "optimization": true,
- "outputHashing": "all",
- "sourceMap": false,
- "namedChunks": false,
- "extractLicenses": true,
- "vendorChunk": false,
- "buildOptimizer": true,
- "budgets": [
- {
- "type": "initial",
- "maximumWarning": "2mb",
- "maximumError": "5mb"
- },
- {
- "type": "anyComponentStyle",
- "maximumWarning": "6kb",
- "maximumError": "500kb"
- }
- ]
- },
- "remote": {
"optimization": true,
"outputHashing": "all",
"sourceMap": false,
@@ -160,12 +104,6 @@
]
},
"production": {
- "fileReplacements": [
- {
- "replace": "src/environments/environment.ts",
- "with": "src/environments/environment.prod.ts"
- }
- ],
"optimization": true,
"outputHashing": "all",
"sourceMap": false,
@@ -192,14 +130,14 @@
"serve": {
"builder": "@angular-builders/custom-webpack:dev-server",
"configurations": {
- "local": {
- "browserTarget": "netex:build:local"
+ "dev": {
+ "browserTarget": "netex:build:development"
},
- "remote": {
- "browserTarget": "netex:build:remote"
+ "old": {
+ "browserTarget": "netex:build:old"
},
"production": {
- "browserTarget": "netex:build:dock1-production"
+ "browserTarget": "netex:build:production"
}
}
},
diff --git a/package.json b/package.json
index 97a725e9..8b3d32f6 100644
--- a/package.json
+++ b/package.json
@@ -3,26 +3,21 @@
"version": "0.9.3",
"scripts": {
"ng": "ng",
- "start:local": "ng serve --configuration=local",
- "start:remote": "ng serve --configuration=remote",
+ "start:dev": "ng serve --configuration=dev",
+ "start:old": "ng serve --configuration=old",
"start:prod": "ng serve --configuration=production",
"build": "ng build",
"test": "ng test",
"lint": "ng lint && htmlhint",
"e2e": "ng e2e",
"build-prod": "ng build --configuration=production --output-hashing=none",
- "build-uhh": "ng build --configuration=uhh-production --output-hashing=none",
- "build-dock1": "ng build --configuration=dock1-production --output-hashing=none",
"build-dev": "ng build --configuration=development --output-hashing=none",
- "build-remote": "ng build --configuration=remote --output-hashing=none",
"package-es5": "cd dist/netex && cat runtime-es5.js polyfills-es5.js main-es5.js > bundle-es5.js",
"package-es2015": "cd dist/netex && cat runtime-es2015.js polyfills-es2015.js main-es2015.js > bundle-es2015.js",
"bundle": "npm run build-prod netex && npm run package-es5 && npm run package-es2015",
"build:netex": "npm run build-prod netex && node build-netex.js",
"build:netex-dev": "npm run build-dev netex && node build-netex.js",
- "build:netex-uhh": "npm run build-uhh netex && node build-netex.js",
- "build:netex-dock1": "npm run build-dock1 netex && node build-netex.js",
- "build:netex-remote": "npm run build-remote netex && node build-netex.js",
+ "build:netex-dock1": "npm run build-old netex && node build-netex.js",
"prefix": "bash prefix_styles.sh",
"prefixcss": "postcss -r drugsTone-build/styles.css"
},
diff --git a/src/environments/environment.dev.ts b/src/environments/environment.dev.ts
index 37b731d6..f10eebdc 100644
--- a/src/environments/environment.dev.ts
+++ b/src/environments/environment.dev.ts
@@ -1,12 +1,7 @@
-// This file can be replaced during build by using the `fileReplacements` array.
-// `ng build --prod` replaces `environment.ts` with `environment.prod.ts`.
-// The list of file replacements can be found in `angular.json`.
-
export const environment = {
production: false,
backend: 'http://localhost:8001/'
};
-
/*
* For easier debugging in development mode, you can import the following file
* to ignore zone related error stack frames such as `zone.run`, `zoneDelegate.invokeTask`.
@@ -14,4 +9,4 @@ export const environment = {
* This import should be commented out in production mode because it will have a negative impact
* on performance if an error is thrown.
*/
-import 'zone.js/plugins/zone-error'; // Included with Angular CLI.
+import 'zone.js/plugins/zone-error';
diff --git a/src/environments/environment.prod.dock1.ts b/src/environments/environment.old.ts
similarity index 99%
rename from src/environments/environment.prod.dock1.ts
rename to src/environments/environment.old.ts
index ac393b40..7372a162 100644
--- a/src/environments/environment.prod.dock1.ts
+++ b/src/environments/environment.old.ts
@@ -2,3 +2,4 @@ export const environment = {
production: true,
backend: 'https://drugst.one/drugstone_api/',
};
+
diff --git a/src/environments/environment.prod.stage.ts b/src/environments/environment.prod.stage.ts
deleted file mode 100644
index 2dec8afe..00000000
--- a/src/environments/environment.prod.stage.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-export const environment = {
- production: true,
- backend: 'https://exbio.wzw.tum.de/drugstone/api/',
-};
diff --git a/src/environments/environment.prod.ts b/src/environments/environment.prod.ts
deleted file mode 100644
index 2dec8afe..00000000
--- a/src/environments/environment.prod.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-export const environment = {
- production: true,
- backend: 'https://exbio.wzw.tum.de/drugstone/api/',
-};
diff --git a/src/environments/environment.prod.uhh.ts b/src/environments/environment.prod.uhh.ts
deleted file mode 100644
index e892d5ee..00000000
--- a/src/environments/environment.prod.uhh.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-export const environment = {
- production: true,
- backend: 'http://ml-s-zbhdock2.ad.uni-hamburg.de/drugstone_api/',
-};
diff --git a/src/environments/environment.ts b/src/environments/environment.ts
index e1e1736a..9554a44b 100644
--- a/src/environments/environment.ts
+++ b/src/environments/environment.ts
@@ -1,17 +1,6 @@
-// This file can be replaced during build by using the `fileReplacements` array.
-// `ng build --prod` replaces `environment.ts` with `environment.prod.ts`.
-// The list of file replacements can be found in `angular.json`.
-
export const environment = {
- production: false,
- backend: 'http://10.162.163.20:8001/',
+ production: true,
+ backend: 'https://api.drugst.one/',
};
-/*
- * For easier debugging in development mode, you can import the following file
- * to ignore zone related error stack frames such as `zone.run`, `zoneDelegate.invokeTask`.
- *
- * This import should be commented out in production mode because it will have a negative impact
- * on performance if an error is thrown.
- */
-import 'zone.js/plugins/zone-error'; // Included with Angular CLI.
+
diff --git a/src/index.html b/src/index.html
index 6f45199e..be55455c 100644
--- a/src/index.html
+++ b/src/index.html
@@ -45,7 +45,7 @@
<network-expander id="netexp1"
pluginId="2"
- config='{"showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#4da300"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590","highlight":{"border":"#F12590","background":"#F12590"}},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
+ config='{"showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
network='{"nodes":[{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"BRCA1","to":"BRCA2","group":"ggi"},{"from":"ATM","to":"BARD1","group":"ggi"},{"from":"BRCA1","to":"CHEK2","group":"ggi"},{"from":"RAD51C","to":"RAD51D","group":"ggi"},{"from":"STK11","to":"TP53","group":"ggi"},{"from":"TP53","to":"PALB2","group":"ggi"},{"from":"TP53","to":"RAD51D","group":"ggi"},{"from":"TP53","to":"NF1","group":"ggi"},{"from":"TP53","to":"BRCA1","group":"ggi"},{"from":"TP53","to":"BRCA2","group":"ggi"},{"from":"PTEN","to":"BRCA1","group":"ggi"},{"from":"PTEN","to":"BRCA2","group":"ggi"},{"from":"TP53","to":"PTEN","group":"ggi"},{"from":"ATM","to":"PTEN","group":"ggi"},{"from":"CDH1","to":"RAD51D","group":"ggi"},{"from":"CDH1","to":"PALB2","group":"ggi"},{"from":"NBN","to":"BRIP1","group":"ggi"},{"from":"BRIP1","to":"PTEN","group":"ggi"},{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'>
}'></network-expander>
</div>
--
GitLab
From 0d12fd4fb2185db27b2a7c905b7ae991ff643dec Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 17:34:16 +0200
Subject: [PATCH 2/8] updates for server change to arenal
---
releases/release_tag.sh | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/releases/release_tag.sh b/releases/release_tag.sh
index ced243e2..74ee6d4e 100755
--- a/releases/release_tag.sh
+++ b/releases/release_tag.sh
@@ -24,4 +24,8 @@ git push
echo "Releasing Version..."
git push origin "$VERSION"
+echo "$1" > latest
+git commit -am "triggered of v$1"
+git push
+
echo "Done!"
--
GitLab
From 82df83dffe836a7359198e2c56b48178e5ebb6f0 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 17:34:17 +0200
Subject: [PATCH 3/8] updates for server change to arenal
---
package-lock.json | 2 +-
package.json | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/package-lock.json b/package-lock.json
index 8c09b57f..3010ba2b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
{
"name": "netex",
- "version": "0.9.3",
+ "version": "0.9.4-rc2",
"lockfileVersion": 1,
"requires": true,
"dependencies": {
diff --git a/package.json b/package.json
index 8b3d32f6..bf2547c8 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "netex",
- "version": "0.9.3",
+ "version": "0.9.4-rc2",
"scripts": {
"ng": "ng",
"start:dev": "ng serve --configuration=dev",
--
GitLab
From 8964349f9e2b4080b4d36a6b1b8d26702e41f23f Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 17:34:33 +0200
Subject: [PATCH 4/8] added latest file
---
releases/latest | 1 +
1 file changed, 1 insertion(+)
create mode 100644 releases/latest
diff --git a/releases/latest b/releases/latest
new file mode 100644
index 00000000..89dc8a23
--- /dev/null
+++ b/releases/latest
@@ -0,0 +1 @@
+0.9.4-rc2
--
GitLab
From a2d58ee11e5918a64257dc6aed3665fa214c3922 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 17:46:27 +0200
Subject: [PATCH 5/8] added option for physics control via config
---
.../analysis-panel/analysis-panel.component.ts | 2 +-
src/app/config.ts | 2 ++
src/app/network-settings.ts | 10 +++++-----
src/app/pages/explorer-page/explorer-page.component.ts | 9 +++++++--
src/index.html | 2 +-
5 files changed, 16 insertions(+), 9 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 83a84414..eb999fc7 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -190,7 +190,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.nodeData.edges = new vis.DataSet(edges);
const container = this.networkEl.nativeElement;
const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis');
+ const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.myConfig.physicsOn);
this.physicsEnabled = !isBig;
this.network = new vis.Network(container, this.nodeData, options);
diff --git a/src/app/config.ts b/src/app/config.ts
index 229c9bb9..2f1de2ff 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -59,6 +59,7 @@ export interface IConfig {
autofillEdges: boolean;
sidebarPos: 'left' | 'right';
interactions?: InteractionDatabase;
+ physicsOn?: boolean;
identifier?: Identifier;
nodeShadow?: boolean;
edgeShadow?: boolean;
@@ -95,6 +96,7 @@ export const defaultConfig: IConfig = {
nodeShadow: true,
edgeShadow: true,
autofillEdges: true,
+ physicsOn: false,
sidebarPos: 'left',
nodeGroups: {
// all NodeGroups but the default group must be set, if not provided by the user, they will be taken from here
diff --git a/src/app/network-settings.ts b/src/app/network-settings.ts
index cbc58a02..e68a102a 100644
--- a/src/app/network-settings.ts
+++ b/src/app/network-settings.ts
@@ -8,7 +8,7 @@ import * as merge from 'lodash/fp/merge';
export class NetworkSettings {
// colors
- private static Grey = '#A0A0A0'
+ private static Grey = '#A0A0A0';
private static White = '#FFFFFF';
private static Black = '#000000';
@@ -68,24 +68,24 @@ export class NetworkSettings {
private static drugNotInTrialShape = 'box';
private static drugInTrialShape = 'triangle';
- static getOptions(network: 'main' | 'analysis' | 'analysis-big') {
+ static getOptions(network: 'main' | 'analysis' | 'analysis-big', physicsOn) {
if (network === 'main') {
return {
layout: this.mainLayout,
edges: this.mainEdges,
- physics: this.mainPhysics,
+ physics: physicsOn || this.mainPhysics ,
};
} else if (network === 'analysis') {
return {
layout: this.analysisLayout,
edges: this.analysisEdges,
- physics: this.analysisPhysics,
+ physics: physicsOn || this.analysisPhysics,
};
} else if (network === 'analysis-big') {
return {
layout: this.analysisLayout,
edges: this.analysisEdges,
- physics: this.analysisBigPhysics,
+ physics: physicsOn || this.analysisBigPhysics,
};
}
}
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 82060744..014884dd 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -89,7 +89,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
// a network exists, save node positions
this.networkPositions = this.networkInternal.getPositions();
}
- this.createNetwork();
+ this.createNetwork().then(() => {
+ if(this.myConfig.physicsOn) {
+ this.updatePhysicsEnabled(true);
+ }
+ });
+
}
}
@@ -400,7 +405,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.nodeData.edges = new vis.DataSet(edges);
const container = this.networkEl.nativeElement;
- const options = NetworkSettings.getOptions('main');
+ const options = NetworkSettings.getOptions('main',this.myConfig.physicsOn);
this.networkInternal = new vis.Network(container, this.nodeData, options);
diff --git a/src/index.html b/src/index.html
index be55455c..4fbfc92c 100644
--- a/src/index.html
+++ b/src/index.html
@@ -45,7 +45,7 @@
<network-expander id="netexp1"
pluginId="2"
- config='{"showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
+ config='{"physicsOn":true, "showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
network='{"nodes":[{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"BRCA1","to":"BRCA2","group":"ggi"},{"from":"ATM","to":"BARD1","group":"ggi"},{"from":"BRCA1","to":"CHEK2","group":"ggi"},{"from":"RAD51C","to":"RAD51D","group":"ggi"},{"from":"STK11","to":"TP53","group":"ggi"},{"from":"TP53","to":"PALB2","group":"ggi"},{"from":"TP53","to":"RAD51D","group":"ggi"},{"from":"TP53","to":"NF1","group":"ggi"},{"from":"TP53","to":"BRCA1","group":"ggi"},{"from":"TP53","to":"BRCA2","group":"ggi"},{"from":"PTEN","to":"BRCA1","group":"ggi"},{"from":"PTEN","to":"BRCA2","group":"ggi"},{"from":"TP53","to":"PTEN","group":"ggi"},{"from":"ATM","to":"PTEN","group":"ggi"},{"from":"CDH1","to":"RAD51D","group":"ggi"},{"from":"CDH1","to":"PALB2","group":"ggi"},{"from":"NBN","to":"BRIP1","group":"ggi"},{"from":"BRIP1","to":"PTEN","group":"ggi"},{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'>
}'></network-expander>
</div>
--
GitLab
From 9a6f23954bb15ae3ed93e769096fe9ffb97c659a Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 18:24:05 +0200
Subject: [PATCH 6/8] renamed component from network-expander to drugst-one
---
src/app/app.module.ts | 3 +--
src/index.html | 4 ++--
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/src/app/app.module.ts b/src/app/app.module.ts
index 9d4402b4..6e159a3b 100644
--- a/src/app/app.module.ts
+++ b/src/app/app.module.ts
@@ -77,10 +77,9 @@ export class AppModule {
faSpinner, faExclamationTriangle, faPlus, faExpand, faInfo, faRocket, faAngleDown, faSearch,
faFastForward, faExternalLinkAlt, faTasks, faFilter, faMinus, faUpload, faAngleDoubleDown,
faSync, faBroom, faAngleDoubleUp);
- // Convert `PopupComponent` to a custom element.
const NetworkExpander = createCustomElement(ExplorerPageComponent, {injector});
// Register the custom element with the browser.
- customElements.define('network-expander', NetworkExpander);
+ customElements.define('drugst-one', NetworkExpander);
}
ngDoBootstrap() {
diff --git a/src/index.html b/src/index.html
index 4fbfc92c..e201022e 100644
--- a/src/index.html
+++ b/src/index.html
@@ -43,11 +43,11 @@
<div >
- <network-expander id="netexp1"
+ <drugst-one id="netexp1"
pluginId="2"
config='{"physicsOn":true, "showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#f0f0f0"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":false,"showLegend":true}'
network='{"nodes":[{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"BRCA1","to":"BRCA2","group":"ggi"},{"from":"ATM","to":"BARD1","group":"ggi"},{"from":"BRCA1","to":"CHEK2","group":"ggi"},{"from":"RAD51C","to":"RAD51D","group":"ggi"},{"from":"STK11","to":"TP53","group":"ggi"},{"from":"TP53","to":"PALB2","group":"ggi"},{"from":"TP53","to":"RAD51D","group":"ggi"},{"from":"TP53","to":"NF1","group":"ggi"},{"from":"TP53","to":"BRCA1","group":"ggi"},{"from":"TP53","to":"BRCA2","group":"ggi"},{"from":"PTEN","to":"BRCA1","group":"ggi"},{"from":"PTEN","to":"BRCA2","group":"ggi"},{"from":"TP53","to":"PTEN","group":"ggi"},{"from":"ATM","to":"PTEN","group":"ggi"},{"from":"CDH1","to":"RAD51D","group":"ggi"},{"from":"CDH1","to":"PALB2","group":"ggi"},{"from":"NBN","to":"BRIP1","group":"ggi"},{"from":"BRIP1","to":"PTEN","group":"ggi"},{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'>
- }'></network-expander>
+ </drugst-one>
</div>
<!--<div >-->
--
GitLab
From 79588028bf4106faf8b8e6f5ad8738b485c8401a Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 18:24:44 +0200
Subject: [PATCH 7/8] network-expander is now drust-one
---
package-lock.json | 2 +-
package.json | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/package-lock.json b/package-lock.json
index 3010ba2b..a1669bfa 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
{
"name": "netex",
- "version": "0.9.4-rc2",
+ "version": "0.9.4-rc3",
"lockfileVersion": 1,
"requires": true,
"dependencies": {
diff --git a/package.json b/package.json
index bf2547c8..51366486 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "netex",
- "version": "0.9.4-rc2",
+ "version": "0.9.4-rc3",
"scripts": {
"ng": "ng",
"start:dev": "ng serve --configuration=dev",
--
GitLab
From dc43f403fe9804162aa7599599179af3f39985a6 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 13 May 2022 18:24:46 +0200
Subject: [PATCH 8/8] triggered of v0.9.4-rc3
---
releases/latest | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/releases/latest b/releases/latest
index 89dc8a23..545cb4af 100644
--- a/releases/latest
+++ b/releases/latest
@@ -1 +1 @@
-0.9.4-rc2
+0.9.4-rc3
--
GitLab