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Development #150

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merged 95 commits into from
May 23, 2024
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d79aa84
fix clustering cutoff
tsheils Sep 19, 2023
cc3fb63
fix tests
tsheils Sep 19, 2023
3fe7689
Merge pull request #114 from tsheils/development
tsheils Sep 19, 2023
5ea1bd1
fix emrichment popup
tsheils Sep 19, 2023
91d0870
Merge branch 'ncats:development' into development
tsheils Sep 19, 2023
eaafe49
Merge pull request #115 from tsheils/development
tsheils Sep 19, 2023
7a77a6c
fix download
tsheils Oct 11, 2023
a68d7cd
Merge pull request #116 from tsheils/development
tsheils Oct 11, 2023
e9864dc
Update token name
bettyli037 Oct 11, 2023
1603e8c
Merge pull request #118 from ncats/bettyli037-patch-1
tsheils Oct 11, 2023
51c91a9
small change to trigger deployment
Oct 16, 2023
45eaef7
Merge branch 'development' of https://github.com/ncats/RaMP-Client in…
Oct 16, 2023
c3e4fa7
small change to trigger deployment
Oct 16, 2023
ff8b42d
small change for deployment
Oct 16, 2023
856564f
Merge pull request #119 from ncats/dev_test
johnbraisted Oct 16, 2023
0128dde
initial commit for RaMP-DB v3.+
johnbraisted Oct 30, 2023
78ea8c1
test_on_sqlite_branch
johnbraisted Oct 30, 2023
fa02bd4
Merge pull request #121 from ncats/ramp_server_3_dev
johnbraisted Oct 30, 2023
2fe0769
explicit RMariaDB::MariaDB() call in db.R
johnbraisted Oct 30, 2023
79263a6
Merge pull request #122 from ncats/ramp_server_3_dev
johnbraisted Oct 30, 2023
a998412
update db.R for ramp v3.0, integer port for qa
johnbraisted Oct 31, 2023
2824e34
mod to db.R for RaMP-DB package v3, needs db_port in config
johnbraisted Oct 31, 2023
c364ce7
Merge pull request #123 from ncats/ramp_server_3_dev
johnbraisted Oct 31, 2023
c78ff68
update install.R to include BiocFileCache installation
johnbraisted Oct 31, 2023
7ed2539
Merge pull request #124 from ncats/ramp_server_3_dev
johnbraisted Oct 31, 2023
c2a833a
Update .travis.yml
tsheils Dec 19, 2023
17b592d
Create build.yml
tsheils Dec 19, 2023
29f16df
Merge pull request #125 from ncats/tsheils-patch-2
tsheils Dec 19, 2023
2eaecb3
Update build.yml
tsheils Dec 19, 2023
354c013
Update build.yml
tsheils Dec 19, 2023
0624528
Update build.yml
tsheils Dec 19, 2023
b3a977a
Update .travis.yml
tsheils Dec 19, 2023
7031aeb
Update .travis.yml
tsheils Dec 19, 2023
134fd3a
update to angular 17, prettify all files
tsheils Jan 12, 2024
88eabe2
convert to standalone components, revamp ngrx effects, remove ngrx fa…
tsheils Jan 18, 2024
ec5d76b
fix header style and ngrx selector imports
tsheils Jan 18, 2024
ec0d2dc
update tsconfig
tsheils Jan 18, 2024
0c4105c
removing flex layout
tsheils Jan 19, 2024
6af745e
implement angular flow control, fix some linting
tsheils Jan 24, 2024
4ee0904
Merge branch 'development' into development
tsheils Jan 24, 2024
734e06d
Merge pull request #126 from tsheils/development
tsheils Jan 24, 2024
1d8e981
fixing chemical enrichment, ui layout
tsheils Jan 24, 2024
12dc22e
Merge pull request #127 from tsheils/development
tsheils Jan 24, 2024
c6ab3b9
added 4 Rhea reaction endpoints
johnbraisted Jan 25, 2024
a262670
Merge pull request #128 from ncats/jb_rxn_plumbing
tsheils Jan 25, 2024
f39c67b
fix structure viewer injection token
tsheils Jan 26, 2024
98fa375
comment in db.R
johnbraisted Jan 26, 2024
1b8f4ff
plumber parameter patch
johnbraisted Jan 26, 2024
88abcd7
Merge pull request #130 from ncats/jb_rxn_plumbing
tsheils Jan 30, 2024
08a2f8e
minor mod to runRamp to trigger RaMP-DB package deployment
johnbraisted Jan 30, 2024
c2dfe88
Merge pull request #131 from ncats/jb_rxn_plumbing
tsheils Jan 31, 2024
3ba2e3b
all linting psses
tsheils Jan 31, 2024
588f46f
Merge branch 'development' of github.com:tsheils/RaMP-Client into dev…
tsheils Jan 31, 2024
30a8460
Merge pull request #132 from tsheils/development
tsheils Jan 31, 2024
8439456
tests passing
tsheils Jan 31, 2024
71affd9
Merge branch 'testing' into development
tsheils Jan 31, 2024
e6bb198
Merge pull request #133 from tsheils/development
tsheils Jan 31, 2024
0276314
updating swagger file and api
tsheils Jan 31, 2024
3c2fbd1
Merge pull request #134 from tsheils/development
tsheils Jan 31, 2024
5a1fd83
updating swagger file
tsheils Feb 1, 2024
8b9b15f
Merge branch 'reactions' into development
tsheils Feb 1, 2024
38d1f31
Merge pull request #135 from tsheils/development
tsheils Feb 1, 2024
0806549
start reactions and fix prerendering
tsheils Mar 22, 2024
bd407cf
test and lint passing, but not actually completing
tsheils Mar 22, 2024
b7432a3
Merge branch 'reactions' into development
tsheils Mar 22, 2024
62d3cb9
Merge branch 'development' of github.com:tsheils/RaMP-Client into dev…
tsheils Mar 22, 2024
17df88a
Merge pull request #136 from tsheils/development
tsheils Mar 22, 2024
9678059
fix enrichment download, lint and tests
tsheils Mar 25, 2024
86c2e95
Merge pull request #137 from tsheils/development
tsheils Mar 25, 2024
66f9874
fix pathway downloads
tsheils Apr 17, 2024
3bac001
Merge branch 'ncats:development' into development
tsheils Apr 17, 2024
5e2552b
Merge pull request #138 from tsheils/development
tsheils Apr 17, 2024
fbde35b
update Ramp to sqlite
tsheils Apr 23, 2024
da4b4da
Merge branch 'development' of github.com:tsheils/RaMP-Client into dev…
tsheils Apr 23, 2024
8980d97
Merge branch 'ncats:development' into development
tsheils Apr 23, 2024
7c2d4de
Merge pull request #139 from tsheils/development
tsheils Apr 23, 2024
c97672d
fix download file
tsheils Apr 26, 2024
a645cdd
Merge branch 'ncats:development' into development
tsheils Apr 26, 2024
0613126
Merge pull request #140 from tsheils/development
tsheils Apr 26, 2024
475d0e4
update api to build from ramp main
tsheils Apr 26, 2024
9686b29
Merge pull request #141 from tsheils/development
tsheils Apr 26, 2024
eef487e
Updated documentation in plumber.R and extensions.yml
andyptt21 Apr 30, 2024
6ef177f
fix common reaction query
tsheils Apr 30, 2024
d2189de
Merge pull request #142 from tsheils/development
johnbraisted Apr 30, 2024
fb2340a
updating plumber
tsheils Apr 30, 2024
76d997c
Merge pull request #143 from tsheils/development
tsheils Apr 30, 2024
cb3654b
adjust models to split by commas instead of semicolon
tsheils May 2, 2024
0dfcef9
Merge pull request #144 from tsheils/development
tsheils May 2, 2024
074f6e8
Update runRamp.R
tsheils May 21, 2024
4834099
Merge branch 'development' into tsheils-patch-1
tsheils May 21, 2024
5ebb29b
Merge pull request #146 from ncats/tsheils-patch-1
tsheils May 21, 2024
0daad72
Merge branch 'development' into ap_doc_update
tsheils May 22, 2024
07eea8c
Merge pull request #148 from ncats/ap_doc_update
tsheils May 22, 2024
48434e0
pre-fetch the sqlite database for the Docker container
KeithKelleher May 23, 2024
5380dea
Merge pull request #149 from ncats/prefetch-sqlite-db
tsheils May 23, 2024
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8 changes: 4 additions & 4 deletions .eslintrc.json
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
{
"root": true,
"ignorePatterns": ["**/*"],
"plugins": ["@nrwl/nx"],
"plugins": ["@nx"],
"overrides": [
{
"files": ["*.ts", "*.tsx", "*.js", "*.jsx"],
"rules": {
"@nrwl/nx/enforce-module-boundaries": [
"@nx/enforce-module-boundaries": [
"error",
{
"enforceBuildableLibDependency": true,
Expand All @@ -23,12 +23,12 @@
},
{
"files": ["*.ts", "*.tsx"],
"extends": ["plugin:@nrwl/nx/typescript"],
"extends": ["plugin:@nx/typescript"],
"rules": {}
},
{
"files": ["*.js", "*.jsx"],
"extends": ["plugin:@nrwl/nx/javascript"],
"extends": ["plugin:@nx/javascript"],
"rules": {}
},
{
Expand Down
32 changes: 32 additions & 0 deletions .github/workflows/build.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs

name: Node.js CI

on:
push:
branches: ['master', 'development']
pull_request:
branches: ['master', 'development']

jobs:
build:
runs-on: ubuntu-latest

strategy:
matrix:
node-version: [18.x, 20.x]
# See supported Node.js release schedule at https://nodejs.org/en/about/releases/

steps:
- uses: actions/checkout@v3
- name: Use Node.js ${{ matrix.node-version }}
uses: actions/setup-node@v3
with:
node-version: ${{ matrix.node-version }}
cache: 'npm'
- run: npm i -g @angular/cli
- run: npm i -g nx
- run: npm i
- run: ng run-many --target=lint
- run: ng run-many --target=test -- --no-watch --no-progress --browsers=ChromeHeadlessCI
5 changes: 5 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,9 @@ yarn-error.log
testem.log
/typings

apps/ramp-client/src/environments/environment*
apps/ramp-client/src/environments/environment.ts

# System Files
.DS_Store
Thumbs.db
Expand All @@ -42,3 +45,5 @@ Thumbs.db
.Rproj.user
RaMP-Client.iml


.nx/cache
6 changes: 6 additions & 0 deletions .prettierignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,9 @@

/dist
/coverage
/.angular
/.idea
/node_modules
/.nx/cache

.angular
7 changes: 4 additions & 3 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
dist: jammy
language: node_js
node_js:
- '16'
- 20

addons:
chrome: stable
Expand All @@ -13,5 +14,5 @@ install:
- npm install

script:
- ng lint
- ng run-many --all --target=test -- --no-watch --no-progress --browsers=ChromeHeadlessCI
- ng run-many --all --target=lint
- ng run-many --all --target=test --no-watch --no-progress --browsers=ChromeHeadlessCI
18 changes: 9 additions & 9 deletions apps/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,31 +15,31 @@ These capabilities include generating applications, libraries, etc as well as th
Below are our core plugins:

- [React](https://reactjs.org)
- `npm install --save-dev @nrwl/react`
- `npm install --save-dev @nx/react`
- Web (no framework frontends)
- `npm install --save-dev @nrwl/web`
- `npm install --save-dev @nx/web`
- [Angular](https://angular.io)
- `npm install --save-dev @nrwl/angular`
- `npm install --save-dev @nx/angular`
- [Nest](https://nestjs.com)
- `npm install --save-dev @nrwl/nest`
- `npm install --save-dev @nx/nest`
- [Express](https://expressjs.com)
- `npm install --save-dev @nrwl/express`
- `npm install --save-dev @nx/express`
- [Node](https://nodejs.org)
- `npm install --save-dev @nrwl/node`
- `npm install --save-dev @nx/node`

There are also many [community plugins](https://nx.dev/community) you could add.

## Generate an application

Run `nx g @nrwl/react:app my-app` to generate an application.
Run `nx g @nx/react:app my-app` to generate an application.

> You can use any of the plugins above to generate applications as well.

When using Nx, you can create multiple applications and libraries in the same workspace.

## Generate a library

Run `nx g @nrwl/react:lib my-lib` to generate a library.
Run `nx g @nx/react:lib my-lib` to generate a library.

> You can also use any of the plugins above to generate libraries as well.

Expand All @@ -51,7 +51,7 @@ Run `nx serve my-app` for a dev server. Navigate to http://localhost:4200/. The

## Code scaffolding

Run `nx g @nrwl/react:component my-component --project=my-app` to generate a new component.
Run `nx g @nx/react:component my-component --project=my-app` to generate a new component.

## Build

Expand Down
8 changes: 2 additions & 6 deletions apps/ramp-client-e2e/project.json
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"projectType": "application",
"targets": {
"e2e": {
"executor": "@nrwl/cypress:cypress",
"executor": "@nx/cypress:cypress",
"options": {
"cypressConfig": "apps/ramp-client-e2e/cypress.json",
"devServerTarget": "ramp-client:serve:development",
Expand All @@ -18,11 +18,7 @@
}
},
"lint": {
"executor": "@nrwl/linter:eslint",
"outputs": ["{options.outputFile}"],
"options": {
"lintFilePatterns": ["apps/ramp-client-e2e/**/*.{js,ts}"]
}
"executor": "@nx/eslint:lint"
}
},
"tags": [],
Expand Down
6 changes: 3 additions & 3 deletions apps/ramp-client-e2e/tsconfig.json
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,12 @@
"forceConsistentCasingInFileNames": true,
"strict": true,
"noImplicitReturns": true,
"noFallthroughCasesInSwitch": true
"noFallthroughCasesInSwitch": true,
},
"include": ["src/**/*.ts", "src/**/*.js"],
"angularCompilerOptions": {
"strictInjectionParameters": true,
"strictInputAccessModifiers": true,
"strictTemplates": true
}
"strictTemplates": true,
},
}
4 changes: 2 additions & 2 deletions apps/ramp-client/.eslintrc.json
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
{
"files": ["*.ts"],
"extends": [
"plugin:@nrwl/nx/angular",
"plugin:@nx/angular",
"plugin:@angular-eslint/template/process-inline-templates"
],
"rules": {
Expand All @@ -29,7 +29,7 @@
},
{
"files": ["*.html"],
"extends": ["plugin:@nrwl/nx/angular-template"],
"extends": ["plugin:@nx/angular-template"],
"rules": {}
}
]
Expand Down
3 changes: 1 addition & 2 deletions apps/ramp-client/CLIENT_INSTRUCTIONS.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,5 +8,4 @@ To run the client application locally, please follow these steps:
4. Change directory (`cd`) to the `apps/ramp-client` directory of this repository
5. Type `ng s` or `nx run ramp-client:serve:development` and hit Enter

To build the application and run it in a container, just build and run the dockerfile in the client directory.

To build the application and run it in a container, just build and run the dockerfile in the client directory.
4 changes: 2 additions & 2 deletions apps/ramp-client/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM node:18.16-alpine3.17 AS build
FROM node:20.11-alpine3.18 AS build

ENV npm_config_unsafe_perm=true

Expand All @@ -20,7 +20,7 @@ RUN npm install -g nx
RUN npm install
RUN nx g @nrwl/workspace:fix-configuration
RUN npm i
RUN NODE_OPTIONS=--max_old_space_size=4096 nx run ramp-client:prerender:production --verbose
RUN NODE_OPTIONS=--max_old_space_size=8192 nx run ramp-client:build:production --verbose

FROM registry.ncats.nih.gov:5000/labshare/docker-base-web

Expand Down
76 changes: 44 additions & 32 deletions apps/ramp-client/project.json
Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,20 @@
"name": "ramp-client",
"$schema": "../../node_modules/nx/schemas/project-schema.json",
"projectType": "application",
"sourceRoot": "apps/ramp-client/src",
"prefix": "ramp-client",
"sourceRoot": "apps/ramp-client/src",
"tags": ["app:ramp-client"],
"targets": {
"build": {
"executor": "@angular-devkit/build-angular:browser",
"executor": "@angular-devkit/build-angular:application",
"outputs": ["{options.outputPath}"],
"options": {
"outputPath": "dist/ramp-client/browser",
"allowedCommonJsDependencies": [
"swagger-ui"
],
"outputPath": "dist/ramp-client",
"index": "apps/ramp-client/src/index.html",
"main": "apps/ramp-client/src/main.ts",
"browser": "apps/ramp-client/src/main.ts",
"polyfills": ["zone.js"],
"tsConfig": "apps/ramp-client/tsconfig.app.json",
"inlineStyleLanguage": "scss",
Expand All @@ -36,20 +40,28 @@
"node_modules/swagger-ui/dist/swagger-ui.css",
"apps/ramp-client/src/styles.scss"
],
"scripts": []
"scripts": [],
"server": "apps/ramp-client/src/main.server.ts",
"prerender": {
"discoverRoutes": false,
"routesFile": "./apps/ramp-client/routes.txt"
},
"ssr": {
"entry": "apps/ramp-client/server.ts"
}
},
"configurations": {
"production": {
"budgets": [
{
"type": "initial",
"maximumWarning": "500kb",
"maximumError": "1000mb"
"maximumWarning": "5000kb",
"maximumError": "10000mb"
},
{
"type": "anyComponentStyle",
"maximumWarning": "2kb",
"maximumError": "500kb"
"maximumWarning": "2000kb",
"maximumError": "5000kb"
}
],
"fileReplacements": [
Expand All @@ -58,15 +70,20 @@
"with": "apps/ramp-client/src/environments/environment.prod.ts"
}
],
"outputHashing": "all"
"outputHashing": "all",
"optimization": {
"scripts": true,
"styles": {
"minify": true,
"inlineCritical": true
},
"fonts": false
}
},
"development": {
"buildOptimizer": false,
"optimization": false,
"vendorChunk": true,
"extractLicenses": false,
"sourceMap": true,
"namedChunks": true
"sourceMap": true
}
},
"defaultConfiguration": "production"
Expand All @@ -75,31 +92,25 @@
"executor": "@angular-devkit/build-angular:dev-server",
"configurations": {
"production": {
"browserTarget": "ramp-client:build:production"
"buildTarget": "ramp-client:build:production"
},
"development": {
"browserTarget": "ramp-client:build:development"
"buildTarget": "ramp-client:build:development"
}
},
"defaultConfiguration": "development"
},
"extract-i18n": {
"executor": "@angular-devkit/build-angular:extract-i18n",
"options": {
"browserTarget": "ramp-client:build"
"buildTarget": "ramp-client:build"
}
},
"lint": {
"executor": "@nrwl/linter:eslint",
"options": {
"lintFilePatterns": [
"apps/ramp-client/src/**/*.ts",
"apps/ramp-client/src/**/*.html"
]
}
"executor": "@nx/eslint:lint"
},
"test": {
"executor": "@nrwl/jest:jest",
"executor": "@nx/jest:jest",
"outputs": ["{workspaceRoot}/coverage/apps/ramp-client"],
"options": {
"jestConfig": "apps/ramp-client/jest.config.ts",
Expand Down Expand Up @@ -128,9 +139,11 @@
]
},
"development": {
"buildOptimizer": false,
"optimization": false,
"sourceMap": true,
"extractLicenses": false
"extractLicenses": false,
"vendorChunk": true
}
},
"defaultConfiguration": "production",
Expand All @@ -150,7 +163,7 @@
}
},
"serve-ssr": {
"executor": "@nguniversal/builders:ssr-dev-server",
"executor": "@angular-devkit/build-angular:ssr-dev-server",
"configurations": {
"development": {
"browserTarget": "ramp-client:build:development",
Expand All @@ -164,10 +177,10 @@
"defaultConfiguration": "development"
},
"prerender": {
"executor": "@nguniversal/builders:prerender",
"executor": "@angular-devkit/build-angular:prerender",
"options": {
"guessRoutes": false,
"routesFile": "./apps/ramp-client/routes.txt"
"routesFile": "./apps/ramp-client/routes.txt",
"discoverRoutes": false
},
"configurations": {
"production": {
Expand All @@ -181,6 +194,5 @@
},
"defaultConfiguration": "production"
}
},
"tags": ["app:ramp-client"]
}
}
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