Merge pull request #37 from ncats/development

Development
ncats · Jun 21, 2021 · 07d9161 · 07d9161
2 parents 33c91e5 + ea1e4aa
commit 07d9161
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Showing 136 changed files with 612 additions and 13,310 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@
 .history/*
 
 .DS_Store
+.profraw
 notebooks
 notebooks/
 env

diff --git a/Dockerfile-ncats b/Dockerfile-ncats
@@ -0,0 +1,30 @@
+FROM node:12 AS build
+
+WORKDIR /opt/adme
+
+COPY client ./
+
+RUN npm install && npm install -g @angular/cli
+
+# parameter for adme.ncats subdomain
+RUN ng build --configuration production --deploy-url=/models/client/ --base-href=/models
+
+FROM continuumio/miniconda:4.7.12
+
+WORKDIR /opt/adme
+
+COPY server ./
+
+RUN conda env create -f environment.yml
+
+ENV PATH /opt/conda/envs/ncats-adme/bin:$PATH
+
+RUN chmod +x startup.sh
+
+# clean existing client folder
+RUN rm -rf client
+COPY --from=build /opt/adme/dist/client client
+
+CMD /bin/bash startup.sh
+
+EXPOSE 5000
diff --git a/Dockerfile-opendata b/Dockerfile-opendata
@@ -0,0 +1,30 @@
+FROM node:12 AS build
+
+WORKDIR /opt/adme
+
+COPY client ./
+
+RUN npm install && npm install -g @angular/cli
+
+# build parameter for opendata subdomain
+RUN ng build --configuration production --deploy-url=/adme/client/ --base-href=/adme
+
+FROM continuumio/miniconda:4.7.12
+
+WORKDIR /opt/adme
+
+COPY server ./
+
+RUN conda env create -f environment.yml
+
+ENV PATH /opt/conda/envs/ncats-adme/bin:$PATH
+
+RUN chmod +x startup.sh
+
+# clean existing client folder
+RUN rm -rf client
+COPY --from=build /opt/adme/dist/client client
+
+CMD /bin/bash startup.sh
+
+EXPOSE 5000
diff --git a/Jenkinsfile-ncats b/Jenkinsfile-ncats
@@ -0,0 +1,63 @@
+pipeline {
+    options {
+        timestamps()
+        disableConcurrentBuilds()
+    }
+    parameters {
+        string(name: 'BUILD_VERSION', defaultValue: '', description: 'The build version to deploy (optional)')
+    }
+    agent {
+        label 'ncatsldvifx01'
+    }
+    triggers {
+        pollSCM('H/5 * * * *')
+    }
+    stages {
+        stage('Build Version') {
+            when {
+                expression {
+                    return !params.BUILD_VERSION
+                }
+            }
+            steps{
+                script {
+                    BUILD_VERSION_GENERATED = VersionNumber(
+                        versionNumberString: 'v${BUILD_YEAR, XX}.${BUILD_MONTH, XX}${BUILD_DAY, XX}.${BUILDS_TODAY}',
+                        projectStartDate:    '1970-01-01',
+                        skipFailedBuilds:    true)
+                    currentBuild.displayName = BUILD_VERSION_GENERATED
+                    env.BUILD_VERSION = BUILD_VERSION_GENERATED
+                    env.BUILD = 'true'
+                }
+            }
+        }
+        stage('Build') {
+            when {
+                expression {
+                    // Skip build when a specific version is provided
+                    return !params.BUILD_VERSION
+                }
+            }
+            steps {
+                sshagent (credentials: ['871f96b5-9d34-449d-b6c3-3a04bbd4c0e4']) {
+                    sh 'git submodule update --init --recursive'
+                    withEnv([
+                        "BUILD_VERSION=" + (params.BUILD_VERSION ?: env.BUILD_VERSION)
+                    ]) {
+                        script {
+                            // build and push for ncats adme image
+                            docker.withRegistry("https://registry.ncats.nih.gov:5000", "564b9230-c7e3-482d-b004-8e79e5e9720a") {
+                                def image = docker.build(
+                                    "ncats-adme:${env.BUILD_VERSION}", 
+                                    "-f Dockerfile-ncats --no-cache ."
+                                )
+                                // Push the image to the registry
+                                image.push("${env.BUILD_VERSION}")
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/server/Jenkinsfile → Jenkinsfile-opendata b/server/Jenkinsfile → Jenkinsfile-opendata
@@ -1,7 +1,6 @@
 pipeline {
     options {
         timestamps()
-        skipDefaultCheckout true
         disableConcurrentBuilds()
     }
     parameters {
@@ -36,28 +35,7 @@ pipeline {
                 }
             }
         }
-        stage('Prepare') {
-            when {
-                expression {
-                    // Skip build when a specific version is provided
-                    return !params.BUILD_VERSION
-                }
-            }
-            steps {
-                sshagent (credentials: ['871f96b5-9d34-449d-b6c3-3a04bbd4c0e4']) {
-                    checkout scm
-                    sh 'git submodule update --init --recursive'
-                    // milestone(1)
-                }
-            }
-        }
         stage('Build') {
-            agent {
-                node { 
-                    label 'ncatsldvifx01'
-                    customWorkspace "${env.WORKSPACE}/server"
-                }
-            }
             when {
                 expression {
                     // Skip build when a specific version is provided
@@ -66,16 +44,16 @@ pipeline {
             }
             steps {
                 sshagent (credentials: ['871f96b5-9d34-449d-b6c3-3a04bbd4c0e4']) {
+                    sh 'git submodule update --init --recursive'
                     withEnv([
                         "IMAGE_NAME=adme",
                         "BUILD_VERSION=" + (params.BUILD_VERSION ?: env.BUILD_VERSION)
                     ]) {
                         script {
-                            // See: https://jenkins.io/doc/book/pipeline/docker/#building-containers
+                            // build and push for opendata adme image
                             docker.withRegistry("https://registry.ncats.nih.gov:5000", "564b9230-c7e3-482d-b004-8e79e5e9720a") {
                                 def image = docker.build(
-                                    "${env.IMAGE_NAME}:${env.BUILD_VERSION}",
-                                    "--no-cache ."
+                                    "${env.IMAGE_NAME}:${env.BUILD_VERSION}", "-f Dockerfile-opendata --no-cache ."
                                 )
                                 // Push the image to the registry
                                 image.push("${env.BUILD_VERSION}")
@@ -87,19 +65,16 @@ pipeline {
         }
         stage('deploy docker') {
             agent {
-               node { label 'ncatsldvifx01'}
+                node { label 'ncatsldvifx01'}
             }
             steps {
                 configFileProvider([
                    configFile(fileId: 'adme-dev-compose', targetLocation: 'docker-compose.yml'),
                    configFile(fileId: 'config.json', targetLocation: 'config.json') 
                 ]) {
-                   sh  """  
-                       chmod 755 config.json
-                   """
-                   script {
+                    script {
                         def docker = new org.labshare.Docker()
-                        docker.deployDockerUI()
+                        docker.deployDockerAPI()
                     }
                 }
             }

diff --git a/client/angular.json b/client/angular.json
@@ -61,33 +61,6 @@
                 }
               ]
             },
-            "adme": {
-              "fileReplacements": [
-                {
-                  "replace": "src/environments/environment.ts",
-                  "with": "src/environments/environment.adme.prod.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": "10kb"
-                }
-              ]
-            },
             "dev": {
               "fileReplacements": [
                 {

diff --git a/client/package.json b/client/package.json
@@ -5,8 +5,8 @@
     "ng": "ng",
     "start:dev": "ng serve --configuration=dev",
     "build": "ng build",
-    "build:embedded:adme": "ng build --configuration=adme --deploy-url=/adme/client/ --base-href=/adme/ && rimraf ../server/client && cpx \"dist/client/**/*\" ../server/client -u",
-    "build:embedded": "ng build --prod --deploy-url=/client/ && rimraf ../server/client && cpx \"dist/client/**/*\" ../server/client -u",
+    "build:embedded:adme": "ng build --deploy-url=/adme/client/ --base-href=/adme/ && rimraf ../server/client && cpx \"dist/client/**/*\" ../server/client -u",
+    "build:embedded": "ng build --prod --deploy-url=/client/ --base-href=/ && rimraf ../server/client && cpx \"dist/client/**/*\" ../server/client -u",
     "test": "ng test",
     "lint": "ng lint",
     "e2e": "ng e2e"

diff --git a/client/src/app/app.component.html b/client/src/app/app.component.html
@@ -6,7 +6,8 @@
     <a class="nav-item" [matMenuTriggerFor]="navMenu" >Models</a>
     <mat-menu #navMenu="matMenu">
       <button mat-menu-item routerLink="/models/rlm">RLM</button>
-      <button mat-menu-item routerLink="/models/pampa">PAMPA</button>
+      <button mat-menu-item routerLink="/models/pampa_ph74">PAMPA pH 7.4</button>
+      <button mat-menu-item routerLink="/models/pampa_ph5">PAMPA pH 5.0</button>
       <button mat-menu-item routerLink="/models/solubility">Solubility</button>
       <button mat-menu-item routerLink="/models/cyp450">CYP450</button>
     </mat-menu>

diff --git a/client/src/app/app.component.ts b/client/src/app/app.component.ts
@@ -3,9 +3,10 @@ import { MatIconRegistry } from '@angular/material/icon';
 import { DomSanitizer } from '@angular/platform-browser';
 import { ResolveEnd, Router, RouterEvent } from '@angular/router';
 import { Subscription } from 'rxjs';
-import { environment } from 'src/environments/environment';
 import { GoogleAnalyticsService } from './google-analytics/google-analytics.service';
 import { DOCUMENT } from '@angular/common';
+import { APP_BASE_HREF } from '@angular/common';
+import { DEPLOY_URL } from './utilities/deploy-url';
 
 @Component({
   selector: 'adme-root',
@@ -20,14 +21,15 @@ export class AppComponent implements OnInit, OnDestroy {
     private router: Router,
     private gaService: GoogleAnalyticsService,
     // tslint:disable-next-line:variable-name
-    @Inject(DOCUMENT) private _document: HTMLDocument
+    @Inject(DOCUMENT) private _document: HTMLDocument,
+    @Inject(DEPLOY_URL) private deployUrl: string
   ) {
     iconRegistry.addSvgIcon(
       'cancel',
-      sanitizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/icons/cancel-24px.svg`));
+      sanitizer.bypassSecurityTrustResourceUrl(`${deployUrl}assets/icons/cancel-24px.svg`));
   }
   ngOnInit() {
-    this._document.getElementById('appFavicon').setAttribute('href', `${environment.baseHref}assets/icons/favicon.ico`);
+    this._document.getElementById('appFavicon').setAttribute('href', `${this.deployUrl}assets/icons/favicon.ico`);
     this.routerSubscription = this.router.events.subscribe((event: RouterEvent) => {
       if (event instanceof ResolveEnd) {
         this.gaService.sendPageView(event.state.root.firstChild.data.pageTitle, event.state.url);

diff --git a/client/src/app/app.module.ts b/client/src/app/app.module.ts
@@ -36,6 +36,7 @@ import { ConfigService } from './config/config.service';
 import { configServiceFactory } from './config/config.factory';
 import { TrackLinkEventDirective } from './google-analytics/track-link-event/track-link-event.directive';
 import { MatMenuModule } from '@angular/material/menu';
+import { APP_BASE_HREF, PlatformLocation } from '@angular/common';
 
 @NgModule({
   declarations: [
@@ -88,6 +89,11 @@ import { MatMenuModule } from '@angular/material/menu';
         useFactory: configServiceFactory,
         deps: [ConfigService],
         multi: true
+    },
+    {
+      provide: APP_BASE_HREF,
+      useFactory: (s: PlatformLocation) => s.getBaseHrefFromDOM(),
+      deps: [PlatformLocation]
     }
   ],
   bootstrap: [AppComponent]

diff --git a/client/src/app/config/config.service.ts b/client/src/app/config/config.service.ts
@@ -1,7 +1,9 @@
-import { Injectable } from '@angular/core';
+import { Injectable, Inject } from '@angular/core';
 import { HttpClient } from '@angular/common/http';
 import { Config } from './config.model';
 import { environment } from 'src/environments/environment';
+import { APP_BASE_HREF } from '@angular/common';
+import { DEPLOY_URL } from '../utilities/deploy-url';
 
 @Injectable({
     providedIn: 'root'
@@ -10,15 +12,18 @@ export class ConfigService {
     // tslint:disable-next-line:variable-name
     private _configData: Config;
 
-    constructor(private http: HttpClient) { }
+    constructor(
+        private http: HttpClient,
+        @Inject(APP_BASE_HREF) public baseHref: string,
+        @Inject(DEPLOY_URL) private deployUrl: string
+    ) { }
 
     // This is the method you want to call at bootstrap
     // Important: It should return a Promise
     load(): Promise<any> {
         this._configData = null;
-
         const configFilePath = environment.configFileLocation ?
-            environment.configFileLocation : `${environment.baseHref || '/'}assets/data/config.json`;
+            environment.configFileLocation : `${this.deployUrl || '/'}assets/data/config.json`;
 
         return this.http
             .get(configFilePath)

diff --git a/client/src/app/contact/contact.component.ts b/client/src/app/contact/contact.component.ts
@@ -1,6 +1,6 @@
-import { Component, OnInit } from '@angular/core';
+import { Component, OnInit, Inject } from '@angular/core';
 import { DomSanitizer, SafeResourceUrl } from '@angular/platform-browser';
-import { environment } from 'src/environments/environment';
+import { DEPLOY_URL } from '../utilities/deploy-url';
 
 @Component({
   selector: 'adme-contact',
@@ -21,20 +21,21 @@ export class ContactComponent implements OnInit {
   epamImgSrc: SafeResourceUrl;
 
   constructor(
-    private domSanatizer: DomSanitizer
+    private domSanatizer: DomSanitizer,
+    @Inject(DEPLOY_URL) public deployUrl: string
   ) {
-    this.vishalImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/siramshettyv2.jpg`);
-    this.pranavImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/shahpa2.png`);
-    this.jorgeImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/neyraj2.jpg`);
-    this.jordanImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/williamsjos.jpg`);
-    this.noelImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/southalln.jpg`);
-    this.trungImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/nguyenda.png`);
-    this.xinImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/profile_images/xux7.jpg`);
+    this.vishalImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/siramshettyv2.jpg`);
+    this.pranavImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/shahpa2.png`);
+    this.jorgeImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/neyraj2.jpg`);
+    this.jordanImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/williamsjos.jpg`);
+    this.noelImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/southalln.jpg`);
+    this.trungImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/nguyenda.png`);
+    this.xinImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/xux7.jpg`);
 
-    this.rdkitImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/images/rdkit.png`);
-    this.pythonImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/images/python.png`);
-    this.angularImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/images/angular.png`);
-    this.epamImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${environment.baseHref}assets/images/epam_ketcher.png`);
+    this.rdkitImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/rdkit.png`);
+    this.pythonImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/python.png`);
+    this.angularImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/angular.png`);
+    this.epamImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/epam_ketcher.png`);
   }
 
   ngOnInit(): void {