Merge pull request #22 from sartography/dev

Dev

.travis.yml

@@ -14,6 +14,15 @@ services:
   - docker
   - xvfb
 
+before_install:
+  - |
+    branches=('dev' 'testing' 'demo' 'training' 'staging')
+    if [[ " ${arr[@]} " =~ " ${TRAVIS_BRANCH} " ]]; then
+      export E2E_TAG="$TRAVIS_BRANCH"
+    else
+      export E2E_TAG="latest"
+    fi
+
 install:
   - npm install
 
@@ -29,7 +38,7 @@ deploy:
   skip_cleanup: true
   on:
     all_branches: true
-    condition: $TRAVIS_BRANCH =~ ^(testing|staging|master)$
+    condition: $TRAVIS_BRANCH =~ ^(dev|testing|demo|training|staging|master|rrt\/.*)$
 
 notifications:
   email:

Dockerfile

@@ -17,9 +17,13 @@ RUN npm install && \
 FROM nginx
 COPY --from=builder /crc-bpmn/dist/* /usr/share/nginx/html/
 COPY --from=builder /crc-bpmn/nginx.conf /etc/nginx/conf.d/default.conf
+
+# Script for substituting environment variables
 COPY ./docker/substitute-env-variables.sh ./entrypoint.sh
 RUN chmod +x ./entrypoint.sh
-ENTRYPOINT ["./entrypoint.sh", "/usr/share/nginx/html/index.html"]
+
+# Substitute environment variables in nginx configuration and index.html
+ENTRYPOINT ["./entrypoint.sh", "/usr/share/nginx/html/index.html,/etc/nginx/conf.d/default.conf"]
 
 ### STAGE 3: Profit! ###
 CMD ["nginx", "-g", "daemon off;"]

deploy.sh

@@ -4,23 +4,45 @@
 pip install --user awscli;
 export PATH=$PATH:$HOME/.local/bin;
 
+function branch_to_tag () {
+  if [ "$1" == "latest" ]; then echo "production"; else echo "$1" ; fi
+}
+
+function branch_to_deploy_group() {
+  if [[ $1 =~ ^(rrt\/.*)$ ]]; then echo "rrt"; else echo "crconnect" ; fi
+}
+
+function branch_to_deploy_stage () {
+  if [ "$1" == "master" ]; then echo "production"; else echo "$1" ; fi
+}
+
+REPO="sartography/cr-connect-bpmn"
+TAG=$(branch_to_tag "$TRAVIS_BRANCH")
+
+DEPLOY_APP="bpmn"
+DEPLOY_GROUP=$(branch_to_deploy_group "$TRAVIS_BRANCH")
+DEPLOY_STAGE=$(branch_to_deploy_stage "$TRAVIS_BRANCH")
+
+if [ "$DEPLOY_GROUP" == "rrt" ]; then
+  IFS='/' read -ra ARR <<< "$TRAVIS_BRANCH"  # Split branch on '/' character
+  TAG=$(branch_to_tag "rrt_${ARR[1]}")
+  DEPLOY_STAGE=$(branch_to_deploy_stage "${ARR[1]}")
+fi
+
+DEPLOY_PATH="$DEPLOY_GROUP/$DEPLOY_STAGE/$DEPLOY_APP"
+echo "REPO = $REPO"
+echo "TAG = $TAG"
+echo "DEPLOY_PATH = $DEPLOY_PATH"
+
 # Build and push Docker image to Docker Hub
 echo "$DOCKER_TOKEN" | docker login -u "$DOCKER_USERNAME" --password-stdin || exit 1
-REPO="sartography/cr-connect-bpmn"
-TAG=$(if [ "$TRAVIS_BRANCH" == "master" ]; then echo "latest"; else echo "$TRAVIS_BRANCH" ; fi)
-COMMIT=${TRAVIS_COMMIT::8}
-
-docker build -f Dockerfile -t "$REPO:$COMMIT" . || exit 1
-docker tag "$REPO:$COMMIT" "$REPO:$TAG" || exit 1
-docker tag "$REPO:$COMMIT" "$REPO:travis-$TRAVIS_BUILD_NUMBER" || exit 1
+docker build -f Dockerfile -t "$REPO:$TAG" . || exit 1
 docker push "$REPO" || exit 1
 
 # Wait for Docker Hub
 echo "Publishing to Docker Hub..."
 sleep 30
 
-# Notify DC/OS that Docker image has been updated
+# Notify UVA DCOS that Docker image has been updated
 echo "Refreshing DC/OS..."
-STAGE=$(if [ "$TRAVIS_BRANCH" == "master" ]; then echo "production"; else echo "$TRAVIS_BRANCH" ; fi)
-echo "STAGE = $STAGE"
-aws sqs send-message --region "$AWS_DEFAULT_REGION" --queue-url "$AWS_SQS_URL" --message-body "crconnect/$STAGE/bpmn" || exit 1
+aws sqs send-message --region "$AWS_DEFAULT_REGION" --queue-url "$AWS_SQS_URL" --message-body "$DEPLOY_PATH" || exit 1

docker/docker-compose.yml

@@ -20,19 +20,20 @@ services:
     container_name: backend
     depends_on:
        - db
-    image: sartography/cr-connect-workflow
+    image: sartography/cr-connect-workflow:$E2E_TAG
     volumes:
       - ./flask-config/config.py:/crc-workflow/instance/config.py
     environment:
       - FLASK_APP=./crc/__init__.py
       - RESET_DB=true
+      - LDAP_URL=ldap
     ports:
       - "5000:5000"
     command: ./wait-for-it.sh db:5432 -t 0 -- ./docker_run.sh
 
   pb:
     container_name: pb
-    image: sartography/protocol-builder-mock
+    image: sartography/protocol-builder-mock:$E2E_TAG
     volumes:
       - ./flask-config/config_pb.py:/protocol-builder-mock/instance/config.py
     environment:
@@ -41,3 +42,8 @@ services:
       - "5001:5001"
     command: ./wait-for-it.sh db:5432 -t 0 -- ./docker_run.sh
 
+  ldap:
+    container_name: ldap
+    image: tuxmonteiro/ldap-mock
+    ports:
+      - "3890"

docker/flask-config/config.py

@@ -2,8 +2,13 @@ import os
 basedir = os.path.abspath(os.path.dirname(__file__))
 
 NAME = "CR Connect Workflow"
-CORS_ENABLED = False
 DEVELOPMENT = True
 SQLALCHEMY_DATABASE_URI = "postgresql://crc_user:crc_pass@db:5432/crc_dev"
 
+# %s/%i placeholders expected for uva_id and study_id in various calls.
+PB_USER_STUDIES_URL = "http://pb:5001/pb/user_studies?uva_id=%s"
+PB_INVESTIGATORS_URL = "http://pb:5001/pb/investigators?studyid=%i"
+PB_REQUIRED_DOCS_URL = "http://pb:5001/pb/required_docs?studyid=%i"
+PB_STUDY_DETAILS_URL = "http://pb:5001/pb/study?studyid=%i"
+
 print('\n\n*** USING INSTANCE CONFIG ***\n\n')

docker/substitute-env-variables.sh

@@ -1,18 +1,25 @@
 #!/bin/bash
 
-# The first parameter is the path to the file which should be substituted
+echo 'Substituting environment variables...'
+
+# The first parameter is a comma-delimited list of paths to files which should be substituted
 if [[ -z $1 ]]; then
-  echo 'ERROR: No target file given.'
+  echo 'ERROR: No target files given.'
   exit 1
 fi
 
-# Replace strings in the given file that have the format ${ENV_VAR}
-envsubst '\$PRODUCTION \$API_URL \$IRB_URL' < "$1" > "$1".tmp && mv "$1".tmp "$1"
+env_list='\$PRODUCTION \$API_URL \$IRB_URL \$HOME_ROUTE \$PORT0'
+for file_path in $(echo $1 | sed "s/,/ /g")
+do
+  echo "replacing $env_list in $file_path"
 
-# Set DEBUG=true in order to log the replaced file
-if [ "$DEBUG" = true ] ; then
-  exec cat $1
-fi
+  # Replace strings in the given file(s) in env_list
+  envsubst "$env_list" < "$file_path" > "$file_path".tmp && mv "$file_path".tmp "$file_path"
+
+  echo '...'
+done
+
+echo 'Finished substituting environment variables.'
 
 # Execute all other commands with parameters
 exec "${@:2}"

e2e/src/app.e2e-spec.ts

@@ -13,7 +13,7 @@ describe('workspace-project App', () => {
   });
 
   it('should click sign-in and navigate to home screen', () => {
-    page.clickAndExpectRoute('#sign_in', '/');
+    page.clickAndExpectRoute('#sign_in', '/home');
     expect(page.getElements('app-workflow-spec-list').count()).toBeGreaterThan(0);
     expect(page.getElements('app-file-list').count()).toBeGreaterThan(0);
   });

nginx.conf

@@ -1,5 +1,5 @@
 server {
-  listen 80;
+  listen $PORT0;
 
   location / {
     root /usr/share/nginx/html;

package-lock.json

@@ -12291,9 +12291,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sartography-workflow-lib": {
-      "version": "0.0.147",
-      "resolved": "https://registry.npmjs.org/sartography-workflow-lib/-/sartography-workflow-lib-0.0.147.tgz",
-      "integrity": "sha512-CaueuOhiZgYmp4NjPsKt9zad3yAqzT/ibnIqC+sIQHt99UKmSzsaFuuDN2l5ux4E/Xe4D33Ew6djXtrgcGROTw=="
+      "version": "0.0.164",
+      "resolved": "https://registry.npmjs.org/sartography-workflow-lib/-/sartography-workflow-lib-0.0.164.tgz",
+      "integrity": "sha512-0sbIR8gkXfPOJOJzHQyzzo7mIS9W8bLiQW/pzp/RWATj0j+MGn9z6aPKQBs6PKUP0KMzAOXfXywkR3e3aPJSoA=="
     },
     "sass": {
       "version": "1.23.3",

package.json

@@ -13,11 +13,14 @@
     "lint": "ng lint",
     "e2e": "./node_modules/protractor/bin/webdriver-manager update && ng e2e",
     "e2e:with-wf": "npm run e2e-wf && ng e2e && npm run e2e-wf:stop && npm run e2e-wf:clean",
-    "e2e-wf:stop": "docker stop db || true && docker stop backend || true",
+    "e2e-wf:stop": "docker stop db || true && docker stop backend || true && docker stop pb || true",
     "e2e-wf:clean": "docker system prune -f && cd docker && docker-compose rm -f -v -s && cd ..",
     "e2e-wf:build": "cd docker && docker-compose pull && docker-compose build --no-cache && cd ..",
     "e2e-wf:start": "cd docker && docker-compose up -d && cd ..",
-    "e2e-wf": "npm run e2e-wf:stop && npm run e2e-wf:clean && npm run e2e-wf:build && npm run e2e-wf:start",
+    "e2e-wf:db-upgrade": "docker exec -it backend pipenv run flask db upgrade",
+    "e2e-wf:db-setup": "docker exec -it backend pipenv run flask load-example-data",
+    "e2e-wf:pb-setup": "docker exec -it pb pipenv run flask db upgrade",
+    "e2e-wf": "npm run e2e-wf:stop && npm run e2e-wf:clean && npm run e2e-wf:build && npm run e2e-wf:start && npm run e2e-wf:db-upgrade && npm run e2e-wf:db-setup && npm run e2e-wf:pb-setup",
     "ci": "npm run lint && npm run test:coverage && npm run e2e:with-wf && sonar-scanner"
   },
   "private": true,
@@ -49,7 +52,7 @@
     "ngx-file-drop": "^8.0.8",
     "ngx-markdown": "^9.0.0",
     "rxjs": "~6.5.4",
-    "sartography-workflow-lib": "^0.0.147",
+    "sartography-workflow-lib": "^0.0.164",
     "tslib": "^1.11.1",
     "uuid": "^7.0.2",
     "zone.js": "^0.10.3"

src/app/app-routing.module.ts

@@ -1,6 +1,7 @@
 import {NgModule} from '@angular/core';
 import {RouterModule, Routes} from '@angular/router';
 import {SessionRedirectComponent} from 'sartography-workflow-lib';
+import {environment} from '../environments/environment.runtime';
 import {HomeComponent} from './home/home.component';
 import {ModelerComponent} from './modeler/modeler.component';
 import {SignInComponent} from './sign-in/sign-in.component';
@@ -10,6 +11,11 @@ import {SignOutComponent} from './sign-out/sign-out.component';
 const routes: Routes = [
   {
     path: '',
+    pathMatch: 'full',
+    redirectTo: environment.homeRoute,
+  },
+  {
+    path: 'home',
     component: HomeComponent
   },
   {

src/app/app.component.html

@@ -1,5 +1,5 @@
 <div class="mat-typography">
-  <app-navbar *ngIf="isSignedIn()" class="mat-elevation-z6" id="globalHeader"></app-navbar>
+  <app-navbar *ngIf="isSignedIn" class="mat-elevation-z6" id="globalHeader"></app-navbar>
   <router-outlet></router-outlet>
   <app-footer></app-footer>
 </div>

src/app/app.component.spec.ts

@@ -1,8 +1,10 @@
+import {HttpClient} from '@angular/common/http';
+import {HttpClientTestingModule} from '@angular/common/http/testing';
 import {Component} from '@angular/core';
 import {async, ComponentFixture, TestBed} from '@angular/core/testing';
 import {BrowserAnimationsModule} from '@angular/platform-browser/animations';
 import {RouterTestingModule} from '@angular/router/testing';
-import {MockEnvironment} from 'sartography-workflow-lib';
+import {ApiService, MockEnvironment} from 'sartography-workflow-lib';
 import {AppComponent} from './app.component';
 
 
@@ -32,10 +34,13 @@ describe('AppComponent', () => {
         MockFooterComponent
       ],
       imports: [
+        HttpClientTestingModule,
         BrowserAnimationsModule,
         RouterTestingModule,
       ],
       providers: [
+        HttpClient,
+        ApiService,
         {provide: 'APP_ENVIRONMENT', useClass: MockEnvironment},
       ],
     })

src/app/app.component.ts

@@ -1,5 +1,5 @@
 import {Component} from '@angular/core';
-import {isSignedIn} from 'sartography-workflow-lib';
+import {ApiService} from 'sartography-workflow-lib';
 
 @Component({
   selector: 'app-root',
@@ -8,5 +8,11 @@ import {isSignedIn} from 'sartography-workflow-lib';
 })
 export class AppComponent {
   title = 'CR Connect Configuration';
-  isSignedIn = isSignedIn;
+
+  constructor(private apiService: ApiService) {
+  }
+
+  get isSignedIn() {
+    return this.apiService.isSignedIn();
+  }
 }

src/app/app.module.ts

@@ -52,6 +52,7 @@ import {WorkflowSpecListComponent} from './workflow-spec-list/workflow-spec-list
 
 @Injectable()
 export class ThisEnvironment implements AppEnvironment {
+  homeRoute = environment.homeRoute;
   production = environment.production;
   api = environment.api;
   irbUrl = environment.irbUrl;

src/app/diagram/diagram.component.ts

@@ -31,6 +31,7 @@ export class DiagramComponent implements ControlValueAccessor, AfterViewInit {
   private diagramType: FileType;
   private modeler: BpmnModeler | DmnModeler;
   private xml = '';
+  private svg;
   private disabled = false;
 
   // Hack so we can spy on this function
@@ -46,12 +47,16 @@ export class DiagramComponent implements ControlValueAccessor, AfterViewInit {
     return this.xml;
   }
 
+  get svgValue(): string {
+    return this.svg;
+  }
+
   ngAfterViewInit() {
     this.initializeModeler(this.diagramType);
     this.openDiagram(this.xml);
   }
 
-  onChange(value: any) {
+  onChange(newValue: string, svgValue: string) {
   }
 
   onTouched() {
@@ -74,12 +79,12 @@ export class DiagramComponent implements ControlValueAccessor, AfterViewInit {
       this.openDiagram(value);
     }
     this.xml = value;
-    this.onChange(this.xml);
+    this.onChange(this.xml, this.svg);
   }
 
   // Allows Angular to register a function to call when the model changes.
   // Save the function as a property to call later here.
-  registerOnChange(fn: (newXmlValue: string) => void): void {
+  registerOnChange(fn: (newXmlValue: string, newSvgValue: string) => void): void {
     this.onChange = fn;
   }
 
@@ -118,9 +123,12 @@ export class DiagramComponent implements ControlValueAccessor, AfterViewInit {
   }
 
   saveDiagram() {
-    this.modeler.saveXML({format: true}, (err, xml) => {
-      this.xml = xml;
-      this.writeValue(xml);
+    this.modeler.saveSVG((svgErr, svg) => {
+      this.svg = svg;
+      this.modeler.saveXML({format: true}, (xmlErr, xml) => {
+        this.xml = xml;
+        this.writeValue(xml);
+      });
     });
   }
 

src/app/home/home.component.html

@@ -1,2 +1,2 @@
-<app-sign-in *ngIf="!isSignedIn()"></app-sign-in>
-<app-workflow-spec-list *ngIf="isSignedIn()"></app-workflow-spec-list>
+<app-sign-in *ngIf="!isSignedIn"></app-sign-in>
+<app-workflow-spec-list *ngIf="isSignedIn"></app-workflow-spec-list>

src/app/home/home.component.spec.ts

@@ -1,6 +1,8 @@
-import {Component, NO_ERRORS_SCHEMA} from '@angular/core';
+import {HttpClient} from '@angular/common/http';
+import {HttpClientTestingModule} from '@angular/common/http/testing';
+import {Component} from '@angular/core';
 import {async, ComponentFixture, TestBed} from '@angular/core/testing';
-import {MockEnvironment} from 'sartography-workflow-lib';
+import {ApiService, MockEnvironment} from 'sartography-workflow-lib';
 
 import {HomeComponent} from './home.component';
 
@@ -9,13 +11,15 @@ import {HomeComponent} from './home.component';
   selector: 'app-sign-in',
   template: ''
 })
-class MockSignInComponent {}
+class MockSignInComponent {
+}
 
 @Component({
   selector: 'app-workflow-spec-list',
   template: ''
 })
-class MockWorkflowSpecListComponent {}
+class MockWorkflowSpecListComponent {
+}
 
 describe('HomeComponent', () => {
   let component: HomeComponent;
@@ -28,8 +32,16 @@ describe('HomeComponent', () => {
         MockSignInComponent,
         MockWorkflowSpecListComponent,
       ],
+      imports: [
+        HttpClientTestingModule
+      ],
+      providers: [
+        HttpClient,
+        ApiService,
+        {provide: 'APP_ENVIRONMENT', useClass: MockEnvironment},
+      ]
     })
-    .compileComponents();
+      .compileComponents();
   }));
 
   beforeEach(() => {
@@ -43,7 +55,7 @@ describe('HomeComponent', () => {
   });
 
   it('should check signed-in state', () => {
-    const result = component.isSignedIn();
+    const result = component.isSignedIn;
     expect(result).toBeDefined();
     expect(typeof result).toEqual('boolean');
   });

src/app/home/home.component.ts

@@ -1,5 +1,5 @@
 import {Component} from '@angular/core';
-import {isSignedIn} from 'sartography-workflow-lib';
+import {ApiService, isSignedIn} from 'sartography-workflow-lib';
 
 @Component({
   selector: 'app-home',
@@ -7,9 +7,11 @@ import {isSignedIn} from 'sartography-workflow-lib';
   styleUrls: ['./home.component.scss']
 })
 export class HomeComponent {
-  isSignedIn = isSignedIn;
 
-  constructor() {
+  constructor(private apiService: ApiService) {
   }
 
+  get isSignedIn(): boolean {
+    return this.apiService.isSignedIn();
+  }
 }

src/app/modeler/modeler.component.ts

@@ -42,6 +42,7 @@ export class ModelerComponent implements AfterViewInit {
   fileTypes = FileType;
   private xml = '';
   private draftXml = '';
+  private svg = '';
   @ViewChild(DiagramComponent) private diagramComponent: DiagramComponent;
   private diagramType: FileType;
   private workflowSpecId: string;
@@ -67,8 +68,9 @@ export class ModelerComponent implements AfterViewInit {
   }
 
   ngAfterViewInit(): void {
-    this.diagramComponent.registerOnChange((newXmlValue: string) => {
+    this.diagramComponent.registerOnChange((newXmlValue: string, newSvgValue: string) => {
       this.draftXml = newXmlValue;
+      this.svg = newSvgValue;
     });
   }
 
@@ -158,6 +160,7 @@ export class ModelerComponent implements AfterViewInit {
   newDiagram(diagramType?: FileType) {
     this.xml = '';
     this.draftXml = '';
+    this.svg = '';
     this.fileName = '';
     this.diagramFileMeta = undefined;
     this.diagramFile = undefined;
@@ -306,6 +309,11 @@ export class ModelerComponent implements AfterViewInit {
     this.xml = this.draftXml;
     this.diagramFileMeta.file = new File([this.xml], this.diagramFileMeta.name, {type: 'text/xml'});
 
+    if (this.svg && this.svg !== '') {
+      const svgFile = new File([this.svg], this.diagramFileMeta.name, {type: 'text/xml'});
+      // this.api.updateFileData();
+    }
+
     this.api.updateFileData(this.diagramFileMeta).subscribe(newFileMeta => {
       this.diagramFileMeta = newFileMeta;
       this.snackBar.open(`Saved changes to file metadata ${this.diagramFileMeta.name}.`, 'Ok', {duration: 5000});

src/app/navbar/navbar.component.html

@@ -1,4 +1,4 @@
-<nav *ngIf="isSignedIn() && user">
+<nav *ngIf="user">
   <a
     [routerLink]="['/']"
     class="site-title mat-display-1"

src/app/navbar/navbar.component.ts

@@ -16,7 +16,7 @@ interface NavItem {
   templateUrl: './navbar.component.html',
   styleUrls: ['./navbar.component.scss']
 })
-export class NavbarComponent implements OnInit {
+export class NavbarComponent {
   navLinks: NavItem[];
   user: User;
   isSignedIn = isSignedIn;
@@ -28,9 +28,6 @@ export class NavbarComponent implements OnInit {
     this._loadUser();
   }
 
-  ngOnInit() {
-  }
-
   isLinkActive(path: string) {
     return path === this.router.url;
   }

src/app/sign-in/sign-in.component.ts

@@ -57,8 +57,7 @@ export class SignInComponent implements OnInit {
   constructor(
     @Inject('APP_ENVIRONMENT') private environment: AppEnvironment,
     private router: Router,
-    private api: ApiService,
-    private platformLocation: PlatformLocation
+    private api: ApiService
   ) {
   }
 
@@ -72,7 +71,7 @@ export class SignInComponent implements OnInit {
 
     // For testing purposes, create a user to simulate login.
     if (!this.environment.production) {
-      this.model.redirect_url = this.platformLocation.href + 'session';
+      this.model.redirect_url = location.origin + '/session';
       this.api.openSession(this.model);
     } else {
       this.error = new Error('This feature does not work in production.');

src/environments/environment.runtime.ts

@@ -2,8 +2,14 @@ import {AppEnvironment} from 'sartography-workflow-lib';
 
 declare var ENV;
 
+const envHas = (key, temp): boolean => (ENV && (ENV[key] !== null) && (ENV[key] !== undefined) && (ENV[key] !== temp));
+
 export const environment: AppEnvironment = {
-  production: ENV && ENV.production === '$PRODUCTION' ? false : (ENV.production === 'true'),
-  api: ENV && ENV.api === '$API_URL' ? 'http://localhost:5000/v1.0' : ENV.api,
-  irbUrl: ENV && ENV.irbUrl === '$IRB_URL' ? 'http://localhost:5001' : ENV.irbUrl,
+  homeRoute: envHas('homeRoute', '$HOME_ROUTE') ? ENV.homeRoute : 'home',
+  production: envHas('production', '$PRODUCTION') ? (ENV.production === 'true') : false,
+  api: envHas('api', '$API_URL') ? ENV.api : 'http://localhost:5000/v1.0',
+  irbUrl: envHas('irbUrl', '$IRB_URL') ? ENV.irbUrl : 'http://localhost:5001',
 };
+
+
+

src/index.html

@@ -6,6 +6,7 @@
   <base href="/">
   <script>
     const ENV = {
+      homeRoute: '$HOME_ROUTE',
       production: '$PRODUCTION',
       api: '$API_URL',
       irbUrl: '$IRB_URL',