Initial local UI+dsub docker compose

Dockerfile.ui

@@ -0,0 +1,5 @@
+FROM node
+
+WORKDIR /app
+ADD ui/package.json /app/
+RUN npm install

api/jobs.yaml

@@ -40,7 +40,7 @@ paths:
         Query jobs by various filter criteria. Returned jobs are ordered from
         newest to oldest submission time.
       parameters:
-        - name: parameters
+        - name: body
           required: true
           in: body
           schema:

docker-compose.yml

@@ -1,6 +1,16 @@
 version: '2'
 services:
-  jobs:
+  ui:
+    build:
+      context: .
+      dockerfile: Dockerfile.ui
+    command: ["npm", "run-script", "ng", "--", "serve", "--host", "ui"]
+    volumes:
+      - ./ui:/app
+      # Hide this subdirectory from the above volume; just use what's already on
+      # the docker image so we don't need to reinstall node modules every time.
+      - /app/node_modules
+  dsub-server:
     # dsub creates the local provider folder in /tmp/dsub-local which can only
     # be written to by the owner. Unless dsub changes the permissions on this
     # folder the docker container must be 'privileged'
@@ -16,6 +26,7 @@ services:
     command: ["-b", ":8190"]
     environment:
       - PROVIDER_TYPE=local
+      - PATH_PREFIX=/api
       # Avoid writing .pyc files back to the volume. Files generated this way
       # have restricted permissions set which cause errors on subsequent docker
       # builds.
@@ -28,3 +39,13 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock
     ports:
       - 8190:8190
+  jobs-proxy:
+    image: nginx
+    volumes:
+      - ./nginx.conf:/etc/nginx/nginx.conf
+    links:
+      - ui
+      - dsub-server
+    ports:
+      - 4200:4200
+

nginx.conf

@@ -0,0 +1,25 @@
+# nginx proxy over the UI and API job manager servers. For directive
+# documentation, see http://nginx.org/en/docs/dirindex.html
+# Required - just leave the defaults for now.
+events {}
+http {
+        # These host names are available in a docker-compose environment via
+        # docker linking.
+        upstream ui {
+                server ui:4200;
+        }
+        upstream api {
+                server dsub-server:8190;
+        }
+        server {
+              listen 4200;
+              # All API requests have a version prefix. Route everything else to
+              # the UI server.
+              location /api {
+                proxy_pass http://api;
+              }
+              location / {
+                proxy_pass http://ui;
+              }
+        }
+}

servers/dsub/jobs/__main__.py

@@ -7,16 +7,6 @@
 from .encoder import JSONEncoder
 from controllers.dsub_client import DSubClient
 
-app = connexion.App(__name__, specification_dir='./swagger/', swagger_ui=False)
-app.app.json_encoder = JSONEncoder
-app.add_api('swagger.yaml')
-
-# Log to stderr.
-handler = logging.StreamHandler()
-handler.setLevel(logging.INFO)
-app.app.logger.addHandler(handler)
-app.app.logger.setLevel(logging.INFO)
-
 # gunicorn flags are passed via env variables, so we use these as the default
 # values. These arguments will rarely be specified as flags directly, aside from
 # occasional use during local debugging.
@@ -26,6 +16,11 @@
     type=str,
     help='The dsub provider type to use for monitoring jobs',
     default=os.environ.get('PROVIDER_TYPE'))
+parser.add_argument(
+    '--path_prefix',
+    type=str,
+    help='Path prefix, e.g. /api to serve from',
+    default=os.environ.get('PATH_PREFIX'))
 
 if __name__ == '__main__':
     parser.add_argument(
@@ -39,8 +34,18 @@
     # gunicorn.
     args, _ = parser.parse_known_args()
 
+app = connexion.App(__name__, specification_dir='./swagger/', swagger_ui=False)
 app.app.config['PROVIDER_TYPE'] = args.provider_type
 app.app.config['CLIENT'] = DSubClient()
 
+# Log to stderr.
+handler = logging.StreamHandler()
+handler.setLevel(logging.INFO)
+app.app.logger.addHandler(handler)
+app.app.logger.setLevel(logging.INFO)
+
+app.app.json_encoder = JSONEncoder
+app.add_api('swagger.yaml', base_path='/api')
+
 if __name__ == '__main__':
     app.run(host='0.0.0.0', port=args.port)

servers/dsub/jobs/controllers/dsub_client.py

@@ -91,9 +91,14 @@ def query_jobs(self, provider, query):
         # https://github.com/googlegenomics/dsub/issues/67
         # Eventually, the pipelines API and dsub should support this query .
 
+        # TODO(https://github.com/googlegenomics/dsub/issues/69): Move this
+        # logic into dsub.
+        statuses = dstat_params['statuses']
+        if not statuses:
+            statuses = ['*']
         jobs = dstat.dstat_job_producer(
             provider=provider,
-            status_list=dstat_params['statuses'],
+            status_list=statuses,
             create_time=dstat_params['create_time'],
             job_name_list=dstat_params['job_name_list'],
             full_output=True).next()

servers/dsub/jobs/controllers/jobs_controller.py

@@ -47,6 +47,8 @@ def get_job(id):
     provider = _get_provider(project_id)
     job = client().get_job(provider, job_id, task_id)
 
+    # Note: dsub local provider does not yet update 'end-time'
+    # https://github.com/googlegenomics/dsub/issues/67
     return JobMetadataResponse(
         id=id,
         status=job_statuses.dsub_to_api(job.get('status')),
@@ -58,17 +60,20 @@ def get_job(id):
         labels=job.get('labels', {}))
 
 
-def query_jobs():
+def query_jobs(body):
     """
     Query jobs by various filter criteria.
 
+    Args:
+        body (dict): The JSON request body.
+
     Returns:
         QueryJobsResponse: Response containing results from query
     """
     if not connexion.request.is_json:
         raise BadRequest("Request body is not JSON formatted")
 
-    query = QueryJobsRequest.from_dict(connexion.request.get_json())
+    query = QueryJobsRequest.from_dict(body)
     jobs = client().query_jobs(_get_provider(query.parent_id), query)
     results = [_query_result(j) for j in jobs]
     return QueryJobsResponse(results=results)

servers/dsub/jobs/swagger/swagger.yaml

@@ -43,7 +43,7 @@ paths:
       operationId: "query_jobs"
       parameters:
       - in: "body"
-        name: "parameters"
+        name: "body"
         required: true
         schema:
           $ref: "#/definitions/QueryJobsRequest"

ui/src/app/app.module.ts

@@ -4,20 +4,12 @@ import {
   HttpModule, Http, BaseRequestOptions
 } from '@angular/http';
 import {BrowserModule} from '@angular/platform-browser';
-import {MockBackend} from '@angular/http/testing';
 
 import {AppRoutingModule} from './app-routing.module';
 import { AppComponent } from './app.component';
 import {JobMonitorService} from './job-monitor.service';
-import {newDefaultMockJobMonitorService, MockJobMonitorService} from './mock-job-monitor.service';
 import {ListJobsComponent} from './components/list-jobs/component';
 
-export function httpFactory(backend: MockBackend, options: BaseRequestOptions,
-                            service: MockJobMonitorService) {
-  service.subscribe(backend);
-  return new Http(backend, options);
-}
-
 @NgModule({
   imports: [
     AppRoutingModule,
@@ -31,18 +23,6 @@ export function httpFactory(backend: MockBackend, options: BaseRequestOptions,
   ],
   providers: [
     JobMonitorService,
-    MockBackend,
-    BaseRequestOptions,
-    {
-      provide: MockJobMonitorService,
-      useFactory: newDefaultMockJobMonitorService,
-    },
-    // TODO(alahwa): Support communication with real backends.
-    {
-      provide: Http,
-      useFactory: httpFactory,
-      deps: [MockBackend, BaseRequestOptions, MockJobMonitorService],
-    }
   ],
   // This specifies the top-level component, to load first.
   bootstrap: [AppComponent]

ui/src/app/components/list-jobs/component.ts

@@ -17,8 +17,10 @@ export class ListJobsComponent implements OnInit {
     private jobMonitorService: JobMonitorService
   ) {}
   ngOnInit(): void {
-    this.jobMonitorService.listAllJobs()
-      .then(response => this.jobs = response.results);
+    this.route.queryParams.subscribe((params: Params) => {
+      this.jobMonitorService.listAllJobs(params['parentId'])
+        .then(response => this.jobs = response.results);
+    });
   }
 
   toggleSelect(job: JobQueryResult): void {

ui/src/app/job-monitor.service.ts

@@ -9,21 +9,27 @@ import {JobAbortResponse} from './model/JobAbortResponse';
 /** Service wrapper for accessing the job monitor API. */
 @Injectable()
 export class JobMonitorService {
-  private apiUrl = '/v1';
+  private apiUrl = '/api';
   private headers = new Headers({'Content-Type': 'application/json'});
 
   constructor(private http: Http) {}
 
-  listAllJobs(): Promise<JobQueryResponse> {
-    return this.http.get(`${this.apiUrl}/jobs`,
-      new RequestOptions({headers: this.headers}))
+  listAllJobs(parentId?: string): Promise<JobQueryResponse> {
+    return this.http.post(
+      `${this.apiUrl}/jobs/query`,
+      {
+        parentId: parentId,
+      },
+      new RequestOptions({
+        headers: this.headers,
+      }))
       .toPromise()
       .then(response => response.json() as JobQueryResponse)
       .catch(this.handleError);
   }
 
   abortJob(id: string): Promise<JobAbortResponse> {
-    return this.http.get(`${this.apiUrl}/jobs/${id}/abort`,
+    return this.http.post(`${this.apiUrl}/jobs/${id}/abort`, {},
       new RequestOptions({headers: this.headers}))
       .toPromise()
       .then(response => response.json() as JobAbortResponse)