Export to firecloud (#1)

Add Export to FireCloud button

Also remove items from menu that don't apply to Commons instance.

Dockerfile

@@ -4,16 +4,15 @@ RUN mkdir -p /usr/src/app
 WORKDIR /usr/src/app
 RUN npm install pm2 -g
 # Install app dependencies
-COPY package.json /usr/src/app/
+COPY . /usr/src/app/
 RUN npm install
-# Bundle app source
-COPY ./dist /usr/src/app/dist
-COPY ./server/dist /usr/src/app/server/dist
-COPY ./views /usr/src/app/views
+RUN npm -g install grunt-cli
+RUN npm -g install [email protected]
+RUN grunt build
+RUN rm boardwalk.zip
+RUN rm -rf spa/node_modules
 
 EXPOSE 3000
 #Set the node env
 ENV NODE_ENV local
 CMD ["pm2-docker", "server/dist/server.js"]
-#RUN chmod a+x run.sh
-#CMD ["./run.sh"]

server/src/lib/config/config-webcontroller.ts

@@ -12,14 +12,15 @@ import { Response as Res } from "express";
 import { Req } from "../../boardwalk";
 import { setupResponseCallback } from "cc-express-utils";
 import { ConfigViewModel } from "./config-view.model";
+import { Response } from "~express/lib/express";
 
 /**
  * Handle request for environment config. Default data URL to "https://carlos.ucsc-cgp-dev.org".
  *
  * @param {Req} req
  * @param {Response} res
  */
-export function getConfig(req: Req, res: Res): void {
+export function getConfig(req: Req, res: Res): Response {
 
     return setupResponseCallback(res)(null, {
         dataURL: process.env.BW_DATA_URL || "https://carlos.ucsc-cgp-dev.org"

spa/ExportToFireCloudTodo.md

@@ -0,0 +1,5 @@
+1. Fix ugly hack in cc-base.dao.ts where added getNoCatch method; but otherwise I don't get the error.
+2. CORS errors provides no details.
+3. `FilesService.exportToFireCloud` returns a string for success and error, then there is an ugly hardcoded test in
+file.effects.ts to see if the string starts with `Error`.
+4. In file.dao.ts, construct FireCloud url from response.

spa/src/app/app.module.ts

@@ -34,6 +34,7 @@ import { CCHamburgerDirective } from "./shared/cc-hamburger/cc-hamburger.directi
 import { CGLSubnavComponent } from "./shared/cgl-subnav/cgl-subnav.component";
 import { CGLToolbarComponent } from "./shared/cgl-toolbar/cgl-toolbar.component";
 import { ConfigService } from "./config/config.service";
+import { CCAlertDialogComponent } from "./shared/cc-alert-dialog/cc-alert-dialog.component";
 
 @NgModule({
     bootstrap: [AppComponent],
@@ -73,6 +74,7 @@ import { ConfigService } from "./config/config.service";
         CCHamburgerDirective,
         CGLSubnavComponent,
         CGLToolbarComponent,
+        CCAlertDialogComponent,
     ],
     providers: [
         UserService,

spa/src/app/cc-http/shared/cc-base.dao.ts

@@ -58,6 +58,11 @@ export class CCBaseDAO {
      */
     public get<T>(url: string, queryStringParams?: any): Observable<T> {
 
+        return this.getNoCatch(url, queryStringParams)
+            .catch(response => this.handleError(response));
+    }
+
+    public getNoCatch<T>(url: string, queryStringParams?: any): Observable<T> {
         // Build up GET headers
         let headers = new Headers();
         this.addAcceptHeader(headers);
@@ -79,8 +84,7 @@ export class CCBaseDAO {
 
         return <Observable<T>>this.http // TODO revisit typing here...
             .get(url, requestOptions)
-            .map(response => this.toJSON(response))
-            .catch(response => this.handleError(response));
+            .map(response => this.toJSON(response));
     }
 
     /**

spa/src/app/files/_ngrx/file-export/file-export.actions.ts

@@ -0,0 +1,27 @@
+import { Action } from "@ngrx/store";
+import { WorkspaceDescriptor } from "./file-export.state";
+
+export class FileExportManifestRequestAction implements Action {
+    public static ACTION_TYPE = "FILE.MANIFEST_EXPORT_REQUEST";
+    public readonly type = FileExportManifestRequestAction.ACTION_TYPE;
+    constructor(public payload: WorkspaceDescriptor) {
+    }
+}
+
+export class FileExportManifestSuccessAction implements Action {
+    public static ACTION_TYPE = "FILE.MANIFEST_EXPORT_SUCCESS";
+    public readonly type = FileExportManifestSuccessAction.ACTION_TYPE;
+    constructor(public fireCloudUrl: string) {
+    }
+}
+
+export class FileExportManifestErrorAction implements Action {
+    public static ACTION_TYPE = "FILE.MANIFEST_EXPORT_ERROR";
+    public readonly type = FileExportManifestErrorAction.ACTION_TYPE;
+    constructor(public errorReason: string) {
+    }
+}
+
+export type All = FileExportManifestRequestAction
+    | FileExportManifestSuccessAction
+    | FileExportManifestErrorAction;

spa/src/app/files/_ngrx/file-export/file-export.reducer.ts

@@ -0,0 +1,23 @@
+import { Action } from "@ngrx/store";
+import {
+    FileExportManifestRequestAction, FileExportManifestErrorAction,
+    FileExportManifestSuccessAction
+} from "./file-export.actions";
+import { FileExportManifestState } from "./file-export.state";
+
+export function reducer(state: FileExportManifestState = FileExportManifestState.getDefaultState(), action: Action): FileExportManifestState {
+    switch (action.type) {
+        case FileExportManifestSuccessAction.ACTION_TYPE: {
+            return new FileExportManifestState((action as FileExportManifestSuccessAction).fireCloudUrl, "success");
+        }
+        case FileExportManifestErrorAction.ACTION_TYPE: {
+            return new FileExportManifestState(null, "error",
+                (action as FileExportManifestErrorAction).errorReason);
+        }
+        case FileExportManifestRequestAction.ACTION_TYPE: {
+            return new FileExportManifestState(null, "request");
+        }
+        default:
+            return state;
+    }
+}

spa/src/app/files/_ngrx/file-export/file-export.state.ts

@@ -0,0 +1,19 @@
+export interface WorkspaceDescriptor {
+    name: string;
+    namespace: string;
+}
+
+export type FileExportManifestStatus = "request" | "success" | "error" | null;
+
+// export interface FileExportStatus
+export class FileExportManifestState {
+    constructor(public fireCloudUrl = "",
+                public status: FileExportManifestStatus = null,
+                public statusMessage = "") {
+    }
+
+    public static getDefaultState() {
+        return new FileExportManifestState();
+    }
+
+}

spa/src/app/files/_ngrx/file.effects.ts

@@ -48,6 +48,10 @@ import {
 } from "./table/table.actions";
 import { TableModel } from "../table/table.model";
 import { DEFAULT_TABLE_PARAMS } from "../table/table-params.model";
+import {
+    FileExportManifestRequestAction, FileExportManifestErrorAction,
+    FileExportManifestSuccessAction
+} from "./file-export/file-export.actions";
 
 @Injectable()
 export class FileEffects {
@@ -90,7 +94,7 @@ export class FileEffects {
      */
 
     /**
-     * Trigger update of file summary if a facet changes (ie term is selected or deseclted. File summary includes the 
+     * Trigger update of file summary if a facet changes (ie term is selected or deseclted. File summary includes the
      * donor count, file count etc that is displayed above the facets.
      *
      * @type {Observable<Action>}
@@ -137,7 +141,7 @@ export class FileEffects {
         });
 
     /**
-     * 
+     *
      */
     @Effect()
     fetchInitialTableData$: Observable<Action> = this.actions$
@@ -190,8 +194,24 @@ export class FileEffects {
             return this.fileService.downloadFileManifest(query);
         });
 
+    @Effect()
+    exportToFireCloud$: Observable<Action> = this.actions$
+        .ofType<FileExportManifestRequestAction>(FileExportManifestRequestAction.ACTION_TYPE)
+        .map(action => action.payload)
+        .withLatestFrom(this.store.select(selectSelectedFileFacets))
+        .switchMap((results) => {
+            const [payload, selectedFacets] = results;
+            return this.fileService.exportToFireCloud(selectedFacets, payload.name, payload.namespace);
+        })
+        .map((fcUrl) => {
+            if (fcUrl.startsWith("Error")) {
+                return new FileExportManifestErrorAction(fcUrl);
+            }
+            return new FileExportManifestSuccessAction(fcUrl);
+        });
+
     private colorWheel: Map<string, string>;
-    
+
     /**
      * Trigger update of facets once a facet term is selected/deselected.
      *
@@ -224,7 +244,7 @@ export class FileEffects {
                     })
             );
         });
-    
+
     /**
      * Trigger update of facet counts on init.
      *

spa/src/app/files/_ngrx/file.reducer.ts

@@ -2,12 +2,14 @@ import * as fileSummaryReducer from "./file-summary/file-summary.reducer";
 import * as fileFacetListReducer from "./file-facet-list/file-facet-list.reducer";
 import * as fileManifestSummaryReducer from "./file-manifest-summary/file-manifest-summary.reducer";
 import * as fileFacetMetadataSummaryReducer from "./file-facet-metadata-summary/file-facet-metadata-summary.reducer";
+import * as fileExportReducer from "./file-export/file-export.reducer";
 import * as tableReducer from "./table/table.reducer";
 
 export const reducer = {
     fileSummary: fileSummaryReducer.reducer,
     fileFacetList: fileFacetListReducer.reducer,
     fileManifestSummary: fileManifestSummaryReducer.reducer,
     fileFacetMetadataSummary: fileFacetMetadataSummaryReducer.reducer,
-    tableState: tableReducer.reducer
+    tableState: tableReducer.reducer,
+    fileExportState: fileExportReducer.reducer
 };

spa/src/app/files/_ngrx/file.selectors.ts

@@ -12,6 +12,7 @@ import { createFeatureSelector, createSelector } from "@ngrx/store";
 import { FileSummaryState } from "./file-summary/file-summary.state";
 import { FileFacetListState } from "./file-facet-list/file-facet-list.state";
 import { FileFacetMetadataSummaryState } from "./file-facet-metadata-summary/file-facet-metadata-summary.state";
+import { FileExportManifestState } from "./file-export/file-export.state";
 import { TableState } from "./table/table.state";
 
 export const selectFileFacets = createFeatureSelector<FileFacetListState>("fileFacetList");
@@ -32,7 +33,7 @@ export const selectTableState = createFeatureSelector<TableState>("tableState");
 
 /**
  * Returns current state of pagination, of file facet table.
- * 
+ *
  * @type {MemoizedSelector<object, PaginationModel>}
  */
 export const selectPagination = createSelector(selectTableState,(tableState: TableState) => {
@@ -50,5 +51,5 @@ export const selectTableQueryParams = createSelector(selectSelectedFacetsMap, se
     return { selectedFacets, pagination };
 });
 
-
+export const selectExportFileState = createFeatureSelector<FileExportManifestState>("fileExportState");
 

spa/src/app/files/_ngrx/file.state.ts

@@ -3,11 +3,13 @@ import { FileFacetListState } from "./file-facet-list/file-facet-list.state";
 import { FileManifestSummaryState } from "./file-manifest-summary/file-manifest-summary.state";
 import { FileFacetMetadataSummaryState } from "./file-facet-metadata-summary/file-facet-metadata-summary.state";
 import { TableState } from "./table/table.state";
+import { FileExportManifestState } from "./file-export/file-export.state";
 
 export interface FileState {
     fileSummary: FileSummaryState;
     fileFacetList: FileFacetListState;
     fileManifestSummary: FileManifestSummaryState;
     fileFacetMetadataSummary: FileFacetMetadataSummaryState;
     tableState: TableState;
+    exportFileManifestState: FileExportManifestState;
 }

spa/src/app/files/file-export/file-export.component.css

@@ -0,0 +1,5 @@
+.column-flex {
+    flex-direction: column;
+    display: flex;
+    font-size: large;
+}

spa/src/app/files/file-export/file-export.component.html

@@ -0,0 +1,24 @@
+<h1 mat-dialog-title>Export to FireCloud</h1>
+<div mat-dialog-content>
+    <mat-progress-bar mode="indeterminate" *ngIf="exporting"></mat-progress-bar>
+    <p *ngIf="exported">The selected files were exported to the FireCloud <a [href]="firecloudUrl" target="_blank">{{data.workspace}} workspace.</a></p>
+    <p *ngIf="errorMessage">There was an error exporting to FireCloud: {{errorMessage}}</p>
+    <div *ngIf="!exported && !errorMessage">
+        <p>Export the selected facets into a new FireCloud workspace.</p>
+        <div class="column-flex">
+            <mat-form-field>
+                <input matInput [(ngModel)]="data.workspace" placeholder="Workspace name" required autofocus [disabled]="exporting">
+            </mat-form-field>
+            <mat-form-field>
+                <mat-select placeholder="Billing project" [(value)]="data.namespace" [disabled]="exporting" required>
+                    <mat-option *ngFor="let namespace of data.namespaces" [value]="namespace">{{namespace}}</mat-option>
+                </mat-select>
+            </mat-form-field>
+        </div>
+    </div>
+</div>
+<div mat-dialog-actions align="end">
+    <button mat-button (click)="onClose()" *ngIf="!exported && !errorMessage">Cancel</button>
+    <button mat-button (click)="onExport()" *ngIf="!exported && !errorMessage" [disabled]="exporting || !data.workspace">Export</button>
+    <button mat-button (click)="onClose()" *ngIf="exported || errorMessage">Close</button>
+</div>

spa/src/app/files/file-export/file-export.component.spec.ts

@@ -0,0 +1,25 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { FileExportComponent } from './file-export.component';
+
+describe('FileExportComponent', () => {
+  let component: FileExportComponent;
+  let fixture: ComponentFixture<FileExportComponent>;
+
+  beforeEach(async(() => {
+    TestBed.configureTestingModule({
+      declarations: [ FileExportComponent ]
+    })
+    .compileComponents();
+  }));
+
+  beforeEach(() => {
+    fixture = TestBed.createComponent(FileExportComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should be created', () => {
+    expect(component).toBeTruthy();
+  });
+});