Merge pull request #201 from geneontology/sprint-1

Sprint 1

src/@noctua.announcement/@noctua.announcement.module.ts

@@ -0,0 +1,25 @@
+import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { AnnouncementPanelComponent } from './components/announcement-panel/announcement-panel.component';
+import { MatIconModule } from '@angular/material/icon';
+import { MatButtonModule } from '@angular/material/button';
+import { MatSidenavModule } from '@angular/material/sidenav';
+import { FlexLayoutModule } from '@angular/flex-layout';
+import { NoctuaSharedModule } from '@noctua/shared.module';
+
+@NgModule({
+  imports: [
+    CommonModule,
+    MatIconModule,
+    MatButtonModule,
+    MatSidenavModule,
+    FlexLayoutModule,
+    NoctuaSharedModule
+  ],
+  exports: [
+    AnnouncementPanelComponent
+  ],
+  declarations: [
+    AnnouncementPanelComponent],
+})
+export class NoctuaAnnouncementModule { }

src/@noctua.announcement/components/announcement-panel/announcement-panel.component.html

@@ -0,0 +1,20 @@
+<form fxLayout="column" fxLayoutAlign="start stretch" class="noc-cam-form noc-drawer h-100-p">
+  <div class="noc-drawer-header" fxLayout="row" fxLayoutAlign="start center">
+    <span class="noc-drawer-header-title">
+      Announcements</span>
+    <span fxFlex></span>
+    <button mat-stroked-button (click)="close()" class="noc-rounded-button noc-sm" color="primary"
+      aria-label="Close dialog">
+      <mat-icon>close</mat-icon> Close
+    </button>
+  </div>
+  <div class="noc-drawer-body w-100-p p-8" noctuaPerfectScrollbar>
+    <div *ngFor="let announcement of announcements" class="alert alert-{{announcement.level}} w-100-p my-8">
+      <strong>{{announcement.title}}</strong><br>
+      {{announcement.description}}
+      <a *ngIf="announcement.descriptionUrl" href="{{announcement.descriptionUrl}}" target="_banl">
+        More Details
+      </a>
+    </div>
+  </div>
+</form>

src/@noctua.announcement/components/announcement-panel/announcement-panel.component.scss

@@ -0,0 +1,46 @@
+@use "@angular/material" as mat;
+@import "src/@noctua/scss/noctua";
+@import "src/@noctua.common/scss/noctua.common";
+
+:host {
+  //width: 100%; // display: block;
+
+  background-color: white;
+  @include mat.elevation(4);
+
+  .noc-cam-form {
+    @include deep-width(500px);
+  }
+
+  .noc-header {
+    @include deep-height(40px);
+    background-color: #eee;
+    border-bottom: #ccc solid 1px;
+
+    mat-icon-button {
+      @include deep-height(40px);
+      @include deep-width(40px);
+      line-height: 40px;
+    }
+
+    .noc-title {
+      font-size: 10px;
+      padding: 0 14px;
+    }
+  }
+
+  .noc-body {
+    padding: 0 14px 14px 14px;
+  }
+
+  .noc-item {
+    @include deep-width(100%);
+    font-size: 12px;
+
+    .noc-title {
+      font-weight: bold;
+      margin-right: 8px;
+      color: #999;
+    }
+  }
+}

src/@noctua.announcement/components/announcement-panel/announcement-panel.component.ts

@@ -0,0 +1,54 @@
+import { Component, Input, OnInit, OnDestroy } from '@angular/core';
+import { MatDrawer, MatSidenav } from '@angular/material/sidenav';
+import { Subject } from 'rxjs';
+import { takeUntil } from 'rxjs/operators';
+import {
+  NoctuaFormMenuService
+} from '@geneontology/noctua-form-base';
+import { NoctuaSearchMenuService } from '@noctua.search/services/search-menu.service';
+import { NoctuaAnnouncementService } from '@noctua.announcement/services/cam.service';
+import { Announcement } from '@noctua.announcement/models/announcement';
+
+
+@Component({
+  selector: 'noc-announcement-panel',
+  templateUrl: './announcement-panel.component.html',
+  styleUrls: ['./announcement-panel.component.scss'],
+})
+
+export class AnnouncementPanelComponent implements OnInit, OnDestroy {
+
+  @Input('sidenav') sidenav: MatSidenav;
+  announcements: Announcement[];
+
+  private _unsubscribeAll: Subject<any>;
+
+  constructor(
+    public noctuaSearchMenuService: NoctuaSearchMenuService,
+    public noctuaFormMenuService: NoctuaFormMenuService,
+    private noctuaAnnouncementService: NoctuaAnnouncementService,
+  ) {
+    this._unsubscribeAll = new Subject();
+  }
+
+  ngOnInit(): void {
+    this.noctuaAnnouncementService.onAnnouncementsChanged.pipe(
+      takeUntil(this._unsubscribeAll))
+      .subscribe((announcements: Announcement[]) => {
+        if (announcements) {
+          this.announcements = announcements
+        }
+      });
+  }
+
+  ngOnDestroy(): void {
+    this._unsubscribeAll.next(null);
+    this._unsubscribeAll.complete();
+  }
+
+  close() {
+    this.sidenav.close();
+  }
+
+
+}

src/@noctua.announcement/models/announcement.ts

@@ -0,0 +1,8 @@
+export class Announcement {
+  type: string;
+  date: string;
+  level: string;
+  title: string;
+  content: string;
+  moreContentUrl?: string;
+}

src/@noctua.announcement/services/cam.service.ts

@@ -0,0 +1,33 @@
+import { HttpClient } from "@angular/common/http";
+import { Injectable } from "@angular/core";
+import { Announcement } from "@noctua.announcement/models/announcement";
+import { environment } from "environments/environment";
+import { BehaviorSubject } from "rxjs";
+
+@Injectable({
+  providedIn: 'root'
+})
+export class NoctuaAnnouncementService {
+  cursor = 0;
+  onAnnouncementsChanged: BehaviorSubject<any>;
+  onAnnouncementChanged: BehaviorSubject<any>;
+
+  constructor(
+    private httpClient: HttpClient) {
+
+    this.onAnnouncementsChanged = new BehaviorSubject(null);
+    this.onAnnouncementChanged = new BehaviorSubject(null);
+
+  }
+
+  getAnnouncement() {
+    return this.httpClient.get(environment.announcementUrl).subscribe((response: Announcement[]) => {
+      if (response) {
+        if (response.length > 0) {
+          this.onAnnouncementChanged.next(response[this.cursor]);
+        }
+        this.onAnnouncementsChanged.next(response);
+      }
+    });
+  }
+}

src/@noctua.common/models/menu-panels.ts

@@ -10,6 +10,8 @@ export enum LeftPanel {
     activityForm = 'activityForm',
     camForm = 'camForm',
     copyModel = 'copyModel',
+    apps = 'apps',
+    announcement = 'announcement'
 };
 
 export enum MiddlePanel {

src/@noctua.common/services/noctua-common-menu.service.ts

@@ -15,6 +15,7 @@ import { WorkbenchId } from '@noctua.common/models/workench-id';
 export class NoctuaCommonMenuService {
 
   onCamSettingsChanged: BehaviorSubject<SettingsOptions>;
+  selectedLeftSidenav: LeftPanel = LeftPanel.apps;
   selectedLeftPanel: LeftPanel;
   selectedMiddlePanel: MiddlePanel;
   selectedRightPanel: RightPanel;
@@ -64,6 +65,10 @@ export class NoctuaCommonMenuService {
     return this._leftSidenav.open();
   }
 
+  selectLeftSidenav(panel: LeftPanel) {
+    this.selectedLeftSidenav = panel;
+  }
+
 
   selectLeftPanel(panel: LeftPanel) {
     this.selectedLeftPanel = panel;

src/@noctua-doctor/services/doctor-menu.service.ts → src/@noctua.doctor/services/doctor-menu.service.ts

@@ -1,6 +1,5 @@
 import { Injectable } from '@angular/core';
 import { MatDrawer } from '@angular/material/sidenav';
-import { NoctuaPerfectScrollbarDirective } from '@noctua/directives/noctua-perfect-scrollbar/noctua-perfect-scrollbar.directive';
 import { PerfectScrollbarDirective } from 'ngx-perfect-scrollbar';
 import { LeftPanel, MiddlePanel, RightPanel } from './../models/menu-panels';
 

src/@noctua.editor/inline-editor/editor-dropdown/editor-dropdown.component.ts

@@ -132,14 +132,15 @@ export class NoctuaEditorDropdownComponent implements OnInit, OnDestroy {
       case EditorCategory.evidenceAll:
         self.noctuaActivityEntityService.addEvidence().then(() => {
           this.close();
-          self.noctuaFormDialogService.openInfoToast('Activity successfully updated.', 'OK');
+          self.noctuaFormDialogService.openInfoToast('Evidence successfully updated.', 'OK');
         });
         break;
-      default:
-        self.noctuaActivityEntityService.saveActivity().then(() => {
+      case EditorCategory.all:
+        self.noctuaActivityEntityService.addIndividual().then(() => {
           this.close();
           self.noctuaFormDialogService.openInfoToast('Activity successfully updated.', 'OK');
         });
+        break;
     }
   }
 

src/@noctua.form/data/config/shape-definition.ts

@@ -248,7 +248,7 @@ export const canInsertEntity = {
             label: 'Add Happens During (Biological Phase)',
             id: ActivityNodeType.GoBiologicalPhase,
             node: <ActivityNodeDisplay>{
-                category: [EntityDefinition.GoBiologicalPhase],
+                category: [EntityDefinition.GoBiologicalPhase, EntityDefinition.UberonStage],
                 type: ActivityNodeType.GoBiologicalPhase,
                 label: 'happens during (Biological Phase)',
                 displaySection: noctuaFormConfig.displaySection.fd,

src/@noctua.form/models/activity/activity.ts

@@ -634,6 +634,17 @@ export class Activity extends SaeGraph<ActivityNode> {
     return saveData;
   }
 
+  createAddIndividual(srcActivity: Activity, predicate: Predicate) {
+    const self = this;
+
+    const addTriples = self.getEdge(predicate.subjectId, predicate.objectId)
+
+    const saveData = {
+      addTriples: addTriples,
+    };
+
+    return saveData;
+  }
 
   createDelete() {
     const self = this;

src/@noctua.form/models/contributor.ts

@@ -24,6 +24,15 @@ export class Contributor {
     get groups() {
         return this._groups;
     }
+
+    static fromResponse(response) {
+        const user = new Contributor()
+        user.orcid = response.uri;
+        user.name = response.nickname;
+        user.groups = response.groups;
+
+        return user;
+    }
 }
 
 export function compareContributor(a: Contributor, b: Contributor): number {

src/@noctua.form/services/activity-entity.service.ts

@@ -102,6 +102,20 @@ export class NoctuaActivityEntityService {
       saveData.removeIds);
   }
 
+  addIndividual() {
+    const self = this;
+
+    self.activityEntityFormToActivity();
+
+    const saveData = self.activity.createAddIndividual(self.currentActivity, self.entity.predicate);
+
+    return self.noctuaGraphService.editActivity(self.cam,
+      [self.entity],
+      [saveData.addTriples],
+      [],
+      []);
+  }
+
   saveSearchDatabase() {
     const self = this;
 

src/@noctua.form/services/cam.service.ts

@@ -57,7 +57,6 @@ export class CamService {
     private curieService: CurieService) {
 
     this.onCamChanged = new BehaviorSubject(null);
-    this.curieUtil = this.curieService.getCurieUtil();
     this.camFormGroup = new BehaviorSubject(null);
     this.camFormGroup$ = this.camFormGroup.asObservable();
 

src/@noctua.form/services/graph.service.ts

@@ -25,10 +25,11 @@ import { Article } from './../models/article';
 import { Contributor, equalContributor } from '../models/contributor';
 import * as moment from 'moment';
 import { HttpClient, HttpHeaders, HttpParams } from '@angular/common/http';
+import { graph as bbopGraph } from 'bbop-graph-noctua';
 
 declare const require: any;
 
-const model = require('bbop-graph-noctua');
+//const model = require('bbop-graph-noctua');
 const barista_client = require('bbop-client-barista');
 const amigo = require('amigo2');
 const barista_response = require('bbop-response-barista');
@@ -158,10 +159,9 @@ export class NoctuaGraphService {
 
   getMetadata(responseData) {
     const self = this;
-    const noctua_graph = model.graph;
     const cam = new Cam()
 
-    cam.graph = new noctua_graph();
+    cam.graph = new bbopGraph();
     cam.graph.load_data_basic(responseData);
 
     cam.id = responseData.id;
@@ -197,18 +197,17 @@ export class NoctuaGraphService {
 
   rebuild(cam: Cam, response) {
     const self = this;
-    const noctua_graph = model.graph;
 
     // cam.loading.status = true;
     // cam.loading.message = 'Loading Model Entities Metadata...';
 
     if (cam.graph) {
-      const inGraph = new noctua_graph();
+      const inGraph = new bbopGraph();
 
       inGraph.load_data_basic(response.data());
       cam.graph.merge_special(inGraph);
     } else {
-      cam.graph = new noctua_graph();
+      cam.graph = new bbopGraph();
       cam.graph.load_data_basic(response.data());
     }
 
@@ -265,9 +264,8 @@ export class NoctuaGraphService {
 
   rebuildFromStoredApi(cam: Cam, activeModel) {
     const self = this;
-    const noctua_graph = model.graph;
 
-    cam.graph = new noctua_graph();
+    cam.graph = new bbopGraph();
     cam.graph.load_data_basic(activeModel);
 
     cam.id = activeModel.id;