Revert "Initial commit"

This reverts commit b8649a6.

.firebaserc

@@ -0,0 +1,5 @@
+{
+  "projects": {
+    "default": "metabmaster"
+  }
+}

.travis.yml

@@ -12,7 +12,7 @@ script:
 deploy:
   provider: surge
   project: ./dist/
-  domain: dar.jcbwndsr.com
+  domain: metabmaster.jcbwndsr.com
   skip_cleanup: true
   on:
     branch: master

README.md

@@ -1,4 +1,5 @@
-# DAR-tool UI
+# MetabMaster
+[![Build Status](https://travis-ci.org/jacobwindsor/MetabMaster.svg?branch=master)](https://travis-ci.org/jacobwindsor/MetabMaster)
 
 This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 1.0.0.
 

database.rules.json

@@ -0,0 +1,21 @@
+{
+  "rules": {
+    "pathways": {
+      ".read": true,
+      "$pathway": {
+        ".read": true,
+        ".write": "(!data.exists() && auth!=null) || (data.exists() && data.child('userId').val() === auth.uid)",
+        ".validate": "newData.hasChildren(['userId', 'title', 'description', 'WPId'])",
+        "title": {
+          ".validate": "newData.isString() && newData.val().length > 0 && newData.val().length < 100"
+        },
+        "WPId": {
+          ".validate": "newData.isNumber() && newData.val() > 0"
+        },
+        "description": {
+          ".validate": "newData.isString() && newData.val().length > 0"
+        }
+      }
+    }
+  }
+}

firebase.json

@@ -0,0 +1,14 @@
+{
+  "database": {
+    "rules": "database.rules.json"
+  },
+  "hosting": {
+    "public": "dist",
+    "rewrites": [
+      {
+        "source": "**",
+        "destination": "/index.html"
+      }
+    ]
+  }
+}

package.json

@@ -1,13 +1,14 @@
 {
-  "name": "dar-tool-ui",
+  "name": "metab-master",
   "version": "0.0.0",
   "license": "MIT",
   "scripts": {
     "ng": "ng",
     "start": "npm run copy:assets && ng serve",
     "build": "ng build && npm run copy:assets",
     "build:prod": "ng build --prod --aot",
-    "copy:assets": "npm run copy:noty",
+    "copy:assets": "npm run copy:pvjs && npm run copy:noty",
+    "copy:pvjs": "rimraf src/assets/pvjs && cp -r node_modules/@wikipathways/pvjs/dist src/assets && mv src/assets/dist src/assets/pvjs && echo 'Fix issue with react-seletize CSS in bridgedb!'",
     "copy:noty": "rimraf src/assets/noty && mkdir src/assets/noty && cp node_modules/noty/lib/noty.css src/assets/noty/noty.css",
     "test": "echo \"Don't test yet. Do tests later for speed\"",
     "lint": "ng lint",
@@ -27,10 +28,14 @@
     "@angular/platform-browser": "^4.0.0",
     "@angular/platform-browser-dynamic": "^4.0.0",
     "@angular/router": "^4.0.0",
+    "@types/react": "^15.0.20",
+    "@wikipathways/kaavio-showdown": "^1.2.0",
+    "@wikipathways/pvjs": "^3.1.4-beta",
     "bootstrap": "^4.0.0-alpha.6",
     "classlist.js": "^1.1.20150312",
     "copy": "^0.3.0",
     "core-js": "^2.4.1",
+    "firebase": "^3.7.5",
     "intl": "^1.2.5",
     "ng2-validators": "^2.1.1",
     "noty": "^3.1.0",

src/app/compounds/compounds.component.spec.ts → src/app/alert/alert.component.spec.ts

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

src/app/alert/alert.component.ts

@@ -0,0 +1,35 @@
+import {Component, Input, OnInit} from '@angular/core';
+import Noty from 'noty';
+
+@Component({
+  selector: 'app-alert',
+  templateUrl: './alert.component.html',
+  styleUrls: ['./alert.component.scss']
+})
+export class AlertComponent implements OnInit {
+  private allowed = ['success', 'warning', 'error', 'alert', 'info'];
+  @Input() type: string;
+  @Input() heading: string;
+  @Input() message: string;
+  constructor() { }
+
+  ngOnInit() {
+    if (! this.allowed.indexOf(this.type)) {
+      // Default to info
+      this.type = 'info';
+    }
+
+    new Noty({
+      type: this.type,
+      text: this.message,
+      timeout: 3000,
+      closeWith: ['click', 'button'],
+      queue: 'global',
+      animation: {
+        open: 'noty_effects_open',
+        close: 'noty_effects_close'
+      },
+    }).show();
+  }
+
+}

src/app/app.component.html

@@ -2,18 +2,24 @@
   <div class="row">
     <md-toolbar color="primary">
       <span class="mr-3">
-        <h1>DAR-tool</h1>
+        <h1>MetabMaster</h1>
       </span>
       <span>
         <button md-button [routerLink]="['/']">Home</button>
       </span>
-      <!--<span *ngIf="auth.authenticated">-->
-        <!--<button md-button [routerLink]="['/compounds/create']">Rank your compounds</button>-->
-      <!--</span>-->
+      <span *ngIf="auth.authenticated">
+        <button md-button [routerLink]="['/pathway/create']">Create a pathway story</button>
+      </span>
       <span class="fill-remaining-space"></span>
       <span>
         <button md-button [routerLink]="['help']">Help</button>
       </span>
+      <span *ngIf="auth.authenticated">
+        <button md-button (click)="logout()">Sign out</button>
+      </span>
+      <span *ngIf="! auth.authenticated">
+        <button md-button [routerLink]="['/signin']">Sign in</button>
+      </span>
     </md-toolbar>
   </div>
   <div class="row mt-3">

src/app/app.component.ts

@@ -1,4 +1,5 @@
 import {Component, ViewEncapsulation} from '@angular/core';
+import {AuthService} from "./auth.service";
 
 @Component({
   selector: 'app-root',
@@ -7,6 +8,9 @@ import {Component, ViewEncapsulation} from '@angular/core';
   encapsulation: ViewEncapsulation.Emulated
 })
 export class AppComponent {
-  constructor() { }
+  constructor(public auth: AuthService) { }
 
+  logout() {
+    this.auth.logout();
+  }
 }

src/app/app.module.ts

@@ -3,29 +3,50 @@ import { NgModule,  CUSTOM_ELEMENTS_SCHEMA } from '@angular/core';
 import {FormsModule, ReactiveFormsModule} from '@angular/forms';
 import { HttpModule } from '@angular/http';
 import { RouterModule} from '@angular/router';
+
 import { AppComponent } from './app.component';
+import { PathwayComponent } from './pathway/pathway.component';
 import {routes} from './app.routes';
 import { MaterialModule } from '@angular/material';
+import { PathwayListComponent } from './pathway-list/pathway-list.component';
+import {FirebaseService} from "./firebase.service";
+import {PathwayService} from "./pathway.service";
+import { SignUpOrSignInComponent } from './sign-up-or-sign-in/sign-up-or-sign-in.component';
+import {AuthService} from "./auth.service";
 import {BrowserAnimationsModule} from "@angular/platform-browser/animations";
+import { PathwayCreateComponent } from './pathway-create/pathway-create.component';
+import {AuthGuard} from "./auth.guard";
 import { HomeComponent } from './home/home.component';
+import { DiagramPresComponent } from './diagram.pres/diagram.pres.component';
+import { PathwayEditComponent } from './pathway-edit/pathway-edit.component';
+import { PathwayUpdateComponent } from './pathway-update/pathway-update.component';
+import { PathwayDeleteDialogComponent } from './pathway-delete-dialog/pathway-delete-dialog.component';
+import { InteractiveDescriptionPresComponent } from './interactive-description.pres/interactive-description.pres.component';
+import {PathwayListService} from "./pathway-list.service";
+import { AlertComponent } from './alert/alert.component';
 import { HelpComponent } from './help/help.component';
 import {NotifierService} from "./notifier.service";
-import { CompoundsComponent } from './compounds/compounds.component';
-import {CompoundService} from "./compound.service";
-import { CompoundDetailComponent } from './compound-detail/compound-detail.component';
 
 @NgModule({
   declarations: [
     AppComponent,
+    PathwayComponent,
+    PathwayListComponent,
+    SignUpOrSignInComponent,
+    PathwayCreateComponent,
     HomeComponent,
-    HelpComponent,
-    CompoundsComponent,
-    CompoundDetailComponent
+    DiagramPresComponent,
+    PathwayEditComponent,
+    PathwayUpdateComponent,
+    PathwayDeleteDialogComponent,
+    InteractiveDescriptionPresComponent,
+    AlertComponent,
+    HelpComponent
   ],
   entryComponents: [
+    PathwayDeleteDialogComponent
   ],
   imports: [
-    RouterModule,
     routes,
     BrowserModule,
     FormsModule,
@@ -35,8 +56,12 @@ import { CompoundDetailComponent } from './compound-detail/compound-detail.compo
     BrowserAnimationsModule
   ],
   providers: [
-    NotifierService,
-    CompoundService
+    FirebaseService,
+    PathwayService,
+    PathwayListService,
+    AuthService,
+    AuthGuard,
+    NotifierService
   ],
   bootstrap: [AppComponent],
   schemas: [CUSTOM_ELEMENTS_SCHEMA]

src/app/app.routes.ts

@@ -1,23 +1,39 @@
 import {Routes, RouterModule} from '@angular/router';
+import {PathwayComponent} from './pathway/pathway.component';
+import {SignUpOrSignInComponent} from "./sign-up-or-sign-in/sign-up-or-sign-in.component";
+import {PathwayCreateComponent} from "./pathway-create/pathway-create.component";
+import {AuthGuard} from "./auth.guard";
 import {HomeComponent} from "app/home/home.component";
+import {PathwayUpdateComponent} from "./pathway-update/pathway-update.component";
 import {HelpComponent} from "./help/help.component";
 
 const appRoutes: Routes = [
-  // {
-  //   path: 'compounds/create',
-  //   //component: PathwayCreateComponent,
-  // },
-  // {
-  //   path: 'compounds/:id',
-  //   //component: PathwayComponent
-  // },
+  {
+    path: 'pathway/create',
+    component: PathwayCreateComponent,
+    canActivate: [AuthGuard]
+  },
+  {
+    path: 'pathway/:id/update',
+    component: PathwayUpdateComponent,
+    canActivate: [AuthGuard]
+  },
+  {
+    path: 'pathway/:id',
+    component: PathwayComponent
+  },
+  {
+    path: 'signin',
+    component: SignUpOrSignInComponent
+  },
   {
     path: 'help',
     component: HelpComponent
   },
   {
     path: '',
     component: HomeComponent
+
   }
 ];
 

src/app/auth.guard.spec.ts

@@ -0,0 +1,15 @@
+import { TestBed, async, inject } from '@angular/core/testing';
+
+import { AuthGuard } from './auth.guard';
+
+describe('AuthGuard', () => {
+  beforeEach(() => {
+    TestBed.configureTestingModule({
+      providers: [AuthGuard]
+    });
+  });
+
+  it('should ...', inject([AuthGuard], (guard: AuthGuard) => {
+    expect(guard).toBeTruthy();
+  }));
+});

src/app/auth.guard.ts

@@ -0,0 +1,23 @@
+import { Injectable } from '@angular/core';
+import {CanActivate, ActivatedRouteSnapshot, RouterStateSnapshot, Router} from '@angular/router';
+import { Observable } from 'rxjs/Observable';
+import {AuthService} from "./auth.service";
+
+@Injectable()
+export class AuthGuard implements CanActivate {
+  constructor(private auth: AuthService, private router: Router) {}
+  canActivate(
+    next: ActivatedRouteSnapshot,
+    state: RouterStateSnapshot): Observable<boolean> | Promise<boolean> | boolean {
+      return this.checkLogin(state.url);
+
+  }
+
+  private checkLogin(url: string): boolean {
+      if (this.auth.authenticated) {
+        return true;
+      }
+
+      this.router.navigate(['/signin']);
+  }
+}

src/app/auth.service.spec.ts

@@ -0,0 +1,15 @@
+import { TestBed, inject } from '@angular/core/testing';
+
+import { AuthService } from './auth.service';
+
+describe('AuthService', () => {
+  beforeEach(() => {
+    TestBed.configureTestingModule({
+      providers: [AuthService]
+    });
+  });
+
+  it('should ...', inject([AuthService], (service: AuthService) => {
+    expect(service).toBeTruthy();
+  }));
+});