From 0059dd7cdec99f85a49a819abddd209a957e5e2f Mon Sep 17 00:00:00 2001
From: ozgur <ozgur@ebi.ac.uk>
Date: Mon, 20 Nov 2023 01:40:36 +0000
Subject: [PATCH] merged with master

---
 .dockerignore                                 |  2 +-
 Dockerfile                                    |  4 +++-
 .../auth/login/login.component.html           |  4 ++--
 .../components/auth/login/login.component.ts  | 10 +++++---
 .../public/guides/guides.component.ts         | 14 ++++-------
 .../public/header/header.component.ts         |  2 +-
 .../public/study/study.component.html         |  2 +-
 .../async-task-status-transform.pipe.ts       | 10 ++++----
 .../shared/nav-bar/nav-bar.component.html     |  4 ++--
 .../shared/nav-bar/nav-bar.component.ts       |  4 ++--
 .../shared/ontology/ontology.component.ts     | 23 +++++++++++++-----
 .../rsync/rsync-status-transform.pipe.ts      | 14 +++++------
 src/app/configuration.mock.service.ts         |  7 +++---
 .../metabolights/metabolights.service.ts      |  9 +++++++
 src/app/services/publications/doi.service.ts  |  7 ++++--
 src/assets/configs/validations.json           | 24 +++++++++----------
 src/environment.interface.ts                  |  1 -
 17 files changed, 82 insertions(+), 59 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index 09e83725..868ce4d8 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,6 +1,6 @@
 nginx.conf
 e2e
-src/assets/configs/*.config.json
+src/assets/configs/*config.json
 dist
 .github
 node_modules
diff --git a/Dockerfile b/Dockerfile
index 58c96010..04227ed0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,12 +4,14 @@ WORKDIR /app-root
 COPY . .
 RUN npm install --save --legacy-peer-deps
 ARG CONFIGURATION=production
+ARG BASE_HREF=/metabolights/editor
 ENV NODE_OPTIONS=--openssl-legacy-provider
-RUN npm run build -- --configuration $CONFIGURATION
+RUN npm run build -- --configuration $CONFIGURATION --base-href="$BASE_HREF/"
 
 # Stage 2, use the compiled app, ready for production with Nginx
 FROM nginx:stable
 LABEL maintainer="MetaboLights (metabolights-help @ ebi.ac.uk)"
+COPY --from=build /app-root/dist/metabolights-editor /editor
 
 COPY --from=build /app-root/dist /editor
 ARG EXPOSED_PORT=8008
diff --git a/src/app/components/auth/login/login.component.html b/src/app/components/auth/login/login.component.html
index 326bc218..36b2e40d 100644
--- a/src/app/components/auth/login/login.component.html
+++ b/src/app/components/auth/login/login.component.html
@@ -7,8 +7,8 @@
           <mat-icon>public</mat-icon> Back to MetaboLights</a
         >
     <br />
-    <span *ngIf="environmentName != null && !environmentName.toLowerCase().startsWith('prod')" style="margin-top: -25px; margin-left: 10px; color: red"
-    > (Environment: {{ environmentName }}, URL: {{ endpoint }})</span
+    <span *ngIf="environmentName != null && environmentName.length > 0" style="margin-top: -25px; margin-left: 10px; color: red"
+    > (Environment: {{ environmentName }} hosted on {{ endpoint }})</span
   >
     <br />
     <nav class="panel bg-white vw40">
diff --git a/src/app/components/auth/login/login.component.ts b/src/app/components/auth/login/login.component.ts
index 64471a2a..608090aa 100644
--- a/src/app/components/auth/login/login.component.ts
+++ b/src/app/components/auth/login/login.component.ts
@@ -10,6 +10,7 @@ import { ConfigurationService } from "src/app/configuration.service";
 import { MtblsJwtPayload } from "src/app/services/headers";
 import jwtDecode  from "jwt-decode";
 import * as toastr from "toastr";
+import {PlatformLocation} from '@angular/common';
 import { stringify } from "querystring";
 @Component({
   selector: "app-login",
@@ -29,10 +30,14 @@ export class LoginComponent implements OnInit {
     private ngRedux: NgRedux<IAppState>,
     public router: Router,
     private editorService: EditorService,
-    private configService: ConfigurationService
+    private configService: ConfigurationService,
+    private platformLocation: PlatformLocation
   ) {
     this.baseHref = this.configService.baseHref;
-    this.environmentName = environment.context;
+    this.environmentName = this.platformLocation.getBaseHrefFromDOM();
+    this.environmentName = this.environmentName.replace("/metabolights/", "");
+    this.environmentName = this.environmentName.replace("/", "");
+
   }
 
   ngOnInit() {
@@ -43,7 +48,6 @@ export class LoginComponent implements OnInit {
       email: ["", [Validators.required, Validators.email]],
       secret: ["", Validators.required],
     });
-    this.domain = this.configService.config.metabolightsWSURL.domain;
     this.endpoint = this.configService.config.endpoint;
     if (this.endpoint.endsWith("/") === false){
       this.endpoint = this.endpoint + "/";
diff --git a/src/app/components/public/guides/guides.component.ts b/src/app/components/public/guides/guides.component.ts
index cd132a25..a17ff57e 100644
--- a/src/app/components/public/guides/guides.component.ts
+++ b/src/app/components/public/guides/guides.component.ts
@@ -48,8 +48,10 @@ export class GuidesComponent implements OnInit {
     if (!environment.isTesting) {
       this.setUpSubscriptions();
     }
-    this.domain = this.configService.config.metabolightsWSURL.domain;
     this.repo = this.configService.config.metabolightsWSURL.guides;
+    if(this.repo.endsWith("/")){
+      this.repo =  this.repo.slice(0, -1);
+    }
   }
 
   setUpSubscriptions() {
@@ -98,7 +100,7 @@ export class GuidesComponent implements OnInit {
       if (img.indexOf("ftp://") > -1) {
         return img;
       }
-      return this.repo + "media/images/" + img;
+      return this.repo + "/media/images/" + img;
     }
   }
 
@@ -143,15 +145,9 @@ export class GuidesComponent implements OnInit {
   }
 
   getURLBase(url) {
-    // const domain = window.location.host.split(".")[0];
-    // if (domain === "www" || domain === "wwwdev") {
-    //   return "/metabolights" + url;
-    // } else {
-    //   return url;
-    // }
     const base = this.platformLocation.getBaseHrefFromDOM();
     if(base.endsWith("/")){
-      return window.location.origin + base.slice(0, base.length-1) + url;
+      return window.location.origin + base.slice(0, -1) + url;
     }
     return window.location.origin + this.platformLocation.getBaseHrefFromDOM() + url;
   }
diff --git a/src/app/components/public/header/header.component.ts b/src/app/components/public/header/header.component.ts
index d33f19f9..2e78d6f6 100644
--- a/src/app/components/public/header/header.component.ts
+++ b/src/app/components/public/header/header.component.ts
@@ -25,7 +25,7 @@ export class HeaderComponent {
       this.setUpSubscription();
       const url = this.configService.config.endpoint;
       if(url.endsWith("/")){
-        this.metabolightsWebsiteUrl = url.slice(0, url.length - 1);
+        this.metabolightsWebsiteUrl = url.slice(0, -1);
       } else {
         this.metabolightsWebsiteUrl = url;
       }
diff --git a/src/app/components/public/study/study.component.html b/src/app/components/public/study/study.component.html
index c6dc2232..43fe2804 100644
--- a/src/app/components/public/study/study.component.html
+++ b/src/app/components/public/study/study.component.html
@@ -25,7 +25,7 @@
         <p>
           <a
             class="button is-small custom-button"
-            [href]="'/metabolights/editor/study/' + requestedStudy"
+            [href]="baseHref + 'study/' + requestedStudy"
             ><mat-icon
               class="mat-icon notranslate material-icons mat-icon-no-color"
               role="img"
diff --git a/src/app/components/shared/async-task/async-task-status-transform.pipe.ts b/src/app/components/shared/async-task/async-task-status-transform.pipe.ts
index 6a9cb425..ed8dadfb 100644
--- a/src/app/components/shared/async-task/async-task-status-transform.pipe.ts
+++ b/src/app/components/shared/async-task/async-task-status-transform.pipe.ts
@@ -7,12 +7,12 @@ import { Pipe, PipeTransform } from "@angular/core";
 export class AsyncStatusTransformPipe implements PipeTransform {
     register = {
         PENDING: '-',
-        INITIATED: 'In Queue ...',
-        STARTED: 'Started ...',
-        SUCCESS: 'Done',
+        INITIATED: 'Task is in queue ...',
+        STARTED: 'Task has started ...',
+        SUCCESS: 'Task has completed.',
         RETRY: 'Retrying ... ',
-        FAILURE: "Failed",
-        REVOKED: "Canceled"
+        FAILURE: "Task has failed.",
+        REVOKED: "Task has canceled."
       };
 
     transform(value: string): string {
diff --git a/src/app/components/shared/nav-bar/nav-bar.component.html b/src/app/components/shared/nav-bar/nav-bar.component.html
index 954786eb..98ae872d 100644
--- a/src/app/components/shared/nav-bar/nav-bar.component.html
+++ b/src/app/components/shared/nav-bar/nav-bar.component.html
@@ -10,8 +10,8 @@
         class="navbar-item"
       >
         <span class="material-icons"> keyboard_backspace </span>&nbsp;Back to MetaboLights
-        <span *ngIf="environmentName != null && !environmentName.toLowerCase().startsWith('prod')" style="margin-left: 16px; color: orange"
-        > &nbsp;(Environment: {{ environmentName }}, URL: {{ endpoint }})</span
+        <span *ngIf="environmentName != null || environmentName.length > 0" style="margin-left: 16px; color: orange"
+        > &nbsp;(Environment: {{ environmentName }} hosted on {{ endpoint }})</span
       >
       </a>
       <ng-template #studyStatus>
diff --git a/src/app/components/shared/nav-bar/nav-bar.component.ts b/src/app/components/shared/nav-bar/nav-bar.component.ts
index 6a303db2..276cb726 100644
--- a/src/app/components/shared/nav-bar/nav-bar.component.ts
+++ b/src/app/components/shared/nav-bar/nav-bar.component.ts
@@ -33,8 +33,8 @@ export class NavBarComponent implements OnInit {
     private platformLocation: PlatformLocation
   ) {
     this.baseHref = this.platformLocation.getBaseHrefFromDOM();
-
-    this.environmentName = environment.context;
+    this.environmentName = this.baseHref.replace("/metabolights/", "");
+    this.environmentName = this.environmentName.replace("/", "");
   }
 
   ngOnInit() {
diff --git a/src/app/components/shared/ontology/ontology.component.ts b/src/app/components/shared/ontology/ontology.component.ts
index 07903600..af9234d3 100644
--- a/src/app/components/shared/ontology/ontology.component.ts
+++ b/src/app/components/shared/ontology/ontology.component.ts
@@ -52,7 +52,7 @@ export class OntologyComponent implements OnInit, OnChanges {
   @ViewChild("input", { read: MatAutocompleteTrigger })
   valueInput: MatAutocompleteTrigger;
 
-  wsDomain = "";
+  baseURL = "";
   loading = false;
   termsLoading = false;
   isforcedOntology = false;
@@ -81,9 +81,21 @@ export class OntologyComponent implements OnInit, OnChanges {
 
   }
 
+  join(path1: string, path2: string){
+
+    if (path2.startsWith("/")){
+      path2 = path2.slice(1);
+    }
+    if (path1.endsWith("/")){
+      path1 = path1.slice(0,-1);
+    }
+    return path1 + "/" + path2;
+
+  }
+
   ngOnInit() {
     this.baseHref = this.configService.baseHref;
-    this.wsDomain = this.configService.config.endpoint;
+    this.baseURL = this.configService.config.metabolightsWSURL.baseURL;
     if (this.values === null || this.values[0] === null) {
       this.values = [];
     }
@@ -99,7 +111,7 @@ export class OntologyComponent implements OnInit, OnChanges {
         this.endPoints = this.validations["recommended-ontologies"].ontology;
         if (this.url !== "") {
           this.editorService
-            .getOntologyTerms(this.wsDomain + "/" + this.url)
+            .getOntologyTerms( this.join(this.baseURL, this.url))
             .subscribe((terms) => {
               this.allvalues = [];
               const jsonConvert: JsonConvert = new JsonConvert();
@@ -144,7 +156,7 @@ export class OntologyComponent implements OnInit, OnChanges {
               this.searchedMore = false;
               this.loading = true;
               this.editorService
-                .getOntologyTerms(this.wsDomain + "/" + this.url + term)
+                .getOntologyTerms(this.join(this.join(this.baseURL, this.url), term))
                 .subscribe((terms) => {
                   this.allvalues = [];
                   this.loading = false;
@@ -256,8 +268,7 @@ export class OntologyComponent implements OnInit, OnChanges {
     this.loading = true;
     this.editorService
       .getOntologyTerms(
-        this.wsDomain + "/" +
-          this.url +
+          this.join(this.baseURL, this.url) +
           term +
           "&queryFields=MTBLS,MTBLS_Zooma,Zooma,OLS,Bioportal}"
       )
diff --git a/src/app/components/study/files/rsync/rsync-status-transform.pipe.ts b/src/app/components/study/files/rsync/rsync-status-transform.pipe.ts
index 22a56cb9..7d392e9c 100644
--- a/src/app/components/study/files/rsync/rsync-status-transform.pipe.ts
+++ b/src/app/components/study/files/rsync/rsync-status-transform.pipe.ts
@@ -8,17 +8,17 @@ export class RsyncStatusTransformPipe implements PipeTransform {
     register = {
         NO_TASK: '-',
         UNKNOWN: 'Unknown',
-        SYNC_NEEDED: 'Done. Sync Needed',
-        SYNC_NOT_NEEDED: 'Done. Sync not Needed',
+        SYNC_NEEDED: 'Task completed. Sync Needed',
+        SYNC_NOT_NEEDED: 'Task completed. Sync not Needed',
         CALCULATING: 'Processing ...',
         CALCULATION_FAILURE: 'Check failure',
-        NOT_FOUND: "Not Found",
-        PENDING: 'In Queue ...',
-        RUNNING: 'Running ...',
-        COMPLETED_SUCCESS: "Done. Sync Completed",
+        NOT_FOUND: "No Task Found",
+        PENDING: 'Task is in Queue ...',
+        RUNNING: 'TAsk is running ...',
+        COMPLETED_SUCCESS: "Task completed. Sync Completed",
         SYNC_FAILURE: "Sync failure",
         START_FAILURE: "Start failure",
-        JOB_SUBMITTED: "Submitted ...",
+        JOB_SUBMITTED: "Task has been submitted ...",
         JOB_SUBMISSION_FAILED: "Start failure"
       };
 
diff --git a/src/app/configuration.mock.service.ts b/src/app/configuration.mock.service.ts
index f6e57a16..e3495360 100644
--- a/src/app/configuration.mock.service.ts
+++ b/src/app/configuration.mock.service.ts
@@ -15,14 +15,13 @@ export class MockConfigurationService {
       javaLogoutURL: "http://localhost:8080/metabolights/logout",
       redirectURL: "console",
       metabolightsWSURL: {
-        domain: "https://www.ebi.ac.uk/metabolights/",
         baseURL: "https://www.ebi.ac.uk/metabolights/ws",
         guides:
-          "https://raw.githubusercontent.com/EBI-Metabolights/guides/test/",
-        ontologyDetails: "https://www.ebi.ac.uk/ols/api/ontologies/",
+          "https://raw.githubusercontent.com/EBI-Metabolights/guides/test",
+        ontologyDetails: "https://www.ebi.ac.uk/ols/api/ontologies",
       },
       doiWSURL: {
-        article: "https://api.crossref.org/works/",
+        article: "https://api.crossref.org/works",
       },
       europePMCURL: {
         article:
diff --git a/src/app/services/metabolights/metabolights.service.ts b/src/app/services/metabolights/metabolights.service.ts
index ec3d9f98..df90e26c 100644
--- a/src/app/services/metabolights/metabolights.service.ts
+++ b/src/app/services/metabolights/metabolights.service.ts
@@ -55,6 +55,15 @@ export class MetabolightsService extends DataService {
   ) {
     super("", http);
     this.url = this.configService.config.metabolightsWSURL;
+    if(this.url.ontologyDetails.endsWith("/")){
+      this.url.ontologyDetails=  this.url.ontologyDetails.slice(0, -1);
+    }
+    if(this.url.baseURL.endsWith("/")){
+      this.url.baseURL=  this.url.baseURL.slice(0, -1);
+    }
+    if(this.url.guides.endsWith("/")){
+      this.url.guides=  this.url.guides.slice(0, -1);
+    }
     this.studyIdentifier.subscribe((value) => (this.id = value));
     this.stateStudy.subscribe((value) => (this.study = value));
   }
diff --git a/src/app/services/publications/doi.service.ts b/src/app/services/publications/doi.service.ts
index 0cee11a5..a0be0fa3 100644
--- a/src/app/services/publications/doi.service.ts
+++ b/src/app/services/publications/doi.service.ts
@@ -14,10 +14,13 @@ export class DOIService extends DataService {
   constructor(http: HttpClient, private configService: ConfigurationService) {
     super("", http);
     this.url = this.configService.config.doiWSURL;
+    if(this.url.article.endsWith("/")){
+      this.url.article =  this.url.article.slice(0, -1);
+    }
   }
 
   getArticleInfo(doi): Observable<ICrossRefDOI> {
-    return this.http.get<ICrossRefDOI>(this.url.article + doi).pipe(
+    return this.http.get<ICrossRefDOI>(this.url.article + "/" + doi).pipe(
       map((res) => this.extractArticleDetails(res)),
       catchError(this.handleError)
     );
@@ -25,7 +28,7 @@ export class DOIService extends DataService {
 
   getArticleKeyWords(doi): Observable<ICrossRefDOI> {
     return this.http
-      .get<ICrossRefDOI>(this.url.article + doi)
+      .get<ICrossRefDOI>(this.url.article + "/" + doi)
       .pipe(catchError(this.handleError));
   }
 
diff --git a/src/assets/configs/validations.json b/src/assets/configs/validations.json
index bc1c9062..afb0f5c3 100644
--- a/src/assets/configs/validations.json
+++ b/src/assets/configs/validations.json
@@ -17,7 +17,7 @@
         "recommended-ontologies": {
           "is-forced-ontology": "false",
           "ontology": {
-            "url": "ws/ebi-internal/ontology?term=",
+            "url": "/ebi-internal/ontology?term=",
             "allowFreeText": true
           }
         }
@@ -252,7 +252,7 @@
           "recommended-ontologies": {
             "is-forced-ontology": "true",
             "ontology": {
-              "url": "ws/ebi-internal/ontology?branch=role&term=",
+              "url": "/ebi-internal/ontology?branch=role&term=",
               "allowFreeText": false
             }
           }
@@ -355,7 +355,7 @@
           "recommended-ontologies": {
             "is-forced-ontology": "true",
             "ontology": {
-              "url": "ws/ebi-internal/ontology?branch=publication&term=",
+              "url": "/ebi-internal/ontology?branch=publication&term=",
               "allowFreeText": true
             }
           }
@@ -381,7 +381,7 @@
       "recommended-ontologies": {
         "is-forced-ontology": "false",
         "ontology": {
-          "url": "ws/ebi-internal/ontology?branch=design%20descriptor&term=",
+          "url": "/ebi-internal/ontology?branch=design%20descriptor&term=",
           "allowFreeText": true
         }
       }
@@ -1278,7 +1278,7 @@
           "recommended-ontologies": {
             "is-forced-ontology": "false",
             "ontology": {
-              "url": "ws/ebi-internal/ontology?branch=factor&term=",
+              "url": "/ebi-internal/ontology?branch=factor&term=",
               "allowFreeText": true
             }
           }
@@ -1326,7 +1326,7 @@
           "recommended-ontologies": {
             "is-forced-ontology": "false",
             "ontology": {
-              "url": "ws/ebi-internal/ontology?branch=factor&term=",
+              "url": "/ebi-internal/ontology?branch=factor&term=",
               "allowFreeText": true
             }
           }
@@ -1365,7 +1365,7 @@
             "recommended-ontologies": {
               "is-forced-ontology": "false",
               "ontology": {
-                "url": "ws/ebi-internal/ontology?branch=taxonomy&term=",
+                "url": "/ebi-internal/ontology?branch=taxonomy&term=",
                 "allowFreeText": true
               }
             }
@@ -1396,7 +1396,7 @@
             "recommended-ontologies": {
               "is-forced-ontology": "false",
               "ontology": {
-                "url": "ws/ebi-internal/ontology?branch=taxonomy&term=",
+                "url": "/ebi-internal/ontology?branch=taxonomy&term=",
                 "allowFreeText": true
               }
             }
@@ -1427,7 +1427,7 @@
             "recommended-ontologies": {
               "is-forced-ontology": "false",
               "ontology": {
-                "url": "ws/ebi-internal/ontology?branch=taxonomy&term=",
+                "url": "/ebi-internal/ontology?branch=taxonomy&term=",
                 "allowFreeText": true
               }
             }
@@ -1458,7 +1458,7 @@
             "recommended-ontologies": {
               "is-forced-ontology": "false",
               "ontology": {
-                "url": "ws/ebi-internal/ontology?branch=taxonomy&term=",
+                "url": "/ebi-internal/ontology?branch=taxonomy&term=",
                 "allowFreeText": true
               }
             }
@@ -1493,7 +1493,7 @@
         "recommended-ontologies": {
           "is-forced-ontology": "false",
           "ontology": {
-            "url": "ws/ebi-internal/ontology?branch=factor&term=",
+            "url": "/ebi-internal/ontology?branch=factor&term=",
             "allowFreeText": true
           }
         }
@@ -1512,7 +1512,7 @@
         "recommended-ontologies": {
           "is-forced-ontology": "false",
           "ontology": {
-            "url": "ws/ebi-internal/ontology?branch=unit&term=",
+            "url": "/ebi-internal/ontology?branch=unit&term=",
             "allowFreeText": true
           }
         }
diff --git a/src/environment.interface.ts b/src/environment.interface.ts
index 36ed1383..75e272ce 100644
--- a/src/environment.interface.ts
+++ b/src/environment.interface.ts
@@ -35,7 +35,6 @@ export interface VideoURL {
 }
 
 interface MWSURL {
-  domain: string; // the domain where editor is running IE localhost:4200/metabolights
   baseURL: string; // the base url for the metabolights webservice ie localhost:4200/metabolighrs/ws
   guides: string; // the url for the guides, usually found in our raw github repo.
   ontologyDetails: string; // the url for ebi's OLS service, usually https://www.ebi.ac.uk/ols/api/ontologies/