MTBLS assignment after validation

.gitlab-ci.yml

@@ -1,5 +1,5 @@
 variables:
-  APP_VERSION: "2.1.0"
+  APP_VERSION: "2.2.0"
 workflow:
   rules:
   - if: $CI_COMMIT_BRANCH == "test" || $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "main" || $CI_COMMIT_BRANCH == "staging" || $CI_COMMIT_BRANCH == "development" || $CI_COMMIT_BRANCH == "migration"

src/app/auth-guard.service.ts

@@ -151,7 +151,11 @@ export class AuthGuard  implements OnInit {
     let obfuscationCode = null;
     if (url.startsWith("/MTBLS")) {
       studyIdentifier = url.split("/")[1];
-    } else if (url.startsWith("/study/MTBLS")) {
+    }if (url.startsWith("/REQ")) {
+      studyIdentifier = url.split("/")[1];
+    }else if (url.startsWith("/study/MTBLS")) {
+      studyIdentifier = url.split("/")[2];
+    }else if (url.startsWith("/study/REQ")) {
       studyIdentifier = url.split("/")[2];
     } else if (url.startsWith("/reviewer")) {
       obfuscationCode = url.split("/")[1].replace("reviewer", "");
@@ -236,14 +240,15 @@ export class AuthGuard  implements OnInit {
   }
 
   async checkStudyUrl(url: string, studyId: string, state: RouterStateSnapshot) {
-    const regEx = new RegExp('^(MTBLS[1-9][0-9]{0,10})($|\\?)', 'g');
+    const regEx = new RegExp('^((MTBLS[1-9][0-9]{0,10})|(REQ[0-9]{1,20}))($|\\?)', 'g');
     const studyIdResults = studyId.match(regEx);
     if (studyIdResults === null || studyIdResults.length === 0) {
-      this.editorService.redirectUrl = url;
-      const errorCode = "E-0001-003";
-      this.router.navigate(["/study-not-found"], { queryParams: { code: errorCode } });
-      return false;
+        this.editorService.redirectUrl = url;
+        const errorCode = "E-0001-003";
+        this.router.navigate(["/study-not-found"], { queryParams: { code: errorCode } });
+        return false;
     }
+
     let studyIdentifier = studyIdResults[0];
     if (studyIdentifier.endsWith("?")) {
       studyIdentifier = studyIdResults[0].slice(0, -1);

src/app/components/guide/create/create.component.html

@@ -10,14 +10,14 @@
             class="is-pulled-left"
             src="{{ baseHref }}assets/img/MetaboLightsLogo.png"
           />
-          <span style="margin-left: 10px">New Study - Get started</span>
+          <span style="margin-left: 10px">New Submission - Get started</span>
         </div>
         <div class="panel-block">
           <div class="column">
             <h3>
               The following steps will guide you through creating your
-              metabolomics study. Once submitted you can view and edit your
-              study through the MetaboLights website.
+              metabolomics study submission request. Once created you can view and edit your
+              submission through the MetaboLights website.
             </h3>
             <br />
             <br />
@@ -27,7 +27,7 @@ <h3>
               >
                 <div class="column">
                   <p class="has-text-centered">
-                    <mat-icon>info</mat-icon> Once you create your study, you
+                    <mat-icon>info</mat-icon> Once you create a request, you
                     can switch between the guided submission and full study view
                     where you see these buttons.
                   </p>
@@ -73,7 +73,7 @@ <h3>
             src="{{ baseHref }}assets/img/MetaboLightsLogo.png"
           />
           <span style="margin-left: 10px"
-            >New Study - Raw / Derived data files</span
+            >New Request - Raw / Derived data files</span
           >
         </div>
         <div class="panel-block">
@@ -135,13 +135,12 @@ <h3>
             class="is-pulled-left"
             src="{{ baseHref }}assets/img/MetaboLightsLogo.png"
           />
-          <span style="margin-left: 10px">New Study - Identifier</span>
+          <span style="margin-left: 10px">New Request</span>
         </div>
         <div class="panel-block">
           <div class="column">
-            <h3><b>MetaboLights study</b></h3>
             <p>
-              Your study has been assigned the unique identifier
+              Your study request has been assigned wit an identifier
               <span class="has-text-link"
                 ><b>{{ newStudy }}</b></span
               >
@@ -152,17 +151,9 @@ <h3><b>MetaboLights study</b></h3>
             <br />
             <h3><b>How to reference your MetaboLights study</b></h3>
             <p>
-              Please use {{ newStudy }} when referencing this study in
-              manuscripts etc. together with the URL
-              <a href="www.ebi.ac.uk/metabolights/{{ newStudy }}"
-                ><b
-                  ><span class="has-text-link"
-                    >www.ebi.ac.uk/metabolights/{{ newStudy }}</span
-                  ></b
-                ></a
-              >
+              A MetaboLights accession number will be assigned to your study after you complete the submission. Please upload your dateset and complete the study metadata as soon as possible.
               <br /><br />
-              <b>Please also cite the following MetaboLights paper</b> <br />
+              <b>While citing MetaboLights, please cite the following paper: </b> <br />
               <a
                 target="_blank"
                 href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1045/7424432"

src/app/components/guide/meta/meta.component.html

@@ -205,7 +205,7 @@ <h3 class="mb5">Do you have a manuscript?</h3>
         </div>
         <div class="panel-block">
           <button
-            (click)="saveMetaData()"
+            (click)="saveMetadataNgxs()"
             class="button is-success is-fullwidth"
           >
             <mat-spinner
@@ -269,7 +269,7 @@ <h3 class="mb5">Do you have a manuscript?</h3>
         </span>
       </div>
       <div class="panel-block">
-        <button (click)="saveMetaData()" class="button is-success is-fullwidth">
+        <button (click)="saveMetadataNgxs()" class="button is-success is-fullwidth">
           <mat-spinner
             [diameter]="20"
             [strokeWidth]="3"
@@ -334,7 +334,7 @@ <h3 class="mb5">Do you have a manuscript?</h3>
         </span>
       </div>
       <div class="panel-block">
-        <button (click)="saveMetaData()" class="button is-success is-fullwidth">
+        <button (click)="saveMetadataNgxs()" class="button is-success is-fullwidth">
           <mat-spinner
             [diameter]="20"
             [strokeWidth]="3"

src/app/components/guide/meta/meta.component.ts

@@ -179,12 +179,12 @@ export class MetaComponent implements OnInit {
   skipMetaData() {
     this.router.navigate(["/guide/assays", this.requestedStudy]);
   }
-  
+
 
   saveMetadataNgxs() {
     this.isLoading = true;
     if (this.isManuscriptValid()) {
-      this.store.dispatch(new Title.Update(this.manuscript.title)).subscribe(
+      this.store.dispatch(new Title.Update({"title": this.manuscript.title})).subscribe(
         (completed) => {
           this.store.dispatch(new StudyAbstract.Update(this.manuscript.abstract)).subscribe(
             (completed) => {
@@ -231,7 +231,7 @@ export class MetaComponent implements OnInit {
                   }
                 )
               } else {
-                this.router.navigate(["/guides/assays", this.requestedStudy]);
+                this.router.navigate(["/guide/assays", this.requestedStudy]);
               }
             },
             (error) => {

src/app/components/guide/progress/progress.component.html

@@ -9,13 +9,13 @@
       </span>
     </div>
     <div class="step-details">
-      <p *ngIf="!study" class="step-title">Create Study</p>
+      <p *ngIf="!study" class="step-title">Create a Request</p>
       <p *ngIf="study" class="step-title">
         <a
           [ngClass]="{ 'has-text-grey': step < 2 }"
           (click)="redirectTo('info', null, 1)"
         >
-          Study Created <br />
+          Request Created <br />
           {{ study }}</a
         >
       </p>

src/app/components/public/study/study.component.ts

@@ -201,7 +201,7 @@ export class PublicStudyComponent implements OnInit {
       .split("/")
       .filter((n) => n);
     if (urlSplit.length >= 2) {
-      if (urlSplit[urlSplit.length - 1].indexOf("MTBLS") < 0) {
+      if (urlSplit[urlSplit.length - 1].indexOf("MTBLS") < 0 && urlSplit[urlSplit.length - 1].indexOf("REQ") < 0) {
         urlSplit.pop();
       }
     }

src/app/components/shared/add-assay/add-assay.component.html

@@ -143,7 +143,8 @@ <h3 class="mb5">Define assay</h3>
         <span
           *ngIf="
             selectedAssayTechnologyOption != null &&
-            selectedAssayTypeOption != null
+            selectedAssayTypeOption != null &&
+            selectedAssayVariantOption != null
           "
         >
           <button (click)="addAssay()" class="button is-primary">

src/app/components/shared/ontology/ontology.component.html

@@ -38,9 +38,9 @@
               />
             </mat-option>
           </span>
-          <!--<ng-template #showMore>
+          <ng-template #showMore>
             <mat-option><small>search more terms on ontology sources</small></mat-option>
-          </ng-template>-->
+          </ng-template>
         </span>
         <mat-option
           class="bb"

src/app/components/shared/ontology/ontology.component.ts

@@ -162,7 +162,7 @@ export class OntologyComponent implements OnInit, OnChanges {
       if (values) {
         let match = false;
         this.values.forEach((ontology) => {
-          if (!match && ontology.annotationValue  && ontology.annotationValue === value.annotationValue
+          if (!match && ontology && ontology.annotationValue  && ontology.annotationValue === value.annotationValue
             && ontology.termAccession && ontology.termAccession === value.termAccession
             && ontology.termSource && ontology.termSource === value.termSource
             ) {

src/app/components/study/assays/assay-details/assay-details.component.ts

@@ -84,7 +84,7 @@ export class AssayDetailsComponent implements OnInit {
 
     });
     this.studySamples$.subscribe((value) => {
-      if (value.data) {
+      if (value && value.data) {
         this.sampleNames = value.data.rows.map((r) => r["Sample Name"]);
         this.filteredSampleNames = this.sampleNames;
       }

src/app/components/study/factors/factor/factor.component.html

@@ -53,7 +53,7 @@
         </div>
         <div class="timeline-item">
           <div class="timeline-marker is-image is-32x32">
-            <img src="https://bulma.io/images/placeholders/32x32.png" />
+            <img src="assets/img/file.png" />
           </div>
           <div class="timeline-content">
             <p class="heading">February 2016</p>

src/app/components/study/files/rsync/rsync-status-transform.pipe.ts

@@ -14,7 +14,7 @@ export class RsyncStatusTransformPipe implements PipeTransform {
         CALCULATION_FAILURE: 'Check failure',
         NOT_FOUND: "No Task Found",
         PENDING: 'Task is in Queue ...',
-        RUNNING: 'TAsk is running ...',
+        RUNNING: 'Task is running ...',
         COMPLETED_SUCCESS: "Task completed. Sync Completed",
         SYNC_FAILURE: "Sync failure",
         START_FAILURE: "Start failure",

src/app/components/study/protocols/protocol/protocol.component.ts

@@ -101,7 +101,7 @@ export class ProtocolComponent implements OnInit, OnChanges {
     });
 
     this.readonly$.subscribe((value) => {
-      if (value !== null) {
+      if (value !== null && this.protocol) {
         this.isStudyReadOnly = value;
         if(!this.isStudyReadOnly) {
           this.protocolGuides$.subscribe((value) => {
@@ -426,7 +426,7 @@ export class ProtocolComponent implements OnInit, OnChanges {
           /**
            * This is an extraordinary antipattern but don't have much of a choice,
            * we can't change the components current protocol via the state without destroying
-           * the component that has the modal rendered. 
+           * the component that has the modal rendered.
            */
           this.protocolSubscription = this.store.select(ProtocolsState.specificProtocol(name))
           .subscribe(
@@ -435,7 +435,7 @@ export class ProtocolComponent implements OnInit, OnChanges {
               this.openModal(this.protocol);
             }
           )
-        
+
         }
         toastr.success(message, "Success", this.toastrSettings)
 

src/app/components/study/status/status.component.ts

@@ -7,7 +7,7 @@ import {
   SimpleChanges,
 } from "@angular/core";
 import Swal from "sweetalert2";
-import { ActivatedRoute } from "@angular/router";
+import { ActivatedRoute, Router } from "@angular/router";
 import { EditorService } from "../../../services/editor.service";
 import * as toastr from "toastr";
 import { environment } from "src/environments/environment";
@@ -19,6 +19,7 @@ import { ValidationState } from "src/app/ngxs-store/study/validation/validation.
 import { ApplicationState } from "src/app/ngxs-store/non-study/application/application.state";
 import { UserState } from "src/app/ngxs-store/non-study/user/user.state";
 import { StudyStatus } from "src/app/ngxs-store/study/general-metadata/general-metadata.actions";
+import { Loading, SetLoadingInfo } from "src/app/ngxs-store/non-study/transitions/transitions.actions";
 
 @Component({
   selector: "mtbls-status",
@@ -51,7 +52,8 @@ export class StatusComponent implements OnInit {
   constructor(
     private editorService: EditorService,
     private route: ActivatedRoute,
-    private store: Store
+    private store: Store,
+    private router: Router,
   ) {
       this.setUpSubscriptionsNgxs();
   }
@@ -65,9 +67,16 @@ export class StatusComponent implements OnInit {
       this.validation = value;
     });
     this.studyStatus$.subscribe((value) => {
+      this.closeModal();
+      this.store.dispatch(new Loading.Disable())
       if (value !== null) {
+        const prevStatus = this.status
         this.status = value;
         this.toStatus = value;
+        if (prevStatus !== null && this.requestedStudy && this.status !== prevStatus) {
+          toastr.success("Study status updated.", "Success", this.toastrSettings);
+          this.router.navigate(["/study", this.requestedStudy]);
+        }
       }
     });
     this.isCurator$.subscribe((value) => {
@@ -105,17 +114,16 @@ export class StatusComponent implements OnInit {
         cancelButtonText: "Back",
       }).then((willChange) => {
         if (willChange.value) {
+
+          this.store.dispatch(new Loading.Enable())
+          this.store.dispatch(new SetLoadingInfo("Updating study status ..."))
+          this.closeModal();
           this.store.dispatch(new StudyStatus.Update(toStatus)).subscribe(
             (completed) => {
-              this.closeModal();
-              toastr.success("Study status updated.", "Success", this.toastrSettings);
-              let readonly = true;
-              if (this.curator) readonly = false;
-              if (toStatus === 'Submitted') readonly = false;
-              this.editorService.loadStudyNgxs(this.requestedStudy, false);
 
             }, (error) => {
               this.closeModal();
+              this.store.dispatch(new Loading.Disable())
               this.toStatus = this.status;
               let message = null;
               typeof error.json === 'function' ? message = error.json().message : "Could not update study status."

src/app/components/study/study.component.ts

@@ -154,7 +154,7 @@ export class StudyComponent implements OnInit, OnDestroy {
       .split("/")
       .filter((n) => n);
     if (urlSplit.length >= 3) {
-      if (urlSplit[urlSplit.length - 1].indexOf("MTBLS") < 0) {
+      if (urlSplit[urlSplit.length - 1].indexOf("MTBLS") < 0 && urlSplit[urlSplit.length - 1].indexOf("REQ") < 0) {
         urlSplit.pop();
       }
     }

src/app/ngxs-store/study/general-metadata/general-metadata.state.ts

@@ -380,7 +380,21 @@ export class GeneralMetadataState {
         const state = ctx.getState();
         this.generalMetadataService.changeStatus(action.status, state.id).subscribe(
             (response) => {
-                ctx.dispatch(new StudyStatus.Set(action.status));
+                const state = ctx.getState();
+                let updated_study_id = state.id;
+                if (response.hasOwnProperty("assigned_study_id")){
+                  updated_study_id = response["assigned_study_id"]
+                  if (state.id !== updated_study_id) {
+                    ctx.dispatch(new Identifier.Set(updated_study_id));
+                  }
+                }
+                let assigned_status = action.status;
+                if (response.hasOwnProperty("assigned_status")){
+                  assigned_status = response["assigned_status"]
+                }
+                if (assigned_status !== state.status) {
+                  ctx.dispatch(new StudyStatus.Set(assigned_status));
+                }
             }
         )
     }

src/assets/configs/validations.json

@@ -2488,24 +2488,6 @@
                 ]
               }
             ]
-          },
-          {
-            "name": "Company/Institutional partner template",
-            "value": "template",
-            "color": "is-danger",
-            "disabled": false,
-            "techniques": [
-              {
-                "name": "Metabolon study",
-                "value": "metabolon",
-                "disabled": true
-              },
-              {
-                "name": "Imperial Phenome Center",
-                "value": "imperial",
-                "disabled": true
-              }
-            ]
           }
         ]
       }