Merge pull request #116 from EBI-Metabolights/MTBLS-607-master

public non curated study management for master
EBI-Metabolights · May 28, 2024 · 23e9792 · 23e9792
2 parents a6fe709 + 8de5413
commit 23e9792
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Showing 15 changed files with 141 additions and 12 deletions.
diff --git a/src/app/components/console/console.component.css b/src/app/components/console/console.component.css
@@ -2,6 +2,11 @@
   border-radius: 4px !important;
 }
 
+.not-curated {
+  background-color: orange;
+  color: white;
+}
+
 .banner {
   font-size: 14px;
   color: red;

diff --git a/src/app/components/console/console.component.html b/src/app/components/console/console.component.html
@@ -122,14 +122,28 @@ <h2 class="has-text-weight-bold">
                 <div class="control py-0 mb0">
                   <div class="tags has-addons">
                     <span class="tag">Status</span>
-                    <span
-                      class="tag"
-                      [class.is-primary]="study.status == 'In Review'"
-                      [class.is-danger]="study.status == 'In Curation'"
-                      [class.is-warning]="study.status == 'Submitted'"
-                      [class.is-success]="study.status == 'Public'"
-                      >{{ study.status }}</span
-                    >
+                    <span *ngIf="study.status == 'Public'; else onlyStatus" >
+                      <span *ngIf="study.curationRequest == 'MANUAL_CURATION'; else noCuration"
+                        class="tag is-success"
+                        >{{ study.status }} - Curated
+                      </span>
+                      <ng-template #noCuration>
+                          <span
+                          class="tag not-curated"
+                          >{{ study.status }} - Not Curated
+                        </span>
+                      </ng-template>
+                  </span>
+                    <ng-template #onlyStatus>
+                        <span
+                          class="tag"
+                          [class.is-primary]="study.status == 'In Review'"
+                          [class.is-danger]="study.status == 'In Curation'"
+                          [class.is-warning]="study.status == 'Submitted'"
+                          [class.is-success]="study.status == 'Public'"
+                          >{{ study.status }}</span
+                        >
+                    </ng-template>
                   </div>
                 </div>
                 <div class="control py-0 mb0">

diff --git a/src/app/components/public/study/study.component.html b/src/app/components/public/study/study.component.html
@@ -72,6 +72,27 @@
       </div>
     </article>
   </div>
+  <div id="status-board" *ngIf="status == 'Public' && curationRequest  == 'NO_CURATION'">
+    <article class="message is-warning">
+      <div class="message-body">
+        <p>
+          <mat-icon class="mat-icon material-icons">info</mat-icon>
+          This study ({{ requestedStudy }}) is publicly accessible upon request from the submitter(s). It <b><u>is not curated</u></b> by MetaboLights team, however it passes the minimum validation requirements of MetaboLights.
+          <br/>
+          <br/>
+          If you have comments or suggestions, please get in touch with the submitter(s) or MetaboLights team (<b>
+            <a
+              [href]="
+                'mailto:[email protected]?subject=Regarding non-curated public study - ' +
+                requestedStudy
+              "
+              >metabolights-help&#64;ebi.ac.uk</a
+            ></b>).
+
+        </p>
+      </div>
+    </article>
+  </div>
   <div
     *ngIf="requestedStudy != undefined && !studyError"
     class="main-wrapper"

diff --git a/src/app/components/public/study/study.component.ts b/src/app/components/public/study/study.component.ts
@@ -23,6 +23,7 @@ export class PublicStudyComponent implements OnInit {
   @select((state) => state.study.identifier) studyIdentifier;
   @select((state) => state.status.user) user;
   @select((state) => state.study.status) studyStatus;
+  @select((state) => state.study.curationRequest) curationRequestState;
   @select((state) => state.study.validation) studyValidation;
   @select((state) => state.status.currentTabIndex) currentIndex: number;
   @select((state) => state.study.investigationFailed) investigationFailed;
@@ -35,6 +36,7 @@ export class PublicStudyComponent implements OnInit {
   status = "submitted";
   tab = "descriptors";
   requestedStudy: string = null;
+  curationRequest = ""
   studyError = false;
   validation: any = {};
   files: any = null;
@@ -139,6 +141,12 @@ export class PublicStudyComponent implements OnInit {
       }
     });
 
+    this.curationRequestState.subscribe((value) => {
+      if(value){
+        this.curationRequest = value;
+      }
+    });
+
     this.studyReviewerLink.subscribe((value) => {
       this.reviewerLink = value;
     });

diff --git a/src/app/components/store.ts b/src/app/components/store.ts
@@ -37,6 +37,7 @@ export const SHARED_INITIAL_STATE: Record<string, any> = {
   info: "",
   configuration: "",
   isCurator: false,
+  curationRequest: null,
   user: null,
   error: false,
   message: "",

diff --git a/src/app/components/study/actions.ts b/src/app/components/study/actions.ts
@@ -5,6 +5,8 @@ export const SET_STUDY_ABSTRACT = "SET_STUDY_ABSTRACT";
 export const SET_STUDY_SUBMISSION_DATE = "SET_STUDY_SUBMISSION_DATE";
 export const SET_STUDY_RELEASE_DATE = "SET_STUDY_RELEASE_DATE";
 export const SET_STUDY_STATUS = "SET_STUDY_STATUS";
+export const SET_STUDY_CURATION_REQUEST = "SET_STUDY_CURATION_REQUEST";
+
 export const SET_STUDY_REVIEWER_LINK = "SET_STUDY_REVIEWER_LINK";
 
 export const SET_STUDY_PUBLICATIONS = "SET_STUDY_PUBLICATIONS";

diff --git a/src/app/components/study/status/status.component.css b/src/app/components/study/status/status.component.css
@@ -1,3 +1,7 @@
 .error-message {
   color: red;
 }
+.not-curated {
+  background-color: orange;
+  color: white;
+}
diff --git a/src/app/components/study/status/status.component.html b/src/app/components/study/status/status.component.html
@@ -1,9 +1,32 @@
 <div class="control">
   <div class="tags has-addons">
     <span class="tag is-dark">Status</span>
-    <span class="tag is-link clickable" (click)="openModal()">{{
-      status
-    }}</span>
+    <div *ngIf="status == 'Public'; else onlyStatus" >
+      <span *ngIf="curationRequest == 'MANUAL_CURATION'; else noCuration">
+        <span class="tag is-link clickable" (click)="openModal()">
+          {{
+            status
+          }} - Curated
+        </span>
+      </span>
+    <ng-template #noCuration>
+      <span class="tag clickable not-curated" (click)="openModal()">
+        {{
+          status
+        }} - Not Curated
+      </span>
+    </ng-template>
+  </div>
+
+    <ng-template #onlyStatus>
+      <span class="tag is-link clickable" (click)="openModal()">
+        {{
+          status
+        }}
+
+      </span>
+    </ng-template>
+
   </div>
 </div>
 <div class="modal" [ngClass]="{ 'is-active': isModalOpen }">

diff --git a/src/app/components/study/status/status.component.ts b/src/app/components/study/status/status.component.ts
@@ -24,6 +24,7 @@ export class StatusComponent implements OnInit {
   @select((state) => state.study.validation) studyValidation;
   @select((state) => state.status.isCurator) isCurator;
   @select((state) => state.study.identifier) studyIdentifier;
+  @select((state) => state.study.curationRequest) curationRequestState;
 
   @select((state) => state.study.readonly) readonly;
   isReadOnly = false;
@@ -33,6 +34,7 @@ export class StatusComponent implements OnInit {
   status: string = null;
   curator = false;
   toStatus = "Submitted";
+  curationRequest: string = null;
   requestedStudy: string = null;
   validation: IValidationSummary;
   constructor(
@@ -43,6 +45,9 @@ export class StatusComponent implements OnInit {
   }
 
   setUpSubscriptions() {
+    this.curationRequestState.subscribe((value) => {
+      this.curationRequest = value;
+    });
     this.studyValidation.subscribe((value) => {
       this.validation = value;
     });

diff --git a/src/app/components/study/store.ts b/src/app/components/study/store.ts
@@ -14,6 +14,7 @@ import {
   SET_STUDY_SUBMISSION_DATE,
   SET_STUDY_RELEASE_DATE,
   SET_STUDY_STATUS,
+  SET_STUDY_CURATION_REQUEST,
   SET_STUDY_REVIEWER_LINK,
   SET_STUDY_ASSAYS,
   SET_STUDY_PUBLICATIONS,
@@ -116,6 +117,10 @@ function setStudyStatus(state, action) {
   return tassign(state, { status: action.body.study.mtblsStudy.studyStatus });
 }
 
+function setCurationRequest(state, action) {
+  return tassign(state, { curationRequest: action.body.study.mtblsStudy.curationRequest });
+}
+
 function setStudyReviewerLink(state, action) {
   return tassign(state, {
     reviewerLink: action.body.study.mtblsStudy.reviewer_link,
@@ -349,9 +354,10 @@ export function studyReducer(
       return setStudyTitle(state, action);
     case SET_STUDY_ABSTRACT:
       return setStudyAbstract(state, action);
-
     case SET_STUDY_STATUS:
       return setStudyStatus(state, action);
+    case SET_STUDY_CURATION_REQUEST:
+      return setCurationRequest(state, action);
     case SET_STUDY_REVIEWER_LINK:
       return setStudyReviewerLink(state, action);
 

diff --git a/src/app/components/study/study.component.html b/src/app/components/study/study.component.html
@@ -83,7 +83,27 @@
       </div>
     </article>
   </div>
+  <div id="status-board" *ngIf="status == 'Public' && curationRequest  == 'NO_CURATION'">
+    <article class="message is-warning">
+      <div class="message-body">
+        <p>
+          <mat-icon class="mat-icon material-icons">info</mat-icon>
+          Your study ({{ requestedStudy }}) is publicly accessible. It <b><u>is not curated</u></b> by MetaboLights team, however it passes the minimum validation requirements of MetaboLights.
+          <br/>
+          <br/>
+          If you have comments or suggestions, please get in touch with MetaboLights team (<b>
+            <a
+              [href]="
+                'mailto:[email protected]?subject=Regarding non-curated public study - ' +
+                requestedStudy
+              "
+              >metabolights-help&#64;ebi.ac.uk</a
+            ></b>).
 
+        </p>
+      </div>
+    </article>
+  </div>
   <div class="main-wrapper" [ngClass]="{ smt: status != 'Submitted' }">
     <div style="margin: 20px">
       <article class="message is-small has-shadow">
@@ -277,6 +297,7 @@
       </div>
     </span>
   </div>
+
 </div>
 <span class="second-bottom-right">
   <a (click)="topFunction()" id="scrollToTop" class="button is-rounded">

diff --git a/src/app/components/study/study.component.ts b/src/app/components/study/study.component.ts
@@ -17,6 +17,8 @@ export class StudyComponent implements OnInit, OnDestroy {
   @select((state) => state.study.validation) studyValidation;
   @select((state) => state.status.currentTabIndex) currentIndex: number;
   @select((state) => state.study.status) studyStatus;
+  @select((state) => state.study.curationRequest) curationRequestState;
+
   @select((state) => state.study.obfuscationCode) studyObfuscationCode;
 
   @select((state) => state.status.bannerMessage) bannerMessage;
@@ -28,6 +30,7 @@ export class StudyComponent implements OnInit, OnDestroy {
   requestedTab = 0;
   tab = "descriptors";
   requestedStudy: string = null;
+  curationRequest = ""
   status = "submitted";
   validation: any = {};
   obfuscationCode: string = null;
@@ -89,6 +92,12 @@ export class StudyComponent implements OnInit, OnDestroy {
       this.status = value;
     });
 
+    this.curationRequestState.subscribe((value) => {
+      if(value){
+        this.curationRequest = value;
+      }
+    });
+
     this.studyValidation.subscribe((value) => {
       this.validation = value;
     });

diff --git a/src/app/models/mtbl/mtbls/interfaces/study-detail.interface.ts b/src/app/models/mtbl/mtbls/interfaces/study-detail.interface.ts
@@ -6,6 +6,7 @@ export interface IStudyDetail {
   status: string;
   title: string;
   description: string;
+  curationRequest: string;
 }
 
 export interface IStudyDetailWrapper {

diff --git a/src/app/models/mtbl/mtbls/interfaces/study-summary.interface.ts b/src/app/models/mtbl/mtbls/interfaces/study-summary.interface.ts
@@ -10,6 +10,9 @@ export interface IStudySummary {
 /*Interface to represent the minute study information returned by our IsaInvestigation endpoint*/
 export interface IMtblsStudySummaryInformation {
   studyStatus: string;
+  curationRequest: string;
+  modifiedTime: string;
+  statusUpdateTime: string;
   read_access: boolean;
   is_curator: boolean;
   write_access: boolean;

diff --git a/src/app/services/editor.service.ts b/src/app/services/editor.service.ts
@@ -654,6 +654,12 @@ export class EditorService {
             study,
           },
         });
+        this.ngRedux.dispatch({
+          type: "SET_STUDY_CURATION_REQUEST",
+          body: {
+            study,
+          },
+        });
         this.ngRedux.dispatch({
           type: "SET_STUDY_REVIEWER_LINK",
           body: {