BI-2380 - Add Delete Option to Samples View

src/breeding-insight/dao/SampleSubmissionDAO.ts

@@ -48,6 +48,20 @@ export class SampleSubmissionDAO {
     }
   }
 
+  static async deleteSubmission(programId: string, submissionId: string): Promise<Result<Error, Void>> {
+    const config: any = {};
+    config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/submissions/${submissionId}`;
+    config.method = 'delete';
+    config.programId = programId;
+    config.submissionId = submissionId;
+    try {
+      await api.call(config);
+      return ResultGenerator.success();
+    } catch (error) {
+      return ResultGenerator.err(error);
+    }
+  }
+
     static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
       const config: any = {};
       config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/submissions/${submissionId}/submit?vendor=dart`;

src/breeding-insight/service/SampleSubmissionService.ts

@@ -61,24 +61,30 @@ export class SampleSubmissionService {
     return await SampleSubmissionDAO.getSubmissionById(programId, submissionId, true);
   }
 
-    static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.submitToDArT(programId, submissionId);
+  static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.submitToDArT(programId, submissionId);
+  }
 
-    static async checkVendorStatus(programId: string, submissionId: string): Promise<Result<Error, SampleSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.checkVendorStatus(programId, submissionId);
+  static async checkVendorStatus(programId: string, submissionId: string): Promise<Result<Error, SampleSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.checkVendorStatus(programId, submissionId);
+  }
 
-    static async updateSubmissionStatus(programId: string, submissionId: string, status: string): Promise<Result<Error, SampleSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.updateSubmissionStatus(programId, submissionId, status);
+  static async updateSubmissionStatus(programId: string, submissionId: string, status: string): Promise<Result<Error, SampleSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.updateSubmissionStatus(programId, submissionId, status);
+  }
+
+  static async deleteSubmission(programId: string, submissionId: string) : Promise<Result<Error, Void>> {
+    return await SampleSubmissionDAO.deleteSubmission(programId, submissionId);
+  }
+
+
 }

src/config/ability.ts

@@ -56,6 +56,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('access', 'Ontology');
     can('access', 'Germplasm');
     can('access', 'SampleManagement');
+    can('delete', 'Submission');
     can('access', 'ProgramAdministration');
     can('access', 'BrAPI');
     can('access', 'JobManagement');
@@ -73,6 +74,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('manage', 'User');
     can('access', 'AdminSection');
     can('submit', 'Submission');
+    can('delete', 'Submission');
     can('access', 'Experiment');
     can('access', 'Ontology');
     can('access', 'Germplasm');

src/views/sample-mgmt/SampleManagement.vue

@@ -99,18 +99,6 @@
         </ExpandableTable>
       </div>
     </div>
-    <GenericModal
-        v-bind:active.sync="showGenerateFileModal"
-        v-bind:msg-title="'Generate Sample Management File'"
-        v-on:deactivate="closeModal()"
-        v-bind:modalClass="'generate-sample-file'"
-    >
-      <h2>Visible!</h2>
-      <template v-slot:footer>
-        <button class="button is-success" v-on:click="closeModal()">Generate</button>
-        <button class="button" v-on:click="closeModal()">Cancel</button>
-      </template>
-    </GenericModal>
   </div>
 </template>
 

src/views/sample-mgmt/SubmissionDetails.vue

@@ -19,6 +19,24 @@
     <router-link v-bind:to="{name: 'sample-management', params: {programId: activeProgram.id}}">
       &lt; Sample Management
     </router-link>
+
+    <template v-if="!submissionDetailsLoading">
+      <ConfirmationModal
+          v-bind:unique-id="submissionId"
+          v-bind:modal-title="`Delete Submission ${submission.name}`"
+          v-bind:confirmedAction="deleteSampleSubmission"
+          v-bind:active="deleteModalActive"
+          modal-class="germplasm-list-deletion-button"
+          v-on:deactivate="deleteModalActive = false"
+          v-on:show-error-notification="$emit('show-error-notification', $event)"
+      >
+        <template #form>
+          <p><strong>{{submission.samples.length}} samples</strong> will be deleted. Are you sure you want to delete the sample submission?</p>
+        </template>
+        <slot />
+      </ConfirmationModal>
+    </template>
+
     <div class="mb-4"/>
     <template v-if="submissionLoading">
       <div class="loading-indicator"></div>
@@ -62,6 +80,7 @@
                       v-on:submit="startOrderSubmission()"
                       v-on:manual-update-status="startManualUpdate()"
                       v-on:check-status="checkVendorStatus()"
+                      v-on:delete="deleteSubmission()"
           />
         </article>
       </div>
@@ -358,15 +377,17 @@ import StatusEnum = VendorOrderStatusResponseResult.StatusEnum;
 import {Plate} from "@/breeding-insight/brapi/model/geno/plate";
 import * as XLSX from "xlsx";
 import {WorkBook} from "xlsx";
+import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 
 @Component({
   components: {
+    ConfirmationModal,
     GenericModal,
     ExpandableTable,
     GermplasmLink,
     PlusCircleIcon,
     ExperimentObservationsDownloadModal,
-    ActionMenu
+    ActionMenu,
   },
   computed: {
     ...mapGetters([
@@ -392,6 +413,7 @@ export default class SubmissionDetails extends ProgramsBase {
   private showUpdateModal = false;
   private updateStarted = false;
   private statusEdit?: string = 'NOT SUBMITTED';
+  private deleteModalActive: boolean = false;
 
   private collator = new Intl.Collator('en', {numeric: true, sensitivity: 'base'});
 
@@ -406,6 +428,12 @@ export default class SubmissionDetails extends ProgramsBase {
     return this.$route.params.submissionId;
   }
 
+  private deleteSuccess() {
+    // Navigate to the submissions table since this submission no longer exists
+    this.$router.push({ name: "sample-management" });
+    this.$emit('show-success-notification', `Successfully deleted sample submission`);
+  }
+
   async getSubmission(showLoading: boolean = true) {
     this.submissionLoading = showLoading;
 
@@ -447,6 +475,12 @@ export default class SubmissionDetails extends ProgramsBase {
       }
     }
 
+    if (this.$ability.can('delete', 'Submission')) {
+      const enabled = !this.submission!.submitted && this.submission!.vendorStatus !== StatusEnum.Completed.toUpperCase();
+
+      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete submission', enabled));
+    }
+
     this.actions = actionsMenuItems;
   }
 
@@ -717,5 +751,36 @@ export default class SubmissionDetails extends ProgramsBase {
     let value = props.data.additionalInfo.gid;
     return Number(value) === (Number(input));
   }
+
+  deleteSubmission() {
+    this.deleteModalActive = true;
+  }
+
+  async deleteSampleSubmission(): Promise<void> {
+    if (this.activeProgram) {
+      try {
+        const result: Result<Error, Void> = await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
+        if (result.isErr()) {
+          const response = result.value.response;
+
+          if (response && response.status === 405) {
+            this.$emit('show-error-notification', `Cannot delete a submission with submitted or completed status`);
+            return;
+          }
+          this.$emit('show-error-notification', `Unknown error deleting submission`);
+
+        } else {
+          this.deleteSuccess();
+        }
+
+      } catch (error) {
+        this.$emit('show-error-notification', `Error while trying to delete the sample submission`);
+      }
+    }
+  }
+
+  cancelDelete(){
+    this.$emit('deactivate');
+  }
 }
 </script>