[BI-1720] - Export Multiple Environment Datasets as Zip

src/assets/scss/main.scss

@@ -900,3 +900,9 @@ tr:nth-child(odd) td.db-filled {
     display: block;
   }
 }
+
+label.environment-option-label {
+  white-space: nowrap;
+  overflow: hidden;
+  text-overflow: ellipsis;
+}

src/breeding-insight/dao/ExperimentDAO.ts

@@ -19,8 +19,6 @@ import {BiResponse, Response} from "@/breeding-insight/model/BiResponse";
 import * as api from "@/util/api";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
 import {Trial} from "@/breeding-insight/model/Trial.ts";
-import * as UUID from "uuid";
-import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
 import {DatasetModel} from "@/breeding-insight/model/DatasetModel";
 
 export class ExperimentDAO {

src/breeding-insight/dao/StudyDAO.ts

@@ -23,15 +23,18 @@ import {BrAPIDAOUtil} from "@/breeding-insight/dao/BrAPIDAOUtil";
 
 export class StudyDAO {
 
-  static async getAllForTrial(programId: string, trialId: string): Promise<Result<Error, BiResponse>> {
+  static async getAllForTrial(programId: string, externalReferenceId: string): Promise<Result<Error, BiResponse>> {
+    // Use GET endpoint to get all Studies for a single Trial by external reference.
+    const { data } = await api.call({
+      url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/studies`,
+      method: 'get',
+      params: {
+        externalReferenceId: externalReferenceId,
+        externalReferenceSource: `${process.env.VUE_APP_BI_REFERENCE_SOURCE}/trials`,
+        pageSize: 1000000 }
+    }) as Response;
 
-    const body = {
-      trialDbIds: [
-        trialId
-      ]
-    };
-
-    return await BrAPIDAOUtil.search(`${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/search/studies`, body);
+    return ResultGenerator.success(new BiResponse(data));
   }
 
   static async getAll(programId: string, paginationQuery: PaginationQuery, full : boolean): Promise<Result<Error, BiResponse>> {

src/breeding-insight/model/ExperimentExportOptions.ts

@@ -17,15 +17,15 @@
 
 import {FileTypeOption} from "@/breeding-insight/model/FileTypeOption";
 import {ExperimentDatasetOption} from "@/breeding-insight/model/ExperimentDatasetOption";
-import {EnvironmentOption} from "@/breeding-insight/model/EnvironmentOption";
 
 // Stores the user selected options for Experiment Observation file export.
 export class ExperimentExportOptions {
 
     public fileExtension: string = FileTypeOption.xls.id;
     public dataset: string = ExperimentDatasetOption.observations.id;
-    public environments: string[] = [EnvironmentOption.all.id];
-    public includeTimestamps: string = 'Yes';
+    public environments: string[] = [];
+    public allEnvironments: boolean = false;
+    public includeTimestamps: string = 'No';
 
     public timestampsTrueFalseString(): string {
         if (this.includeTimestamps.toLowerCase() === 'yes')

src/breeding-insight/model/Study.ts

@@ -15,6 +15,8 @@
  * limitations under the License.
  */
 
+import {ExternalReferences} from "@/breeding-insight/brapi/model/externalReferences";
+
 export class Study {
   id?: string;
   name?: string;
@@ -24,6 +26,8 @@ export class Study {
   endDate?: Date | null;
   location?: string;
   active?: boolean;
+  externalReferences?: ExternalReferences;
+
 
   constructor(id?: string,
               name?: string,
@@ -32,7 +36,8 @@ export class Study {
               startDate?: string,
               endDate?: string,
               location?: string,
-              active?: boolean
+              active?: boolean,
+              externalReferences?: ExternalReferences
               ) {
     this.id = id;
     this.name = name;
@@ -50,13 +55,14 @@ export class Study {
     } else {
       this.active = true;
     }
+    this.externalReferences = externalReferences;
   }
 
   static assign(study: Study): Study {
     const start: string | undefined = study.startDate ? study.startDate.toISOString() : undefined;
     const end: string | undefined = study.endDate ? study.endDate.toISOString() : undefined;    
 
-    return new Study(study.id, study.name, study.description, study.type, start, end, study.location, study.active);
+    return new Study(study.id, study.name, study.description, study.type, start, end, study.location, study.active, study.externalReferences);
   }
 
   equals(study?: Study): boolean {

src/breeding-insight/service/BrAPIService.ts

@@ -44,7 +44,7 @@ export class BrAPIService {
       params['sortOrder'] = sort.order;
     }
     if (pagination.page || pagination.page == 0) { //have to account for 0-index pagination since 0 falsy
-      params ['page'] = pagination.page;
+      params['page'] = pagination.page;
     }
     if (pagination.pageSize) {
       params['pageSize'] = pagination.pageSize;

src/breeding-insight/service/ProgramService.ts

@@ -38,7 +38,7 @@ export class ProgramService {
       if (program.id === undefined) {
         ProgramDAO.create(program).then((biResponse) => {
           const result: any = biResponse.result;
-          const newProgram = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl);
+          const newProgram = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl, result.key);
           resolve(newProgram);
 
         }).catch((error) => {
@@ -68,7 +68,7 @@ export class ProgramService {
       if (program.id) {
         ProgramDAO.update(program.id, program).then((biResponse) => {
           const result: any = biResponse.result;
-          const newProgram = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl);
+          const newProgram = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl, result.key);
           resolve(newProgram);
 
         }).catch((error) => reject(error));
@@ -125,7 +125,7 @@ export class ProgramService {
 
       ProgramDAO.getOne(programId).then((biResponse) => {
         const result = biResponse.result;
-        const program = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl);
+        const program = new Program(result.id, result.name, result.species.id, result.numUsers, result.brapiUrl, result.key);
         resolve(program);
       }).catch((error) => reject(error));
 

src/breeding-insight/service/StudyService.ts

@@ -21,10 +21,11 @@ import {BiResponse, Metadata} from "@/breeding-insight/model/BiResponse";
 import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
 import {PaginationUtilities} from "@/breeding-insight/model/view_models/PaginationUtilities";
 import {Result, ResultGenerator } from "@/breeding-insight/model/Result";
+import {Trial} from "@/breeding-insight/model/Trial";
+import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
 
 export class StudyService {
-
-  static async getAll(programId: string, trialId?: string, paginationQuery?: PaginationQuery, full?: boolean): Promise<Result<Error, [Study[], Metadata]>> {
+  static async getAll(programId: string, trial?: Trial, paginationQuery?: PaginationQuery, full?: boolean): Promise<Result<Error, [Study[], Metadata]>> {
 
     if (paginationQuery === undefined){
       paginationQuery = new PaginationQuery(0, 0, true);
@@ -38,8 +39,11 @@ export class StudyService {
       if(!programId) throw new Error('missing or invalid program id');
 
       let response: Result<Error, BiResponse>;
-      if (trialId) {
-        response = await StudyDAO.getAllForTrial(programId, trialId) as Result<Error, BiResponse>;
+      if (trial !== undefined && trial.externalReferences !== undefined) {
+        let externalReferenceId = BrAPIUtils.getBreedingInsightId(trial.externalReferences, '/trials');
+        // Throw if trial is missing ExternalReferenceId.
+        if (externalReferenceId === undefined) throw new Error("Trial is missing external reference.");
+        response = await StudyDAO.getAllForTrial(programId, externalReferenceId) as Result<Error, BiResponse>;
       } else {
         response = await StudyDAO.getAll(programId, paginationQuery, full) as Result<Error, BiResponse>;
       }
@@ -52,7 +56,7 @@ export class StudyService {
 
         data = PaginationUtilities.mockSortRecords(data);
         studies = data.map((study: any) => {
-          return new Study(study.studyDbId, study.studyName, study.studyDescription, study.studyType, study.startDate, study.endDate, study.locationName, study.active);
+          return new Study(study.studyDbId, study.studyName, study.studyDescription, study.studyType, study.startDate, study.endDate, study.locationName, study.active, study.externalReferences);
         });
 
         let newPagination;

src/components/experiments/ExperimentObservationsDownloadButton.vue

@@ -17,7 +17,7 @@
 
 <template>
   <DownloadButton
-    v-bind:unique-id="trialDbId"
+    v-bind:unique-id="trialId"
     v-bind:modal-title="modalTitle"
     v-bind:download="downloadList"
     v-bind:anchor-class="anchorClass"
@@ -26,17 +26,17 @@
   >
     <template #form>
       <div class="columns mb-4">
-        <!-- DatasetModel Select -->
+        <!-- Dataset Select -->
         <div class="column control">
           <div class="field">
             <label
               class="label"
-              v-bind:for="`dataset-select-${trialDbId}`"
-            ><span>DatasetModel</span></label>
+              v-bind:for="`dataset-select-${trialId}`"
+            ><span>Dataset</span></label>
             <div class="control">
               <div class="select">
                 <select
-                  v-bind:id="`dataset-select-${trialDbId}`"
+                  v-bind:id="`dataset-select-${trialId}`"
                   v-model="fileOptions.dataset"
                 >
                   <option
@@ -57,16 +57,29 @@
             <legend class="label required">
               <span class="required">Environment(s)</span>
             </legend>
+            <div class="control">
+              <label
+                class="checkbox environment-option-label"
+              >
+                <input
+                  v-model="fileOptions.allEnvironments"
+                  type="checkbox"
+                  value="all"
+                >
+                All Environments
+              </label>
+            </div>
             <div
               v-for="option in environmentOptions"
               v-bind:key="option.id"
               class="control"
             >
-              <label class="checkbox">
+              <label class="checkbox environment-option-label">
                 <input
                   v-model="fileOptions.environments"
                   type="checkbox"
                   v-bind:value="option.id"
+                  v-bind:disabled="fileOptions.allEnvironments"
                 >
                 {{ option.name }}
               </label>
@@ -92,7 +105,7 @@
             </legend>
             <div class="field">
               <input
-                v-bind:id="`timestamps-switch-${trialDbId}`"
+                v-bind:id="`timestamps-switch-${trialId}`"
                 v-model="fileOptions.includeTimestamps"
                 type="checkbox"
                 true-value="Yes"
@@ -101,8 +114,8 @@
                 class="switch is-info is-rounded"
               >
               <label
-                v-bind:id="`timestamps-label-${trialDbId}`"
-                v-bind:for="`timestamps-switch-${trialDbId}`"
+                v-bind:id="`timestamps-label-${trialId}`"
+                v-bind:for="`timestamps-switch-${trialId}`"
               >{{ fileOptions.includeTimestamps }}</label>
             </div>
           </fieldset>
@@ -145,9 +158,14 @@ import {Program} from "@/breeding-insight/model/Program";
 import {ExperimentExportOptions} from "@/breeding-insight/model/ExperimentExportOptions";
 import {FileTypeOption} from "@/breeding-insight/model/FileTypeOption";
 import {ExperimentDatasetOption} from "@/breeding-insight/model/ExperimentDatasetOption";
-import {EnvironmentOption} from "@/breeding-insight/model/EnvironmentOption";
 import {AlertTriangleIcon} from 'vue-feather-icons';
 import DownloadButton from "@/components/DownloadButton.vue";
+import {Trial} from "@/breeding-insight/model/Trial";
+import {Metadata} from "@/breeding-insight/model/BiResponse";
+import {Study} from "@/breeding-insight/model/Study";
+import {StudyService} from "@/breeding-insight/service/StudyService";
+import {Result} from "@/breeding-insight/model/Result";
+import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
 
 @Component({
   mixins: [validationMixin],
@@ -163,7 +181,9 @@ export default class ExperimentObservationsDownloadButton extends Vue {
   @Prop()
   active!: boolean;
   @Prop()
-  trialDbId!: string;
+  trialId!: string;
+  @Prop()
+  experiment!: Trial;
   @Prop()
   modalTitle?: string;
   @Prop()
@@ -174,7 +194,21 @@ export default class ExperimentObservationsDownloadButton extends Vue {
   private showEnvironmentsValidationError: boolean = false;
   private fileExtensionOptions: object[] = Object.values(FileTypeOption);
   private datasetOptions: object[] = Object.values(ExperimentDatasetOption);
-  private environmentOptions: object[] = Object.values(EnvironmentOption);
+  private environmentOptions: object[] = [];
+
+  async mounted() {
+    // Fetch all environments (studies) for this experiment.
+    try {
+      const response: Result<Error, [Study[], Metadata]> = await StudyService.getAll(this.activeProgram!.id!, this.experiment);
+      if(response.isErr()) throw response.value;
+      let [studies, metadata] = response.value;
+      // Set environment options.
+      this.environmentOptions = studies.map((s) => ({id: BrAPIUtils.getBreedingInsightId(s.externalReferences!, '/studies'), name: s.name}));
+    } catch (error) {
+      // Display error that studies cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load studies');
+    }
+  }
 
   downloadList(): boolean {
     // Validate selected options.
@@ -185,13 +219,12 @@ export default class ExperimentObservationsDownloadButton extends Vue {
             + '/v1/programs/'
             + this.activeProgram.id
             + '/experiments/'
-            + this.trialDbId
+            + this.trialId
             + '/export?fileExtension='
             + this.fileOptions.fileExtension
             + '&dataset='
             + this.fileOptions.dataset
-            // + '&environments='
-            // + this.fileOptions.environments
+            + (this.fileOptions.allEnvironments ? '' : ('&environments=' + this.fileOptions.environments))
             + '&includeTimestamps='
             + this.fileOptions.timestampsTrueFalseString(),
             '_blank');
@@ -209,7 +242,8 @@ export default class ExperimentObservationsDownloadButton extends Vue {
   }
 
   validateOptions(): boolean {
-    if (this.fileOptions.environments.length === 0){
+    // Either "All environments" or one or more specific environments must be selected.
+    if (this.fileOptions.environments.length === 0 && !this.fileOptions.allEnvironments){
       this.$emit('show-error-notification', 'One or more environments must be selected.');
       this.showEnvironmentsValidationError = true;
       return false;

src/components/experiments/ExperimentsObservationsTable.vue

@@ -54,8 +54,9 @@
       </b-table-column>
       <b-table-column field="data.listDbId" sortable v-slot="props" :th-attrs="(column) => ({scope:'col'})">
         <ExperimentObservationsDownloadButton
+          v-bind:experiment="props.row.data"
           v-bind:modal-title="`Download ${props.row.data.trialName}`"
-          v-bind:trial-db-id="BrAPIUtils.getBreedingInsightId(props.row.data.externalReferences, '/trials')"
+          v-bind:trial-id="BrAPIUtils.getBreedingInsightId(props.row.data.externalReferences, '/trials')"
           v-on:show-error-notification="$emit('show-error-notification', $event)"
         >
           Download