Merge branch 'develop' into feature/BI-1473

README.md

@@ -96,8 +96,8 @@ npx npm-check -u
 See [Configuration Reference](https://cli.vuejs.org/config/).
 
 ## Style and layout
-A guide to visual design conventions and writing style can be found at `/styleguide` after authentication.
-For example, if you are running the app locally on port 8080, the style guide URL would be [http://localhost:8080/styleguide].
+A guide to visual design conventions and writing style can be found at `/style-guide` after authentication.
+For example, if you are running the app locally on port 8080, the style guide URL would be [http://localhost:8080/style-guide](http://localhost:8080/style-guide).
 
 ## Layout template usage standards
 General guidance for using each of the layout templates in `/components/layouts`:

package.json

@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.8.0+519",
+  "version": "v0.8.0+527",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -93,5 +93,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.6.10"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/8939ce282fdba86a7b50f3ce735ef713d2dfc2b4"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/b6c481fedb53107564dd3723be0f69794f7f9e87"
 }

src/breeding-insight/model/BaseFilter.ts

@@ -0,0 +1,24 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+export enum BaseField {
+  DateFormat = "dateDisplayFormat",
+}
+
+export class BaseFilter {
+  [BaseField.DateFormat]: string = "yyyy-MM-dd";
+}

src/breeding-insight/model/Filter.ts → src/breeding-insight/model/GermplasmFilter.ts

@@ -15,25 +15,24 @@
  * limitations under the License.
  */
 
-
-// germplasm
 import {GermplasmSortField} from "@/breeding-insight/model/Sort";
+import {BaseFilter} from "@/breeding-insight/model/BaseFilter";
 
 export enum GermplasmBIField {
-  ListDbId = "listDbId",
-  ListName = "listName",
+    ListDbId = "listDbId",
+    ListName = "listName",
 }
 
-export class GermplasmFilter {
-  [GermplasmBIField.ListDbId]: string;
-  [GermplasmBIField.ListName]: string;
-  [GermplasmSortField.AccessionNumber]: string;
-  [GermplasmSortField.DefaultDisplayName]: string;
-  [GermplasmSortField.BreedingMethod]: string;
-  [GermplasmSortField.SeedSource]: string;
-  [GermplasmSortField.Pedigree]: string;
-  [GermplasmSortField.FemaleParent]: string;
-  [GermplasmSortField.MaleParent]: string;
-  [GermplasmSortField.CreatedDate]: string;
-  [GermplasmSortField.UserName]: string;
+export class GermplasmFilter extends BaseFilter {
+    [GermplasmBIField.ListDbId]: string;
+    [GermplasmBIField.ListName]: string;
+    [GermplasmSortField.AccessionNumber]: string;
+    [GermplasmSortField.DefaultDisplayName]: string;
+    [GermplasmSortField.BreedingMethod]: string;
+    [GermplasmSortField.SeedSource]: string;
+    [GermplasmSortField.Pedigree]: string;
+    [GermplasmSortField.FemaleParent]: string;
+    [GermplasmSortField.MaleParent]: string;
+    [GermplasmSortField.CreatedDate]: string;
+    [GermplasmSortField.UserName]: string;
 }

src/breeding-insight/service/GermplasmService.ts

@@ -24,7 +24,7 @@ import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
 import {SortOrder} from "@/breeding-insight/model/Sort";
 import * as api from "@/util/api";
-import {GermplasmFilter} from "@/breeding-insight/model/Filter";
+import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
 
 export class GermplasmService {
 

src/breeding-insight/utils/BrAPIDateTime.ts

@@ -0,0 +1,25 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// DateTime format strings based on the BrAPI spec,
+// see https://plant-breeding-api.readthedocs.io/en/latest/docs/best_practices/Dates_and_Times.html
+// for more information.
+
+// The Java BI API interpretable format for displayed Date values, e.g. 2023-03-31.
+export const JAVA_BRAPI_DATE_FORMAT = 'yyyy-MM-dd';
+// The moment.js interpretable format for displayed Date values, e.g. 2023-03-31.
+export const MOMENT_BRAPI_DATE_FORMAT = 'YYYY-MM-DD';

src/breeding-insight/utils/GermplasmUtils.ts

@@ -19,6 +19,10 @@ import moment from "moment";
 import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
 import {ExternalReferences} from "@/breeding-insight/brapi/model/externalReferences";
 import {GermplasmService} from "@/breeding-insight/service/GermplasmService";
+import {MOMENT_BRAPI_DATE_FORMAT} from "@/breeding-insight/utils/BrAPIDateTime";
+
+// The moment.js interpretable format for Date values sent and received via the BI API.
+export const MOMENT_DATE_PERSISTED_FORMAT = 'DD/MM/YYYY h:mm:ss';
 
 export class GermplasmUtils {
     static getExternalUID(germplasm: Germplasm): string | undefined {
@@ -33,8 +37,8 @@ export class GermplasmUtils {
 
     static getCreatedDate(germplasm: Germplasm): string | undefined {
         if (germplasm.additionalInfo && germplasm.additionalInfo.createdDate) {
-            let dateTime = moment(germplasm.additionalInfo!.createdDate!, "DD/MM/YYYY h:mm:ss");
-            return dateTime.format("YYYY-MM-DD");
+            let dateTime = moment(germplasm.additionalInfo!.createdDate!, MOMENT_DATE_PERSISTED_FORMAT);
+            return dateTime.format(MOMENT_BRAPI_DATE_FORMAT);
         }
         return "";
     }

src/components/germplasm/GermplasmListsTable.vue

@@ -95,6 +95,8 @@ import {
 } from "@/breeding-insight/model/Sort";
 import {UPDATE_EXPERIMENT_SORT} from "@/store/sorting/mutation-types";
 import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
+import {BaseFilter} from "@/breeding-insight/model/BaseFilter";
+import {MOMENT_BRAPI_DATE_FORMAT} from "@/breeding-insight/utils/BrAPIDateTime";
 
 @Component({
   mixins: [validationMixin],
@@ -134,7 +136,7 @@ export default class GermplasmListsTable extends Vue {
   private fileOptions = Object.values(FileType);
 
   private germplasmListSort!: GermplasmListSort;
-  private filters: any = {};
+  private filters: BaseFilter = new BaseFilter();
   private germplasmListCallStack?: CallStack;
 
   private updateSort!: (sort: GermplasmListSort) => void;
@@ -147,7 +149,10 @@ export default class GermplasmListsTable extends Vue {
   };
 
   initSearch(filter: any) {
-    this.filters = filter;
+
+    // Merge, overriding any properties of this.filters that exist in filter.
+    this.filters = {...this.filters, ...filter};
+
     // When filtering the list, set the page to the first page.
     this.paginationController.updatePage(1);
   }
@@ -197,7 +202,7 @@ export default class GermplasmListsTable extends Vue {
   }
 
   formatDate(date: Date) {
-    return moment(date).format('YYYY-MM-DD');
+    return moment(date).format(MOMENT_BRAPI_DATE_FORMAT);
   }
 
   setSort(field: string, order: string) {

src/components/germplasm/GermplasmTable.vue

@@ -94,6 +94,7 @@ import {
 import {UPDATE_GERMPLASM_SORT} from "@/store/sorting/mutation-types";
 import {GermplasmService} from "@/breeding-insight/service/GermplasmService";
 import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
+import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
 
 @Component({
   mixins: [validationMixin],
@@ -127,7 +128,7 @@ export default class GermplasmTable extends Vue {
   private paginationController: PaginationController = new PaginationController();
   private germplasmLoading: Boolean = true;
   private germplasm: Germplasm[] = [];
-  private filters: any = {};
+  private filters: GermplasmFilter = new GermplasmFilter();
 
   private germplasmCallStack?: CallStack;
 
@@ -201,8 +202,9 @@ export default class GermplasmTable extends Vue {
   }
 
   initSearch(filters: any) {
-    
-    this.filters = filters;
+
+    // Merge, overriding any properties of this.filters that exist in filters.
+    this.filters = {...this.filters, ...filters};
 
     // When filtering the list, set a page to the first page.
     this.paginationController.updatePage(1);

src/router/index.ts

@@ -65,7 +65,7 @@ import GermplasmByList from "@/views/germplasm/GermplasmByList.vue";
 import GermplasmLists from "@/views/germplasm/GermplasmLists.vue";
 import BreedingMethods from "@/views/germplasm/BreedingMethods.vue";
 import GermplasmDetails from "@/views/germplasm/GermplasmDetails.vue";
-import OntologySharing from "@/views/program/OntologySharing.vue";
+import ProgramConfiguration from "@/views/program/ProgramConfiguration.vue";
 import JobManagement from '@/views/program/JobManagement.vue';
 import GermplasmPedigreesView from "@/components/germplasm/GermplasmPedigreesView.vue";
 import GermplasmGenotypeView from "@/components/germplasm/GermplasmGenotypeView.vue";
@@ -223,13 +223,13 @@ const routes = [
         component: BreedingMethods
       },
       {
-        path: 'ontology-sharing',
-        name: 'ontology-sharing',
+        path: 'configuration',
+        name: 'configuration',
         meta: {
-          title: 'Ontology Sharing',
+          title: 'Configuration',
           layout: layouts.userSideBar
         },
-        component: OntologySharing
+        component: ProgramConfiguration
       }
     ]
   },

src/store/filtering/getters.ts

@@ -18,7 +18,7 @@
 import {GetterTree} from 'vuex';
 import {RootState} from "@/store/types";
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/Filter";
+import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
 
 export const getters: GetterTree<FilterState, RootState> = {
     // germplasm

src/store/filtering/index.ts

@@ -20,7 +20,7 @@ import {getters} from '@/store/filtering/getters';
 import {mutations} from '@/store/filtering/mutations';
 import {RootState} from '@/store/types';
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/Filter";
+import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
 
 export let state: FilterState;
 state = {

src/store/filtering/mutations.ts

@@ -17,7 +17,7 @@
 
 import {MutationTree} from 'vuex';
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/Filter";
+import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
 import {UPDATE_GERMPLASM_FILTER} from "@/store/filtering/mutation-types";
 
 export const mutations: MutationTree<FilterState> = {

src/store/filtering/types.ts

@@ -1,4 +1,4 @@
-import { GermplasmFilter } from "@/breeding-insight/model/Filter";
+import { GermplasmFilter } from "@/breeding-insight/model/GermplasmFilter";
 
 export interface FilterState {
     // germplasm table

src/views/import/ImportExperiment.vue

@@ -30,7 +30,7 @@
 
       <template v-slot:importInfoTemplateMessageBox>
         <ImportInfoTemplateMessageBox v-bind:import-type-name="'Experiments & Observations'"
-                                      v-bind:template-url="'https://cornell.box.com/shared/static/wp6tmlt0585ryid3csccj3q1w2fiyg9d.xls'"
+                                      v-bind:template-url="'https://cornell.box.com/shared/static/28k65fg3mrrcv5s8hm86ap9qijbbi06b.xls'"
                                       class="mb-5">
           <strong>Before You Import...</strong>
           <br/>

src/views/import/ImportGermplasm.vue

@@ -30,7 +30,7 @@
 
       <template v-slot:importInfoTemplateMessageBox>
         <ImportInfoTemplateMessageBox v-bind:import-type-name="'Germplasm'"
-                                      v-bind:template-url="'https://cornell.box.com/shared/static/7ct5k3tljr20uzo2wt2qlc5jgi46sopg.xls'"
+                                      v-bind:template-url="'https://cornell.box.com/shared/static/raxqv3pbz858jjdb33ymsepbyizt9imd.xls'"
                                       class="mb-5">
           <strong>Before You Import...</strong>
           <br/>

src/views/program/OntologySharing.vue → src/views/program/ProgramConfiguration.vue

@@ -16,7 +16,7 @@
   -->
 
 <template>
-  <div id="ontology-sharing">
+  <div id="program-configuration">
       <SharedOntologyConfiguration
           v-on="$listeners"
           class="mb-6"
@@ -51,7 +51,7 @@ import BreedingMethods from "@/views/germplasm/BreedingMethods.vue";
     ])
   }
 })
-export default class OntologySharing extends ProgramsBase {
+export default class ProgramConfiguration extends ProgramsBase {
   // Change tracker to pass to children for refresh
   private subscribeAction: number = 0;
   private shareAction: number = 0;

src/views/program/ProgramManagement.vue

@@ -43,9 +43,9 @@
           </router-link>
           <router-link
               v-if="$ability.can('access', 'ProgramConfiguration')"
-              v-bind:to="{name: 'ontology-sharing', params: {programId: activeProgram.id}}"
+              v-bind:to="{name: 'configuration', params: {programId: activeProgram.id}}"
               tag="li" active-class="is-active">
-            <a>Ontology Sharing</a>
+            <a>Configuration</a>
           </router-link>
         </ul>
       </nav>

src/views/trait/TraitsImport.vue

@@ -178,7 +178,7 @@ export default class TraitsImport extends ProgramsBase {
   private showAbortModal = false;
 
   private yesAbortId: string = "traitsimport-yes-abort";
-  private templateUrl: string = "https://cornell.box.com/shared/static/7vtd4vkzc2efrdlion74miql9surugqd.xls";
+  private templateUrl: string = "https://cornell.box.com/shared/static/2erlubbeobuv1tochwkbuq5jghdayuei.xls";
 
   private confirmImportState: DataFormEventBusHandler = new DataFormEventBusHandler();