v1.4 Release

.env.development

@@ -15,6 +15,7 @@ VUE_APP_LOG_LEVEL=${WEB_LOG_LEVEL}
 
 # The reference source
 VUE_APP_BI_REFERENCE_SOURCE=${BRAPI_REFERENCE_SOURCE}
+VUE_APP_MAX_GENOTYPE_UPLOAD_MB=${MAX_GENOTYPE_UPLOAD_MB}
 
 # feature flags
 VUE_APP_BRAPI_VENDOR_SUBMISSION_ENABLED=${BRAPI_VENDOR_SUBMISSION_ENABLED}

AGENTS.md

@@ -0,0 +1,105 @@
+# AGENTS.md
+
+Instructions for automated coding agents working in this repository.
+
+## Scope
+
+These instructions apply to the whole repository.
+
+## Project Overview
+
+`bi-web` is a Vue 2.7 frontend for Breeding Insight. It uses Vue CLI 4,
+TypeScript, Vuex, Vue Router, Buefy/Bulma, Vuelidate, CASL abilities, and an
+axios wrapper for API calls.
+
+Important directories:
+
+- `src/views`: route-level pages.
+- `src/components`: reusable Vue components and layout templates.
+- `src/store`: Vuex root store and feature modules.
+- `src/breeding-insight/model`: application domain models.
+- `src/breeding-insight/dao`: raw API access using `src/util/api`.
+- `src/breeding-insight/service`: business logic and response mapping.
+- `src/breeding-insight/brapi/model`: generated BrAPI/OpenAPI models.
+- `tests/unit`: Jest and Vue Test Utils unit tests.
+- `tests/e2e`: Cypress end-to-end tests.
+- `task`: Node task wrappers used by npm scripts.
+
+## Setup
+
+- Use npm and `package-lock.json`; do not introduce Yarn or pnpm.
+- Use `npm install` for local setup, or `npm ci` for clean/install-in-CI style
+  runs.
+- The Dockerfile uses Node 14 and npm 8.12.1. Avoid dependency or syntax changes
+  that require a newer runtime unless the runtime is intentionally updated.
+- `npm run githooks` configures the repository's commit message hook.
+- Local environment overrides belong in ignored `.env.local` or `.env.*.local`
+  files, not in tracked env files.
+
+## Common Commands
+
+- `npm run serve`: start the dev server. The default port is `8080`; `PORT`
+  overrides it.
+- `npm run build`: production build. The task wrapper runs npm audit checks
+  before building.
+- `npm run lint`: run Vue CLI ESLint.
+- `npm run test:unit`: run existing Jest unit tests only when explicitly
+  requested.
+- `npm run test:e2e`: run existing Cypress e2e tests only when explicitly
+  requested.
+- `npm run test:accessibility`: run pa11y accessibility checks. This expects
+  the dev server to be running and `task/.pa11yTargets.json` to exist; use it
+  only when explicitly requested.
+
+This repository does not add or maintain tests as part of normal feature or bug
+work. Do not create new tests, update existing tests, add test-only selectors,
+or spend time repairing unrelated test failures unless the user explicitly asks
+for test work. Prefer `npm run lint`, `npm run build`, or a focused manual smoke
+check for verification when practical.
+
+## Coding Conventions
+
+- Preserve the existing Apache 2.0 notice header when editing files that have
+  it. Add the same header to new `.ts`, `.js`, and `.vue` source files.
+- Keep TypeScript strictness in mind. Prefer explicit domain models and local
+  service/DAO patterns over loose `any` unless surrounding code already forces
+  it.
+- Use the `@/` alias for imports from `src` when consistent with nearby files.
+- Vue components commonly use class-style components with
+  `vue-property-decorator`; match the surrounding component style.
+- ESLint requires long-form Vue directives: use `v-bind:` and `v-on:` instead
+  of shorthand in templates.
+- Keep API calls centralized through `src/util/api`. DAOs should make HTTP
+  requests, while services should handle application mapping and user-facing
+  error logic.
+- `src/breeding-insight/brapi/model` files are generated by Swagger/OpenAPI.
+  Do not hand-edit them unless the task explicitly calls for it.
+- Reuse existing layouts in `src/components/layouts` and visual conventions
+  from the authenticated `/style-guide` page. Prefer existing Buefy/Bulma
+  patterns and the configured Feather icon pack.
+
+## Configuration Notes
+
+`vue.config.js` derives frontend runtime values from environment variables:
+
+- `VUE_APP_BI_API_ROOT` defaults to `http://localhost`.
+- `VUE_APP_BI_API_V1_PATH` is computed as `${VUE_APP_BI_API_ROOT}/v1`.
+- `VUE_APP_LOG_LEVEL` defaults to `error`.
+- `VUE_APP_BRAPI_VENDOR_SUBMISSION_ENABLED` and
+  `VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED` are enabled only when set to the
+  string `true`.
+
+`.env.development` maps these values from shell environment variables such as
+`API_BASE_URL`, `SANDBOX_MODE`, and `WEB_LOG_LEVEL`.
+
+## Working Safely
+
+- Check `git status --short` before editing and do not overwrite unrelated
+  local changes.
+- Do not commit generated output, `node_modules`, `dist`, local env files, IDE
+  files, Cypress screenshots/videos, or task logs.
+- Do not change `package-lock.json` unless dependency changes are intentional.
+- Keep changes scoped to the requested behavior. Avoid broad refactors unless
+  they are required to make the requested change safely.
+- If backend behavior is relevant, make the frontend assumption explicit in the
+  code review or final notes; this repository only contains the web client.

package.json

@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.3.0",
+  "version": "v1.4.0+989",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/releases/tag/v1.3.0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/d54d28db116a99e278f5c055d8868cd8d790df29"
 }

src/breeding-insight/dao/GenoDAO.ts

@@ -17,17 +17,18 @@
 
 import * as api from '@/util/api';
 import { BiResponse, Response } from '@/breeding-insight/model/BiResponse';
+import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
+import { GenotypeImportFilters, GenotypeImportSort } from '@/breeding-insight/model/Sort';
 
 export class GenoDAO {
 
-  static async uploadData(programId: string, experimentId: string, file: File): Promise<any> {
+  static async uploadData(programId: string, submissionId: string, file: File): Promise<any> {
 
     var formData = new FormData();
     formData.append("file", file);
-    formData.append("filename", file.name);
 
     const {data} = await api.call({
-      url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/geno/import`,
+      url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/submissions/${submissionId}/geno/import`,
       method: 'post', data: formData}
     ) as Response;
 
@@ -42,4 +43,25 @@ export class GenoDAO {
 
     return new BiResponse(data);
   }
-}
+
+  static async fetchGenotypeImports(
+      programId: string,
+      {page, pageSize}: PaginationQuery,
+      {field, order}: GenotypeImportSort,
+      filters: GenotypeImportFilters
+  ): Promise<BiResponse> {
+    const {data} = await api.call({
+      url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/geno/imports`,
+      method: 'get',
+      params: {
+        ...filters,
+        page,
+        pageSize,
+        sortField: field,
+        sortOrder: order
+      }
+    }) as Response;
+
+    return new BiResponse(data);
+  }
+}

src/breeding-insight/model/ExperimentExportOptions.ts

@@ -24,7 +24,7 @@ export class ExperimentExportOptions {
     public fileExtension: string = FileTypeOption.xls.id;
     public datasetId: string;
     public environments: string[] = [];
-    public allEnvironments: boolean = false;
+    public allEnvironments: boolean = true;
     public includeTimestamps: string = 'No';
 
     public timestampsTrueFalseString(): string {

src/breeding-insight/model/GenotypeImport.ts

@@ -0,0 +1,44 @@
+/*
+ * 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 class GenotypeImport {
+  genotypeImportId?: string;
+  sampleSubmissionId?: string;
+  projectNameForSampleSubmission?: string;
+  sampleSubmissionCreatedBy?: string;
+  genotypingFileName?: string;
+  genotypingImportDate?: string;
+  genotypingImportBy?: string;
+
+  constructor({
+                genotypeImportId,
+                sampleSubmissionId,
+                projectNameForSampleSubmission,
+                sampleSubmissionCreatedBy,
+                genotypingFileName,
+                genotypingImportDate,
+                genotypingImportBy
+              }: GenotypeImport = {}) {
+    this.genotypeImportId = genotypeImportId;
+    this.sampleSubmissionId = sampleSubmissionId;
+    this.projectNameForSampleSubmission = projectNameForSampleSubmission;
+    this.sampleSubmissionCreatedBy = sampleSubmissionCreatedBy;
+    this.genotypingFileName = genotypingFileName;
+    this.genotypingImportDate = genotypingImportDate;
+    this.genotypingImportBy = genotypingImportBy;
+  }
+}

src/breeding-insight/model/Sort.ts

@@ -168,6 +168,7 @@ export enum GermplasmSortField {
   Pedigree = "pedigree",
   FemaleParent = "femaleParentGID",
   MaleParent = "maleParentGID",
+  ExternalUID = "externalUID",
   CreatedDate = "createdDate",
   UserName = "createdByUserName"
 }
@@ -217,4 +218,24 @@ export class GermplasmListSort {
     this.field = field;
     this.order = order;
   }
-}
+}
+
+export enum GenotypeImportSortField {
+  ProjectNameForSampleSubmission = 'projectNameForSampleSubmission',
+  SampleSubmissionCreatedBy = 'sampleSubmissionCreatedBy',
+  GenotypingFileName = 'genotypingFileName',
+  GenotypingImportDate = 'genotypingImportDate',
+  GenotypingImportBy = 'genotypingImportBy'
+}
+
+export type GenotypeImportFilters = Partial<Record<GenotypeImportSortField, string>>;
+
+export class GenotypeImportSort {
+  field: GenotypeImportSortField;
+  order: SortOrder;
+
+  constructor(field: GenotypeImportSortField, order: SortOrder) {
+    this.field = field;
+    this.order = order;
+  }
+}

src/breeding-insight/model/import/germplasm/ExternalUID.ts

@@ -18,17 +18,16 @@
 export class ExternalUID {
 
   /**
-   * Get ExternalUID value from germplasm BrAPI external references array based
-   * on the seedSource value
+   * Get ExternalUID value from germplasm BrAPI external references array using
+   * the canonical External UID reference source.
    *
    * @param externalReferences
-   * @param source
    */
-  public static getExternalUIDFromExternalReferences(externalReferences: Array<any>, source : string) : string | undefined {
-    if (externalReferences === undefined || source === undefined) {
+  public static getExternalUIDFromExternalReferences(externalReferences: Array<any>) : string | undefined {
+    if (externalReferences === undefined) {
       return undefined;
     }
-    const externalUID = externalReferences.find( ({ referenceSource }) => referenceSource === source );
+    const externalUID = externalReferences.find( ({ referenceSource }) => referenceSource === "External UID" );
     if (externalUID !== undefined) {
       return externalUID.referenceID;
     } else

src/breeding-insight/service/GenoService.ts

@@ -16,21 +16,24 @@
  */
 
 import { GenoDAO } from '@/breeding-insight/dao/GenoDAO';
-import { BiResponse } from '@/breeding-insight/model/BiResponse';
+import { BiResponse, Metadata } from '@/breeding-insight/model/BiResponse';
 import { ImportResponse } from '@/breeding-insight/model/import/ImportResponse';
 import { GermplasmGenotype } from '@/breeding-insight/model/GermplasmGenotype';
+import { GenotypeImport } from '@/breeding-insight/model/GenotypeImport';
+import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
+import { GenotypeImportFilters, GenotypeImportSort } from '@/breeding-insight/model/Sort';
 
 export class GenoService {
 
-  static async uploadData(programId: string, experimentId: string, file: File): Promise<ImportResponse> {
+  static async uploadData(programId: string, submissionId: string, file: File): Promise<ImportResponse> {
     if (!programId) {
       throw 'Program ID not provided';
     }
-    if (!experimentId) {
-      throw 'Experiment ID not provided';
+    if (!submissionId) {
+      throw 'Submission ID not provided';
     }
 
-    const response: BiResponse = await GenoDAO.uploadData(programId, experimentId, file);
+    const response: BiResponse = await GenoDAO.uploadData(programId, submissionId, file);
     const data: any = response.result;
     return new ImportResponse(data);
   }
@@ -47,4 +50,26 @@ export class GenoService {
 
     return resp.result as GermplasmGenotype;
   }
-}
+
+  static async fetchGenotypeImports(
+      programId: string,
+      paginationQuery: PaginationQuery,
+      sort: GenotypeImportSort,
+      filters: GenotypeImportFilters
+  ): Promise<[GenotypeImport[], Metadata]> {
+    if (!programId) {
+      throw 'Program ID not provided';
+    }
+
+    const response = await GenoDAO.fetchGenotypeImports(programId, paginationQuery, sort, filters);
+    const responseData = response.result && response.result.data ? response.result.data : response.result;
+
+    if (!Array.isArray(responseData)) {
+      return [[], response.metadata];
+    }
+
+    const genotypeImports = responseData.map((record: GenotypeImport) => new GenotypeImport(record));
+
+    return [genotypeImports, response.metadata];
+  }
+}

src/breeding-insight/utils/GermplasmUtils.ts

@@ -18,15 +18,16 @@
 import moment from "moment";
 import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
 import {MOMENT_BRAPI_DATE_FORMAT} from "@/breeding-insight/utils/BrAPIDateTime";
+import {ExternalReferences} from "@/breeding-insight/brapi/model/externalReferences";
 
 // 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 {
         let val;
-        if (germplasm.externalReferences && germplasm.seedSource) {
-            val = germplasm.externalReferences!.filter(ref => ref.referenceSource == germplasm.seedSource!)
+        if (germplasm.externalReferences) {
+            val = germplasm.externalReferences!.filter(ref => ref.referenceSource == "External UID")
                 .map(ref => ref.referenceID);
             return val ? val[0]: "";
         }

src/components/VueFeatherIconPack.vue

@@ -27,6 +27,8 @@ import { ArrowDownIcon,
   ChevronLeftIcon,
   ChevronRightIcon,
   ChevronUpIcon,
+  DownloadIcon,
+  UploadIcon,
   LogOutIcon,
   UserIcon} from "vue-feather-icons";
 
@@ -39,7 +41,9 @@ export default {
     ArrowUpIcon,
     ArrowDownIcon,
     LogOutIcon,
-    UserIcon
+    UserIcon,
+    DownloadIcon,
+    UploadIcon
   },
   props: {
     icon: [String, Array],