Release/1.1

.github/pull_request_template.md

@@ -20,3 +20,4 @@ _Please include any details needed for reviewers to test this code_
 - [ ] I have commented my code, particularly in hard-to-understand areas
 - [ ] I have made corresponding changes to documentation
 - [ ] I have run TAF: _\<link to TAF run>_
+- [ ] I have run SiteImprove on pages impacted by changes 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0",
+  "version": "v1.1.0+832",
   "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/v1.0.0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/939aade34a7566e58dfaeb3896904c6e897c764c"
 }

src/assets/scss/main.scss

@@ -945,7 +945,7 @@ tr:nth-child(odd) td.db-filled {
   margin-right: 10px;
 }
 
-.sub-entity-dataset-modal, .experiment-observations-download-button, .experiment-observation-add-collaborator-button, .experiment-observation-remove-collaborator-button {
+.sub-entity-dataset-modal, .experiment-observations-download-button, .experiment-observation-add-collaborator-button, .experiment-observation-remove-collaborator-button, .germplasm-list-deletion-button {
   .modal {
     .modal-card {
       width: $medium-modal-content-width;

src/breeding-insight/dao/ExperimentDAO.ts

@@ -108,6 +108,29 @@ export class ExperimentDAO {
         }
     }
 
+
+    static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
+        config.method = 'delete';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.params = {
+            hard : ! softDelete,
+        };
+        try {
+            const response = await api.call(config);
+            // Check if the status code indicates success
+            if (response.status >= 200 && response.status < 300) {
+                return ResultGenerator.success(true);
+            } else {
+                throw new Error(`Unexpected status code: ${response.status}`);
+            }
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
     static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
         const config: any = {};
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/datasets`;

src/breeding-insight/dao/GermplasmDAO.ts

@@ -30,7 +30,7 @@ export class GermplasmDAO {
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists`;
         config.method = 'get';
         config.programId = programId;
-        config.params = {listType: ListType.Germplasm};
+        config.params = {listType: ListType.GERMPLASM};
         if (paginationQuery.page) config.params.page = paginationQuery.page - 1;
         if (paginationQuery.pageSize) config.params.pageSize = paginationQuery.pageSize;
 

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

@@ -18,14 +18,17 @@
 import {GermplasmSortField} from "@/breeding-insight/model/Sort";
 import {BaseFilter} from "@/breeding-insight/model/BaseFilter";
 
-export enum GermplasmBIField {
+export enum ListBIField {
     ListDbId = "listDbId",
     ListName = "listName",
 }
 
-export class GermplasmFilter extends BaseFilter {
-    [GermplasmBIField.ListDbId]: string;
-    [GermplasmBIField.ListName]: string;
+export class ListFilter extends BaseFilter {
+    [ListBIField.ListDbId]: string;
+    [ListBIField.ListName]: string;
+}
+
+export class GermplasmFilter extends ListFilter {
     [GermplasmSortField.AccessionNumber]: string;
     [GermplasmSortField.DefaultDisplayName]: string;
     [GermplasmSortField.BreedingMethod]: string;

src/breeding-insight/service/ExperimentService.ts

@@ -100,4 +100,14 @@ export class ExperimentService {
         }
         return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
     }
+
+    static async deleteExperiment(programId: string | undefined, experimentId: string, hasObsUnits: boolean): Promise<Result<Error, boolean>> {
+        if (!programId) {
+            return ResultGenerator.err(new Error('Missing or invalid program id'));
+        }
+        let response: Result<Error, boolean>;
+        response = await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
+        if(response.isErr()) throw response.value;
+        return response;
+    }
 }

src/breeding-insight/service/GermplasmService.ts

@@ -24,7 +24,8 @@ 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/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
+
 
 export class GermplasmService {
 
@@ -34,7 +35,7 @@ export class GermplasmService {
                          { listDbId, listName, ...brapiFilters  }: GermplasmFilter):
         Promise<BiResponse> {
         //Form the query params including sorting, pagination, and filtering
-        let params: any = { ...brapiFilters };
+        let params: any = {listDbId: listDbId, ...brapiFilters };
 
         if (sort.field) {
             params['sortField'] = sort.field;
@@ -67,8 +68,8 @@ export class GermplasmService {
             }
 
             //Get the list germplasm
-            const {data} = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/germplasm/lists/${listId}/records`,
+            const {data}: any = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/germplasm`,
                 method: 'get',
                 params: params
             }) as Response;

src/breeding-insight/service/ListService.ts

@@ -0,0 +1,93 @@
+/*
+ * 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.
+ */
+
+import {BiResponse} from "@/breeding-insight/model/BiResponse";
+import {SortOrder} from "@/breeding-insight/model/Sort";
+import * as api from "@/util/api";
+import {ListType} from "@/util/ListType";
+
+export class ListService {
+    static async deleteList(programId: string | undefined, listDbId: string) {
+        if (programId == undefined) {
+            throw new Error("Not valid program");
+        }
+        try {
+            const response = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists/${listDbId}`,
+                method: 'delete',
+                params: { hardDelete: true }
+            }) as Response;
+
+            // If we get here, it means the call was successful (likely 200 OK)
+            return new BiResponse({ success: true });
+
+        } catch (error) {
+            // Check if the error is actually a 204 No Content response since http clients can be configured to
+            // automatically throw an error if the response has no content
+            if (error.response && error.response.status === 204) {
+                // This is actually a successful deletion
+                return new BiResponse({ success: true });
+            }
+
+            // For other errors, log and rethrow
+            console.error('Error in deleteList:', error);
+            throw error;
+        }
+    }
+
+    static async getLists<T>(listType: ListType,
+                             programId: string,
+                             sort: { field: T, order: SortOrder },
+                             pagination: {pageSize: number, page: number},
+                             filters?: any): Promise<BiResponse> {
+        if (!programId) throw 'Program ID required';
+
+        // Set list type, sort, and pagination
+        let params: any = { listType };
+
+        if(filters) {
+            params = { listType, ...filters };
+        }
+
+        if (sort.field) {
+            params['sortField'] = sort.field;
+        }
+        if (sort.order) {
+            params['sortOrder'] = sort.order;
+        }
+        if (pagination.page || pagination.page == 0) { //have to account for 0-index pagination since 0 falsy
+            params['page'] = pagination.page;
+        }
+        if (pagination.pageSize) {
+            params['pageSize'] = pagination.pageSize;
+        }
+
+        // Make the GET call
+        try {
+            const { data }: any = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists`,
+                method: 'get',
+                params: params
+            });
+
+            return new BiResponse(data);
+
+        } catch (error) {
+            throw error;
+        }
+    }
+}

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);
+  }
+
+
 }