Merge release/1.1.1 into main

package.json

@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0",
+  "version": "v1.2.0+873",
   "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/v1.1.0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/5c4d461021cff1e8ce8e69a4b2de0d43468358d7"
 }

src/breeding-insight/dao/UserDAO.ts

@@ -21,6 +21,7 @@ import {BiResponse} from "@/breeding-insight/model/BiResponse";
 import {Role} from "@/breeding-insight/model/Role";
 import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
 import {UserSort} from "@/breeding-insight/model/Sort";
+import {SearchRequest} from "@/breeding-insight/model/SearchRequest";
 
 export class UserDAO {
 
@@ -101,6 +102,40 @@ export class UserDAO {
 
   }
 
+  static getById(id: string): Promise<BiResponse> {
+    return new Promise<BiResponse>((resolve, reject) => {
+      api.call({ url: `${process.env.VUE_APP_BI_API_V1_PATH}/users/${id}`, method: 'get' })
+          .then((response: any) => {
+            const biResponse = new BiResponse(response.data);
+            resolve(biResponse);
+          }).catch((error) => reject(error));
+    });
+  }
+
+  static search(searchRequest: SearchRequest, {page, pageSize}: PaginationQuery, {field, order}: UserSort): Promise<BiResponse> {
+
+    return new Promise<BiResponse>(((resolve, reject) => {
+      const config = {
+        url: `${process.env.VUE_APP_BI_API_V1_PATH}/users/search`,
+        method: 'post',
+        data: searchRequest,
+        params: {
+          sortField: field,
+          sortOrder: order,
+          page,
+          pageSize
+        }
+      }
+      api.call(config)
+          .then((response: any) => {
+            const biResponse = new BiResponse(response.data);
+            resolve(biResponse);
+          }).catch((error) => {
+        reject(error);
+      })
+    }));
+  }
+
   static updateSystemRoles(id: string, systemRoles: Array<Role>) {
 
     return new Promise<BiResponse>((resolve, reject) => {

src/breeding-insight/model/FilterRequest.ts

@@ -0,0 +1,26 @@
+/*
+ * 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 FilterRequest {
+    field: string;
+    value: string;
+
+    constructor(field: string, value: string) {
+        this.field = field;
+        this.value = value;
+    }
+}

src/breeding-insight/model/SearchRequest.ts

@@ -0,0 +1,26 @@
+/*
+ * 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 {FilterRequest} from "@/breeding-insight/model/FilterRequest";
+
+export class SearchRequest {
+    filters: FilterRequest[] = [];
+
+    constructor(filters: FilterRequest[]) {
+        this.filters = filters;
+    }
+}

src/breeding-insight/service/UserService.ts

@@ -24,13 +24,16 @@ import {Program} from "@/breeding-insight/model/Program";
 import {ProgramUser} from "@/breeding-insight/model/ProgramUser";
 import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
 import {ProgramSort, SortOrder, UserSort, UserSortField} from "@/breeding-insight/model/Sort";
+import {SearchRequest} from "@/breeding-insight/model/SearchRequest";
 
 export class UserService {
 
   static duplicateEmailMessage : string = 'Email is already in use.';
   static errorCreateUser: string = 'Unable to create user';
   static errorDeleteUser: string = 'Unable to archive user';
-  static errorGetUsers: string = 'Error while trying to load roles';
+  static errorGetUsers: string = 'Error while trying to load users';
+  static errorSearchUsers: string = 'Error while searching users';
+  static errorGetUser: string = 'User not found';
   static errorDeleteUserNotFound: string = 'Unable to find user to deactivate';
   static errorDeleteUserNotAllowed: string = 'You are not allowed to deactivate this user.';
   static errorPermissionsEditUser: string = "You don't have permissions to edit the roles of this user.";
@@ -153,6 +156,45 @@ export class UserService {
     }));
   }
 
+  static getById(id: string): Promise<User> {
+    return new Promise<User>((resolve, reject) => {
+      UserDAO.getById(id).then((biResponse: BiResponse) => {
+        const result: any = biResponse.result;
+        const role: Role | undefined = this.parseSystemRoles(result.systemRoles);
+        const programRoles: ProgramUser[] | undefined = this.parseProgramRoles(result.programRoles);
+        const user = new User(result.id, result.name, result.orcid, result.email, role, programRoles);
+        resolve(user);
+      }).catch((error) => {
+        error['errorMessage'] = this.errorGetUser;
+        reject(error);
+      });
+    });
+  }
+
+  static search(searchRequest: SearchRequest,
+                paginationQuery: PaginationQuery = new PaginationQuery(1, 50, true),
+                sort: UserSort = new UserSort(UserSortField.Name, SortOrder.Ascending)): Promise<[User[], Metadata]> {
+    return new Promise<[User[], Metadata]>(((resolve, reject) => {
+
+      UserDAO.search(searchRequest, paginationQuery, sort).then((biResponse) => {
+
+        // Parse our users into the vue users param
+        let users = biResponse.result.data.map((user: any) => {
+          const role: Role | undefined = this.parseSystemRoles(user.systemRoles);
+          const programRoles: ProgramUser[] | undefined = this.parseProgramRoles(user.programRoles);
+          return new User(user.id, user.name, user.orcid, user.email, role, programRoles);
+        });
+
+        resolve([users, biResponse.metadata]);
+
+      }).catch((error) => {
+        error['errorMessage'] = this.errorSearchUsers;
+        reject(error)
+      });
+
+    }));
+  }
+
   static updateSystemRoles(user: User): Promise<User> {
 
     return new Promise<User>((resolve, reject) => {

src/components/program/ProgramUsersTable.vue

@@ -191,6 +191,8 @@
   import {
     UPDATE_PROGRAM_USER_SORT
   } from "@/store/sorting/mutation-types";
+  import {SearchRequest} from "@/breeding-insight/model/SearchRequest";
+  import {FilterRequest} from "@/breeding-insight/model/FilterRequest";
 
 @Component({
   components: { ExpandableTable, NewDataForm, BasicInputField, BasicSelectField, TableColumn,
@@ -218,7 +220,6 @@ export default class ProgramUsersTable extends Vue {
   private activeProgram?: Program;
   private activeUser?: User;
   public users: ProgramUser[] = [];
-  public systemUsers: User[] = [];
 
   private deactivateActive: boolean = false;
   private newUserActive: boolean = false;
@@ -252,7 +253,6 @@ export default class ProgramUsersTable extends Vue {
 
   mounted() {
     this.getRoles();
-    this.getSystemUsers();
     this.paginationChanged();
   }
 
@@ -333,41 +333,40 @@ export default class ProgramUsersTable extends Vue {
 
   }
 
-  saveUser() {
+  async saveUser() {
 
     this.newUser.program = this.activeProgram;
 
     try {
-      this.newUser = this.checkExistingUserByEmail(this.newUser, this.systemUsers);
+      this.newUser = await this.checkExistingUserByEmail(this.newUser);
     } catch (err) {
       this.$emit('show-error-notification', err);
       this.newUserFormState.bus.$emit(DataFormEventBusHandler.SAVE_COMPLETE_EVENT);
       return;
     }
 
+    // if we found a system user by email in checkExistingUserByEmail then system user exists
+    const systemUserExisted = this.newUser.id !== undefined;
+
     ProgramUserService.create(this.newUser).then((user: ProgramUser) => {
       this.paginationController.updatePage(1);
       this.paginationController.updateOnAdd();
       this.getUsers();
-      this.getSystemUsers();
 
       // See if the user already existed
-      //TODO: Reconsider when user search feature is added
-      if (this.getSystemUserById(user, this.systemUsers)) {
+      if (systemUserExisted) {
         this.$emit('show-success-notification', 'Success! Existing user ' + user.name + ' added to program.');
       } else {
         this.$emit('show-success-notification', 'Success! ' + this.newUser.name + ' added.');
       }
 
       if(this.newUser.email === this.activeUser!.email) this.updateActiveUser();
 
-      this.getSystemUsers();
       this.newUser = new ProgramUser();
       this.newUserActive = false;
     }).catch((error) => {
       this.$emit('show-error-notification', error.errorMessage);
       this.getUsers();
-      this.getSystemUsers();
     }).finally(() => this.newUserFormState.bus.$emit(DataFormEventBusHandler.SAVE_COMPLETE_EVENT))
 
   }
@@ -379,47 +378,42 @@ export default class ProgramUsersTable extends Vue {
     Vue.prototype.$ability.update(rules);
   }
 
-  //TODO: Reconsider when user search feature is added
-  getSystemUsers() {
+  //TODO: Do we still want this since orcid entry is removed?
+  async checkExistingUserByEmail(user: ProgramUser): Promise<ProgramUser> {
+    user.id = undefined;
+    // api call to check if user exists for email
+    // this was done on front-end before because we didn't have search endpoint at the time
+    const filter = new FilterRequest('email', user.email);
+    const request = new SearchRequest(filter);
 
-    UserService.getAll().then(([users, metadata]) => {
-      this.systemUsers = users;
-    }).catch((error) => {
+    try {
+      const [users, metadata] = await UserService.search(request);
+      // email exists
+      if (users.length === 1) {
+        user.id = users[0].id;
+      }
+    } catch (error) {
       // Display error that users cannot be loaded
       this.$emit('show-error-notification', 'Error while trying to load system users');
       throw error;
-    });
-
-  }
-
-  //TODO: Reconsider when user search feature is added
-  //TODO: Do we still want this since orcid entry is removed?
-  checkExistingUserByEmail(user: ProgramUser, systemUsers: User[]): ProgramUser {
-    user.id = undefined;
-    let usersFound = 0;
-    for (const systemUser of systemUsers){
-      if (user.email === systemUser.email){
-        usersFound += 1;
-        if (systemUser.id){
-          user.id = systemUser.id;
-        }
-      }
     }
 
-    if (usersFound > 1){
-      throw "Email matches two different users.";
-    }
 
     return user;
   }
 
-  //TODO: Reconsider when user search feature is added
-  getSystemUserById(user: ProgramUser, systemUsers: User[]): User | undefined {
-    for (const systemUser of systemUsers){
-      if (user.id === systemUser.id){
-        return systemUser;
+  getSystemUserById(user: ProgramUser): User | undefined {
+
+    UserService.getById(user.id).then(([users, metadata]) => {
+      if (users.length === 1) {
+        return users[0];
       }
-    }
+    }).catch((error) => {
+      // Display error that users cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load system user');
+      throw error;
+    });
+
     return undefined;
   }
 

src/views/experiments-and-observations/ExperimentDetails.vue

@@ -222,7 +222,7 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-import-file', 'import-file', 'Import file', this.$ability.can('create', 'Import')),
       new ActionMenuItem('experiment-download-file', 'download-file', 'Download file'),
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
-      // new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset'),
+      new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset'),
       new ActionMenuItem('experiment-delete', 'delete-experiment', 'Delete experiment', this.$ability.can('delete', 'Experiment'))
   ];
 

src/views/import/Dataset.vue

@@ -123,6 +123,7 @@
         <b-table-column
             v-slot="props"
             field="data.expUnitId"
+            :custom-sort="sortExpUnitId"
             label="Exp Unit ID"
             sortable
             searchable
@@ -403,6 +404,18 @@ export default class Dataset extends ProgramsBase {
     }
   }
 
+  // This sorts the Exp Unit ID's in Alphanumeric order (ie. B300,BO2, B1 would sort to B1, B02, B300)
+  sortExpUnitId(a: any, b: any, isAsc: boolean){
+    let first :any = (a.data.expUnitId);
+    let second :any = (b.data.expUnitId);
+    if (isAsc) {
+      return first.toString().localeCompare(second.toString(), 'en', {numeric: true});
+    }
+    else {
+      return second.toString().localeCompare(first.toString(), 'en', {numeric: true});
+    }
+  }
+
   /*
   * remove the '[....]' found at the end of the string
   * */

src/views/import/ImportGermplasm.vue

@@ -81,8 +81,7 @@
             <p>New Germplasm count: {{ statistics.Germplasm.newObjectCount }}</p>
             <p>New Pedigree Connections: {{ statistics["Pedigree Connections"].newObjectCount }}</p>
             <template v-if="duplicatesPresent(rows)">
-              <p>Duplicate names detected and are highlighted in yellow and show a <alert-triangle-icon size="1.2x" class="icon-align"/> icon.
-                Upon import duplicates will become independent database entries.</p>
+              <p>Duplicate names detected and are highlighted in yellow and show a <alert-triangle-icon size="1.2x" class="icon-align"/> icon.</p>
             </template>
 
           </div>

task/serve.js

@@ -25,10 +25,13 @@ const port = process.env.PORT || JSON.parse(fs.readFileSync('package.json', 'utf
 (async () => {
   let spinner = ora({prefixText: ' ', color: 'yellow'});
   try {
+    // TODO: figure out the issue here
+    /*
     spinner = spinner.start('sort package.json');
     await execa('npx', ['sort-package-json@3.0.0'], {preferLocal: true});
     spinner = spinner.clear()
                      .succeed('package.json sorted');
+     */
 
     console.log(`App running at http://localhost:${port}`);
     await execa.command(`vue-cli-service\ serve --port ${port}`);