Feature/bi 1817

src/breeding-insight/dao/ExperimentDAO.ts

@@ -15,10 +15,13 @@
  * limitations under the License.
  */
 
-import { Response} from "@/breeding-insight/model/BiResponse";
+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 {
 
@@ -37,4 +40,25 @@ export class ExperimentDAO {
             return ResultGenerator.err(error);
         }
     }
+    static getDatasetById(programId: string, experimentId: string, datasetId: string, stats: boolean): Promise<Result<Error, DatasetModel>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/dataset/${datasetId}`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.datasetId = datasetId;
+        config.params = {
+            stat : stats,
+        };
+        return new Promise<Result<Error, DatasetModel>>(((resolve, reject) => {
+            api.call(config)
+                .then((response: any) => {
+                    const biResponse = new BiResponse(response.data);
+                    resolve(biResponse);
+                }).catch((error) => {
+                    reject(error);
+                })
+        }))
+    }
+
 }

src/breeding-insight/model/DatasetModel.ts

@@ -0,0 +1,61 @@
+/*
+ * 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 {Observation} from "@/breeding-insight/model/Observation";
+import {ObservationUnit} from "@/breeding-insight/model/ObservationUnit";
+import {ObservationVariable} from "@/breeding-insight/model/ObservationVariable";
+
+export class DatasetModel {
+  id?: string;
+  experimentId?: string;
+  additionalInfo?: any;
+  data?: Observation[];
+  observationUnits?: ObservationUnit[];
+  observationVariables?: ObservationVariable[];
+
+
+  constructor(id?: string,
+              experimentId?: string,
+              additionalInfo?: any,
+              data?: Observation[],
+              observationUnits?: ObservationUnit[],
+              observationVariables?: ObservationVariable[]
+              ) {
+    this.id = id;
+    this.experimentId = experimentId;
+    this.additionalInfo = additionalInfo;
+    this.data = data;
+    this.observationUnits = observationUnits;
+    this.observationVariables = observationVariables;
+  }
+
+  static assign(dataset: DatasetModel): DatasetModel {
+
+    return new DatasetModel(
+        dataset.id,
+        dataset.experimentId,
+        dataset.additionalInfo,
+        dataset.data,
+        dataset.observationUnits
+        );
+  }
+
+  equals(dataset?: DatasetModel): boolean {
+    if (!dataset) {return false;}
+    return (this.id === dataset.id)
+  }
+}

src/breeding-insight/service/ExperimentService.ts

@@ -18,6 +18,7 @@
 import {ExperimentDAO} from "@/breeding-insight/dao/ExperimentDAO";
 import {Trial} from "@/breeding-insight/model/Trial.ts";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
+import {DatasetModel} from "@/breeding-insight/model/DatasetModel";
 
 export class ExperimentService {
 
@@ -27,4 +28,12 @@ export class ExperimentService {
         }
         return await ExperimentDAO.getSingleExperiment(programId, experimentId, stats);
     }
+
+    static async getDatasetModel(programId: string, experimentId: string, datasetId: string): Promise<Result<Error, DatasetModel>> {
+        if (!programId) {
+            return ResultGenerator.err(new Error('Missing or invalid program id'));
+        }
+        return await ExperimentDAO.getDatasetById(programId,experimentId, datasetId, true);
+    }
+
 }

src/components/experiments/ExperimentObservationsDownloadButton.vue

@@ -26,13 +26,13 @@
   >
     <template #form>
       <div class="columns mb-4">
-        <!-- Dataset Select -->
+        <!-- DatasetModel Select -->
         <div class="column control">
           <div class="field">
             <label
               class="label"
               v-bind:for="`dataset-select-${trialDbId}`"
-            ><span>Dataset</span></label>
+            ><span>DatasetModel</span></label>
             <div class="control">
               <div class="select">
                 <select

src/router/index.ts

@@ -25,6 +25,7 @@ import BrapiAuthorize from '@/views/BrAPI/BrapiAuthorize.vue'
 import BrAPIInfo from '@/views/BrAPI/BrAPIInfo.vue'
 import ProgramManagement from '@/views/program/ProgramManagement.vue'
 import ExperimentDetails from "@/views/experiments-and-observations/ExperimentDetails";
+import Dataset from "@/views/import/Dataset.vue";
 import StudiesList from "@/views/trials-and-studies/StudiesList.vue";
 import ObservationsList from '@/views/observations/ObservationsList.vue';
 import AdminProgramManagement from '@/views/admin/AdminProgramManagement.vue'
@@ -366,7 +367,24 @@ const routes = [
       layout: layouts.userSideBar
     },
     component: ExperimentDetails,
-    beforeEnter: processProgramNavigation
+    redirect: (to: Route) => ({name: 'experiment_obs_dataset', params: {datasetId: 'observation', programId: to.params.programId, experimentId: to.params.experimentId}}),
+    beforeEnter: processProgramNavigation,
+    children: [
+      {
+        path: 'dataset/:datasetId',
+        name: 'experiment_obs_dataset',
+        meta: {
+          title: 'Observation Dataset',
+          layout: layouts.userSideBar
+        },
+        component: Dataset,
+        props: (route: any) => {
+          return ({
+            ...route.params
+          })
+        }
+      }
+    ]
   },
   {
     path: '/programs/:programId/import',

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

@@ -69,6 +69,25 @@
       </div>
 
     </div>
+    <section>
+      <nav class="tabs is-boxed">
+        <ul>
+          <router-link
+              v-bind:to="{name: 'experiment_obs_dataset', params: {programId: activeProgram.id, experimentId: experimentUUID, datasetId: 'observation'}}"
+              tag="li" active-class="is-active">
+            <a>Observation DatasetModel</a>
+          </router-link>
+          <!--TODO: Will need to loop through a list of datasets and add a tab for each.-->
+        </ul>
+      </nav>
+    </section>
+    <div class="tab-content">
+      <router-view
+          @show-success-notification="$emit('show-success-notification', $event)"
+          @show-info-notification="$emit('show-info-notification', $event)"
+          @show-error-notification="$emit('show-error-notification', $event)"
+      />
+    </div>
   </div>
 </template>
 

src/views/import/Dataset.vue

@@ -0,0 +1,146 @@
+<!--
+  - 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.
+  -->
+
+<template>
+  <div id="data_set">
+    <div v-if="loading">
+      loading dataset...
+      <progress class="progress is-normal" max="80"></progress>
+    </div>
+    <article
+      v-if="!loading"
+      class="message is-success"
+    >
+      <div class="message-body">
+        <div class="columns is-multiline">
+          <div class="column is-one-fifth">
+            <div class="has-text-right">
+              <b>Observation unit: </b> <span style="width: 30px;" class="is-inline-block has-text-left">{{ observationUnit }}</span><br>
+              <b>Phenotypes: </b> <span style="width: 30px;" class="is-inline-block has-text-left">{{ phenotypesCount }}</span><br>
+              <b>Total observations: </b> <span style="width: 30px;" class="is-inline-block has-text-left">{{ totalObservationsCount }}</span><br>
+              <b>Observations with data: </b> <span style="width: 30px;" class="is-inline-block has-text-left">{{ observationsWithData }}</span><br>
+              <b>Observations without data: </b> <span style="width: 30px;" class="is-inline-block has-text-left">{{ observationsWithoutData }}</span><br>
+            </div>
+          </div>
+        </div>
+      </div>
+    </article>
+  </div>
+</template>
+
+<script lang="ts">
+import {Component, Prop, Vue, Watch} from 'vue-property-decorator'
+import ProgramsBase from "@/components/program/ProgramsBase.vue";
+import {Result} from "@/breeding-insight/model/Result";
+import {DatasetModel} from "@/breeding-insight/model/DatasetModel";
+import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
+import {Program} from "@/breeding-insight/model/Program";
+import {mapGetters} from "vuex";
+
+@Component({
+  computed: {
+    ...mapGetters([
+      'activeProgram'
+    ])
+  }
+})
+export default class Dataset extends ProgramsBase {
+  private activeProgram: Program;
+  private datasetModel: DatasetModel;
+  private experiment: Experiment;
+  private loading: boolean = true;
+  private resultDatasetId: string;
+
+
+  mounted () {
+    this.getDatasetModelAndExperiment();
+  }
+
+  @Prop()
+  private datasetId?: string;
+
+  get experimentUUID(): string {
+    return this.$route.params.experimentId;
+  }
+
+  get observationUnit(): string{
+    let ou = "NA"
+    if(this.experiment && this.experiment.additionalInfo && this.experiment.additionalInfo.defaultObservationLevel){
+      ou = this.experiment.additionalInfo.defaultObservationLevel;
+    }
+    return ou;
+  }
+
+  get phenotypesCount(): number{
+    let count = 0;
+
+    if(this.datasetModel && this.datasetModel.observationVariables){
+      count = this.datasetModel.observationVariables.length;
+    }
+    return count
+  }
+
+  // Total observations
+  get totalObservationsCount(): number {
+    let count = 0;
+
+    if(this.datasetModel && this.datasetModel.observationUnits){
+      let ouCount = this.datasetModel.observationUnits.length;
+      count = ouCount * this.phenotypesCount;
+    }
+    return count
+  }
+
+  // Observations with data
+  get observationsWithData(): number {
+    let count = 0;
+    if(this.datasetModel && this.datasetModel.data){
+      count = this.datasetModel.data.length;
+    }
+    return count
+  }
+
+  // Observations without data
+  get observationsWithoutData(): number {
+    return this.totalObservationsCount-this.observationsWithData
+  }
+
+  @Watch('$route')
+  async getDatasetModelAndExperiment () {
+    this.loading = true;
+    let experimentResult =  await ExperimentService.getSingleExperiment(this.activeProgram!.id!, this.experimentUUID,false);
+    this.experiment = experimentResult.value;
+
+    if( this.datasetId==='observation'){
+      this.resultDatasetId = this.experiment.additionalInfo.observationDatasetId;
+    }
+    else{
+      this.resultDatasetId = this.datasetId;
+    }
+    try {
+      const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, this.resultDatasetId);
+      this.datasetModel = response.result;
+    } catch (err) {
+      // Display error that experiment cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load data set' + err.message());
+      throw err;
+    } finally {
+      this.loading = false;
+    }
+  }
+}
+</script>