BI-1647 (View Experiments: Observation Dataset Table)

src/assets/scss/main.scss

@@ -906,3 +906,19 @@ label.environment-option-label {
   overflow: hidden;
   text-overflow: ellipsis;
 }
+
+.missing-data {
+  /* using an opacity instead of a muted color (for example
+    'gray') to preserve some difference in row color when
+    a table is striped.
+   */
+  background-color: black;
+  opacity: 17%;
+  }
+
+#data_set th {
+  min-width: 5em;
+}
+
+
+

src/breeding-insight/dao/ExperimentDAO.ts

@@ -46,7 +46,7 @@ export class ExperimentDAO {
         config.experimentId = experimentId;
         config.datasetId = datasetId;
         config.params = {
-            stat : stats,
+            stats : stats,
         };
         return new Promise<Result<Error, DatasetModel>>(((resolve, reject) => {
             api.call(config)

src/breeding-insight/model/DatasetModel.ts

@@ -20,21 +20,22 @@ import {ObservationUnit} from "@/breeding-insight/model/ObservationUnit";
 import {ObservationVariable} from "@/breeding-insight/model/ObservationVariable";
 
 export class DatasetModel {
-  id?: string;
-  experimentId?: string;
+  id: string;
+  experimentId: string;
+  data: Observation[];
+  observationUnits: ObservationUnit[];
+  observationVariables: ObservationVariable[];
   additionalInfo?: any;
-  data?: Observation[];
-  observationUnits?: ObservationUnit[];
-  observationVariables?: ObservationVariable[];
-
-
-  constructor(id?: string,
-              experimentId?: string,
-              additionalInfo?: any,
-              data?: Observation[],
-              observationUnits?: ObservationUnit[],
-              observationVariables?: ObservationVariable[]
-              ) {
+
+
+
+  constructor(id: string,
+              experimentId: string,
+              data: Observation[],
+              observationUnits: ObservationUnit[],
+              observationVariables: ObservationVariable[],
+              additionalInfo?: any
+  ) {
     this.id = id;
     this.experimentId = experimentId;
     this.additionalInfo = additionalInfo;
@@ -48,10 +49,10 @@ export class DatasetModel {
     return new DatasetModel(
         dataset.id,
         dataset.experimentId,
-        dataset.additionalInfo,
         dataset.data,
-        dataset.observationUnits
-        );
+        dataset.observationUnits,
+        dataset.additionalInfo
+    );
   }
 
   equals(dataset?: DatasetModel): boolean {

src/breeding-insight/model/DatasetTableRow.ts

@@ -0,0 +1,83 @@
+/*
+ * 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 DatasetTableRow {
+  germplasmName?: string;
+  gid?: string;
+  testOrCheck?: string;
+  env?: string;
+  envLocation?: string;
+  envYear?: string;
+  expUnitId?: string;
+  expReplicate?: number;
+  expBlock?: number;
+  row?: string;
+  column?: string;
+  obsUnitId?: string;
+  traitValues?: string[] = [];
+
+
+  constructor(germplasmName?: string,
+              gid?: string,
+              testOrCheck?: string,
+              env?: string,
+              envLocation?: string,
+              envYear?: string,
+              expUnitId?: string,
+              expReplicate?: number,
+              expBlock?: number,
+              row?: string,
+              column?: string,
+              obsUnitId?: string,
+              traitValues?: string[]) {
+    this.germplasmName = germplasmName;
+    this.gid = gid;
+    this.testOrCheck = testOrCheck;
+    this.env = env;
+    this.envLocation = envLocation;
+    this.envYear = envYear;
+    this.expUnitId = expUnitId;
+    this.expReplicate = expReplicate;
+    this.expBlock = expBlock;
+    this.row = row;
+    this.column = column;
+    this.obsUnitId = obsUnitId;
+    this.traitValues = traitValues;
+
+  }
+
+  static assign(dataset: DatasetTableRow): DatasetTableRow {
+
+    return new DatasetTableRow(
+        dataset.germplasmName,
+        dataset.gid,
+        dataset.testOrCheck,
+        dataset.env,
+        dataset.envLocation,
+        dataset.envYear,
+        dataset.expUnitId,
+        dataset.expReplicate,
+        dataset.expBlock,
+        dataset.row,
+        dataset.column,
+        dataset.obsUnitId,
+        dataset.traitValues
+        );
+  }
+
+
+}

src/breeding-insight/model/Observation.ts

@@ -17,10 +17,10 @@
 
 export class Observation {
   id?: string;
-  studyId?: string;
-  germplasmId?: string;
-  observationUnitId?: string;
-  observationVariableId?: string;
+  studyDbId?: string;
+  germplasmDbId?: string;
+  observationUnitDbId?: string;
+  observationVariableDbId?: string;
   germplasmName?: string;
   observationUnitName?: string;
   observationVariableName?: string;
@@ -33,10 +33,10 @@ export class Observation {
   observationTimeStamp?: string;
 
   constructor(id?: string,
-              studyId?: string,
-              germplasmId?: string,
-              observationUnitId?: string,
-              observationVariableId?: string,
+              studyDbId?: string,
+              germplasmDbId?: string,
+              observationUnitDbId?: string,
+              observationVariableDbId?: string,
               germplasmName?: string,
               observationUnitName?: string,
               observationVariableName?: string,
@@ -48,10 +48,10 @@ export class Observation {
               value?: any
               ) {
     this.id = id;
-    this.studyId = studyId;
-    this.germplasmId = germplasmId;
-    this.observationUnitId = observationUnitId;
-    this.observationVariableId = observationVariableId;
+    this.studyDbId = studyDbId;
+    this.germplasmDbId = germplasmDbId;
+    this.observationUnitDbId = observationUnitDbId;
+    this.observationVariableDbId = observationVariableDbId;
     this.germplasmName = germplasmName;
     this.observationUnitName = observationUnitName;
     this.observationVariableName = observationVariableName;
@@ -72,10 +72,10 @@ export class Observation {
     const stamp: string | undefined = observation.timeStamp ? observation.timeStamp.toISOString() : undefined;
 
     return new Observation(observation.id,
-                           observation.studyId,
-                           observation.germplasmId,
-                           observation.observationUnitId,
-                           observation.observationVariableId,
+                           observation.studyDbId,
+                           observation.germplasmDbId,
+                           observation.observationUnitDbId,
+                           observation.observationVariableDbId,
                            observation.germplasmName,
                            observation.observationUnitName,
                            observation.observationVariableName,
@@ -90,10 +90,10 @@ export class Observation {
   equals(observation?: Observation): boolean {
     if (!observation) {return false;}
     return (this.id === observation.id) &&
-      (this.studyId === observation.studyId) &&
-      (this.germplasmId === observation.germplasmId) &&
-      (this.observationUnitId === observation.observationUnitId) &&
-      (this.observationVariableId === observation.observationVariableId) &&
+      (this.studyDbId === observation.studyDbId) &&
+      (this.germplasmDbId === observation.germplasmDbId) &&
+      (this.observationUnitDbId === observation.observationUnitDbId) &&
+      (this.observationVariableDbId === observation.observationVariableDbId) &&
       (this.germplasmName === observation.germplasmName) &&
       (this.observationUnitName === observation.observationUnitName) &&
       (this.observationVariableName === observation.observationVariableName) &&

src/breeding-insight/model/ObservationUnit.ts

@@ -15,22 +15,72 @@
  * limitations under the License.
  */
 
+import {ExternalReferences} from "@/breeding-insight/brapi/model/externalReferences";
+
 export class ObservationUnit {
-  id?: string;
-  name?: string;
-  position?: ObservationUnitPosition;
-
-  constructor(id?:string, name?:string, position?:ObservationUnitPosition) {
-    this.id = id;
-    this.name = name;
-    this.position = position;
+  observationUnitDbId: string;
+  germplasmDbId?: string;
+  germplasmName: string;
+  locationDbI?: string;
+  locationName: string;
+  observationUnitName?: string;
+  observationUnitPUI?: string;
+  programDbId?: string;
+  programName?: string;
+  studyDbId?: string;
+  studyName: string;
+  trialDbId?: string;
+  trialName?: string;
+  observationUnitPosition?: ObservationUnitPosition;
+  externalReferences?: ExternalReferences;
+  additionalInfo?: any;
+  treatments?: any;
+
+
+  constructor(observationUnitDbId:string, observationUnitName?:string, observationUnitPosition?:ObservationUnitPosition, externalReferences?: ExternalReferences) {
+    this.observationUnitDbId = observationUnitDbId;
+    this.observationUnitName = observationUnitName;
+    this.observationUnitPosition = observationUnitPosition;
+    this.externalReferences = externalReferences;
   }
 }
 
 export class ObservationUnitPosition {
   level?: string;
+  observationLevelRelationships?: ObservationLevelRelationship[];
+  positionCoordinateXType?: string;
+  positionCoordinateX?: string;
+  positionCoordinateYType?: string;
+  positionCoordinateY?: string;
+  entryType?: string;
 
-  constructor(level?:string) {
+  constructor(level?:string,
+              observationLevelRelationships?: ObservationLevelRelationship[],
+              positionCoordinateXType?: string,
+              positionCoordinateX?: string,
+              positionCoordinateYType?: string,
+              positionCoordinateY?: string,
+              entryType?: string,
+              ) {
     this.level = level;
+    this.observationLevelRelationships = observationLevelRelationships;
+    this.positionCoordinateXType = positionCoordinateXType;
+    this.positionCoordinateX = positionCoordinateX;
+    this.positionCoordinateYType = positionCoordinateYType;
+    this.positionCoordinateY = positionCoordinateY;
+    this.entryType = entryType
+  }
+}
+
+
+export class ObservationLevelRelationship {
+  levelName?: string;
+  levelOrder?: string;
+  levelCode?: number;
+
+  constructor(levelName?: string, levelOrder?: string, levelCode?: number) {
+    this.levelName = levelName;
+    this.levelOrder = levelOrder;
+    this.levelCode = levelCode;
   }
 }

src/breeding-insight/model/ObservationVariable.ts

@@ -21,20 +21,20 @@ import {Scale} from "@/breeding-insight/model/Scale";
 
 // TODO: eventually refactor Trait into Observation Variable to be consistent with the BrAPI model
 export class ObservationVariable {
-  id?: string;
+  observationVariableDbId?: string;
   observationVariableName?: string;
   additionalInfo?: OVAdditionalInfo;
   trait?: Trait;
   method?: Method;
   scale?: Scale;
 
-  constructor(id?:string,
+  constructor(observationVariableDbId?:string,
               observationVariableName?:string,
               additionalInfo?:OVAdditionalInfo,
               trait?:Trait,
               method?:Method,
               scale?:Scale) {
-    this.id = id;
+    this.observationVariableDbId = observationVariableDbId;
     this.observationVariableName = observationVariableName;
     if (additionalInfo){
       this.additionalInfo = OVAdditionalInfo.assign({...additionalInfo} as OVAdditionalInfo);

src/breeding-insight/utils/BrAPIUtils.ts

@@ -18,7 +18,10 @@
 import {ExternalReferences} from "@/breeding-insight/brapi/model/externalReferences";
 
 export class BrAPIUtils {
-    static getBreedingInsightId(references: ExternalReferences, referenceSourcePath: string = ""): string | undefined {
+    static getBreedingInsightId(references: ExternalReferences|undefined, referenceSourcePath: string = ""): string | undefined {
+        if(!references){
+            return undefined;
+        }
         let val = references.find(ref => ref.referenceSource === process.env.VUE_APP_BI_REFERENCE_SOURCE + referenceSourcePath);
         return val ? val.referenceID : "";
     }