Feature/bi 1146

src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentImportService.java

@@ -0,0 +1,75 @@
+/*
+ * 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.
+ */
+package org.breedinginsight.brapps.importer.model.imports.experimentObservation;
+
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
+import org.breedinginsight.brapps.importer.model.ImportUpload;
+import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
+import org.breedinginsight.brapps.importer.model.imports.BrAPIImportService;
+import org.breedinginsight.brapps.importer.model.imports.germplasm.GermplasmImport;
+import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
+import org.breedinginsight.brapps.importer.services.processors.*;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.model.User;
+import org.breedinginsight.services.exceptions.UnprocessableEntityException;
+import org.breedinginsight.services.exceptions.ValidatorException;
+import tech.tablesaw.api.Table;
+
+import javax.inject.Inject;
+import javax.inject.Provider;
+import javax.inject.Singleton;
+import java.util.List;
+
+@Singleton
+@Slf4j
+public class ExperimentImportService extends BrAPIImportService {
+
+    private final String IMPORT_TYPE_ID = "ExperimentImport";
+
+    private Provider<ExperimentProcessor> experimentProcessorProvider;
+    private Provider<ProcessorManager> processorManagerProvider;
+
+    @Inject
+    public ExperimentImportService(Provider<ExperimentProcessor> experimentProcessorProvider, Provider<ProcessorManager> processorManagerProvider)
+    {
+        this.experimentProcessorProvider = experimentProcessorProvider;
+        this.processorManagerProvider = processorManagerProvider;
+    }
+
+    @Override
+    public ExperimentObservation getImportClass() {
+        return new ExperimentObservation();
+    }
+
+    @Override
+    public String getImportTypeId() {
+        return IMPORT_TYPE_ID;
+    }
+
+    @Override
+    public ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
+            throws UnprocessableEntityException, ValidatorException, ApiException {
+
+        ImportPreviewResponse response = null;
+        List<Processor> processors = List.of(experimentProcessorProvider.get());
+        response = processorManagerProvider.get().process(brAPIImports, processors, program, upload, user, commit);
+        return response;
+
+    }
+}
+

src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java

@@ -0,0 +1,227 @@
+/*
+ * 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.
+ */
+
+package org.breedinginsight.brapps.importer.model.imports.experimentObservation;
+
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import org.brapi.v2.model.core.*;
+import org.brapi.v2.model.pheno.*;
+import org.breedinginsight.brapps.importer.model.config.*;
+import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.utilities.Utilities;
+
+import java.math.BigInteger;
+import java.util.*;
+import java.util.function.Supplier;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@ImportConfigMetadata(id="ExperimentImport", name="Experiment Import",
+        description = "This import is used to create Observation Unit and Experiment data")
+public class ExperimentObservation implements BrAPIImport {
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="germplasmName", name="Germplasm Name", description = "Name of germplasm")
+    private String germplasmName;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="gid", name="Germplasm GID", description = "Unique germplasm identifier")
+    private String gid;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="test_or_check", name="Test or Check", description = "T test (T) and check (C) germplasm")
+    private String testOrCheck;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="exp_title", name="Experiment Title", description = "Title of experiment")
+    private String expTitle;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="expDescription", name="Experiment Description", description = "Description of experiment")
+    private String expDescription;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="expUnit", name="Experiment Unit", description = "experiment unit  (Examples: plots, plant, tanks, hives, etc.)")
+    private String expUnit;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="expType", name="Experiment Type", description = "Description of experimental type (Examples: Performance trial, crossing block, seed orchard, etc)")
+    private String expType;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="env", name="Environment", description = "Free-text unique identifier for environment within the experiment. Common examples include: 1,2,3…n and/or a concationation of environment location and year")
+    private String env;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="envLocation", name="Environment Location", description = "Location of the environment")
+    private String envLocation;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.INTEGER)
+    @ImportFieldMetadata(id="envYear", name="Environment Year", description = "Year corresponding to the environment")
+    private String envYear;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="expUnitId", name="Experiment Unit ID", description = "Human-readable alphanumeric identifier for experimental units unique within environment. Examples, like plot number, are often a numeric sequence.")
+    private String expUnitId;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.INTEGER)
+    @ImportFieldMetadata(id="expReplicateNo", name="Experiment Replicate Number", description = "Sequential number of experimental replications")
+    private String expReplicateNo;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.INTEGER)
+    @ImportFieldMetadata(id="expBlockNo", name="Experiment Block Number", description = "Sequential number of blocks in an experimental design")
+    private String expBlockNo;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="row", name="Row", description = "Horizontal (y-axis) position in 2D Cartesian space.")
+    private String row;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="column", name="Column", description = "Vertical (x-axis) position in 2D Cartesian space.")
+    private String column;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="treatmentFactors", name="Exp Treatment Factor Name", description = "treatement factors in an experiment with applied variables, like fertilizer or water regimens.")
+    private String treatmentFactors;
+
+    @ImportFieldType(type= ImportFieldTypeEnum.TEXT)
+    @ImportFieldMetadata(id="ObsUnitID", name="Observation Unit ID", description = "A database generated unique identifier for experimental observation units")
+    private String ObsUnitID;
+
+    public BrAPITrial constructBrAPITrial(Program program, boolean commit) {
+        BrAPIProgram brapiProgram = program.getBrapiProgram();
+        BrAPITrial trial = new BrAPITrial();
+        if( commit ){
+            trial.setTrialName( getTrialNameWithProgramKey( program ));
+        }
+        else{
+            trial.setTrialName( getExpTitle() );
+        }
+        trial.setTrialDescription(getExpDescription());
+        trial.setActive(true);
+        trial.setProgramDbId(brapiProgram.getProgramDbId());
+        trial.setProgramName(brapiProgram.getProgramName());
+
+        // TODO: Get to a constant
+        trial.putAdditionalInfoItem("defaultObservationLevel", getExpUnit());
+        trial.putAdditionalInfoItem("experimentType", getExpType());
+        return trial;
+    }
+
+    public String getTrialNameWithProgramKey(Program program){
+        return String.format("%s [%s]", getExpTitle(), program.getKey());
+    }
+
+    public BrAPILocation constructBrAPILocation() {
+        BrAPILocation location = new BrAPILocation();
+        location.setLocationName(getEnvLocation());
+        return location;
+    }
+
+    public BrAPIStudy constructBrAPIStudy(Program program, Supplier<BigInteger> nextVal, boolean commit) {
+        BrAPIStudy study = new BrAPIStudy();
+        if ( commit ){
+            study.setStudyName(Utilities.appendProgramKey(getEnv(), program.getKey(), nextVal.get().toString()));
+        }
+        else {
+            study.setStudyName(getEnv());
+        }
+        study.setActive(true);
+        study.setStudyType(getExpType());
+        study.setLocationName(getEnvLocation());
+        study.setTrialName(getExpTitle());
+        study.setSeasons( List.of( getEnvYear()==null ? "" : getEnvYear() ) );
+        /*
+        TODO: Not used
+        BrAPIStudyExperimentalDesign design = new BrAPIStudyExperimentalDesign();
+        design.setPUI(getExperimentalDesignPUI());
+        study.setExperimentalDesign(design);
+        */
+
+        return study;
+    }
+
+    public BrAPIObservationUnit constructBrAPIObservationUnit(Program program, Supplier<BigInteger> nextVal, boolean commit) {
+
+        BrAPIObservationUnit observationUnit = new BrAPIObservationUnit();
+        if( commit){
+            observationUnit.setObservationUnitName( Utilities.appendProgramKey(getExpUnitId(), program.getKey(), nextVal.get().toString()));
+        }
+        else {
+            observationUnit.setObservationUnitName(getExpUnitId());
+        }
+        observationUnit.setStudyName(getEnv());
+
+        // TODO: Set the germplasm
+        //observationUnit.setGermplasmName(getGermplasm().getReferenceValue());
+
+        BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
+        BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
+        level.setLevelName(getExpUnit());
+        position.setObservationLevel(level);
+
+        // Exp Unit
+        List<BrAPIObservationUnitLevelRelationship> levelRelationships = new ArrayList<>();
+        if( getExpReplicateNo() !=null ) {
+            BrAPIObservationUnitLevelRelationship repLvl = new BrAPIObservationUnitLevelRelationship();
+            repLvl.setLevelName("replicate");
+            repLvl.setLevelCode(getExpReplicateNo());
+            levelRelationships.add(repLvl);
+        }
+
+        // Block number
+        if( getExpBlockNo() != null ) {
+            BrAPIObservationUnitLevelRelationship repLvl = new BrAPIObservationUnitLevelRelationship();
+            repLvl.setLevelName("block");
+            repLvl.setLevelCode(getExpBlockNo());
+            levelRelationships.add(repLvl);
+        }
+        position.setObservationLevelRelationships(levelRelationships);
+
+        // Test or Check
+        if("C".equals(getTestOrCheck())){
+            position.setEntryType(BrAPIEntryTypeEnum.CHECK);
+        } else {
+            position.setEntryType(BrAPIEntryTypeEnum.TEST);
+        }
+
+        // X and Y coordinates
+        if (getRow() != null) {
+            position.setPositionCoordinateX(getRow());
+            position.setPositionCoordinateXType(BrAPIPositionCoordinateTypeEnum.GRID_ROW);
+        }
+        if (getColumn() != null) {
+            position.setPositionCoordinateY(getColumn());
+            position.setPositionCoordinateYType(BrAPIPositionCoordinateTypeEnum.GRID_ROW);
+        }
+        observationUnit.setObservationUnitPosition(position);
+
+        // Treatment factors
+        if (getTreatmentFactors() != null) {
+            BrAPIObservationTreatment treatment = new BrAPIObservationTreatment();
+            treatment.setFactor(getTreatmentFactors());
+            observationUnit.setTreatments(List.of(treatment));
+        }
+
+        return observationUnit;
+    }
+
+}