[BI-2923] Associate Observation Variables with BrAPI Program

src/main/java/io/swagger/model/pheno/ObservationVariable.java

@@ -21,6 +21,12 @@ public class ObservationVariable extends VariableBaseClass  {
   @JsonProperty("observationVariableName")
   private String observationVariableName = null;
 
+  @JsonProperty("programDbId")
+  private String programDbId = null;
+
+  @JsonProperty("programName")
+  private String programName = null;
+
   public ObservationVariable observationVariableDbId(String observationVariableDbId) {
     this.observationVariableDbId = observationVariableDbId;
     return this;
@@ -61,6 +67,21 @@ public void setObservationVariableName(String observationVariableName) {
     this.observationVariableName = observationVariableName;
   }
 
+  public String getProgramDbId() {
+    return programDbId;
+  }
+
+  public void setProgramDbId(String programDbId) {
+    this.programDbId = programDbId;
+  }
+
+  public String getProgramName() {
+    return programName;
+  }
+
+  public void setProgramName(String programName) {
+    this.programName = programName;
+  }
 
   @Override
   public boolean equals(java.lang.Object o) {

src/main/java/io/swagger/model/pheno/ObservationVariableNewRequest.java

@@ -17,6 +17,9 @@ public class ObservationVariableNewRequest extends VariableBaseClass {
 	@JsonProperty("observationVariableName")
 	private Optional<String> observationVariableName = null;
 
+	@JsonProperty("programDbId")
+	private String programDbId = null;
+
 	public ObservationVariableNewRequest observationVariableName(String observationVariableName) {
 		this.observationVariableName = UpdateUtility.setField(observationVariableName);
 		return this;
@@ -30,6 +33,14 @@ public void setObservationVariableName(String observationVariableName) {
 		this.observationVariableName = UpdateUtility.setField(observationVariableName);
 	}
 
+	public String getProgramDbId() {
+		return programDbId;
+	}
+
+	public void setProgramDbId(String programDbId) {
+		this.programDbId = programDbId;
+	}
+
 	@Override
 	public boolean equals(java.lang.Object o) {
 		if (this == o) {
@@ -54,6 +65,7 @@ public String toString() {
 		sb.append("class ObservationVariableNewRequest {\n");
 		sb.append("    ").append(toIndentedString(super.toString())).append("\n");
 		sb.append("    observationVariableName: ").append(toIndentedString(observationVariableName)).append("\n");
+		sb.append("    programDbId: ").append(toIndentedString(programDbId)).append("\n");
 		sb.append("}");
 		return sb.toString();
 	}

src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationVariableEntity.java

@@ -1,6 +1,7 @@
 package org.brapi.test.BrAPITestServer.model.entity.pheno;
 
 import jakarta.persistence.*;
+import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
 
 import java.util.List;
 
@@ -13,6 +14,8 @@ public class ObservationVariableEntity extends VariableBaseEntity{
 	private String pui;
 	@OneToMany(mappedBy="observationVariable", fetch = FetchType.LAZY)
 	private List<ObservationEntity> observations;
+	@ManyToOne(fetch = FetchType.LAZY)
+	private ProgramEntity program;
 
 	public String getPui() {
 		return pui;
@@ -32,4 +35,10 @@ public List<ObservationEntity> getObservations() {
 	public void setObservations(List<ObservationEntity> observations) {
 		this.observations = observations;
 	}
+	public ProgramEntity getProgram() {
+		return program;
+	}
+	public void setProgram(ProgramEntity program) {
+		this.program = program;
+	}
 }

src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationVariableService.java

@@ -7,6 +7,7 @@
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
 import org.brapi.test.BrAPITestServer.model.entity.core.CropEntity;
+import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.*;
 import org.brapi.test.BrAPITestServer.repository.primaryEntities.core.TraitRepository;
 import org.brapi.test.BrAPITestServer.repository.primaryEntities.pheno.MethodRepository;
@@ -17,6 +18,7 @@
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
 import org.brapi.test.BrAPITestServer.service.UpdateUtility;
 import org.brapi.test.BrAPITestServer.service.core.CropService;
+import org.brapi.test.BrAPITestServer.service.core.ProgramService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -47,11 +49,12 @@ public class ObservationVariableService {
 	private final MethodService methodService;
 	private final ScaleService scaleService;
 	private final TraitService traitService;
+	private final ProgramService programService;
 
 	@Autowired
 	public ObservationVariableService(ObservationVariableRepository observationVariableRepository,
-									  OntologyService ontologyService, CropService cropService, MethodService methodService,
-									  ScaleService scaleService, TraitService traitService, MethodRepository methodRepository, ScaleRepository scaleRepository, TraitRepository traitRepository) {
+	                                  OntologyService ontologyService, CropService cropService, MethodService methodService,
+	                                  ScaleService scaleService, TraitService traitService, MethodRepository methodRepository, ScaleRepository scaleRepository, TraitRepository traitRepository, ProgramService programService) {
 		this.observationVariableRepository = observationVariableRepository;
 		this.methodRepository = methodRepository;
 		this.scaleRepository = scaleRepository;
@@ -61,6 +64,7 @@ public ObservationVariableService(ObservationVariableRepository observationVaria
 		this.methodService = methodService;
 		this.scaleService = scaleService;
 		this.traitService = traitService;
+		this.programService = programService;
 	}
 
 	public List<ObservationVariable> findObservationVariables(String observationVariableDbId,
@@ -124,7 +128,8 @@ public List<ObservationVariable> findObservationVariables(ObservationVariableSea
 				   .leftJoinFetch("method", "varMethod")
 				   .leftJoinFetch("ontology", "varOntology")
 				   .leftJoinFetch("scale", "varScale")
-				   .leftJoinFetch("trait", "varTrait");
+				   .leftJoinFetch("trait", "varTrait")
+				   .leftJoinFetch("program", "varProgram");
 		if (request.getStudyDbId() != null) {
 			searchQuery = searchQuery.join("observations", "observation").appendList(request.getStudyDbId(),
 					"*observation.observationUnit.study.id");
@@ -136,7 +141,10 @@ public List<ObservationVariable> findObservationVariables(ObservationVariableSea
 				.appendList(request.getOntologyDbIds(), "ontology.id").appendList(request.getScaleDbIds(), "scale.id")
 				.appendList(request.getTraitClasses(), "trait.traitClass")
 				.appendList(request.getTraitDbIds(), "trait.id")
-				.appendEnumList(request.getDataTypes(), "scale.dataType");
+				.appendList(request.getTraitNames(), "trait.name")
+				.appendEnumList(request.getDataTypes(), "scale.dataType")
+				.appendList(request.getProgramDbIds(), "program.id")
+				.appendList(request.getProgramNames(), "program.name");
 
 		log.debug("Starting variable search");
 		Page<ObservationVariableEntity> page = observationVariableRepository.findAllBySearchAndPaginate(searchQuery, pageReq);
@@ -201,6 +209,11 @@ private ObservationVariable convertFromEntity(ObservationVariableEntity entity)
 		var.setObservationVariableName(entity.getName());
 		var.setObservationVariableDbId(entity.getId().toString());
 
+		if (entity.getProgram() != null) {
+			var.setProgramDbId(entity.getProgram().getId().toString());
+			var.setProgramName(entity.getProgram().getName());
+		}
+
 		return var;
 	}
 
@@ -240,6 +253,11 @@ private void updateEntity(ObservationVariableEntity entity, ObservationVariableN
 			throws BrAPIServerException {
 		updateBaseEntity(entity, request);
 		entity.setName(UpdateUtility.replaceField(request.getObservationVariableName(), entity.getName()));
+
+		if (request.getProgramDbId() != null) {
+			ProgramEntity programEntity = programService.getProgramEntity(request.getProgramDbId());
+			entity.setProgram(programEntity);
+		}
 	}
 
 	public void updateBaseEntity(VariableBaseEntity entity, VariableBaseClass request) throws BrAPIServerException {

src/main/resources/db/migration/V006_005__add_program_id_to_observation_variable_and_migrate.sql

@@ -0,0 +1,40 @@
+ALTER TABLE observation_variable
+    ADD COLUMN program_id UUID;
+
+ALTER TABLE observation_variable
+    ADD CONSTRAINT observation_variable_program_fk
+        FOREIGN KEY (program_id)
+            REFERENCES public.program(id);
+
+CREATE INDEX observation_var_program_idx ON observation_variable (program_id, id);
+
+UPDATE observation_variable set program_id = pquery.program_id
+    FROM (
+        SELECT ov.id AS obs_var_id, p.id AS program_id
+        FROM observation_variable ov
+        JOIN variable_base_entity_external_references ovex ON ov.id = ovex.variable_base_entity_id
+        JOIN external_reference ex ON ex.id = ovex.external_references_id
+        JOIN external_reference ex2 ON ex2.external_reference_id = ex.external_reference_id
+        JOIN program_external_references pex ON pex.external_references_id = ex2.id
+        JOIN program p ON p.id = pex.program_entity_id
+        WHERE ex.external_reference_source = 'breedinginsight.org/programs' AND ex2.external_reference_source = 'breedinginsight.org') pquery
+WHERE id = pquery.obs_var_id;
+
+-- Assertion to ensure all observation variables are now associated with a program
+DO $$
+    DECLARE
+obs_vars_without_program_count integer;
+
+BEGIN
+SELECT COUNT(*)
+INTO obs_vars_without_program_count
+FROM observation_variable ov
+WHERE ov.program_id IS NULL;
+
+IF obs_vars_without_program_count <> 0 THEN
+                RAISE EXCEPTION
+                    'V006.005 After migration, expected all observation_variable rows to have program_id set, but there are % rows with program_id not set',
+                    obs_vars_without_program_count;
+END IF;
+END
+$$;