Concept Set Compare Feature

src/main/java/org/ohdsi/webapi/conceptset/ConceptSetComparison.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.ohdsi.webapi.conceptset;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
@@ -18,45 +13,154 @@
 @JsonInclude(JsonInclude.Include.ALWAYS)
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class ConceptSetComparison {
-    @JsonProperty("conceptId")
-    public Long conceptId;    
-
-    @JsonProperty("conceptIn1Only")
-    public Long conceptIn1Only;
-
-    @JsonProperty("conceptIn2Only")
-    public Long conceptIn2Only;
-
-    @JsonProperty("conceptIn1And2")
-    public Long conceptIn1And2;
-
-    @JsonProperty("conceptName")
-    public String conceptName;
-
-    @JsonProperty("standardConcept")
-    public String standardConcept;
-
-    @JsonProperty("invalidReason")
-    public String invalidReason;
-
-    @JsonProperty("conceptCode")
-    public String conceptCode;
-
-    @JsonProperty("domainId")
-    public String domainId;
-
-    @JsonProperty("vocabularyId")
-    public String vocabularyId;
-
-    @JsonProperty("validStartDate")
-    public Date validStartDate;
-
-    @JsonProperty("validEndDate")
-    public Date validEndDate;
-
-    @JsonProperty("conceptClassId")
-    public String conceptClassId;
-
-    @JsonProperty("nameMismatch")
-    public boolean nameMismatch;
-}
+	@JsonProperty("isSourceCode")
+	public boolean isSourceCode;
+
+	@JsonProperty("conceptId")
+	public Long conceptId;
+
+	// Concept Set membership flags
+	@JsonProperty("conceptInCS1Only")
+	public Long conceptInCS1Only;
+
+	@JsonProperty("conceptInCS2Only")
+	public Long conceptInCS2Only;
+
+	@JsonProperty("conceptInCS1AndCS2")
+	public Long conceptInCS1AndCS2;
+
+	// Concept names from both vocabularies
+	@JsonProperty("vocab1ConceptName")
+	public String vocab1ConceptName;
+
+	@JsonProperty("vocab2ConceptName")
+	public String vocab2ConceptName;
+
+	// Standard concept from both vocabularies
+	@JsonProperty("vocab1StandardConcept")
+	public String vocab1StandardConcept;
+
+	@JsonProperty("vocab2StandardConcept")
+	public String vocab2StandardConcept;
+
+	@JsonProperty("standardConcept")
+	public String standardConcept;
+
+	// Invalid reason from both vocabularies
+	@JsonProperty("vocab1InvalidReason")
+	public String vocab1InvalidReason;
+
+	@JsonProperty("vocab2InvalidReason")
+	public String vocab2InvalidReason;
+
+	@JsonProperty("invalidReason")
+	public String invalidReason;
+
+	// Concept code from both vocabularies
+	@JsonProperty("vocab1ConceptCode")
+	public String vocab1ConceptCode;
+
+	@JsonProperty("vocab2ConceptCode")
+	public String vocab2ConceptCode;
+
+	@JsonProperty("conceptCode")
+	public String conceptCode;
+
+	// Domain ID from both vocabularies
+	@JsonProperty("vocab1DomainId")
+	public String vocab1DomainId;
+
+	@JsonProperty("vocab2DomainId")
+	public String vocab2DomainId;
+
+	@JsonProperty("domainId")
+	public String domainId;
+
+	// Vocabulary ID from both vocabularies
+	@JsonProperty("vocab1VocabularyId")
+	public String vocab1VocabularyId;
+
+	@JsonProperty("vocab2VocabularyId")
+	public String vocab2VocabularyId;
+
+	@JsonProperty("vocabularyId")
+	public String vocabularyId;
+
+	// Concept class ID from both vocabularies
+	@JsonProperty("vocab1ConceptClassId")
+	public String vocab1ConceptClassId;
+
+	@JsonProperty("vocab2ConceptClassId")
+	public String vocab2ConceptClassId;
+
+	@JsonProperty("conceptClassId")
+	public String conceptClassId;
+
+	// Valid start date from both vocabularies
+	@JsonProperty("vocab1ValidStartDate")
+	public Date vocab1ValidStartDate;
+
+	@JsonProperty("vocab2ValidStartDate")
+	public Date vocab2ValidStartDate;
+
+	@JsonProperty("validStartDate")
+	public Date validStartDate;
+
+	// Valid end date from both vocabularies
+	@JsonProperty("vocab1ValidEndDate")
+	public Date vocab1ValidEndDate;
+
+	@JsonProperty("vocab2ValidEndDate")
+	public Date vocab2ValidEndDate;
+
+	@JsonProperty("validEndDate")
+	public Date validEndDate;
+
+	// Mismatch flags for each field
+	@JsonProperty("nameMismatch")
+	public boolean nameMismatch;
+
+	@JsonProperty("standardConceptMismatch")
+	public boolean standardConceptMismatch;
+
+	@JsonProperty("invalidReasonMismatch")
+	public boolean invalidReasonMismatch;
+
+	@JsonProperty("conceptCodeMismatch")
+	public boolean conceptCodeMismatch;
+
+	@JsonProperty("domainIdMismatch")
+	public boolean domainIdMismatch;
+
+	@JsonProperty("vocabularyIdMismatch")
+	public boolean vocabularyIdMismatch;
+
+	@JsonProperty("conceptClassIdMismatch")
+	public boolean conceptClassIdMismatch;
+
+	@JsonProperty("validStartDateMismatch")
+	public boolean validStartDateMismatch;
+
+	@JsonProperty("validEndDateMismatch")
+	public boolean validEndDateMismatch;
+
+	// Vocabulary info for vocab 1
+	@JsonProperty("vocab1SourceKey")
+	public String vocab1SourceKey;
+
+	@JsonProperty("vocab1SourceName")
+	public String vocab1SourceName;
+
+	@JsonProperty("vocab1SourceVersion")
+	public String vocab1SourceVersion;
+
+	// Vocabulary info for vocab 2
+	@JsonProperty("vocab2SourceKey")
+	public String vocab2SourceKey;
+
+	@JsonProperty("vocab2SourceName")
+	public String vocab2SourceName;
+
+	@JsonProperty("vocab2SourceVersion")
+	public String vocab2SourceVersion;
+}

src/main/java/org/ohdsi/webapi/conceptset/ConceptSetRepository.java

@@ -15,10 +15,12 @@
  */
 package org.ohdsi.webapi.conceptset;
 
+import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
 
+import java.util.Date;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
@@ -27,7 +29,7 @@
  *
  * @author fdefalco
  */
-public interface ConceptSetRepository extends CrudRepository<ConceptSet, Integer> {
+public interface ConceptSetRepository extends CrudRepository<ConceptSet, Integer>, JpaSpecificationExecutor<ConceptSet> {
   ConceptSet findById(Integer conceptSetId);
 
   @Deprecated
@@ -44,4 +46,31 @@ public interface ConceptSetRepository extends CrudRepository<ConceptSet, Integer
 
   @Query("SELECT DISTINCT cs FROM ConceptSet cs JOIN FETCH cs.tags t WHERE lower(t.name) in :tagNames")
   List<ConceptSet> findByTags(@Param("tagNames") List<String> tagNames);
+
+	@Query("SELECT cs FROM ConceptSet cs WHERE " +
+		"(:createdFrom IS NULL OR cs.createdDate >= :createdFrom) AND " +
+		"(:createdTo IS NULL OR cs.createdDate <= :createdTo) AND " +
+		"(:updatedFrom IS NULL OR cs.modifiedDate >= :updatedFrom) AND " +
+		"(:updatedTo IS NULL OR cs.modifiedDate <= :updatedTo)")
+	List<ConceptSet> findByDateFilters(
+		@Param("createdFrom") Date createdFrom,
+		@Param("createdTo") Date createdTo,
+		@Param("updatedFrom") Date updatedFrom,
+		@Param("updatedTo") Date updatedTo
+	);
+
+	@Query("SELECT DISTINCT cs FROM ConceptSet cs " +
+		"JOIN cs.tags t " +
+		"WHERE t.id IN :tagIds AND " +
+		"(:createdFrom IS NULL OR cs.createdDate >= :createdFrom) AND " +
+		"(:createdTo IS NULL OR cs.createdDate <= :createdTo) AND " +
+		"(:updatedFrom IS NULL OR cs.modifiedDate >= :updatedFrom) AND " +
+		"(:updatedTo IS NULL OR cs.modifiedDate <= :updatedTo)")
+	List<ConceptSet> findByTagsAndDateFilters(
+		@Param("tagIds") List<Integer> tagIds,
+		@Param("createdFrom") Date createdFrom,
+		@Param("createdTo") Date createdTo,
+		@Param("updatedFrom") Date updatedFrom,
+		@Param("updatedTo") Date updatedTo
+	);
 }

src/main/java/org/ohdsi/webapi/estimation/EstimationController.java

@@ -26,7 +26,7 @@
 import org.springframework.core.convert.support.GenericConversionService;
 import org.springframework.stereotype.Controller;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.DELETE;
 import javax.ws.rs.DefaultValue;

src/main/java/org/ohdsi/webapi/estimation/EstimationServiceImpl.java

@@ -56,7 +56,7 @@
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import javax.ws.rs.InternalServerErrorException;
 import java.io.ByteArrayOutputStream;
 import java.io.File;

src/main/java/org/ohdsi/webapi/executionengine/service/ScriptExecutionServiceImpl.java

@@ -45,7 +45,7 @@
 
 import javax.annotation.PostConstruct;
 import javax.net.ssl.HttpsURLConnection;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import javax.ws.rs.InternalServerErrorException;
 import javax.ws.rs.NotFoundException;
 import javax.ws.rs.client.Entity;

src/main/java/org/ohdsi/webapi/job/JobArtifactController.java

@@ -0,0 +1,45 @@
+package org.ohdsi.webapi.job;
+
+import org.ohdsi.webapi.job.artifact.JobArtifactService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.ws.rs.GET;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.Produces;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+
+/**
+ * Controller for managing job execution artifacts (reports, results, etc.)
+ */
+@Path("/job")
+@Component
+public class JobArtifactController {
+
+	private static final Logger logger = LoggerFactory.getLogger(JobArtifactController.class);
+
+	private final JobArtifactService artifactService;
+
+	public JobArtifactController(JobArtifactService artifactService) {
+		this.artifactService = artifactService;
+	}
+
+	/**
+	 * Download artifact for a specific job execution
+	 *
+	 * @param executionId the job execution ID
+	 * @return Response containing the artifact file
+	 */
+	@GET
+	@Path("/{executionId}/artifact")
+	@Produces(MediaType.APPLICATION_OCTET_STREAM)
+	@Transactional
+	public Response downloadArtifact(@PathParam("executionId") Long executionId) {
+		logger.info("Artifact download requested for job execution ID: {}", executionId);
+		return artifactService.downloadArtifact(executionId);
+	}
+}

src/main/java/org/ohdsi/webapi/job/JobExecutionResource.java

@@ -33,8 +33,11 @@ public class JobExecutionResource {
 
     @JsonProperty("ownerType")
     private JobOwnerType ownerType;
-
-    public JobExecutionResource() {
+
+	  @JsonProperty("hasArtifact")
+	  private Boolean hasArtifact;  
+
+	public JobExecutionResource() {
         //needed for json deserialization
     }
 
@@ -129,4 +132,12 @@ public JobOwnerType getOwnerType() {
     public void setOwnerType(JobOwnerType ownerType) {
         this.ownerType = ownerType;
     }
+
+	public Boolean getHasArtifact() {
+		return hasArtifact;
+	}
+
+	public void setHasArtifact(Boolean hasArtifact) {
+		this.hasArtifact = hasArtifact;
+	}
 }