Temporal annual distribution functionality and temporal FeatureExtraction capability enablement

pom.xml

@@ -23,7 +23,7 @@
     <shiro.version>1.12.0</shiro.version>
     <dom4j.version>2.1.3</dom4j.version>
     <hydra.version>0.4.0</hydra.version>
-    <featureExtraction.version>3.2.0</featureExtraction.version>
+    <featureExtraction.version>3.7.0-SNAPSHOT</featureExtraction.version>
     <tomcat.embed.version>8.5.87</tomcat.embed.version>
 
     <commons-fileupload.version>1.5</commons-fileupload.version>
@@ -1122,7 +1122,7 @@
     <dependency>
       <groupId>org.ohdsi</groupId>
       <artifactId>SkeletonCohortCharacterization</artifactId>
-      <version>1.2.1</version>
+      <version>2.0.0-SNAPSHOT</version>
       <exclusions>
         <exclusion>
           <groupId>org.ohdsi</groupId>

src/main/java/org/ohdsi/webapi/cohortcharacterization/CcController.java

@@ -18,6 +18,7 @@
 import org.ohdsi.webapi.cohortcharacterization.dto.CcPrevalenceStat;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcResult;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcShortDTO;
+import org.ohdsi.webapi.cohortcharacterization.dto.CcTemporalResult;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcVersionFullDTO;
 import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
 import org.ohdsi.webapi.cohortcharacterization.dto.ExportExecutionResultRequest;
@@ -257,7 +258,7 @@ public CohortCharacterizationDTO update(@PathParam("id") final Long id, final Co
         final CohortCharacterizationEntity entity = conversionService.convert(dto, CohortCharacterizationEntity.class);
         entity.setId(id);
         final CohortCharacterizationEntity updatedEntity = service.updateCc(entity);
-        return conversionService.convert(updatedEntity, CohortCharacterizationDTO.class);
+        return convertCcToDto(updatedEntity);
     }
 
     /**
@@ -445,6 +446,14 @@ public List<CcResult> getGenerationsResults(
         return service.findResultAsList(generationId, thresholdLevel);
     }
 
+    @GET
+    @Path("/generation/{generationId}/temporalresult")
+    @Produces(MediaType.APPLICATION_JSON)
+    @Consumes(MediaType.APPLICATION_JSON)
+    public List<CcTemporalResult> getGenerationTemporalResults(@PathParam("generationId") final Long generationId) {
+        return service.findTemporalResultAsList(generationId);
+    }
+
     @POST
     @Path("/generation/{generationId}/result")
     @Produces(MediaType.APPLICATION_JSON)

src/main/java/org/ohdsi/webapi/cohortcharacterization/CcService.java

@@ -6,6 +6,7 @@
 import org.ohdsi.webapi.cohortcharacterization.dto.CcPrevalenceStat;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcResult;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcShortDTO;
+import org.ohdsi.webapi.cohortcharacterization.dto.CcTemporalResult;
 import org.ohdsi.webapi.cohortcharacterization.dto.CcVersionFullDTO;
 import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
 import org.ohdsi.webapi.cohortcharacterization.dto.ExecutionResultRequest;
@@ -15,6 +16,8 @@
 import org.ohdsi.webapi.cohortdefinition.event.CohortDefinitionChangedEvent;
 import org.ohdsi.webapi.feanalysis.event.FeAnalysisChangedEvent;
 import org.ohdsi.webapi.job.JobExecutionResource;
+import org.ohdsi.webapi.shiro.annotations.CcGenerationId;
+import org.ohdsi.webapi.shiro.annotations.DataSourceAccess;
 import org.ohdsi.webapi.tag.domain.HasTags;
 import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
 import org.ohdsi.webapi.versioning.domain.CharacterizationVersion;
@@ -64,6 +67,9 @@ public interface CcService extends HasTags<Long> {
 
     List<CcGenerationEntity> findGenerationsByCcIdAndSource(Long id, String sourceKey);
 
+    @DataSourceAccess
+    List<CcTemporalResult> findTemporalResultAsList(@CcGenerationId Long generationId);
+
     GenerationResults findResult(Long generationId, ExecutionResultRequest params);
 
     List<CcResult> findResultAsList(Long generationId, float thresholdLevel);

src/main/java/org/ohdsi/webapi/cohortcharacterization/GenerateCohortCharacterizationTasklet.java

@@ -22,6 +22,7 @@
 import org.ohdsi.sql.SqlSplit;
 import org.ohdsi.sql.SqlTranslate;
 import org.ohdsi.webapi.cohortcharacterization.converter.SerializedCcToCcConverter;
+import org.ohdsi.webapi.cohortcharacterization.domain.CcFeAnalysisEntity;
 import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
 import org.ohdsi.webapi.cohortcharacterization.repository.AnalysisGenerationInfoEntityRepository;
 import org.ohdsi.webapi.common.generation.AnalysisTasklet;
@@ -37,6 +38,7 @@
 
 import java.sql.SQLException;
 import java.util.Map;
+import java.util.Optional;
 
 import static org.ohdsi.webapi.Constants.Params.*;
 
@@ -75,9 +77,13 @@ protected String[] prepareQueries(ChunkContext chunkContext, CancelableJdbcTempl
         final String cohortTable = jobParams.get(TARGET_TABLE).toString();
         final String sessionId = jobParams.get(SESSION_ID).toString();
         final String tempSchema = SourceUtils.getTempQualifier(source);
+        boolean includeAnnual = cohortCharacterization.getCcFeatureAnalyses().stream()
+                .anyMatch(fe -> Optional.ofNullable(fe.getIncludeAnnual()).orElse(false));
+        boolean includeTemporal = cohortCharacterization.getCcFeatureAnalyses().stream()
+                .anyMatch(fe -> Optional.ofNullable(fe.getIncludeTemporal()).orElse(false));
         CCQueryBuilder ccQueryBuilder = new CCQueryBuilder(cohortCharacterization, cohortTable, sessionId,
                 SourceUtils.getCdmQualifier(source), SourceUtils.getResultsQualifier(source),
-                SourceUtils.getVocabularyQualifier(source), tempSchema, jobId);
+                SourceUtils.getVocabularyQualifier(source), tempSchema, jobId, includeAnnual, includeTemporal);
         String sql = ccQueryBuilder.build();
 
         /*

src/main/java/org/ohdsi/webapi/cohortcharacterization/converter/BaseCcDTOToCcEntityConverter.java

@@ -5,6 +5,7 @@
 import org.ohdsi.analysis.CohortMetadata;
 import org.ohdsi.analysis.Utils;
 import org.ohdsi.analysis.cohortcharacterization.design.CcResultType;
+import org.ohdsi.webapi.cohortcharacterization.domain.CcFeAnalysisEntity;
 import org.ohdsi.webapi.cohortcharacterization.domain.CcStrataConceptSetEntity;
 import org.ohdsi.webapi.cohortcharacterization.domain.CcParamEntity;
 import org.ohdsi.webapi.cohortcharacterization.domain.CcStrataEntity;
@@ -51,7 +52,16 @@ public CohortCharacterizationEntity convert(T source) {
         fa.setStatType(CcResultType.PREVALENCE);
       }
     });
-    cohortCharacterization.setFeatureAnalyses(converterUtils.convertSet(source.getFeatureAnalyses(), FeAnalysisEntity.class));
+    cohortCharacterization.setFeatureAnalyses(
+            source.getFeatureAnalyses().stream().map(fa -> {
+              CcFeAnalysisEntity feAnalysisEntity = new CcFeAnalysisEntity();
+              feAnalysisEntity.setFeatureAnalysis(conversionService.convert(fa, FeAnalysisEntity.class));
+              feAnalysisEntity.setCohortCharacterization(cohortCharacterization);
+              feAnalysisEntity.setIncludeAnnual(fa.getIncludeAnnual());
+              feAnalysisEntity.setIncludeTemporal(fa.getIncludeTemporal());
+              return feAnalysisEntity;
+            }).collect(Collectors.toSet())
+    );
 
     cohortCharacterization.setParameters(converterUtils.convertSet(source.getParameters(), CcParamEntity.class));
     cohortCharacterization.setStratas(converterUtils.convertSet(source.getStratas(), CcStrataEntity.class));

src/main/java/org/ohdsi/webapi/cohortcharacterization/converter/CcToCcDTOConverter.java

@@ -15,7 +15,7 @@ public CohortCharacterizationDTO convert(final CohortCharacterizationEntity sour
         final CohortCharacterizationDTO cohortCharacterizationDTO = super.convert(source);
 
         cohortCharacterizationDTO.setCohorts(converterUtils.convertSet(source.getCohortDefinitions(), CohortMetadataImplDTO.class));
-        cohortCharacterizationDTO.setFeatureAnalyses(converterUtils.convertSet(source.getFeatureAnalyses(), FeAnalysisShortDTO.class));
+        cohortCharacterizationDTO.setFeatureAnalyses(converterUtils.convertSet(source.getCcFeatureAnalyses(), FeAnalysisShortDTO.class));
         return cohortCharacterizationDTO;
     }
 

src/main/java/org/ohdsi/webapi/cohortcharacterization/domain/CcFeAnalysisEntity.java

@@ -0,0 +1,115 @@
+package org.ohdsi.webapi.cohortcharacterization.domain;
+
+import org.hibernate.annotations.GenericGenerator;
+import org.hibernate.annotations.Parameter;
+import org.ohdsi.analysis.cohortcharacterization.design.FeatureAnalysis;
+import org.ohdsi.analysis.cohortcharacterization.design.FeatureAnalysisDomain;
+import org.ohdsi.analysis.cohortcharacterization.design.FeatureAnalysisType;
+import org.ohdsi.webapi.feanalysis.domain.FeAnalysisEntity;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import java.util.Optional;
+import java.util.function.Function;
+import java.util.function.Supplier;
+
+@Entity
+@Table(name = "cc_analysis")
+public class CcFeAnalysisEntity implements FeatureAnalysis {
+
+    @Id
+    @GenericGenerator(
+            name = "cc_analysis_generator",
+            strategy = "org.hibernate.id.enhanced.SequenceStyleGenerator",
+            parameters = {
+                    @Parameter(name = "sequence_name", value = "cc_analysis_seq"),
+                    @Parameter(name = "increment_size", value = "1")
+            }
+    )
+    @GeneratedValue(generator = "cc_analysis_generator")
+    private Long id;
+    @ManyToOne(optional = false)
+    @JoinColumn(name = "cohort_characterization_id")
+    private CohortCharacterizationEntity cohortCharacterization;
+    @ManyToOne(optional = false)
+    @JoinColumn(name = "fe_analysis_id")
+    private FeAnalysisEntity featureAnalysis;
+    @Column(name = "include_annual")
+    private Boolean includeAnnual;
+    @Column(name = "include_temporal")
+    private Boolean includeTemporal;
+
+    public CohortCharacterizationEntity getCohortCharacterization() {
+        return cohortCharacterization;
+    }
+
+    public void setCohortCharacterization(CohortCharacterizationEntity cohortCharacterization) {
+        this.cohortCharacterization = cohortCharacterization;
+    }
+
+    public FeAnalysisEntity getFeatureAnalysis() {
+        return featureAnalysis;
+    }
+
+    public void setFeatureAnalysis(FeAnalysisEntity featureAnalysis) {
+        this.featureAnalysis = featureAnalysis;
+    }
+
+    public Long getId() {
+        return id;
+    }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
+    public Boolean getIncludeAnnual() {
+        return includeAnnual;
+    }
+
+    public void setIncludeAnnual(Boolean includeAnnual) {
+        this.includeAnnual = includeAnnual;
+    }
+
+    public Boolean getIncludeTemporal() {
+        return includeTemporal;
+    }
+
+    public void setIncludeTemporal(Boolean includeTemporal) {
+        this.includeTemporal = includeTemporal;
+    }
+
+    private <T> T mapFeatureAnalysis(Function<FeAnalysisEntity, T> getter) {
+        return Optional.ofNullable(featureAnalysis).map(getter).orElse(null);
+    }
+
+    @Override
+    public FeatureAnalysisType getType() {
+        return mapFeatureAnalysis(FeatureAnalysis::getType);
+    }
+
+    @Override
+    public String getName() {
+        return mapFeatureAnalysis(FeatureAnalysis::getName);
+    }
+
+    @Override
+    public FeatureAnalysisDomain getDomain() {
+        return mapFeatureAnalysis(FeatureAnalysis::getDomain);
+    }
+
+    @Override
+    public String getDescr() {
+        return mapFeatureAnalysis(FeatureAnalysis::getDescr);
+    }
+
+    @Override
+    public Object getDesign() {
+        return mapFeatureAnalysis(FeatureAnalysis::getDesign);
+    }
+}

src/main/java/org/ohdsi/webapi/cohortcharacterization/domain/CohortCharacterizationEntity.java

@@ -1,6 +1,7 @@
 package org.ohdsi.webapi.cohortcharacterization.domain;
 
 import java.util.*;
+import java.util.stream.Collectors;
 
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -52,11 +53,9 @@ public class CohortCharacterizationEntity extends CommonEntityExt<Long> implemen
             inverseJoinColumns = @JoinColumn(name = "cohort_id", referencedColumnName = "id"))
     private Set<CohortDefinition> cohortDefinitions = new HashSet<>();
 
-    @ManyToMany(targetEntity = FeAnalysisEntity.class, fetch = FetchType.LAZY)
-    @JoinTable(name = "cc_analysis",
-            joinColumns = @JoinColumn(name = "cohort_characterization_id", referencedColumnName = "id"),
-            inverseJoinColumns = @JoinColumn(name = "fe_analysis_id", referencedColumnName = "id"))
-    private Set<FeAnalysisEntity> featureAnalyses = new HashSet<>();
+    @OneToMany(orphanRemoval = true)
+    @JoinColumn(name = "cohort_characterization_id", insertable = false, updatable = false, nullable = false)
+    private Set<CcFeAnalysisEntity> featureAnalyses = new HashSet<>();
 
     @OneToMany(mappedBy = "cohortCharacterization", fetch = FetchType.LAZY, targetEntity = CcParamEntity.class)
     private Set<CcParamEntity> parameters = new HashSet<>();
@@ -89,6 +88,12 @@ public Set<CohortDefinition> getCohorts() {
 
     @Override
     public Set<FeAnalysisEntity> getFeatureAnalyses() {
+        return featureAnalyses != null ?
+                featureAnalyses.stream().map(CcFeAnalysisEntity::getFeatureAnalysis).collect(Collectors.toSet()) :
+                Collections.emptySet();
+    }
+
+    public Set<CcFeAnalysisEntity> getCcFeatureAnalyses() {
         return featureAnalyses;
     }
 
@@ -97,6 +102,10 @@ public Set<CcParamEntity> getParameters() {
         return parameters;
     }
 
+    public void setFeatureAnalyses(Set<CcFeAnalysisEntity> featureAnalyses) {
+        this.featureAnalyses = featureAnalyses;
+    }
+
     @Override
     public Long getId() {
         return id;
@@ -126,10 +135,6 @@ public void setParameters(final Set<CcParamEntity> parameters) {
         this.parameters = parameters;
     }
 
-    public void setFeatureAnalyses(final Set<FeAnalysisEntity> featureAnalyses) {
-        this.featureAnalyses = featureAnalyses;
-    }
-
     public Set<CohortDefinition> getCohortDefinitions() {
         return cohortDefinitions;
     }