Cohort Definition Validation Feature API

src/main/java/org/ohdsi/webapi/annotation/annotation/Annotation.java

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+package org.ohdsi.webapi.annotation.annotation;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.ManyToOne;
+import javax.persistence.JoinColumn;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.GenericGenerator;
+import org.hibernate.annotations.Parameter;
+import org.ohdsi.webapi.annotation.set.QuestionSet;
+
+@Entity(name = "Annotation")
+@Table(
+  name = "annotation"
+)
+public class Annotation {
+
+  @Id
+  @GenericGenerator(
+    name="annotation_generator",
+    strategy = "org.hibernate.id.enhanced.SequenceStyleGenerator",
+    parameters = {
+      @Parameter(name="sequence_name",value="annotation_seq"),
+      @Parameter(name="increment_size",value="1")
+    }
+  )
+  @GeneratedValue(generator = "annotation_generator")
+  @Column(name = "annotation_id")
+  private int id;
+
+  @Column(name = "subject_id")
+  private int subjectId;
+
+  @Column(name = "cohort_sample_id")
+  private int cohortSampleId;
+
+  @ManyToOne
+  @JoinColumn(name = "question_set_id")
+  private QuestionSet questionSet;
+
+  //***** GETTERS/SETTERS ******
+
+  /**
+   * @return the id
+   */
+  public int getId() {
+    return id;
+  }
+
+  /**
+	 * @param id the id to set
+	 */
+  public void setId(int id) {
+    this.id = id;
+  }
+
+  /**
+   * @return the subjectId
+   */
+  public int getSubjectId() {
+    return subjectId;
+  }
+
+  /**
+   * @param subjectId the subjectId to set
+   */
+  public void setSubjectId(int subjectId) {
+    this.subjectId = subjectId;
+  }
+
+  /**
+   * @return the cohortId
+   */
+  public int getCohortSampleId() {
+    return cohortSampleId;
+  }
+
+  /**
+   * @param cohortSampleId the cohortId to set
+   */
+  public void setCohortSampleId(int cohortSampleId) {
+    this.cohortSampleId = cohortSampleId;
+  }
+
+  /**
+   * @return the set
+   */
+  public QuestionSet getQuestionSet() {
+    return questionSet;
+  }
+
+  /**
+   * @param set the set to set
+   */
+  public void setQuestionSet(QuestionSet questionSet) {
+    this.questionSet = questionSet;
+  }
+
+}

src/main/java/org/ohdsi/webapi/annotation/annotation/AnnotationController.java

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+package org.ohdsi.webapi.annotation.annotation;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.ws.rs.GET;
+import javax.ws.rs.POST;
+import javax.ws.rs.Path;
+import javax.ws.rs.Consumes;
+import javax.ws.rs.Produces;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.QueryParam;
+import javax.ws.rs.PathParam;
+import org.json.JSONObject;
+import org.json.JSONArray;
+import org.ohdsi.webapi.annotation.result.ResultService;
+import org.ohdsi.webapi.annotation.study.Study;
+import org.ohdsi.webapi.annotation.study.StudyService;
+import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
+import org.ohdsi.webapi.cohortdefinition.CohortDefinitionRepository;
+import org.ohdsi.webapi.cohortsample.CohortSample;
+import org.ohdsi.webapi.cohortsample.CohortSampleRepository;
+import org.ohdsi.webapi.cohortsample.CohortSamplingService;
+import org.ohdsi.webapi.cohortsample.dto.SampleElementDTO;
+import org.ohdsi.webapi.source.Source;
+import org.ohdsi.webapi.source.SourceService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.ohdsi.webapi.annotation.set.QuestionSetRepository;
+import org.ohdsi.webapi.annotation.set.QuestionSet;
+import org.springframework.web.bind.annotation.RequestBody;
+
+
+@Path("annotations")
+@Component
+public class AnnotationController {
+
+  @Autowired
+  private StudyService studyService;
+
+  @Autowired
+  private ResultService resultService;
+
+  @Autowired
+  private CohortDefinitionRepository cohortDefinitionRepository;
+
+  @Autowired
+  private CohortSamplingService cohortSamplingService;
+
+  @Autowired
+  private CohortSampleRepository sampleRepository;
+
+  @Autowired
+  private AnnotationService annotationService;
+
+  @Autowired
+  private QuestionSetRepository questionSetRepository;
+
+  @Autowired
+  private SourceService sourceService;
+
+  @GET
+  @Path("/")
+  @Produces(MediaType.APPLICATION_JSON)
+  public List<AnnotationSummary> getAnnotations(
+    @QueryParam("cohortSampleId") final int cohortSampleId,
+    @QueryParam("subjectId") final int subjectId,
+    @QueryParam("setId") final int setId
+  ) {
+    List<Annotation> returnAnnotations;
+    returnAnnotations = getFullAnnotations(cohortSampleId,subjectId,setId);
+    List<AnnotationSummary> summaries = new ArrayList();
+    for(Annotation singleAnno : returnAnnotations){
+//      can we see about doing this in a more performant manner?
+      AnnotationSummary tempAnnoSummary=new AnnotationSummary(singleAnno);
+      summaries.add(tempAnnoSummary);
+    }
+    return summaries;
+  }
+
+  @GET
+  @Path("/fullquestion")
+  @Produces(MediaType.APPLICATION_JSON)
+  public List<Annotation> getFullAnnotations(
+          @QueryParam("cohortSampleId") final int cohortSampleId,
+          @QueryParam("subjectId") final int subjectId,
+          @QueryParam("setId") final int setId
+          ) {
+    List<Annotation> returnAnnotations=null;
+    if (cohortSampleId != 0 && subjectId != 0 && setId != 0) {
+      System.out.println("made it into the search function");
+      returnAnnotations= annotationService.getAnnotationByCohortSampleIdAndBySubjectIdAndByQuestionSetId(cohortSampleId, subjectId, setId);
+    }
+    else if (cohortSampleId !=0 && setId!=0){
+      returnAnnotations= annotationService.getAnnotationByCohortSampleIdAndByQuestionSetId(cohortSampleId,setId);
+    }
+    else if(cohortSampleId!=0){
+      returnAnnotations= annotationService.getAnnotationsByCohortSampleId(cohortSampleId);
+    }
+    else if(setId !=0){
+      returnAnnotations= annotationService.getAnnotationsByQuestionSetId(setId);
+    }
+    else{
+      returnAnnotations=annotationService.getAnnotations();
+    }
+    return returnAnnotations;
+  }
+
+  @POST
+  @Path("/")
+  @Consumes(MediaType.APPLICATION_JSON)
+  @Produces(MediaType.APPLICATION_JSON)
+  public void addResult(@RequestBody String payload) {
+    System.out.println(payload);
+    JSONObject jsonpayload = new JSONObject(payload);
+    System.out.println(jsonpayload);
+    System.out.println(jsonpayload.get("results"));
+    System.out.printf("cohortId: %s\n",jsonpayload.get("cohortId").toString());
+    System.out.printf("cohortSampleId: %s\n",jsonpayload.get("cohortSampleId").toString());
+    System.out.printf("subjectId: %s\n",jsonpayload.get("subjectId").toString());
+    System.out.printf("setId: %s\n",jsonpayload.get("setId").toString());
+    Annotation tempAnnotation = annotationService.getAnnotationsByAnnotationId(jsonpayload.getInt("id"));
+    System.out.printf("annotationID:%d\n",tempAnnotation.getId());
+    JSONArray array = jsonpayload.getJSONArray("results");
+    Study study = studyService.getStudyByQuestionSetIdAndSampleId(jsonpayload.getInt("setId"),jsonpayload.getInt("cohortSampleId") );
+    resultService.insertResults(tempAnnotation,array,study);
+  }
+
+  @POST
+  @Path("/sample")
+  @Consumes(MediaType.APPLICATION_JSON)
+  @Produces(MediaType.APPLICATION_JSON)
+  public void addAnnotation(@RequestBody String payload) {
+    JSONObject jsonpayload = new JSONObject(payload);
+    int cohortSampleId = Integer.parseInt(jsonpayload.get("sampleId").toString());
+    CohortSample cohortSample =sampleRepository.findById(cohortSampleId);
+    List<SampleElementDTO> temp = cohortSamplingService.getSample(cohortSampleId, false).getElements();
+    Study study = new Study();
+    int questionSetId = Integer.parseInt(jsonpayload.get("annotationSetId").toString());
+    QuestionSet questionSet = questionSetRepository.findById(questionSetId);
+    study.setQuestionSet(questionSetRepository.findById(questionSetId));
+    study.setCohortSample(cohortSample);
+    CohortDefinition cohortDefinition= cohortDefinitionRepository.findOneWithDetail(cohortSample.getCohortDefinitionId());
+    study.setCohortDefinition(cohortDefinition);
+    Source source = sourceService.findBySourceKey(jsonpayload.get("sourceKey").toString());
+    study.setSource(source);
+    studyService.addStudy(study);
+    for (SampleElementDTO element : temp){
+      System.out.println("element"+element);
+      System.out.println("element GetPersonID"+element.getPersonId());
+      Annotation annotation = new Annotation();
+      annotation.setSubjectId(Integer.parseInt(element.getPersonId()));
+      annotation.setCohortSampleId(cohortSampleId);
+      annotation.setQuestionSet(questionSet);
+      annotationService.addAnnotation(annotation);
+    }
+  }
+
+  @GET
+  @Path("/{annotationID}")
+  @Produces(MediaType.APPLICATION_JSON)
+  public Annotation getResults(@PathParam("annotationID") String annotationID) {
+    int annotationIdInt=Integer.parseInt(annotationID);
+    Annotation ourAnno =annotationService.getAnnotationsByAnnotationId(annotationIdInt);
+    return ourAnno;
+  }
+}
+

src/main/java/org/ohdsi/webapi/annotation/annotation/AnnotationDto.java

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+package org.ohdsi.webapi.annotation.annotation;
+
+import java.util.HashSet;
+import java.util.Set;
+import org.ohdsi.webapi.annotation.result.ResultDto;
+
+public class AnnotationDto {
+
+  private int id;
+  private int subjectId;
+  private int sampleId;
+  private int annotationSetId;
+  private String name;
+  private Set<ResultDto> results = new HashSet();
+
+  //***** GETTERS/SETTERS ******
+
+  /**
+   * @return the id
+   */
+  public int getId() {
+    return id;
+  }
+
+  /**
+   * @param id the id to set
+   */
+  public void setId(int id) {
+    this.id = id;
+  }
+
+  /**
+   * @return the subjectId
+   */
+  public int getSubjectId() {
+    return subjectId;
+  }
+
+  /**
+	 * @param subjectId the subjectId to set
+	 */
+  public void setSubjectId(int subjectId) {
+    this.subjectId = subjectId;
+  }
+
+  /**
+   * @return the cohortId
+   */
+  public int getsampleId() {
+    return sampleId;
+  }
+
+  /**
+   * @param sampleId the cohortId to set
+   */
+  public void setsampleId(int sampleId) {
+    this.sampleId = sampleId;
+  }
+
+  /**
+   * @return the setId
+   */
+  public int getannotationSetId() {
+    return annotationSetId;
+  }
+
+  /**
+   * @param setId the setId to set
+   */
+  public void setannotationSetId(int setId) {
+    this.annotationSetId = setId;
+  }
+
+	/**
+	 * @return the results
+	 */
+	public Set<ResultDto> getResults() {
+			return new HashSet<ResultDto>(results);
+	}
+
+	/**
+	 * @param results the results to set
+	 */
+	protected void setResults(Set<ResultDto> results) {
+			this.results = results;
+  }
+
+  /**
+   * @return the sample name
+   */
+  public String getSampleName() {
+    return name;
+  }
+
+  /**
+   * @param name to the slected sample name
+   */
+  public void setSampleName(String name) {
+    this.name = name;
+  }
+
+}

src/main/java/org/ohdsi/webapi/annotation/annotation/AnnotationRepository.java

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+package org.ohdsi.webapi.annotation.annotation;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import java.util.List;
+import java.util.Set;
+import org.ohdsi.webapi.annotation.annotation.Annotation;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+public interface AnnotationRepository extends JpaRepository<Annotation, Integer> {
+
+  public Set<Annotation> findOneByCohortSampleIdAndSubjectIdAndQuestionSetId(int cohortSampleId, int subjectId, int questionSetId);
+  public List<Annotation> findByCohortSampleIdAndQuestionSetId(int cohortSampleId, int questionSetId);
+  public List<Annotation> findByCohortSampleId(int cohortSampleId);
+  public List<Annotation> findByQuestionSetId(int questionSetId);
+  public Annotation findById(int annotation_id);
+}