Examples with PageRequest org.pmiops.workbench.cohortreview.util.PageRequest used on opensource projects

Example 1 with PageRequest

use of org.pmiops.workbench.cohortreview.util.PageRequest in project workbench by all-of-us.

the class CohortReviewController method getParticipantProcedures.

@Override
public ResponseEntity<ParticipantProceduresListResponse> getParticipantProcedures(String workspaceNamespace, String workspaceId, Long cohortId, Long cdrVersionId, Long participantId, PageFilterRequest request) {
    CohortReview review = validateRequestAndSetCdrVersion(workspaceNamespace, workspaceId, cohortId, cdrVersionId, WorkspaceAccessLevel.READER);
    // this validates that the participant is in the requested review.
    cohortReviewService.findParticipantCohortStatus(review.getCohortReviewId(), participantId);
    PageRequest pageRequest = createPageRequest(request);
    QueryResult result = bigQueryService.executeQuery(bigQueryService.filterBigQueryConfig(reviewTabQueryBuilder.buildQuery(ReviewTabQueries.PROCEDURE, participantId, pageRequest)));
    Map<String, Integer> rm = bigQueryService.getResultMapper(result);
    ParticipantProceduresListResponse response = new ParticipantProceduresListResponse();
    SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
    for (List<FieldValue> row : result.iterateAll()) {
        ParticipantProcedure procedure = new ParticipantProcedure().itemDate(sdf.format(bigQueryService.getDate(row, rm.get("item_date")))).standardVocabulary(bigQueryService.getString(row, rm.get("standard_vocabulary"))).standardName(bigQueryService.getString(row, rm.get("standard_name"))).sourceValue(bigQueryService.getString(row, rm.get("source_value"))).sourceVocabulary(bigQueryService.getString(row, rm.get("source_vocabulary"))).sourceName(bigQueryService.getString(row, rm.get("source_name"))).age(bigQueryService.getLong(row, rm.get("age")).intValue());
        response.addItemsItem(procedure);
    }
    result = bigQueryService.executeQuery(bigQueryService.filterBigQueryConfig(reviewTabQueryBuilder.buildCountQuery(ReviewTabQueries.PROCEDURE, participantId)));
    rm = bigQueryService.getResultMapper(result);
    List<FieldValue> row = result.iterateAll().iterator().next();
    response.count(bigQueryService.getLong(row, rm.get("count")));
    response.setPageRequest(new org.pmiops.workbench.model.PageRequest().page(pageRequest.getPageNumber()).pageSize(pageRequest.getPageSize()).sortOrder(pageRequest.getSortOrder()).sortColumn(pageRequest.getSortColumn()));
    return ResponseEntity.ok(response);
}

Example 2 with PageRequest

use of org.pmiops.workbench.cohortreview.util.PageRequest in project workbench by all-of-us.

the class CohortReviewController method getParticipantConditions.

@Override
public ResponseEntity<ParticipantConditionsListResponse> getParticipantConditions(String workspaceNamespace, String workspaceId, Long cohortId, Long cdrVersionId, Long participantId, PageFilterRequest request) {
    CohortReview review = validateRequestAndSetCdrVersion(workspaceNamespace, workspaceId, cohortId, cdrVersionId, WorkspaceAccessLevel.READER);
    // this validates that the participant is in the requested review.
    cohortReviewService.findParticipantCohortStatus(review.getCohortReviewId(), participantId);
    PageRequest pageRequest = createPageRequest(request);
    QueryResult result = bigQueryService.executeQuery(bigQueryService.filterBigQueryConfig(reviewTabQueryBuilder.buildQuery(ReviewTabQueries.CONDITION, participantId, pageRequest)));
    Map<String, Integer> rm = bigQueryService.getResultMapper(result);
    ParticipantConditionsListResponse response = new ParticipantConditionsListResponse();
    SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
    for (List<FieldValue> row : result.iterateAll()) {
        ParticipantCondition condition = new ParticipantCondition().itemDate(sdf.format(bigQueryService.getDate(row, rm.get("item_date")))).standardVocabulary(bigQueryService.getString(row, rm.get("standard_vocabulary"))).standardName(bigQueryService.getString(row, rm.get("standard_name"))).sourceValue(bigQueryService.getString(row, rm.get("source_value"))).sourceVocabulary(bigQueryService.getString(row, rm.get("source_vocabulary"))).sourceName(bigQueryService.getString(row, rm.get("source_name")));
        response.addItemsItem(condition);
    }
    result = bigQueryService.executeQuery(bigQueryService.filterBigQueryConfig(reviewTabQueryBuilder.buildCountQuery(ReviewTabQueries.CONDITION, participantId)));
    rm = bigQueryService.getResultMapper(result);
    List<FieldValue> row = result.iterateAll().iterator().next();
    response.count(bigQueryService.getLong(row, rm.get("count")));
    response.setPageRequest(new org.pmiops.workbench.model.PageRequest().page(pageRequest.getPageNumber()).pageSize(pageRequest.getPageSize()).sortOrder(pageRequest.getSortOrder()).sortColumn(pageRequest.getSortColumn()));
    return ResponseEntity.ok(response);
}

Example 3 with PageRequest

use of org.pmiops.workbench.cohortreview.util.PageRequest in project workbench by all-of-us.

the class CohortReviewControllerTest method assertFindByCohortIdAndCdrVersionId.

private void assertFindByCohortIdAndCdrVersionId(String namespace, String name, long cohortId, long cdrVersionId, Integer page, Integer pageSize, SortOrder sortOrder, ParticipantCohortStatusColumns sortColumn) {
    Integer pageParam = page == null ? 0 : page;
    Integer pageSizeParam = pageSize == null ? 25 : pageSize;
    sortColumn = (sortColumn == null || sortColumn.name().equals(sortColumn.PARTICIPANTID)) ? ParticipantCohortStatusColumns.PARTICIPANTID : sortColumn;
    sortOrder = sortOrder == null ? SortOrder.ASC : sortOrder;
    ParticipantCohortStatusKey key = new ParticipantCohortStatusKey().cohortReviewId(cohortId).participantId(participantId);
    final Date dob = new Date(System.currentTimeMillis());
    ParticipantCohortStatus dbParticipant = new ParticipantCohortStatus().participantKey(key).status(CohortStatus.INCLUDED).birthDate(dob).ethnicityConceptId(1L).genderConceptId(1L).raceConceptId(1L);
    org.pmiops.workbench.model.ParticipantCohortStatus respParticipant = new org.pmiops.workbench.model.ParticipantCohortStatus().participantId(1L).status(CohortStatus.INCLUDED).birthDate(dob.getTime()).ethnicityConceptId(1L).genderConceptId(1L).raceConceptId(1L);
    org.pmiops.workbench.model.CohortReview respCohortReview = new org.pmiops.workbench.model.CohortReview().cohortReviewId(1L).cohortId(cohortId).cdrVersionId(cdrVersionId).matchedParticipantCount(1000L).reviewedCount(0L).reviewSize(200L).page(pageParam).pageSize(pageSizeParam).sortOrder(sortOrder.toString()).sortColumn(sortColumn.toString()).participantCohortStatuses(Arrays.asList(respParticipant));
    List<ParticipantCohortStatus> participants = new ArrayList<ParticipantCohortStatus>();
    participants.add(dbParticipant);
    CohortReview cohortReviewAfter = new CohortReview();
    cohortReviewAfter.setCohortReviewId(1L);
    cohortReviewAfter.setCohortId(cohortId);
    cohortReviewAfter.setCdrVersionId(cdrVersionId);
    cohortReviewAfter.setMatchedParticipantCount(1000);
    cohortReviewAfter.setReviewSize(200);
    cohortReviewAfter.setCreationTime(new Timestamp(System.currentTimeMillis()));
    Cohort cohort = new Cohort();
    cohort.setWorkspaceId(1);
    Map<String, Map<Long, String>> concepts = new HashMap<>();
    concepts.put(GenderRaceEthnicityType.RACE.name(), new HashMap<>());
    concepts.put(GenderRaceEthnicityType.GENDER.name(), new HashMap<>());
    concepts.put(GenderRaceEthnicityType.ETHNICITY.name(), new HashMap<>());
    GenderRaceEthnicityConcept greConcept = new GenderRaceEthnicityConcept(concepts);
    when(cohortReviewService.findCohortReview(cohortId, cdrVersionId)).thenReturn(cohortReviewAfter);
    when(cohortReviewService.findAll(key.getCohortReviewId(), Collections.<Filter>emptyList(), new PageRequest(pageParam, pageSizeParam, sortOrder, sortColumn.toString()))).thenReturn(participants);
    when(cohortReviewService.validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER)).thenReturn(new Workspace());
    when(cohortReviewService.findCohort(cohortId)).thenReturn(cohort);
    ParticipantCohortStatuses request = new ParticipantCohortStatuses();
    request.page(page);
    request.pageSize(pageSize);
    request.sortOrder(sortOrder);
    request.sortColumn(sortColumn);
    request.pageFilterType(PageFilterType.PARTICIPANTCOHORTSTATUSES);
    ResponseEntity<org.pmiops.workbench.model.CohortReview> response = reviewController.getParticipantCohortStatuses(namespace, name, cohortId, cdrVersionId, request);
    org.pmiops.workbench.model.CohortReview actualCohortReview = response.getBody();
    respCohortReview.setCreationTime(actualCohortReview.getCreationTime());
    assertEquals(respCohortReview, response.getBody());
    verify(cohortReviewService, atLeast(1)).validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER);
    verify(cohortReviewService, atLeast(1)).findCohortReview(cohortId, cdrVersionId);
    verify(cohortReviewService, times(1)).findAll(key.getCohortReviewId(), Collections.<Filter>emptyList(), new PageRequest(pageParam, pageSizeParam, sortOrder, sortColumn.toString()));
    verify(cohortReviewService, atLeast(1)).findCohort(cohortId);
    verifyNoMoreMockInteractions();
}

Example 4 with PageRequest

use of org.pmiops.workbench.cohortreview.util.PageRequest in project workbench by all-of-us.

the class ParticipantCohortStatusDaoTest method findAllSearchCriteriaIn.

@Test
public void findAllSearchCriteriaIn() throws Exception {
    PageRequest pageRequest = new PageRequest(page, pageSize, SortOrder.ASC, ParticipantCohortStatusColumns.PARTICIPANTID.toString());
    List<Filter> filters = new ArrayList<>();
    filters.add(new Filter().property(ParticipantCohortStatusColumns.PARTICIPANTID).operator(Operator.IN).values(Arrays.asList("1", "2")));
    filters.add(new Filter().property(ParticipantCohortStatusColumns.STATUS).operator(Operator.IN).values(Arrays.asList(CohortStatus.INCLUDED.toString(), CohortStatus.EXCLUDED.toString())));
    filters.add(new Filter().property(ParticipantCohortStatusColumns.BIRTHDATE).operator(Operator.IN).values(Arrays.asList(new Date(System.currentTimeMillis()).toString())));
    filters.add(new Filter().property(ParticipantCohortStatusColumns.GENDER).operator(Operator.IN).values(Arrays.asList("MALE", "FEMALE")));
    filters.add(new Filter().property(ParticipantCohortStatusColumns.RACE).operator(Operator.IN).values(Arrays.asList("Asian", "White")));
    filters.add(new Filter().property(ParticipantCohortStatusColumns.ETHNICITY).operator(Operator.IN).values(Arrays.asList("Not Hispanic", "Hispanic")));
    List<ParticipantCohortStatus> results = participantCohortStatusDao.findAll(1L, filters, pageRequest);
    assertEquals(2, results.size());
    ParticipantCohortStatus expectedPCS1 = createExpectedPCSWithConceptValues(new ParticipantCohortStatusKey().cohortReviewId(COHORT_REVIEW_ID).participantId(1), CohortStatus.INCLUDED);
    expectedPCS1.setBirthDate(results.get(0).getBirthDate());
    ParticipantCohortStatus expectedPCS2 = createExpectedPCSWithConceptValues(new ParticipantCohortStatusKey().cohortReviewId(COHORT_REVIEW_ID).participantId(2), CohortStatus.EXCLUDED);
    expectedPCS2.setBirthDate(results.get(0).getBirthDate());
    assertEquals(expectedPCS1, results.get(0));
    assertEquals(expectedPCS2, results.get(1));
}

Example 5 with PageRequest

use of org.pmiops.workbench.cohortreview.util.PageRequest in project workbench by all-of-us.

the class ParticipantCohortStatusDaoTest method findAllBadFilterTypes.

@Test
public void findAllBadFilterTypes() throws Exception {
    PageRequest pageRequest = new PageRequest(page, pageSize, SortOrder.ASC, ParticipantCohortStatusColumns.PARTICIPANTID.toString());
    List<Filter> filters = new ArrayList<>();
    filters.add(new Filter().property(ParticipantCohortStatusColumns.PARTICIPANTID).operator(Operator.EQUAL).values(Arrays.asList("z")));
    assertBadRequest(pageRequest, filters, "Problems parsing participantId: For input string: \"z\"");
    filters.clear();
    filters.add(new Filter().property(ParticipantCohortStatusColumns.STATUS).operator(Operator.EQUAL).values(Arrays.asList("z")));
    assertBadRequest(pageRequest, filters, "Problems parsing status: No enum constant org.pmiops.workbench.model.CohortStatus.z");
    filters.clear();
    filters.add(new Filter().property(ParticipantCohortStatusColumns.BIRTHDATE).operator(Operator.EQUAL).values(Arrays.asList("z")));
    assertBadRequest(pageRequest, filters, "Problems parsing birthDate: Unparseable date: \"z\"");
}