Examples with SearchParameter org.pmiops.workbench.model.SearchParameter used on opensource projects

Example 11 with SearchParameter

use of org.pmiops.workbench.model.SearchParameter in project workbench by all-of-us.

the class CohortBuilderControllerTest method countSubjectsICD10ConditionOccurrenceChild.

@Test
public void countSubjectsICD10ConditionOccurrenceChild() throws Exception {
    SearchParameter icd10 = createSearchParameter(icd10ConditionChild, "A09");
    SearchRequest searchRequest = createSearchRequests(icd10ConditionChild.getType(), Arrays.asList(icd10));
    assertParticipants(controller.countParticipants(cdrVersion.getCdrVersionId(), searchRequest), 1);
}

Example 12 with SearchParameter

use of org.pmiops.workbench.model.SearchParameter in project workbench by all-of-us.

the class CohortBuilderControllerTest method countSubjectsICD9MeasurementParent.

@Test
public void countSubjectsICD9MeasurementParent() throws Exception {
    SearchParameter icd9 = createSearchParameter(icd9MeasurementParent, "003");
    SearchRequest searchRequest = createSearchRequests(icd9MeasurementParent.getType(), Arrays.asList(icd9));
    assertParticipants(controller.countParticipants(cdrVersion.getCdrVersionId(), searchRequest), 1);
}

Example 13 with SearchParameter

use of org.pmiops.workbench.model.SearchParameter in project workbench by all-of-us.

the class CodesQueryBuilder method buildQueryJobConfig.

@Override
public QueryJobConfiguration buildQueryJobConfig(QueryParameters params) {
    Map<GroupType, ListMultimap<String, SearchParameter>> paramMap = getMappedParameters(params.getParameters());
    List<String> queryParts = new ArrayList<String>();
    Map<String, QueryParameterValue> queryParams = new HashMap<>();
    for (GroupType group : paramMap.keySet()) {
        ListMultimap<String, SearchParameter> domainMap = paramMap.get(group);
        for (String domain : domainMap.keySet()) {
            final List<SearchParameter> searchParameterList = domainMap.get(domain);
            final SearchParameter parameter = searchParameterList.get(0);
            final String type = parameter.getType();
            final String subtype = parameter.getSubtype();
            List<String> codes = searchParameterList.stream().map(SearchParameter::getValue).collect(Collectors.toList());
            if (group.equals(GroupType.NOT_GROUP)) {
                buildNotGroupQuery(type, subtype, queryParts, queryParams, domain, codes);
            } else {
                buildGroupQuery(type, subtype, queryParts, queryParams, domain, codes);
            }
        }
    }
    String finalSql = OUTER_SQL_TEMPLATE.replace("${innerSql}", String.join(UNION_TEMPLATE, queryParts));
    return QueryJobConfiguration.newBuilder(finalSql).setNamedParameters(queryParams).setUseLegacySql(false).build();
}

Example 14 with SearchParameter

use of org.pmiops.workbench.model.SearchParameter in project workbench by all-of-us.

the class ParticipantCounterTest method buildParticipantCounterQuery.

@Test
public void buildParticipantCounterQuery() throws Exception {
    String genderNamedParameter = "";
    String conditionNamedParameter = "";
    String procedureNamedParameter = "";
    String cmConditionParameter = "";
    String procConditionParameter = "";
    String cmProcedureParameter = "";
    String procProcedureParameter = "";
    SearchParameter parameter1 = new SearchParameter().domain("Condition").group(false).type("ICD9").value("001.1");
    SearchParameter parameter2 = new SearchParameter().subtype("GEN").conceptId(8507L);
    SearchParameter parameter3 = new SearchParameter().domain("Procedure").group(false).type("CPT").value("001.2");
    SearchGroupItem searchGroupItem1 = new SearchGroupItem().type("ICD9").addSearchParametersItem(parameter1);
    SearchGroupItem searchGroupItem2 = new SearchGroupItem().type("DEMO").addSearchParametersItem(parameter2);
    SearchGroupItem searchGroupItem3 = new SearchGroupItem().type("CPT").addSearchParametersItem(parameter3);
    SearchGroup searchGroup1 = new SearchGroup().addItemsItem(searchGroupItem1);
    SearchGroup searchGroup2 = new SearchGroup().addItemsItem(searchGroupItem2);
    SearchGroup searchGroup3 = new SearchGroup().addItemsItem(searchGroupItem3);
    SearchRequest request = new SearchRequest().addIncludesItem(searchGroup1).addIncludesItem(searchGroup2).addExcludesItem(searchGroup3);
    QueryJobConfiguration actualRequest = participantCounter.buildParticipantCounterQuery(new ParticipantCriteria(request));
    for (String key : actualRequest.getNamedParameters().keySet()) {
        if (key.startsWith("gen")) {
            genderNamedParameter = key;
        } else if (key.startsWith("Condition")) {
            conditionNamedParameter = key;
            cmConditionParameter = "cm" + key.replace("Condition", "");
            procConditionParameter = "proc" + key.replace("Condition", "");
        } else if (key.startsWith("Procedure")) {
            procedureNamedParameter = key;
            cmProcedureParameter = "cm" + key.replace("Procedure", "");
            procProcedureParameter = "proc" + key.replace("Procedure", "");
        }
    }
    final String expectedSql = "select count(*) as count\n" + "from `${projectId}.${dataSetId}.person` person\n" + "where\n" + "person.person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.person` p\n" + "where person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.condition_occurrence` a, `${projectId}.${dataSetId}.concept` b\n" + "where a.condition_source_concept_id = b.concept_id\n" + "and b.vocabulary_id in (@" + cmConditionParameter + ",@" + procConditionParameter + ")\n" + "and b.concept_code in unnest(@" + conditionNamedParameter + ")\n" + ")\n" + ")\n" + "and person.person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.person` p\n" + "where\n" + "p.gender_concept_id in unnest(@" + genderNamedParameter + ")\n" + ")\n" + "and not exists\n" + "(select 'x' from\n" + "(select person_id\n" + "from `${projectId}.${dataSetId}.person` p\n" + "where person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.procedure_occurrence` a, `${projectId}.${dataSetId}.concept` b\n" + "where a.procedure_source_concept_id = b.concept_id\n" + "and b.vocabulary_id in (@" + cmProcedureParameter + ",@" + procProcedureParameter + ")\n" + "and b.concept_code in unnest(@" + procedureNamedParameter + ")\n" + ")\n" + ")\n" + "x where x.person_id = person.person_id)\n";
    assertEquals(expectedSql, actualRequest.getQuery());
    assertEquals("8507", actualRequest.getNamedParameters().get(genderNamedParameter).getArrayValues().get(0).getValue());
    assertEquals(parameter1.getValue(), actualRequest.getNamedParameters().get(conditionNamedParameter).getArrayValues().get(0).getValue());
}

Example 15 with SearchParameter

use of org.pmiops.workbench.model.SearchParameter in project workbench by all-of-us.

the class ParticipantCounterTest method buildParticipantCounterQuery_ExcludesWithoutIncludes.

@Test
public void buildParticipantCounterQuery_ExcludesWithoutIncludes() throws Exception {
    String genderNamedParameter = "";
    SearchParameter parameter1 = new SearchParameter().subtype("GEN").conceptId(8507L);
    SearchGroupItem searchGroupItem1 = new SearchGroupItem().type("DEMO").addSearchParametersItem(parameter1);
    SearchGroup searchGroup1 = new SearchGroup().addItemsItem(searchGroupItem1);
    SearchRequest request = new SearchRequest().addExcludesItem(searchGroup1);
    QueryJobConfiguration actualRequest = participantCounter.buildParticipantCounterQuery(new ParticipantCriteria(request));
    for (String key : actualRequest.getNamedParameters().keySet()) {
        if (key.startsWith("gen")) {
            genderNamedParameter = key;
        }
    }
    final String expectedSql = "select count(*) as count\n" + "from `${projectId}.${dataSetId}.person` person\n" + "where\n" + "person.person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.person` p\n" + "where\n" + "p.gender_concept_id in unnest(@" + genderNamedParameter + ")\n" + ")\n";
    assertEquals(expectedSql, actualRequest.getQuery());
    assertEquals("8507", actualRequest.getNamedParameters().get(genderNamedParameter).getArrayValues().get(0).getValue());
}