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

Example 16 with SearchParameter

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

the class CodesQueryBuilderTest method getMappedParameters.

@Test
public void getMappedParameters() throws Exception {
    final SearchParameter searchParam1 = new SearchParameter().group(false).domain("Condition").value("001");
    final SearchParameter searchParam2 = new SearchParameter().group(false).domain("Procedure").value("002");
    final SearchParameter searchParam3 = new SearchParameter().group(false).domain("Procedure").value("003");
    final SearchParameter searchParam4 = new SearchParameter().group(true).domain("Procedure").value("0");
    SearchGroupItem item = new SearchGroupItem().type("ICD9").searchParameters(Arrays.asList(searchParam1, searchParam2, searchParam3, searchParam4));
    Map<CodesQueryBuilder.GroupType, ListMultimap<String, SearchParameter>> mappedParemeters = queryBuilder.getMappedParameters(item.getSearchParameters());
    assertEquals(2, mappedParemeters.keySet().size());
    assertEquals(new HashSet<CodesQueryBuilder.GroupType>(Arrays.asList(CodesQueryBuilder.GroupType.GROUP, CodesQueryBuilder.GroupType.NOT_GROUP)), mappedParemeters.keySet());
    assertEquals(Arrays.asList(searchParam1), mappedParemeters.get(CodesQueryBuilder.GroupType.NOT_GROUP).get("Condition"));
    assertEquals(Arrays.asList(searchParam2, searchParam3), mappedParemeters.get(CodesQueryBuilder.GroupType.NOT_GROUP).get("Procedure"));
    assertEquals(Arrays.asList(searchParam4), mappedParemeters.get(CodesQueryBuilder.GroupType.GROUP).get("Procedure"));
}

Example 17 with SearchParameter

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

the class CodesQueryBuilderTest method buildQueryJobConfigICD9Group.

@Test
public void buildQueryJobConfigICD9Group() throws Exception {
    String procedureNamedParameter = "";
    String cmProcedureParameter = "";
    String procProcedureParameter = "";
    String conditionNamedParameter = "";
    String cmConditionParameter = "";
    String procConditionParameter = "";
    String measurementNamedParameter = "";
    String cmMeasurementParameter = "";
    String procMeasurementParameter = "";
    List<SearchParameter> params = new ArrayList<>();
    params.add(new SearchParameter().group(false).type("ICD9").domain("Condition").value("10.1"));
    params.add(new SearchParameter().group(false).type("ICD9").domain("Condition").value("20.2"));
    params.add(new SearchParameter().group(true).type("ICD9").domain("Measurement").value("0"));
    params.add(new SearchParameter().group(true).type("ICD9").domain("Procedure").value("1"));
    /* Check the generated querybuilder */
    QueryJobConfiguration queryJobConfiguration = queryBuilder.buildQueryJobConfig(new QueryParameters().type("ICD9").parameters(params));
    for (String key : queryJobConfiguration.getNamedParameters().keySet()) {
        if (key.startsWith("Condition")) {
            conditionNamedParameter = key;
            cmConditionParameter = "cm" + key.replace("Condition", "");
            procConditionParameter = "proc" + key.replace("Condition", "");
        } else if (key.startsWith("Measurement")) {
            measurementNamedParameter = key;
            cmMeasurementParameter = "cm" + key.replace("Measurement", "");
            procMeasurementParameter = "proc" + key.replace("Measurement", "");
        } else if (key.startsWith("Procedure")) {
            procedureNamedParameter = key;
            cmProcedureParameter = "cm" + key.replace("Procedure", "");
            procProcedureParameter = "proc" + key.replace("Procedure", "");
        }
    }
    String expected = "select person_id\n" + "from `${projectId}.${dataSetId}.person` p\n" + "where person_id in (select person_id\n" + "from `${projectId}.${dataSetId}.measurement` a, `${projectId}.${dataSetId}.concept` b\n" + "where a.measurement_source_concept_id = b.concept_id\n" + "and b.vocabulary_id in (@" + cmMeasurementParameter + ",@" + procMeasurementParameter + ")\n" + "and b.concept_code like @" + measurementNamedParameter + "\n" + " union all\n" + "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 like @" + procedureNamedParameter + "\n" + " union all\n" + "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";
    assertEquals(expected, queryJobConfiguration.getQuery());
    /* Check the querybuilder parameters */
    List<QueryParameterValue> conditionCodes = queryJobConfiguration.getNamedParameters().get(conditionNamedParameter).getArrayValues();
    assertTrue(conditionCodes.contains(QueryParameterValue.newBuilder().setValue("10.1").setType(StandardSQLTypeName.STRING).build()));
    assertTrue(conditionCodes.contains(QueryParameterValue.newBuilder().setValue("20.2").setType(StandardSQLTypeName.STRING).build()));
    String measurementCode = queryJobConfiguration.getNamedParameters().get(measurementNamedParameter).getValue();
    assertTrue("0%".equals(measurementCode));
    String procedureCode = queryJobConfiguration.getNamedParameters().get(procedureNamedParameter).getValue();
    assertTrue("1%".equals(procedureCode));
    assertEquals("ICD9CM", queryJobConfiguration.getNamedParameters().get(cmConditionParameter).getValue());
    assertEquals("ICD9Proc", queryJobConfiguration.getNamedParameters().get(procConditionParameter).getValue());
}

Example 18 with SearchParameter

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

the class CodesQueryBuilderTest method buildQueryJobConfigICD9NotGroup.

@Test
public void buildQueryJobConfigICD9NotGroup() throws Exception {
    String measurementNamedParameter = "";
    String conditionNamedParameter = "";
    String cmConditionParameter = "";
    String procConditionParameter = "";
    String cmMeasurementParameter = "";
    String procMeasurementParameter = "";
    List<SearchParameter> params = new ArrayList<>();
    params.add(new SearchParameter().group(false).type("ICD9").domain("Condition").value("10.1"));
    params.add(new SearchParameter().group(false).type("ICD9").domain("Condition").value("20.2"));
    params.add(new SearchParameter().group(false).type("ICD9").domain("Measurement").value("30.3"));
    /* Check the generated querybuilder */
    QueryJobConfiguration queryJobConfiguration = queryBuilder.buildQueryJobConfig(new QueryParameters().type("ICD9").parameters(params));
    for (String key : queryJobConfiguration.getNamedParameters().keySet()) {
        if (key.startsWith("Condition")) {
            conditionNamedParameter = key;
            cmConditionParameter = "cm" + key.replace("Condition", "");
            procConditionParameter = "proc" + key.replace("Condition", "");
        } else if (key.startsWith("Measurement")) {
            measurementNamedParameter = key;
            cmMeasurementParameter = "cm" + key.replace("Measurement", "");
            procMeasurementParameter = "proc" + key.replace("Measurement", "");
        }
    }
    String expected = "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" + " union all\n" + "select person_id\n" + "from `${projectId}.${dataSetId}.measurement` a, `${projectId}.${dataSetId}.concept` b\n" + "where a.measurement_source_concept_id = b.concept_id\n" + "and b.vocabulary_id in (@" + cmMeasurementParameter + ",@" + procMeasurementParameter + ")\n" + "and b.concept_code in unnest(@" + measurementNamedParameter + ")\n" + ")\n";
    assertEquals(expected, queryJobConfiguration.getQuery());
    /* Check the querybuilder parameters */
    List<QueryParameterValue> conditionCodes = queryJobConfiguration.getNamedParameters().get(conditionNamedParameter).getArrayValues();
    assertTrue(conditionCodes.contains(QueryParameterValue.newBuilder().setValue("10.1").setType(StandardSQLTypeName.STRING).build()));
    assertTrue(conditionCodes.contains(QueryParameterValue.newBuilder().setValue("20.2").setType(StandardSQLTypeName.STRING).build()));
    List<QueryParameterValue> measurementCodes = queryJobConfiguration.getNamedParameters().get(measurementNamedParameter).getArrayValues();
    assertTrue(measurementCodes.contains(QueryParameterValue.newBuilder().setValue("30.3").setType(StandardSQLTypeName.STRING).build()));
    assertEquals("ICD9CM", queryJobConfiguration.getNamedParameters().get(cmConditionParameter).getValue());
    assertEquals("ICD9Proc", queryJobConfiguration.getNamedParameters().get(procConditionParameter).getValue());
}

Example 19 with SearchParameter

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

the class PhecodesQueryBuilderTest method buildQueryJobConfig.

@Test
public void buildQueryJobConfig() throws Exception {
    String pheCodesNamedParameter = "";
    List<SearchParameter> params = new ArrayList<>();
    params.add(new SearchParameter().value("008"));
    params.add(new SearchParameter().value("010"));
    params.add(new SearchParameter().value("031"));
    /* Check the generated querybuilder */
    QueryJobConfiguration queryJobConfiguration = queryBuilder.buildQueryJobConfig(new QueryParameters().type("PHECODE").parameters(params));
    for (String key : queryJobConfiguration.getNamedParameters().keySet()) {
        if (key.startsWith("PheCodes")) {
            pheCodesNamedParameter = key;
        }
    }
    String expected = "select person_id\n" + "from `${projectId}.${dataSetId}.condition_occurrence` co\n" + "where co.condition_source_concept_id in (select concept_id\n" + "from `${projectId}.${dataSetId}.concept`\n" + "where concept_code in\n" + "(select icd9 from `${projectId}.${dataSetId}.phecode_criteria_icd`\n" + "where phecode in unnest(@" + pheCodesNamedParameter + "))\n" + "and vocabulary_id in ('ICD9Proc', 'ICD9CM')\n" + ")\n" + "union all\n" + "select person_id\n" + "from `${projectId}.${dataSetId}.procedure_occurrence` po\n" + "where po.procedure_source_concept_id in (select concept_id\n" + "from `${projectId}.${dataSetId}.concept`\n" + "where concept_code in\n" + "(select icd9 from `${projectId}.${dataSetId}.phecode_criteria_icd`\n" + "where phecode in unnest(@" + pheCodesNamedParameter + "))\n" + "and vocabulary_id in ('ICD9Proc', 'ICD9CM')\n" + ")\n" + "union all\n" + "select person_id\n" + "from `${projectId}.${dataSetId}.measurement` m\n" + "where m.measurement_source_concept_id in (select concept_id\n" + "from `${projectId}.${dataSetId}.concept`\n" + "where concept_code in\n" + "(select icd9 from `${projectId}.${dataSetId}.phecode_criteria_icd`\n" + "where phecode in unnest(@" + pheCodesNamedParameter + "))\n" + "and vocabulary_id in ('ICD9Proc', 'ICD9CM')\n" + ")\n" + "union all\n" + "select person_id\n" + "from `${projectId}.${dataSetId}.observation` o\n" + "where o.observation_source_concept_id in (select concept_id\n" + "from `${projectId}.${dataSetId}.concept`\n" + "where concept_code in\n" + "(select icd9 from `${projectId}.${dataSetId}.phecode_criteria_icd`\n" + "where phecode in unnest(@" + pheCodesNamedParameter + "))\n" + "and vocabulary_id in ('ICD9Proc', 'ICD9CM')\n" + ")\n";
    assertEquals(expected, queryJobConfiguration.getQuery());
    /* Check the querybuilder parameters */
    List<QueryParameterValue> pheCodes = queryJobConfiguration.getNamedParameters().get(pheCodesNamedParameter).getArrayValues();
    assertTrue(pheCodes.contains(QueryParameterValue.newBuilder().setValue("008").setType(StandardSQLTypeName.STRING).build()));
    assertTrue(pheCodes.contains(QueryParameterValue.newBuilder().setValue("010").setType(StandardSQLTypeName.STRING).build()));
    assertTrue(pheCodes.contains(QueryParameterValue.newBuilder().setValue("031").setType(StandardSQLTypeName.STRING).build()));
}

Example 20 with SearchParameter

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

the class SearchRequests method genderRequest.

public static SearchRequest genderRequest(long... conceptIds) {
    SearchGroupItem searchGroupItem = new SearchGroupItem().id("id1").type(DEMO_TYPE);
    for (long conceptId : conceptIds) {
        SearchParameter parameter = new SearchParameter().domain(DEMO_DOMAIN).subtype(GENDER_SUBTYPE).conceptId(conceptId);
        searchGroupItem.addSearchParametersItem(parameter);
    }
    return searchRequest(searchGroupItem);
}