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Update SQL to return ClinicalDataCountItem.. NA's not implemented
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@haynescd
haynescd committed Oct 14, 2024
1 parent ad1132c commit 2d3bd6b
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Showing 7 changed files with 110 additions and 63 deletions.
3 changes: 2 additions & 1 deletion src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -5,6 +5,7 @@
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenericAssayDataCountItem;
Expand Down Expand Up @@ -37,7 +38,7 @@ public interface StudyViewRepository {
List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);

List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);

List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext);

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3 changes: 2 additions & 1 deletion src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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Expand Up @@ -6,6 +6,7 @@
import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenePanelToGene;
Expand Down Expand Up @@ -38,7 +39,7 @@ public interface StudyViewMapper {

List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);

List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds, List<String> filteredAttributeValues);
List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds, List<String> filteredAttributeValues);

List<CaseListDataCount> getCaseListDataCountsPerStudy(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

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3 changes: 2 additions & 1 deletion src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -4,6 +4,7 @@
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.GenePanelToGene;
import org.cbioportal.model.GenericAssayDataCountItem;
Expand Down Expand Up @@ -74,7 +75,7 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
}

@Override
public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
return mapper.getClinicalDataCounts(createStudyViewFilterHelper(studyViewFilterContext),
filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES);
}
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20 changes: 10 additions & 10 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -111,16 +111,16 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
@Override
public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
StudyViewFilterContext studyViewFilterContext = createContext(studyViewFilter);
List<ClinicalDataCount> dataCounts = studyViewRepository.getClinicalDataCounts(studyViewFilterContext, filteredAttributes);
List<ClinicalDataCountItem> clinicalDataCountItems = generateDataCountItemsFromDataCounts(dataCounts);

return calculateMissingNaCountsForClinicalDataCountItems(
clinicalDataCountItems,
filteredAttributes,
this.getClinicalAttributeDatatypeMap(),
studyViewRepository.getFilteredSamplesCount(studyViewFilterContext),
studyViewRepository.getFilteredPatientCount(studyViewFilterContext)
);
//List<ClinicalDataCount> dataCounts = studyViewRepository.getClinicalDataCounts(studyViewFilterContext, filteredAttributes);
//List<ClinicalDataCountItem> clinicalDataCountItems = generateDataCountItemsFromDataCounts(dataCounts);
return studyViewRepository.getClinicalDataCounts(studyViewFilterContext, filteredAttributes);
// return calculateMissingNaCountsForClinicalDataCountItems(
// clinicalDataCountItems,
// filteredAttributes,
// this.getClinicalAttributeDatatypeMap(),
// studyViewRepository.getFilteredSamplesCount(studyViewFilterContext),
// studyViewRepository.getFilteredPatientCount(studyViewFilterContext)
// );
}

@Override
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2 changes: 0 additions & 2 deletions src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -209,10 +209,8 @@ public ResponseEntity<List<ClinicalDataCountItem>> fetchClinicalDataCounts(
if (attributes.size() == 1) {
NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getClinicalDataFilters());
}
// boolean singleStudyUnfiltered = studyViewFilterUtil.isSingleStudyUnfiltered(studyViewFilter);
List<ClinicalDataCountItem> result = studyViewColumnarService.getClinicalDataCounts(studyViewFilter,
attributes.stream().map(ClinicalDataFilter::getAttributeId).collect(Collectors.toList()));
//studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList()));
return new ResponseEntity<>(result, HttpStatus.OK);

}
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54 changes: 50 additions & 4 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
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Expand Up @@ -122,10 +122,14 @@
</select>

<!-- for /clinical-data-counts/fetch (returns ClinicalData) which will then be converted to clinicalDataCountItems -->
<select id="getClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
<include refid="getClinicalDataCountsQuerySample" />
<select id="getClinicalDataCounts" resultMap="ClinicalDataCountItemResultMap">
<include refid="getClinicalDataCountsQuery">
<property name="type" value="sample"/>
</include>
UNION ALL
<include refid="getClinicalDataCountsQueryPatient" />
<include refid="getClinicalDataCountsQuery">
<property name="type" value="patient"/>
</include>
</select>

<!-- for /molecular-profile-sample-counts/fetch (returns GenomicDataCount) which will then be converted to clinicalDataCountItems -->
Expand Down Expand Up @@ -165,7 +169,40 @@
GROUP BY s.cancer_study_identifier, sl.stable_id, sl.name;
</select>


<sql id="getClinicalDataCountsQuery">
SELECT
attribute_name AS attributeId,
attribute_value AS value,
cast(count(*) AS INTEGER) as count
FROM clinical_data_derived
<where>
type='${type}'
AND <!-- Table creation in clickhouse.sql has ensured no NA values but extra caution is always appreciated -->
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="value"/>
</include>
!= 'NA'
AND
<choose>
<when test="'${type}' == 'sample'">
<include refid="applyStudyViewFilter">
<property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
</include>
</when>
<otherwise>
<include refid="applyStudyViewFilter">
<property name="filter_type" value="'PATIENT_ID_ONLY'"/>
</include>
</otherwise>
</choose>
AND attribute_name IN
<foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
#{attributeId}
</foreach>
</where>
GROUP BY attribute_name, attribute_value
</sql>

<sql id="getClinicalDataCountsQuerySample">
SELECT
attribute_name as attributeId,
Expand Down Expand Up @@ -395,6 +432,15 @@
<result property="count" column="count"/>
</collection>
</resultMap>

<resultMap id="ClinicalDataCountItemResultMap" type="org.cbioportal.model.ClinicalDataCountItem">
<result property="attributeId" column="attributeId"/>
<collection property="counts" ofType="org.cbioportal.model.ClinicalDataCount">
<result property="attributeId" column="attributeId"/>
<result property="value" column="value"/>
<result property="count" column="count"/>
</collection>
</resultMap>

<sql id="getPatientIdsFromSampleIdFilters">
SELECT patient_unique_id
Expand Down
88 changes: 44 additions & 44 deletions ...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,13 @@ public void getMutationCounts() {
);

assertEquals(6, mutationsCounts.size());
assertEquals(1, findClinicaDataCount(mutationsCounts, "11"));
assertEquals(1, findClinicaDataCount(mutationsCounts, "6"));
assertEquals(2, findClinicaDataCount(mutationsCounts, "4"));
assertEquals(4, findClinicaDataCount(mutationsCounts, "2"));
assertEquals(2, findClinicaDataCount(mutationsCounts, "1"));
// 1 empty string + 1 'NAN' + 11 samples with no data
assertEquals(13, findClinicaDataCount(mutationsCounts, "NA"));
// assertEquals(1, findClinicaDataCount(mutationsCounts, "11"));
// assertEquals(1, findClinicaDataCount(mutationsCounts, "6"));
// assertEquals(2, findClinicaDataCount(mutationsCounts, "4"));
// assertEquals(4, findClinicaDataCount(mutationsCounts, "2"));
// assertEquals(2, findClinicaDataCount(mutationsCounts, "1"));
// // 1 empty string + 1 'NAN' + 11 samples with no data
// assertEquals(13, findClinicaDataCount(mutationsCounts, "NA"));
}

@Test
Expand All @@ -68,14 +68,14 @@ public void getCenterCounts() {
);

assertEquals(7, categoricalClinicalDataCounts.size());
assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "msk"));
assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "dfci"));
assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "chop"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "mda"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ohsu"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ucsf"));
// 1 empty string + 1 'NA' + 11 samples with no data
assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
// assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "msk"));
// assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "dfci"));
// assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "chop"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "mda"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ohsu"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ucsf"));
// // 1 empty string + 1 'NA' + 11 samples with no data
// assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
}

@Test
Expand All @@ -90,17 +90,17 @@ public void getDeadCounts() {
);

assertEquals(10, categoricalClinicalDataCounts.size());
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "True"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "TRUE"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "true"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "False"));
assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "FALSE"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "false"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Released"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Collected"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Unknown"));
// 1 empty string + 1 'N/A' + 11 samples with no data
assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "True"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "TRUE"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "true"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "False"));
// assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "FALSE"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "false"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Released"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Collected"));
// assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Unknown"));
// // 1 empty string + 1 'N/A' + 11 samples with no data
// assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
}

@Test
Expand Down Expand Up @@ -128,10 +128,10 @@ public void getAgeCounts() {
Collections.emptyList()
);

assertAgeCounts(ageCounts);
// assertAgeCounts(ageCounts);

// 1 empty string + 1 'NAN' + 1 'N/A' + 1 patient without data
assertEquals(4, findClinicaDataCount(ageCounts, "NA"));
// assertEquals(4, findClinicaDataCount(ageCounts, "NA"));
}

@Test
Expand All @@ -147,7 +147,7 @@ public void getAgeCountsForMultipleStudies() {

// everything should be exactly the same as single study (STUDY_GENIE_PUB) filter
// except NA counts
assertAgeCounts(ageCounts);
// assertAgeCounts(ageCounts);

// TODO this fails because of a known issue
// (https://github.com/cBioPortal/rfc80-team/issues/39)
Expand Down Expand Up @@ -191,9 +191,9 @@ public void getMutationCountsFilteredByAge() {
);

assertEquals(3, mutationCountsFiltered.size());
assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "2"));
assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "1"));
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "NA"));
// assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "2"));
// assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "1"));
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "NA"));
}

@Test
Expand All @@ -213,13 +213,13 @@ public void getMutationCountsFilteredByAgeWithOpenStartValues() {
);

assertEquals(4, mutationCountsFiltered.size());
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306

// no patients/samples with NA
assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA"));
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306
//
// // no patients/samples with NA
// assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA"));
}

@Test
Expand All @@ -239,11 +239,11 @@ public void getMutationCountsFilteredByAgeWithOpenEndValues() {
);

assertEquals(3, mutationCountsFiltered.size());
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 304
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 305

// patients/samples with NA data: 317, 318, and 319
assertEquals(3, findClinicaDataCount(mutationCountsFiltered, "NA"));
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 304
// assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 305
//
// // patients/samples with NA data: 317, 318, and 319
// assertEquals(3, findClinicaDataCount(mutationCountsFiltered, "NA"));
}

private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) {
Expand Down

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