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Added chromosome query parameter for copy number segments endpoint #5321

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merged 1 commit into from
Nov 26, 2018
Merged

Added chromosome query parameter for copy number segments endpoint #5321

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12 changes: 6 additions & 6 deletions ...persistence-api/src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,17 +7,17 @@

public interface CopyNumberSegmentRepository {

List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String projection,
List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome, String projection,
Integer pageSize, Integer pageNumber, String sortBy,
String direction);

BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId);
BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome);

List<Integer> fetchSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds);
List<Integer> fetchSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome);

List<CopyNumberSeg> fetchCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String projection);
List<CopyNumberSeg> fetchCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome, String projection);

BaseMeta fetchMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds);
BaseMeta fetchMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome);

List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId, String projection);
List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId, String chromosome, String projection);
}
8 changes: 4 additions & 4 deletions ...nce-mybatis/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java
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Expand Up @@ -7,12 +7,12 @@

public interface CopyNumberSegmentMapper {

List<CopyNumberSeg> getCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String projection,
List<CopyNumberSeg> getCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome, String projection,
Integer limit, Integer offset, String sortBy, String direction);

List<Integer> getSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds);
List<Integer> getSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome);

BaseMeta getMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds);
BaseMeta getMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome);

List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId, String projection);
List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId, String chromosome, String projection);
}
28 changes: 16 additions & 12 deletions .../src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java
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Expand Up @@ -20,43 +20,47 @@ public class CopyNumberSegmentMyBatisRepository implements CopyNumberSegmentRepo


@Override
public List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId,
public List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome,
String projection, Integer pageSize,
Integer pageNumber, String sortBy,
String direction) {

return copyNumberSegmentMapper.getCopyNumberSegments(Arrays.asList(studyId), Arrays.asList(sampleId),
return copyNumberSegmentMapper.getCopyNumberSegments(Arrays.asList(studyId), Arrays.asList(sampleId), chromosome,
projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
}

@Override
public BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId) {
public BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome) {

return copyNumberSegmentMapper.getMetaCopyNumberSegments(Arrays.asList(studyId), Arrays.asList(sampleId));
return copyNumberSegmentMapper.getMetaCopyNumberSegments(Arrays.asList(studyId), Arrays.asList(sampleId), chromosome);
}

@Override
public List<Integer> fetchSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds) {
return copyNumberSegmentMapper.getSamplesWithCopyNumberSegments(studyIds, sampleIds);
public List<Integer> fetchSamplesWithCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome) {
return copyNumberSegmentMapper.getSamplesWithCopyNumberSegments(studyIds, sampleIds, chromosome);
}

@Override
public List<CopyNumberSeg> fetchCopyNumberSegments(List<String> studyIds, List<String> sampleIds,
public List<CopyNumberSeg> fetchCopyNumberSegments(List<String> studyIds,
List<String> sampleIds,
String chromosome,
String projection) {

return copyNumberSegmentMapper.getCopyNumberSegments(studyIds, sampleIds, projection, 0, 0, null, null);
return copyNumberSegmentMapper.getCopyNumberSegments(studyIds, sampleIds, chromosome, projection, 0, 0, null, null);
}

@Override
public BaseMeta fetchMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds) {
public BaseMeta fetchMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome) {

return copyNumberSegmentMapper.getMetaCopyNumberSegments(studyIds, sampleIds);
return copyNumberSegmentMapper.getMetaCopyNumberSegments(studyIds, sampleIds, chromosome);
}

@Override
public List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId,
public List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId,
String sampleListId,
String chromosome,
String projection) {

return copyNumberSegmentMapper.getCopyNumberSegmentsBySampleListId(studyId, sampleListId, projection);
return copyNumberSegmentMapper.getCopyNumberSegmentsBySampleListId(studyId, sampleListId, chromosome, projection);
}
}
16 changes: 15 additions & 1 deletion ...mybatis/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml
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Expand Up @@ -42,7 +42,12 @@
INNER JOIN patient ON sample.PATIENT_ID=patient.INTERNAL_ID
INNER JOIN cancer_study ON patient.CANCER_STUDY_ID=cancer_study.CANCER_STUDY_ID
<include refid="where"/>
AND EXISTS (SELECT * from copy_number_seg where sample.INTERNAL_ID=copy_number_seg.SAMPLE_ID)
AND EXISTS (
SELECT * from copy_number_seg where sample.INTERNAL_ID=copy_number_seg.SAMPLE_ID
<if test="chromosome != null and !chromosome.isEmpty()">
AND copy_number_seg.CHR=#{chromosome}
</if>
)
</select>


Expand All @@ -51,6 +56,9 @@
<include refid="select"/>
<include refid="from"/>
<include refid="where"/>
<if test="chromosome != null and !chromosome.isEmpty()">
AND copy_number_seg.CHR=#{chromosome}
</if>
<if test="sortBy != null and projection != 'ID'">
ORDER BY ${sortBy} ${direction}
</if>
Expand All @@ -67,13 +75,19 @@
COUNT(*) AS totalCount
<include refid="from"/>
<include refid="where"/>
<if test="chromosome != null and !chromosome.isEmpty()">
AND copy_number_seg.CHR=#{chromosome}
</if>
</select>

<select id="getCopyNumberSegmentsBySampleListId" resultType="org.cbioportal.model.CopyNumberSeg">
SELECT
<include refid="select"/>
<include refid="from"/>
WHERE cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId}
<if test="chromosome != null and !chromosome.isEmpty()">
AND copy_number_seg.CHR=#{chromosome}
</if>
AND copy_number_seg.SAMPLE_ID IN
(
SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
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