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Fix profiling count issues in legacy #11105

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merged 7 commits into from
Oct 29, 2024
Merged

Fix profiling count issues in legacy #11105

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a2437bc
Fix errant genetic profile matches due to overlapping type suffix
alisman Oct 22, 2024
3d7953c
fix legacy broken profile counts
alisman Oct 22, 2024
bfc6179
Fix clinical event availability grouping (broken for multi study wher…
alisman Oct 22, 2024
8ac5d44
Fix genomic profile filtering
alisman Oct 29, 2024
a004d91
Fix casing of table name
alisman Oct 29, 2024
7e53ba2
Fix another casing issue
alisman Oct 29, 2024
9143285
Fix another casing issue
alisman Oct 29, 2024
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2 changes: 1 addition & 1 deletion src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@
</if>
</if>
</where>
Group by clinical_event.EVENT_TYPE, patient.STABLE_ID
Group by clinical_event.EVENT_TYPE, patient.INTERNAL_ID
</select>

</mapper>
2 changes: 2 additions & 0 deletions src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml
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Expand Up @@ -121,6 +121,7 @@
<include refid="selectGenePanelData"/>
<include refid="fromGenePanelData"/>
WHERE
SAMPLE_ID IS NOT NULL AND
genetic_profile.STABLE_ID IN
<foreach item="item" collection="collection" open="(" separator="," close=")">
#{item}
Expand All @@ -132,6 +133,7 @@
<include refid="selectGenePanelData"/>
<include refid="fromGenePanelData"/>
<where>
SAMPLE_ID IS NOT NULL
<choose>
<when test="list == null or list.isEmpty()">
AND NULL
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8 changes: 5 additions & 3 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
SELECT * FROM (
<foreach item="ANDGroup" collection="studyViewFilterHelper.studyViewFilter.genomicProfiles" separator="INTERSECT">
SELECT sample_derived.sample_unique_id
FROM sample_profile
FROM sample_profile GYMP
JOIN genetic_profile gp ON sample_profile.genetic_profile_id = gp.genetic_profile_id
JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id
JOIN sample_derived on sample_profile.sample_id = sample_derived.internal_id
Expand All @@ -48,8 +48,10 @@
#{studyId}
</foreach>
AND
<foreach item="genomicProfileId" collection="ANDGroup" open="(" separator="OR" close=")">
gp.stable_id LIKE concat('%_', #{genomicProfileId})
<foreach item="studyId" collection="studyViewFilterHelper.studyViewFilter.studyIds" open="(" close=")" separator="OR">
<foreach item="genomicProfileId" collection="ANDGroup" open="(" separator=" OR " close=")">
gp.stable_id=concat(#{studyId}, '_', #{genomicProfileId})
</foreach>
</foreach>
</where>
</foreach>
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