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Custom sample filtering performance and security improvement #11296

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merged 2 commits into from
Dec 19, 2024
Merged

Custom sample filtering performance and security improvement #11296

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0bc04ff
Use prepared statements to avoid injection attack and clickhouse nati…
dippindots Nov 27, 2024
8607377
Dynamically calculate sample identifiers in study view filter helper
dippindots Dec 17, 2024
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10 changes: 10 additions & 0 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,16 @@ public List<CustomSampleIdentifier> customDataSamples() {
return this.customDataSamples;
}

public String[] filteredSampleIdentifiers() {
if (studyViewFilter != null && studyViewFilter.getSampleIdentifiers() != null) {
return studyViewFilter.getSampleIdentifiers().stream()
.map(sampleIdentifier -> sampleIdentifier.getStudyId() + "_" + sampleIdentifier.getSampleId())
.toArray(String[]::new);
} else {
return new String[0];
}
}

public List<String> involvedCancerStudies() {
return involvedCancerStudies;
}
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11 changes: 11 additions & 0 deletions src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ public class CustomSampleIdentifier extends SampleIdentifier implements Serializ

private boolean isFilteredOut = false;
private String value;
private String uniqueSampleId;

public boolean getIsFilteredOut() {
return isFilteredOut;
Expand All @@ -22,4 +23,14 @@ public String getValue() {
public void setValue(String value) {
this.value = value;
}

// Generating unique SampleId by concatenating studyId and sampleId
public String getUniqueSampleId() {
// Assuming studyId and sampleId are available in SampleIdentifier
// Concatenate with "_" in between if both values are not null
if (getStudyId() != null && getSampleId() != null) {
return getStudyId() + "_" + getSampleId();
}
return null; // or return null if either studyId or sampleId is null
}
}
21 changes: 12 additions & 9 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 @@ -60,15 +60,15 @@
)

</if>

<if test="studyViewFilterHelper.studyViewFilter.sampleIdentifiers != null and !studyViewFilterHelper.studyViewFilter.sampleIdentifiers.isEmpty()">
INTERSECT
<bind name="filteredSampleIdentifiers" value="studyViewFilterHelper.filteredSampleIdentifiers()" />
<if test="filteredSampleIdentifiers != null and filteredSampleIdentifiers.length > 0">
INTERSECT
SELECT sample_unique_id
FROM sample_derived
WHERE sample_unique_id IN
<foreach item="sampleIdentifier" collection="studyViewFilterHelper.studyViewFilter.sampleIdentifiers" open="(" separator="," close=")">
'${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
</foreach>
(
#{filteredSampleIdentifiers, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
)
</if>
<if test="studyViewFilterHelper.studyViewFilter.customDataFilters != null and !studyViewFilterHelper.studyViewFilter.customDataFilters.isEmpty() and studyViewFilterHelper.customDataSamples != null">
INTERSECT
Expand All @@ -86,8 +86,8 @@
sample_unique_id IN (
'',
<foreach item="sampleIdentifier" collection="studyViewFilterHelper.customDataSamples" separator=",">
<if test="!sampleIdentifier.getIsFilteredOut()">
'${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
<if test="!sampleIdentifier.getIsFilteredOut() and sampleIdentifier.getUniqueSampleId() != null">
#{sampleIdentifier.uniqueSampleId}
</if>
</foreach>
)
Expand All @@ -97,8 +97,11 @@
<if test="customDataFilterValue.value eq 'NA'">
OR
sample_unique_id NOT IN (
'',
<foreach item="sampleIdentifier" collection="studyViewFilterHelper.customDataSamples" separator=",">
'${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
<if test="sampleIdentifier.getUniqueSampleId() != null">
#{sampleIdentifier.uniqueSampleId}
</if>
</foreach>
)
</if>
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