Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Custom sample filtering performance and security improvement #11235

Merged
merged 1 commit into from
Nov 29, 2024
Merged

Custom sample filtering performance and security improvement #11235

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,21 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil
private final StudyViewFilter studyViewFilter;
private final CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter;
private final List<CustomSampleIdentifier> customDataSamples;
private final String[] filteredSampleIdentifiers;

private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter,
@NonNull Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
this.studyViewFilter = studyViewFilter;
this.categorizedGenericAssayDataCountFilter = extractGenericAssayDataCountFilters(studyViewFilter, genericAssayProfilesMap);
this.customDataSamples = customDataSamples;
if (studyViewFilter != null && studyViewFilter.getSampleIdentifiers() != null) {
this.filteredSampleIdentifiers = studyViewFilter.getSampleIdentifiers().stream()
.map(sampleIdentifier -> sampleIdentifier.getStudyId() + "_" + sampleIdentifier.getSampleId())
.toArray(String[]::new);
} else {
this.filteredSampleIdentifiers = new String[0];
}
}

public StudyViewFilter studyViewFilter() {
Expand All @@ -54,6 +62,10 @@ public CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFi
public List<CustomSampleIdentifier> customDataSamples() {
return this.customDataSamples;
}

public String[] filteredSampleIdentifiers() {
return this.filteredSampleIdentifiers;
}

private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilters(final StudyViewFilter studyViewFilter, Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap) {
if ((studyViewFilter.getGenericAssayDataFilters() == null || genericAssayProfilesMap.isEmpty()))
Expand Down
10 changes: 10 additions & 0 deletions src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,4 +22,14 @@ 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 a default value if either studyId or sampleId is null
}
}
18 changes: 10 additions & 8 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,14 +59,14 @@

</if>

<if test="studyViewFilterHelper.studyViewFilter.sampleIdentifiers != null and !studyViewFilterHelper.studyViewFilter.sampleIdentifiers.isEmpty()">
INTERSECT
<if test="studyViewFilterHelper.filteredSampleIdentifiers != null and studyViewFilterHelper.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>
(
#{studyViewFilterHelper.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 @@ -84,8 +84,8 @@
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.getUniqueSampleId}
</if>
</foreach>
)
Expand All @@ -96,7 +96,9 @@
OR
sample_unique_id NOT IN (
<foreach item="sampleIdentifier" collection="studyViewFilterHelper.customDataSamples" separator=",">
'${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
<if test="sampleIdentifier.getUniqueSampleId != null">
#{sampleIdentifier.getUniqueSampleId}
</if>
</foreach>
)
</if>
Expand Down
Loading