Demo rfc80 poc mutation data count specific gene parameter #10975

fuzhaoyuan · 2024-09-04T19:54:55Z

Fix cBioPortal/rfc80-team#38 and cBioPortal/rfc80-team#43

Describe changes proposed in this pull request:

Add basic unit tests
Overload mutatedGenes and populateAlterationCounts related methods to provide a way to query limited list of genes, thus fasten the speed of endpoint 'mutation-data-count'

alisman · 2024-09-04T20:34:06Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -27,7 +27,7 @@ public interface StudyViewRepository {

 List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);


@haynescd @fuzhaoyuan is there a way to indicate that this is optional rather than forcing people to pass null? I think that's called overloading at method, right?

Also, I think maybe just "hugoGeneSymbol" is enough. specificHugGeneSymbol seems redundant. There should be a comment explaining that we pass in a genesymbol if we only want counts for that gene. i also wonder whether we should just make it an array since it seems inevitable that we'll want to target multiple genes.

I would honestly create a new method called getMutatedGene that would reuse the sql in the mapper file for getMutatedGenes...

Kinda doesn't make sense to have getMutatedGenes that returns one gene

Yeah I'll look into it

maybe two methods (they could be overloaded )
getMutatedGenes
getMutatedGenes(StudyViewFilter, String... geneToQuery)

haynescd · 2024-09-05T14:39:37Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -27,7 +27,7 @@ public interface StudyViewRepository {

 List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);


I would honestly create a new method called getMutatedGene that would reuse the sql in the mapper file for getMutatedGenes...

Kinda doesn't make sense to have getMutatedGenes that returns one gene

haynescd · 2024-09-05T14:40:27Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -42,11 +42,11 @@ public interface StudyViewRepository {

 List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);

- Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+ Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol);


Same as above. We are overloading something that returns multiples to return a single

haynescd · 2024-09-05T14:52:18Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -27,7 +27,7 @@ public interface StudyViewRepository {

 List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);


maybe two methods (they could be overloaded )
getMutatedGenes
getMutatedGenes(StudyViewFilter, String... geneToQuery)

haynescd · 2024-09-05T14:57:26Z

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java



 public interface StudyViewMapper {
 List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

 List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);


If you just overload the Repository layer.. you could just keep this the same except pass a list or null then you could just reuse the sql as well

Think I got it. Thanks!

fuzhaoyuan · 2024-09-05T17:47:57Z

src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java

 final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
- var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
- final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
+ var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), specificHugoGeneSymbol);


@haynescd Do you think I should change it to list or overload? Same applies to the one below.

haynescd

Changed to use vararg to make it easier

haynescd · 2024-09-06T13:25:54Z

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java

 List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
+
+ AlterationCountByGene getMutatedGene(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);


Am I missing this? I don't see it defined in the xml?

Oh sorry I must forgot to remove it

haynescd · 2024-09-06T13:25:58Z

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java



 public interface StudyViewMapper {
 List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

 List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, List<String> hugoGeneSymbols);


maybe a better variable name is genesToQuery?

haynescd · 2024-09-06T13:36:59Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -29,6 +29,8 @@ public interface StudyViewRepository {

 List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);

+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);


Suggested change

List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);

Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String... genesToQuery);

This is what I want. So when calling the function you can do the following...

studyViewRepository.getTotalProfiledCounts(studyViewFilter, alterationType, "TP53", "GENEA"); //or studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());

Oh wow that's cool

haynescd · 2024-09-06T13:37:38Z

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -43,11 +45,15 @@ public interface StudyViewRepository {
 List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);

 Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+
+ Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols);


Change the variable name to genesToQuery

sonarcloud · 2024-09-06T19:42:34Z

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
18.5% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

This was linked to issues Sep 4, 2024

Slight mutation count discrepancy on genie cBioPortal/rfc80-team#38

Closed

Mutation data count service not returning "Not Profiled" count cBioPortal/rfc80-team#43

Closed

alisman reviewed Sep 4, 2024

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haynescd requested changes Sep 5, 2024

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fuzhaoyuan commented Sep 5, 2024

View reviewed changes

fuzhaoyuan requested a review from haynescd September 5, 2024 18:38

alisman added the RFC80 label Sep 5, 2024

fuzhaoyuan requested a review from alisman September 5, 2024 18:54

fuzhaoyuan added 4 commits September 5, 2024 18:11

Basic unit tests

7dc5c1c

Fix on mutation counts

22da8e4

Add optional specific gene parameter for populateAlterationCounts

7476bec

Overload methods

72a5175

fuzhaoyuan force-pushed the demo-rfc80-poc-mutation_data_count-specific-gene branch from a73857b to 72a5175 Compare September 5, 2024 22:21

haynescd requested changes Sep 6, 2024

View reviewed changes

Varargs. Need to fix filter

601d340

fuzhaoyuan closed this Sep 9, 2024

fuzhaoyuan deleted the demo-rfc80-poc-mutation_data_count-specific-gene branch September 9, 2024 19:29

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Demo rfc80 poc mutation data count specific gene parameter #10975

Demo rfc80 poc mutation data count specific gene parameter #10975

fuzhaoyuan commented Sep 4, 2024 •

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sonarcloud bot commented Sep 6, 2024

		List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);

		AlterationCountByGene getMutatedGene(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);

		@@ -29,6 +29,8 @@ public interface StudyViewRepository {

		List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);

		List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);

	List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);
	Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String... genesToQuery);

Demo rfc80 poc mutation data count specific gene parameter #10975

Demo rfc80 poc mutation data count specific gene parameter #10975

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fuzhaoyuan commented Sep 4, 2024 • edited Loading

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sonarcloud bot commented Sep 6, 2024

Quality Gate passed

fuzhaoyuan commented Sep 4, 2024 •

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