(GSoC) Generic Assay Categorical/Binary data implementation Backend #10303

Djokovic0311 · 2023-07-28T16:20:48Z

Changes proposed

Implement new Services and Controller to provide generic assay categorical and binary data enrichments for group comparision.
Implement Fisher's exact test for binary data and the chi-square test for categorical data.
Add tests for Services.

Display

Binary data visualisation:

Categorical data visualisation:

dippindots

Hi @Djokovic0311, your code looks good to me. Good job!! I think most of my comments are related to the refactoring and some code styles. We can talk about this tomorrow. I still need to figure out why the tests are not passing.

dippindots · 2023-08-07T21:30:50Z

web/src/main/java/org/cbioportal/web/GenericAssayBinaryDataController.java

+@RestController
+@Validated
+@Api(tags = "Generic Assay Binary Data", description = " ")
+public class GenericAssayBinaryDataController {


let's merge this controller and the other controller together and rename it GenericAssayEnrichmentController

dippindots · 2023-08-07T21:33:07Z

web/src/main/java/org/cbioportal/web/GenericAssayBinaryDataController.java

+
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @RequestMapping(value = "/generic-assay-enrichments/binary/fetch",


Let's try to use similar naming structure with other endpoints

Suggested change

@RequestMapping(value = "/generic-assay-enrichments/binary/fetch",

@RequestMapping(value = "/generic-assay-binary-enrichments/fetch",

web/src/main/java/org/cbioportal/web/GenericAssayCategoricalDataController.java

dippindots · 2023-08-07T21:53:36Z

web/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java

+    public static final String GENERIC_ASSAY_CATEGORICAL_ENRICHMENT_FETCH_PATH = "/generic-assay-enrichments/categorical/fetch";
+    public static final String GENERIC_ASSAY_BINARY_ENRICHMENT_FETCH_PATH = "/generic-assay-enrichments/binary/fetch";


These two also need to be changed accordingly.

service/src/main/java/org/cbioportal/service/GenericAssayBinaryDataService.java

dippindots · 2023-08-07T22:32:07Z

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

+    private void validateMolecularProfile(MolecularProfile molecularProfile,
+                                          List<MolecularProfile.MolecularAlterationType> validMolecularAlterationTypes) throws MolecularProfileNotFoundException {
+        if (!validMolecularAlterationTypes.contains(molecularProfile.getMolecularAlterationType())) {
+            throw new MolecularProfileNotFoundException(molecularProfile.getStableId());


We should also check if a molecularProfile has the correct datatype (e.g. BINARY for binary method and CATEGORICAL for categorical method)

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

dippindots · 2023-08-07T22:48:40Z

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

+        });
+
+        // Extract pValues and calculate qValues.
+        BigDecimal[] pValues = genericAssayBinaryEnrichments.stream().map(a -> a.getpValue()).toArray(BigDecimal[]::new);


It's better to refer its actual type here

Suggested change

BigDecimal[] pValues = genericAssayBinaryEnrichments.stream().map(a -> a.getpValue()).toArray(BigDecimal[]::new);

BigDecimal[] pValues = genericAssayBinaryEnrichments.stream().map(GenericAssayBinaryEnrichment ::getpValue).toArray(BigDecimal[]::new);

dippindots · 2023-08-07T22:54:44Z

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

+import java.util.stream.Collectors;
+
+@Service
+public class GenericAssayCategoricalDataServiceImpl implements GenericAssayCategoricalDataService {


Please see shared comments in GenericAssayCategoricalDataServiceImpl.java

dippindots · 2023-08-07T23:22:46Z

...ce/src/test/java/org/cbioportal/service/impl/GenericAssayCategoricalDataServiceImplTest.java

+
+    @Spy
+    @InjectMocks
+    private ExpressionEnrichmentUtil expressionEnrichmentUtil;


It seems this is not being used anywhere, I know this is probably coming from our example test, but since we found it, let's remove it.

Okay. I will have a look at your comments. Thanks for your efforts! @dippindots

dippindots · 2023-08-07T23:36:55Z

@Djokovic0311 There is one update for fisher tests we just merged (this is why we see the conflicts in the service/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java). The change was to use a two-sided fisher test instead of a one-sided one. We should also update the fisher method we used. See #10288 for more details.

JREastonMarks

Overall, this looks good but I would like to see inline comments describing some of the logic. In parts of cBioPortal we have some complicated data manipulations that we perform and without good documentation it is hard for the next person to work on that code.

model/src/main/java/org/cbioportal/model/ExpressionEnrichment.java

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

JREastonMarks · 2023-08-09T15:54:14Z

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

+        if (!validMolecularAlterationTypes.contains(molecularProfile.getMolecularAlterationType())) {
+            throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
+        }
+        if(isBinary) {


Why the nested if statements? Is the second one needed?

There are two types of generic assay data calling this validation, so the second one is used to verify all the data fetched by getGenericAssayBinaryEnrichments are Binary type, not Categorical, Limited Value or null. This will ensure frontend display the right things.

JREastonMarks · 2023-08-09T15:56:05Z

service/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java

-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
+import java.util.*;


No * imports please

Yes, done. Thanks!

It looks like the * made it back in

Djokovic0311 · 2023-08-11T14:42:01Z

@JREastonMarks Thanks for all your comments reminding me about the inline comments issue. I previously planned to put the instructions in my final report documentation which is ongoing now. At the same time, I will put them in my codes in next commit.

JREastonMarks

@Djokovic0311 Sorry, found a few more * imports.

JREastonMarks · 2023-08-16T21:26:32Z

service/src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java

@@ -0,0 +1,261 @@
+package org.cbioportal.service.impl;
+
+import org.cbioportal.model.*;


Please remove the * import. Sorry, I caught another one.

Sorry I noticed the ExpressionEnrichmentTest has the * import, so I just left it here aligned with them.Now I find other test files avoid import *. I have pushed modified version. Shall I modify ExpressionEnrichmentTest as well?

JREastonMarks · 2023-08-16T21:26:48Z

web/src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java

+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;


Please remove the * import

…1/cbioportal into GenericAssay-Jiahang

sonarqubecloud · 2023-08-17T20:09:57Z

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dippindots · 2023-08-18T17:04:57Z

@Djokovic0311 Just confirmed with @JREastonMarks that we are good to go, thanks @JREastonMarks for helping us review the code. The local e2e tests are not related, I will squash your commits into one and merge it. Good job @Djokovic0311 !!!

@dippindots

* fix #9461 - mutations api endpoint - modified java files to remove unused properties and changes to tests - db changes, mutationmapper.xml - Update seed_mini.sql roll back changes for refseqMrnaId roll back changes for refseqMrnaId Update ExtendedMutation.java Added required property setOncotatorRefseqMrnaId and getOncotatorRefseqMrnaId * Updated more files for removed fields Updated more files for removed fields Remove unused oncotator fields Remove unused oncotator fields ONCOTATOR_DBSNP_RS ONCOTATOR_UNIPROT_ENTRY_NAME remove fields from sql file ONCOTATOR_DBSNP_RS and ONCOTATOR_UNIPROT_ENTRY_NAME removal from sql file * db changes and renaming the column prefixes from oncotator to mutation db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files * Update SQL statements Update testSql.sql updating testSql for the name change of columns from ONCOTATOR to MUTATION Update DaoMutation.java The data files still use the old column prefix of ONCOTATOR instead of MUTATION Update DaoMutation.java Update migration.sql Adding quotes around column names * db changes and renaming the column prefixes from oncotator to mutation db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files * Update migration.sql Update migration.sql fix syntax errors in mysql change column Update migration.sql fix syntax errors in mysql change column setting db version setting db version * Removed Link columns Removed Link columns and modified the documentation * Update news.md * update news.md * update cosmic importer for new cosmic datafiles * Update DB version and renaming mutation_event fields * Update Mutation model * Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy and add support for multiple database impls to support mysql and h2 * Allow binning and filtering of custom (numerical and categorical) data * Several small fixes and cleanup after feedback @dippindots * Remove excess whitespace * Fix combined Entrez Gene Id and Stuct Var Query in StructuralVariantMapper.xml * update bilkent members * Frontend v5.3.0 * Update ClinicalEventMyBatisRepositoryTest.java We need to update this test because it's not java 8 compatible. * Address java8 compatible issues in more tests * Add importer and validator section to release-drafter.yml * Fix release-drafter.yml error * Update news.md * Frontend v5.3.1 * Update News.md * Use custom driver annotations in sv counts * Test custom driver annotations filter in sv count query * Differentiate between test svs by making annotations unique * Fix sv whereSite1IsNot2 clause, add es0 sv custom driver data * Remove unused DriverManagerDataSource fields from db tests * Add comment to mybatis sv whereSite1IsNot2 clause * Fix validation result_report.html: include new sv * Frontend v5.3.2 * Update News.md * fixed swagger page validation errors * Frontend v5.3.3 * Add MSK database migration documentation (#10115) Co-authored-by: Ino de Bruijn <[email protected]> * Do not call next study view filter when no samples left (#10124) * Add studyId to CancerStudyTag entity * Frontend v5.3.4 * 🔧 Add Configuration Properties for study view summary limits * add sitemaps for retype adding url should fix this * Frontend v5.3.5 * Add tutorials from others * Add Farhan Haq tutorial video * 🔧 Add StudyDownloadUrl to portal.properties * Frontend v5.3.6 * Update News-Genie.md * Fix study tag search when no studies present * Add dsnparse Python requirement Needed for future PR concerning using db.connection_string to connect to the database * add jeremy to about page * Documentation markdown fixes (#10186) * Fix broken hyperlink to retype * Move development files under development directory * Fix markdown links for table of contents * Frontend v5.3.7 * Update gene set version and update tests * Fix integration test * Frontend v5.3.8 * 📚 Update Priority Documentation * ✨ Add ability to set priority to -1 for clinical attr * add statistical tests in FAQ Fixed #10198 * extend File-Formats.md with mutational signature datatype (#10172) * Frontend v5.3.9 * change docker compose cmds * fix contact email in dev section * fix release notes docs link * fix release procedure info * Frontend v5.3.10 * Add note about official releases * Add AACR GENIE BPC tutorial videos (#10215) * Adding new features news (#10149) * Adding new features news from 2022/05 to current Co-authored-by: Ino de Bruijn <[email protected]> * Update web-API-and-Clients.md (#10209) Add description of cbioportalR in web API section * Frontend v5.3.11 * Paginate clinical table response using Page and Pagable spring interfaces * Use PaginatedClinicalData * Add query to count items in clinical table * Replace spring page with page response headers * Fix page size when sorting clinical table * Sort clinical table by sample and patient ID * Fix distinct in patient attr sorting * Fix difference h2 and mysql in sorting nulls last * Rename *SampleClinicalTable* methods * update members about us page add calla & bryan, move several people to alumni * Revert controler rename to keep backward compatible * Impl. Struct Var count endpoint for Study View * Remove unused imports PR feedback Gaofei * Correct variable name PR feedback Gaofei * Change HashMap to Set PR feedback Gaofei * Return counts when gene 1 or gene2 is null * Change missing site1 or site2 gene for SV to INFO log level Was WARN before. * Update result report * Create property to show reference genome in study list * Frontend v5.3.12 * fix contributor last name * Frontend v5.3.13 * Impl. Struct Var filter queries for /filtered-samples/fetch endpoint * Add unit tests for resolveEntrezGeneIds * Changes after PR reviews - Rename StructVar* to StructuralVariant* - Revert JsonInclude Always to NON_NULL - * Add Java 11 as requirement * modify documentation for skin.hide_download_controls * Improve treatment data api performance * Improve study view treatment api performance * Update download control options (#10264) * Add more tests and comments * fix 10221 - 403 issue fix 10221 - 403 issue; swagger annotations cause issue in authentication object. If user authorization is enabled, authentication object is obtained from SecurityContextHolder * Update Pyyaml package See yaml/pyyaml#724 for details of this update * Frontend v5.3.14 * Changes related to download group * Allow ProfiledCasesCounter to add counts to empty alteration count list (#10255) * Update about us page * Frontend v5.3.15 * Cache treatment endpoints (#10282) * update one-sided fisher test to two-sided * Allow redis service unavailable when Redis is enabled * Frontend v5.3.16 * Update two-sided fisher tests news (#10312) * Add two-sided fisher tests news --------- Co-authored-by: Ino de Bruijn <[email protected]> * Genomic data counts study-view endpoint (#10300) * implement getting CNA types for a gene specific * add tests for genomic-data-counts endpoint * change CopyNumberDataCounterFilter to StudyViewFilter and GenomicDataCountFilter * change to molecularDataService to fetch data * add filter logic for DISCRETE molecular profiles * Refactor * count NA and clean up codes * Updates * Update StudyViewServiceImplTest.java --------- Co-authored-by: Qi-Xuan Lu <[email protected]> Co-authored-by: Karthik <[email protected]> * Frontend v5.3.17 * Add defaults for genomic evolution tab in patient view (#10309) * Add defaults for mutation heatmap and line chart checkboxes * Update text --------- Co-authored-by: Gaofei Zhao <[email protected]> * Add data access token user role filter feature (#10315) * Add data access token user role filter feature * Update and more tests * Update failing test --------- Co-authored-by: Jeremy R. Easton-Marks <[email protected]> * Update About-Us.md (#10196) Update About-Us.md * Add label check test for pull request * Frontend v5.3.18 * add info about adding labels * add property show_web_tours (#10333) * (GSoC) Generic Assay Categorical/Binary data implementation Backend (#10303) * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update imports * Update GenericAssayEnrichment.java --------- Co-authored-by: Prasanna Kumar Jagannathan <[email protected]> Co-authored-by: sbabyanusha <[email protected]> Co-authored-by: matthijspon <[email protected]> Co-authored-by: Gaofei <[email protected]> Co-authored-by: haynescd <[email protected]> Co-authored-by: Charles Haynes <[email protected]> Co-authored-by: Pim van Nierop <[email protected]> Co-authored-by: Bas Leenknegt <[email protected]> Co-authored-by: Ino de Bruijn <[email protected]> Co-authored-by: sbabyanusha <[email protected]> Co-authored-by: John Konecny <[email protected]> Co-authored-by: alisman <[email protected]> Co-authored-by: ritikakundra <[email protected]> Co-authored-by: Tali Mazor <[email protected]> Co-authored-by: Justin Jao <[email protected]> Co-authored-by: JJ Gao <[email protected]> Co-authored-by: Matthijs Pon <[email protected]> Co-authored-by: karissawhiting <[email protected]> Co-authored-by: oplantalech <[email protected]> Co-authored-by: Onur Sumer <[email protected]> Co-authored-by: Qi-Xuan Lu <[email protected]> Co-authored-by: Karthik <[email protected]> Co-authored-by: Bryan Lai <[email protected]> Co-authored-by: qi-xuan.lu <[email protected]> Co-authored-by: Beking0912 <[email protected]> Co-authored-by: Jiahang Li <[email protected]>

…BioPortal#10303) * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update imports * Update GenericAssayEnrichment.java

dippindots requested review from dippindots and fuzhaoyuan July 28, 2023 18:09

dippindots assigned Djokovic0311 Jul 28, 2023

dippindots reviewed Aug 7, 2023

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inodb requested a review from JREastonMarks August 8, 2023 16:11

inodb added api gsoc labels Aug 8, 2023

Djokovic0311 changed the title ~~Generic Assay Categorical/Binary data implementation~~ (GSoC) Generic Assay Categorical/Binary data implementation Aug 8, 2023

JREastonMarks reviewed Aug 9, 2023

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Djokovic0311 force-pushed the GenericAssay-Jiahang branch from 55b258c to 38911ab Compare August 13, 2023 20:53

Djokovic0311 changed the title ~~(GSoC) Generic Assay Categorical/Binary data implementation~~ (GSoC) Generic Assay Categorical/Binary data implementation Backend Aug 15, 2023

Djokovic0311 added 17 commits August 15, 2023 14:55

update backend

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modify controller file structure

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modify import

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update backend

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finish tests

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modify controller file structure

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refactor some variables

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modify enrichment compare and validate issue

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refactor the controllers and services

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refactor test

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Update GenericAssayEnrichmentServiceImpl.java

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fixed simplification issues

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add inline comments

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modify import

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solve core test issue

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test check

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Djokovic0311 added 18 commits August 16, 2023 13:40

finish tests

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modify controller file structure

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modify import

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finish tests

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modify controller file structure

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refactor some variables

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modify enrichment compare and validate issue

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refactor the controllers and services

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refactor test

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Update GenericAssayEnrichmentServiceImpl.java

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fixed simplification issues

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modify import

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solve core test issue

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test check

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modify expressionenrichment

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modify imports

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Djokovic0311 force-pushed the GenericAssay-Jiahang branch from 732f24e to 13ea407 Compare August 16, 2023 17:40

JREastonMarks suggested changes Aug 16, 2023

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Djokovic0311 added 3 commits August 16, 2023 18:26

Merge branch 'GenericAssay-Jiahang' of https://github.com/Djokovic031…

7bf56d2

…1/cbioportal into GenericAssay-Jiahang

update imports

24158cd

Update GenericAssayEnrichment.java

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dippindots merged commit 901406f into cBioPortal:master Aug 18, 2023

Djokovic0311 mentioned this pull request Aug 22, 2023

Generic assay binary types #10335

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Djokovic0311 mentioned this pull request Aug 25, 2023

(GSoC) Generic Assay Categorical/Binary data implementation Frontend cBioPortal/cbioportal-frontend#4686

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(GSoC) Generic Assay Categorical/Binary data implementation Backend #10303

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		@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
		@RequestMapping(value = "/generic-assay-enrichments/binary/fetch",

		public static final String GENERIC_ASSAY_CATEGORICAL_ENRICHMENT_FETCH_PATH = "/generic-assay-enrichments/categorical/fetch";
		public static final String GENERIC_ASSAY_BINARY_ENRICHMENT_FETCH_PATH = "/generic-assay-enrichments/binary/fetch";

	BigDecimal[] pValues = genericAssayBinaryEnrichments.stream().map(a -> a.getpValue()).toArray(BigDecimal[]::new);
	BigDecimal[] pValues = genericAssayBinaryEnrichments.stream().map(GenericAssayBinaryEnrichment ::getpValue).toArray(BigDecimal[]::new);

		@@ -0,0 +1,261 @@
		package org.cbioportal.service.impl;

		import org.cbioportal.model.*;

(GSoC) Generic Assay Categorical/Binary data implementation Backend #10303

(GSoC) Generic Assay Categorical/Binary data implementation Backend #10303

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Djokovic0311 commented Jul 28, 2023

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