Code

Clickhouse mode of study view#11224

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alisman merged 150 commits intomastercBioPortal/cbioportal:masterfrom demo-rfc80-poccBioPortal/cbioportal:demo-rfc80-pocCopy head branch name to clipboardDec 19, 2024

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Commits on Nov 24, 2024

• ➕ Add infra to support multi db and Columnar DataSource Properties

  

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• Add Columnar support for Mybatis

  

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• Add Columnar Study View Controller /api/column-store

  

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• Feature/ch/update poc base branch (#10776)

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• ✅ Add Unit test for StudyViewMapper Clickhouse

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• use regular views instead of materialized views (#10793)

  

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• Feature/mutated genes AlterationFilter and Fix unit test (#10803)

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• Add missing POC clinical data binning function (#10778)

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• Create sample materialized view and use it (#10822)

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• Feature/mutated genes total profiled counts and gene panels (#10824)

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• RFC80:density plot endpoint(#10837)

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• Fix clinical data counts query/filter using new derived table (#10833)

  

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• Molecular-profile-counts service implementation (#10840)

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• Fix clinical data scatterplot (point at new derived cd table) (#10846)

  

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• Rfc80/add cna genes endpoint (#10845)

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• ✨ Add StructuralVariant-genes endpoint (#10854)

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• Implement study view sample-lists-counts endpoint in Clickhouse (#10849)

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• Fix class import (#10856)

  

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• Move ClinicalCategoricalFilter to repository (#10847)

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• Rfc80/fix patient level filtering for alteration counts endpoints (#10857)

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• 🐛 Fix totalCount calculation when WES not available (#10858)

  

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• Consolidate SQL files used to create CH Tables (#10867)

  

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• Demo rfc80 poc violin plot (#10863)

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• replace sample_mv references with sample_derived (#10880)

  

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• 🔧 Update Sonar Cloud Token (#10888)

  

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• Simplify clinical data binning related SQL (#10823)

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• Fix patient_derived table population (patient stable id was getting base64) (#10898)

  

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• Always load frontend over https (localdev mode) (#10901)

  

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• Rfc80/clinical event timeline endpoint (#10899)

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• Fix alteration count services (#10911)

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• Rfc80/treatments patients endpoint (#10903)

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• Hide replacement clickhouse endpoints from swagger (except new treatment) (#10919)

  

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• Rfc80/sample treatment endpoint (#10927)

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• Rfc80/update open api annotation for sampleTreatment Endpoint (#10929)

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• Molecular-profile-counts-service (#10934)

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• Add entrez_id to alteration Count endpoints (#10936)

  

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• Demo rfc80 poc mutation data counts & genomic data counts (#10807)

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• Add tests for case list sample counts endpoint (#10935)

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• add unit tests for clinical data counts sql (#10933)

  

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• Implement custom-data-bin-counts endpoint (#10827)

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• normalize clinical data (#10943)

  

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• improve numerical clinical data filter (#10951)

  

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• Update Treatment Endpoint to handle event_type TREATMENT, previously … (#10959)

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• Remove need to filter via Patient-IDs, All filters utilize sample-ids (#10974)

  

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• add api test specs to backend (#10979)

  

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• fix api test merge writer (#10980)

  

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• Genomic and Generic Assay bin counts endpoints (#10964)

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• Fix clinical data NA counts for multiple studies (#10978)

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• Demo rfc80 poc mutation data count unit tests (#10981)

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• Delete custom specs (#10987)

  

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• Fix GenomicDataFilterTest

  

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• Rfc80/add tests mutated-genes,cna-genes,structural-variants filters (#10986)

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• Set custom http header with elapsed time on all api endpoints (#10994)

  

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• fix clinical data NA count logic (#10991)

  

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• Remove Sample Treatments with no counts (#10995)

  

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• All custom header elapsed-time on CORS headers (#10999)

  

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• Remove caching from cd-bin-counts (#11001)

  

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• We have to cast all numbers to floats in Clickhouse SQL in order to compare them properly (#11021)

  

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• Merge Alteration Counts that have conflicting HugoSymbols for Study V… (#11026)

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• Add clickhouse custom data endpoints (#10963)

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• Add samples field to custom filters to allow fetching samples without session (#10998)

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• Add support for NA in genomic-data-bin-counts (#11006)

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• Update to add QValue for Alteration Count Services (#11034)

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• Demo rfc80 poc na count for generic assay (#11039)

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• Normalize data counts in a generic case-insensitive way (#11037)

  

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• filter out null labels when counting sample lists (#11045)

  

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• Rfc80/add na clinical data filtering (#11050)

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• Add generic-assay-data-counts endpoint (#11059)

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• Update SQL to remove duplicate Reference Genome entry (#11060)

  

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• Add checks to prevent null pointer on alterations in geneFilterQuery (#11071)

  

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• remove duplicate attributes when calculating missing NA (#11076)

  

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• Re-apply caching to all study view service methods (#11091)

  

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• fetch missing patient clinical data for violin plot (#11092)

  

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• Update to allow Qvalue when filtered cohort returns samples from a single study (#11093)

  

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• Add new property for clickhouse cache enabling (#11109)

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• Fix trim trailing error (#11085)

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• SQL variable format clean up (#11110)

  

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• ClinicalViolinPlot Serializable (#11124)

  

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• Add isUnfiltered condition to cacheable clickhouse methods (#11120)

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• Fix violin plot sample filtering and counting issues (#11122)

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• fetch missing patient clinical data for the density plot (#11132)

  

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• Fix profiling count issues in legacy (#11105)

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• add internal id to sample and clinical data SQL queries (#11139)

  

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• use case-insensitive ILIKE instead of case-sensitive LIKE when looking for sample acquisition and specimen (#11143)

  

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• ignore non-numeric values for violin plot to prevent number format exceptions (#11135)

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• Rfc80/clinical data counts refactor (#11084)

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• Filter out Mutations with Status UnCalled for Counts (#11166)

  

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  eff0c23

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• Update Profiled counts to use WES count when gene panel is not available

  

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• Update to handle use case when sampleProfileWithoutGenePanel is 0 then assume total Profile Count

  

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• add custom driver filtering unit tests

  

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• add missing study filter param to clickhouse method for caching condition

  

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• CNA profile counts should only count samples once

  

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• Add back NA counts when corresponding samples are filtered out of study view (#11185)

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• Update generic assay table schema (#11189)

  

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• Do not used prepared statements for the studyid lists (#11191)

  

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• Api Tests Config for CircleCI (#11188)

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• Revert "add custom driver filtering unit tests" (#11203)

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• Update Total profile Count to filter on genetic profile (#11198)

  

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• Add tests for profiled counts (#11190)

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• Remove test failing due to legacy miscount (#11205)

  

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• cast all data filter start and end values to float (#11207)

  

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• Split clickhouse integration tests into separate files for each method (#11209)

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• Adding option for extracting study ids from sample identifiers for clinical data counts endpoint (#11192)

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• Add missing DROP TABLE statements (#11211)

  

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• Use PR-specific image for circleci api tests (#11217)

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• Pretty print portal info in api-test logs

  

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• Add a frontend prop for clickhouse mode (#11219)

  

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• require approval for restricted tests

  

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• rename approval job for circleci tests

  

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• add integration tests for cna-genes and sv-genes (#11221)

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Commits on Nov 25, 2024

• Fix Rebase issues with master

  

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• Merge branch 'master' into demo-rfc80-poc

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• Use upstream repo for api-tests

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• Fix swagger decorators for rfc80 clickhouse controller (#11230)

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• check for non-numerical values in numerical clinical data count filter

  

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• unify numerical data filters in one sql

  

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• do not normalize attribute value if not NA

  

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• add unit tests

  

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Commits on Dec 2, 2024

• Add TransactionManager to handle lazy loading of data from db (cursor obj)

  

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Commits on Dec 3, 2024

• add unit tests for logic in service and repository methods

  

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• fix error with case list counts method

  

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• Add categorical patient level filtering for generic-assay-data-counts (#11155)

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• Fix unfiltered method call in cacheable condition (#11250)

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Commits on Dec 4, 2024

• skip web-and-data image build for api tests (#11255)

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Commits on Dec 5, 2024

• run cbioportal instance in clickhouse mode for apitests

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• pass env var to circleci environment

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Commits on Dec 6, 2024

• Merge pull request #11257 from cBioPortal/fix/circleci-clickhouse

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• Update cBioPortal to dynamically load ch Components only when property clickhouse_enabled is set (#11256)

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Commits on Dec 7, 2024

• Optimize bins filtering by merging bins (#11248)

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  fuzhaoyuan

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  alisman

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  b31fe9e

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Commits on Dec 10, 2024

• Fix CNA query (#11265)

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  onursumer

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Commits on Dec 11, 2024

• make CaseListDataCount serializable (#11267)

  onursumer

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• Fix CH primary keying of genetic-alteration-derived (#11268)

  alisman

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• Make sure study ids exist before using them in filter SQL (#11272)

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  onursumer

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Commits on Dec 12, 2024

• automate connection checks

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• Merge pull request #11276 from cBioPortal/fix/circleci-test-script

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  fa1e4f3

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• skip build step if image exists

  zainasir

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• streamline shell checks

  zainasir

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• fix docker tags

  zainasir

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  1bcd1c9

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• use double quotes

  zainasir

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• Merge pull request #11277 from cBioPortal/fix/apitest-docker-build

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Commits on Dec 13, 2024

• Add more unit tests for clickhouse service related methods (#11262)

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  gblaih

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  Bryan Lai

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Commits on Dec 16, 2024

• rollback gene panel mapper changes from profiling counts fix (#11292)

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  gblaih

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  Bryan Lai

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Commits on Dec 18, 2024

• Custom sample filtering performance and security improvement (#11274)

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  dippindots

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• Revert "Custom sample filtering performance and security improvement (#11274)"

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  alisman

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• Merge branch 'master' into demo-rfc80-poc

  alisman

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• add a comment for elapsed-time header intercept (#11297)

  alisman

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Commits on Dec 19, 2024

• Update api-tests to use master branch of cbioportal-frontend

  zainasir

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  b8090ea

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• simplify circleci apitests dependencies

  zainasir

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• Custom sample filtering performance and security improvement (#11296)

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  dippindots

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• Update rfc80 poc (#11298)

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  haynescd

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  haynescd

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  8703b87

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