PR8/15: import six services verbatim (subtree, full history)#267

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Gcolon021 wants to merge 1764 commits into

psar/07-remove-legacyfrom

psar/08-service-imports

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Commits on Oct 10, 2024

Commits on Oct 11, 2024

[CHORE] GH actions fix

Luke Sikina
authored and
Luke-Sikina
committed
Add Javadoc comments to model classes (#223)
Gcolon021
authored

Commits on Oct 16, 2024

[CHORE] This is not an error

Luke Sikina
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Luke-Sikina
committed

Commits on Oct 21, 2024

[ALS-7575] Add cache inspection and eviction services (#222)
Gcolon021
authored

Commits on Oct 22, 2024

Fix bucket index loading for non-variant explorer environments (#123)
ramari16
authored

Commits on Oct 23, 2024

Commits on Oct 24, 2024

ALS-7635: Upgrade avro version (#124)
ramari16
authored

Commits on Oct 25, 2024

Remove superflous file load attempt (#125)
ramari16
authored

Commits on Oct 30, 2024

[ALS-7687] Create PSAMA cache unit test (#232)
Gcolon021
authored

Commits on Nov 15, 2024

Commits on Nov 20, 2024

ALS-7810: Add data dictionary table to PFB output (#127)
ramari16
authored

Commits on Dec 6, 2024

Commits on Dec 9, 2024

ALS-7882: Add locale for checkmarx
ramari16
committed

Commits on Dec 13, 2024

Update dependencies in pom.xml to latest versions (#233)
Gcolon021
authored

Commits on Dec 18, 2024

[ALS-5053] pen test medium stacktrace error (#85)

Gcolon021
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ramari16
committed

Commits on Dec 19, 2024

[ALS-5050] Ignore invalid concept paths in anyRecordOf queries (#87)
ramari16
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Add deps to label checker + release config update

Luke Sikina
authored and
ramari16
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- Create endpoint for writing data to file

Luke Sikina
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ramari16
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[ALS-5656] Make TimeSeriesProcessor handle missing concept paths

Luke Sikina
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ramari16
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[ALS-0000] Quick fix to time series. Use different batch size

Luke Sikina
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ramari16
committed

Commits on Dec 20, 2024

Fix path traversal issue

Luke Sikina
authored and
ramari16
committed
Fix export headers

Gcolon021
authored and
ramari16
committed
[ALS-5755] Switch time series processor to ISO timestamps

Luke Sikina
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ramari16
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[ALS-6344] - Make new query that retuns patient count and concept count

Luke Sikina
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ramari16
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[ALS-6265] Add any record of multi support to time series processor

Luke Sikina
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ramari16
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[ALS-6467] Configurable VCF excerpt info column ordering

Luke Sikina
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ramari16
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[CHORE] NPEs for timestamps

Luke Sikina
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ramari16
committed
[ALS-7539] Test file creation for uploader

Luke Sikina
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ramari16
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[ALS-7199] Files mved from tomcat's tmp dir to a mounted fs failed to delete

Luke Sikina
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ramari16
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Fix merge issue
ramari16
committed

Commits on Jan 6, 2025

[ALS-6818] Data Dictionary Loader Job from HPDS (#130)
Gcolon021
authored

Commits on Jan 8, 2025

ALS-4380: Add code formatting commit hook
ramari16
committed

Commits on Jan 9, 2025

Update branch references from 'master' to 'main'
Gcolon021
committed

Commits on Jan 10, 2025

[ALS-8098] Produce a list of all patients involved in query

Luke Sikina
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Luke-Sikina
committed

Commits on Jan 13, 2025

Dockerize maven install (#133)
Gcolon021
authored

Commits on Jan 23, 2025

Release (#238)
Gcolon021
authored

Commits on Jan 29, 2025

Merge pull request #134 from hms-dbmi/genomic-v2
ramari16
authored

Commits on Feb 5, 2025

[ALS-7437] Switch study to dataset for concept node detail
Luke Sikina
committed
Lint things
Luke Sikina
committed
[ALS-7751] Java Opts can now be passed to docker container (#52)

Gcolon021
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Luke Sikina
committed
[CHORE] Simple caching
Luke Sikina
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[ALS-7760] Replicate Old Search in new Data-Dictionary (#53)

Gcolon021
and
Luke Sikina
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Refactor legacy search query processing (#57)

Gcolon021
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Luke Sikina
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[ALS-7809] DRS URI: Data Dictionary API (#56)

Gcolon021
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Luke Sikina
committed
[CHORE] Fix duplicate type fields (no one told me)
Luke Sikina
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Revert "[CHORE] Fix duplicate type fields (no one told me)"
Luke Sikina
committed
[ALS-7694] Add DashboardDrawer feature with controller, service, and repository (#55)

TDeSain
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Luke Sikina
committed
Fix conditional logic for string length checks (#59)

Gcolon021
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Luke Sikina
committed
Return empty string for NULL dataset full name (#60)

Gcolon021
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Luke Sikina
committed
[ALS-5375] Configurable All-in-one to select public datasets of interest (#61)

Gcolon021
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Luke Sikina
committed
ALS-7867 (#62)

TDeSain
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Luke Sikina
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Update Postgres Volume Mounts for All-In-One (#63)

Gcolon021
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Luke Sikina
committed
[ALS-7415] - Force value matches to top of search results
Luke Sikina
committed
[ALS-8191] Switch from study to dataset for weights job
Luke Sikina
committed
[ALS-8191] Link facet and concept filtering a bit better
Luke Sikina
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Update schema.sql

sharra44
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Luke-Sikina
committed

Commits on Feb 18, 2025

[ALS-7113] Enhance sequential loader

Luke Sikina
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Luke-Sikina
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[CHORE] Add spotless to pom

Luke Sikina
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Luke-Sikina
committed

Commits on Mar 11, 2025

[CUMULUS] Update write endpoint to support PATIENT result type

Luke Sikina
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Luke-Sikina
committed

Commits on Mar 14, 2025

[ALS-8396] When no meta exists, dont filter out var

Luke Sikina
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Luke-Sikina
committed

Commits on Mar 21, 2025

Commits on Mar 26, 2025

Add logging file output configuration to application.properties (#244)
Gcolon021
authored

Commits on Mar 28, 2025

[ALS-6074] Fix uploader auth timeouts for instance profile

Luke Sikina
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Luke-Sikina
committed
[ALS-7538] Make docker-compose standalone for uploader

Luke Sikina
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Luke-Sikina
committed
[ALS-7539] - Get rid of super complex self refreshing client

Luke Sikina
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Luke-Sikina
committed
[ALS-7539] Test HPDS connection

Luke Sikina
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Luke-Sikina
committed
[ALS-7200] Upload large files via multipart

Luke Sikina
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Luke-Sikina
committed
[CHIP-1] Add query.json and patients.txt

Luke Sikina
authored and
Luke-Sikina
committed
[ALS-8610] Add cumulus upload logic

Luke Sikina
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Luke-Sikina
committed
[ALS-7716] - Use AVL role

Luke Sikina
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Luke-Sikina
committed
Add logging configuration to application properties files (#139)
Gcolon021
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ALS-8474 (#69)
Gcolon021
authored

Commits on Mar 31, 2025

ALS-8728: Various bug fixes and performance enhancements for variant explorer (#144)
ramari16
authored

Commits on Apr 9, 2025

ALS-8667: Fix issues with metadata in PFB (#145)
ramari16
authored

Commits on Apr 18, 2025

[ALS-8712][ALS-8727] (#146)
Gcolon021
authored

Commits on Apr 22, 2025

[ALS-8535] Set up migrations for dictionary

Luke Sikina
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Luke-Sikina
committed

Commits on Apr 25, 2025

ALS-8899: Update Job to build bucket index files, etc (#147)
ramari16
authored

Commits on Apr 28, 2025

[ALS-8534] Dump endpoint

Luke Sikina
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Luke-Sikina
committed

Commits on Apr 29, 2025

ALS-8837: Cleanup noisy logs (#148)
ramari16
authored

Commits on May 7, 2025

Commits on May 13, 2025

[ALS-8535] Local dump service

Luke Sikina
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Luke-Sikina
committed
[ALS-8538] Devops for agg dict

Luke Sikina
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Luke-Sikina
committed

Commits on May 14, 2025

[ALS-8952] [ALS-8085] Reconsile docker networks + allow reupload when stuck

Luke Sikina
authored and
Luke-Sikina
committed
Refactor to replace Float with Double for ContinuousConcept (#75)
Gcolon021
authored

Commits on May 15, 2025

[ALS-8583] Fix for networks, migrations

Luke Sikina
authored and
Luke-Sikina
committed
[ALS-8756] Support table / study logic for longer concepts

Luke Sikina
authored and
Luke-Sikina
committed

Commits on May 16, 2025

[ALS-9020] Check db version before updating

Luke Sikina
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Luke-Sikina
committed

Commits on May 20, 2025

[ALS-9113] Tree for concepts didnt work b/c sort was wrong

Luke Sikina
authored and
Luke-Sikina
committed

Commits on May 21, 2025

[ALS-8608] Missed break statement
Luke-Sikina
committed

Commits on May 27, 2025

[ALS-9114] getValuesForKeys did not work with unsorted sets
Luke Sikina
committed
Revert "[ALS-9114] getValuesForKeys did not work with unsorted sets"
Luke Sikina
committed
[ALS-9114] getValuesForKeys did not work with unsorted sets

Luke Sikina
authored and
Luke-Sikina
committed

Commits on Jun 3, 2025

Update docker-compose.yml
Luke-Sikina
committed

Commits on Jun 11, 2025

ALS-9245: Fix exception being thrown getting cross counts with SNP filter (#155)
ramari16
authored

Commits on Jun 23, 2025

"~/code/bch/picsure-dictionary/.git/COMMIT_EDITMSG" 33L, 1299B …

Luke Sikina
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Luke-Sikina
committed

Commits on Jun 27, 2025

ALS-9092: Upgrade to Java 24 (#159)
ramari16
authored

Commits on Jul 8, 2025

ALS-9386: Upgrade hpds-etl to java 24 (#161)
ramari16
authored

Commits on Jul 25, 2025

[CHORE] Make tree endpoint for all datasets

Luke Sikina
authored and
Luke-Sikina
committed
Update src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptController.java
Luke-Sikina
committed

Commits on Jul 28, 2025

[ALS-9500] Facet endpoint performance fix

Luke Sikina
authored and
Luke-Sikina
committed

Commits on Jul 31, 2025

ALS-9303: Implement rest controller for new Query entity (#164)
ramari16
authored

Commits on Aug 4, 2025

ALS-9576: Fix maven tests by upgrading plugin versions, update a bunch of other versions (#165)
ramari16
authored

Commits on Aug 6, 2025

ALS-9303: Refactoring and cleanup from previous PR (#166)
ramari16
authored

Commits on Aug 13, 2025

ALS-9639: Revert CSV library upgrade (#167)
ramari16
authored

Commits on Sep 3, 2025

Make picsureId a UUID in new Query (#168)
ramari16
authored

Commits on Sep 15, 2025

Commits on Sep 16, 2025

[ALS-9230] Findings from UTHSC prod: schema was altered

Luke Sikina
authored and
Luke-Sikina
committed

Commits on Sep 17, 2025

ALS-9852: Add better error messaging for VcfIndex parsing (#169)
ramari16
authored

Commits on Sep 30, 2025

Commits on Oct 23, 2025

ALS-9868: Add test for cross counts (#171)
ramari16
authored

Commits on Oct 29, 2025

ALS-10129: Create endpoint to get concept hierarchy for a concept (#86)
ramari16
authored

Commits on Nov 3, 2025

Release (#265)

authored

Commits on Nov 24, 2025

Improve error handling and logging in FENCEAuthenticationService (#266)
Gcolon021
authored

Commits on Dec 2, 2025

ALS-10388: Move cache configuration to properties files (#89)
ramari16
authored

Commits on Dec 3, 2025

Commits on Dec 16, 2025

ALS-9955: Add tests to confirm handling of nulls in timestamp values (#173)
ramari16
authored

Commits on Dec 17, 2025

ALS-10113: Add swagger documentation for new query (#174)
ramari16
authored

Commits on Jan 8, 2026

Commits on Jan 13, 2026

ALS-8744: Upgrade to java 24 (#267)
ramari16
authored

Commits on Jan 16, 2026

Add httpcore5 dependency to pic-sure-auth-services pom file (#268)
Gcolon021
authored

Commits on Feb 3, 2026

Commits on Feb 13, 2026

Commits on Feb 19, 2026

Commits on Feb 21, 2026

Commits on Feb 23, 2026

Commits on Feb 25, 2026

Remove session_id and logged_in from AppConfig
JamesPeck
authored

Commits on Mar 10, 2026

Commits on Mar 20, 2026

Commits on Mar 24, 2026

Merge pull request #184 from hms-dbmi/ALS-10763
TDeSain
authored

Commits on Mar 25, 2026

Commits on Mar 28, 2026

Handle Session ids as first class
JamesPeck
committed

Commits on Mar 30, 2026

Fix id batch size parameter (#188)
ramari16
authored

Commits on Mar 31, 2026

Commits on Apr 1, 2026

[bug] Add info endpoint (#5)
JamesPeck
authored

Commits on Apr 2, 2026

Commits on Apr 8, 2026

ALS-11368: Add configuration to require authorization filters for all queries (#190)
ramari16
authored

Commits on Apr 9, 2026

ALS-11390: Allow topmed and parent concepts to be used by everyone (#279)
ramari16
authored

Commits on Apr 10, 2026

[CHORE] Refactor key (#6)
JamesPeck
authored

Commits on Apr 13, 2026

[ALS-10712] Dockerize Build (#96)
JamesPeck
authored

Commits on Apr 19, 2026

ALS-11520: Fix bug where user consents were not getting updated (#281)
ramari16
authored

Commits on Apr 20, 2026

Update searchable fields and language configuration in TSVector
TDeSain
committed

Commits on Apr 27, 2026

Require authorization filter by default (#193)
ramari16
authored

Commits on Apr 28, 2026

Commits on May 4, 2026

[ALS-11555] Log helpful things with inspect (#283)
JamesPeck
authored

Commits on May 7, 2026

ALS-11662: Add logging when query invalid for missing auth filter (#196)
ramari16
authored

Commits on May 27, 2026

Commits on May 28, 2026

Commits on Jun 2, 2026

Bump org.apache.avro:avro from 1.12.0 to 1.12.1 (#181)
dependabot[bot]
authored

Commits on Jun 3, 2026

Commits on Jun 5, 2026

Als 10196 fix roles (#286)
Gcolon021
authored

Commits on Jun 9, 2026

ALS-11710: Enable v3 queries in aim-ahead (#288)
ramari16
authored

Commits on Jun 16, 2026

[ALS-10714] Pass thru the obfuscation #10
JamesPeck
committed

Commits on Jun 22, 2026

added documentation for the application properties file for dictionary to describe difference between unfilterable concept list and no show list (#105)
sharra44
authored

Commits on Jun 23, 2026

[ALS-11493] Optimize query performance with parallel execution and indexing (#103)
TDeSain
authored

Commits on Jun 30, 2026

ALS-12219: Schema-qualify dict tables in flyway migrations V7 and V10 (#109)
Gcolon021
authored

Commits on Jul 1, 2026

Emit caller as a top-level audit field (#9)
Gcolon021
authored

Commits on Jul 7, 2026