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0d5271d
Create maven.yml
Luke-Sikina Oct 10, 2024
5086b49
ALS-6330: Fix variant explorer functionality (#115)
ramari16 Oct 10, 2024
047f9bf
[CHORE] GH actions fix
Oct 10, 2024
84b3dc8
Add Javadoc comments to model classes (#223)
Gcolon021 Oct 11, 2024
63e4cd9
[CHORE] This is not an error
Oct 14, 2024
f6cf294
[ALS-7575] Add cache inspection and eviction services (#222)
Gcolon021 Oct 21, 2024
86f8197
Fix bucket index loading for non-variant explorer environments (#123)
ramari16 Oct 22, 2024
7c1ab7d
[ALS-7554] User should not be able to search without a valid token (#…
Gcolon021 Oct 23, 2024
84ec20e
Test github actions (#228)
Gcolon021 Oct 23, 2024
1924562
ALS-7635: Upgrade avro version (#124)
ramari16 Oct 24, 2024
52ded18
Remove superflous file load attempt (#125)
ramari16 Oct 25, 2024
d8a368c
[ALS-7687] Create PSAMA cache unit test (#232)
Gcolon021 Oct 30, 2024
94cbe4b
ALS-7581: Implement multiple values per patient in CSV output (#122)
ramari16 Nov 15, 2024
1183064
ALS-7242: Spring profile per bdc environment (#126)
ramari16 Nov 15, 2024
5ba5522
ALS-7810: Add data dictionary table to PFB output (#127)
ramari16 Nov 20, 2024
09057b6
ALS-7882: Checkmarx related cleanup
ramari16 Dec 6, 2024
c5433e4
Fix last commit
ramari16 Dec 6, 2024
78b2dca
ALS-7882: Add locale for checkmarx
ramari16 Dec 9, 2024
108b5ba
Update dependencies in pom.xml to latest versions (#233)
Gcolon021 Dec 13, 2024
85d873d
[ALS-5053] pen test medium stacktrace error (#85)
Gcolon021 Oct 13, 2023
184b676
[ALS-5050] Ignore invalid concept paths in anyRecordOf queries (#87)
ramari16 Oct 23, 2023
dc562bd
Add deps to label checker + release config update
Dec 19, 2023
0b7e258
- Create endpoint for writing data to file
Nov 16, 2023
24a97d0
[ALS-5656] Make TimeSeriesProcessor handle missing concept paths
Jan 10, 2024
57ac3cc
[ALS-0000] Quick fix to time series. Use different batch size
Jan 14, 2024
e7e7682
Fix path traversal issue
Jan 16, 2024
6ce5e1b
Fix export headers
Gcolon021 Apr 11, 2024
2611e06
[ALS-5755] Switch time series processor to ISO timestamps
Jan 23, 2024
f4310fa
[ALS-6344] - Make new query that retuns patient count and concept count
Apr 25, 2024
ee18a05
[ALS-6265] Add any record of multi support to time series processor
Jun 14, 2024
f65411f
[ALS-6467] Configurable VCF excerpt info column ordering
Jun 14, 2024
c1af53a
[CHORE] NPEs for timestamps
Aug 29, 2024
6f9066e
[ALS-7539] Test file creation for uploader
Nov 27, 2024
eadb0bf
[ALS-7199] Files mved from tomcat's tmp dir to a mounted fs failed to…
Nov 28, 2024
6b8288f
Fix merge issue
ramari16 Dec 20, 2024
44b039d
[ALS-6818] Data Dictionary Loader Job from HPDS (#130)
Gcolon021 Jan 6, 2025
4af4af4
ALS-4380: Add code formatting commit hook
ramari16 Jan 8, 2025
a831c5e
Update branch references from 'master' to 'main'
Gcolon021 Jan 9, 2025
e62d942
[ALS-8098] Produce a list of all patients involved in query
Dec 23, 2024
fadbac8
Dockerize maven install (#133)
Gcolon021 Jan 13, 2025
29f93be
Release (#238)
Gcolon021 Jan 23, 2025
932b9a5
Merge pull request #134 from hms-dbmi/genomic-v2
ramari16 Jan 29, 2025
68fd8b3
[ALS-7437] Switch study to dataset for concept node detail
Oct 10, 2024
a5bbb7e
Lint things
Oct 11, 2024
88f95ff
[ALS-7751] Java Opts can now be passed to docker container (#52)
Gcolon021 Nov 4, 2024
9da1060
[CHORE] Simple caching
Oct 31, 2024
a82d8ce
[ALS-7760] Replicate Old Search in new Data-Dictionary (#53)
Gcolon021 Nov 18, 2024
eb2f50f
Refactor legacy search query processing (#57)
Gcolon021 Nov 19, 2024
8b346a3
[ALS-7809] DRS URI: Data Dictionary API (#56)
Gcolon021 Nov 20, 2024
0f496ea
[CHORE] Fix duplicate type fields (no one told me)
Nov 20, 2024
48ca5fd
Revert "[CHORE] Fix duplicate type fields (no one told me)"
Nov 20, 2024
40539de
[ALS-7694] Add DashboardDrawer feature with controller, service, and …
TDeSain Nov 20, 2024
1ce4b20
Fix conditional logic for string length checks (#59)
Gcolon021 Nov 21, 2024
4051242
Return empty string for NULL dataset full name (#60)
Gcolon021 Dec 3, 2024
54053eb
[ALS-5375] Configurable All-in-one to select public datasets of inter…
Gcolon021 Jan 6, 2025
f92c457
ALS-7867 (#62)
TDeSain Jan 8, 2025
2f2eaa8
Update Postgres Volume Mounts for All-In-One (#63)
Gcolon021 Jan 15, 2025
f3fe512
[ALS-7415] - Force value matches to top of search results
Jan 25, 2025
5cbc72e
[ALS-8191] Switch from study to dataset for weights job
Jan 29, 2025
684e645
[ALS-8191] Link facet and concept filtering a bit better
Jan 30, 2025
4651c69
Update schema.sql
sharra44 Feb 5, 2025
ddfedb6
[ALS-7113] Enhance sequential loader
Feb 4, 2025
5d78fe8
[CHORE] Add spotless to pom
Feb 14, 2025
3a80cab
[CUMULUS] Update write endpoint to support PATIENT result type
Feb 18, 2025
0890baa
[ALS-8396] When no meta exists, dont filter out var
Mar 13, 2025
e61f0bf
ALS-7737: Better support for splitting genomic data by chromosome (#137)
ramari16 Mar 21, 2025
fce785b
Bump postgresql from 42.2.12 to 42.4.1 in /etl (#46)
dependabot[bot] Mar 21, 2025
f6efc6e
Bump org.postgresql:postgresql from 42.4.1 to 42.4.4 in /etl (#140)
dependabot[bot] Mar 21, 2025
07cddcb
Bump htsjdk from 2.19.0 to 3.0.1 in /etl (#52)
dependabot[bot] Mar 21, 2025
3426290
Bump com.google.guava:guava from 30.0-jre to 32.0.0-jre (#141)
dependabot[bot] Mar 21, 2025
eb0f9b9
Bump org.apache.commons:commons-compress from 1.21 to 1.26.0 in /etl …
dependabot[bot] Mar 21, 2025
4e25809
Bump commons-io:commons-io from 2.7 to 2.14.0 (#142)
dependabot[bot] Mar 21, 2025
e378a31
Add logging file output configuration to application.properties (#244)
Gcolon021 Mar 26, 2025
a4faa40
[ALS-6074] Fix uploader auth timeouts for instance profile
Jul 10, 2024
364a7fc
[ALS-7538] Make docker-compose standalone for uploader
Nov 22, 2024
4fbcb63
[ALS-7539] - Get rid of super complex self refreshing client
Nov 26, 2024
af6545a
[ALS-7539] Test HPDS connection
Nov 28, 2024
483306d
[ALS-7200] Upload large files via multipart
Dec 30, 2024
60cf6cd
[CHIP-1] Add query.json and patients.txt
Dec 31, 2024
2bc4e6d
[ALS-8610] Add cumulus upload logic
Mar 4, 2025
3ed64b8
[ALS-7716] - Use AVL role
Mar 28, 2025
2ab2fed
Add logging configuration to application properties files (#139)
Gcolon021 Mar 28, 2025
1709a26
ALS-8474 (#69)
Gcolon021 Mar 28, 2025
49b6521
ALS-8728: Various bug fixes and performance enhancements for variant …
ramari16 Mar 31, 2025
1ad624a
ALS-8667: Fix issues with metadata in PFB (#145)
ramari16 Apr 9, 2025
5d373d6
[ALS-8712][ALS-8727] (#146)
Gcolon021 Apr 18, 2025
9335808
[ALS-8535] Set up migrations for dictionary
Apr 17, 2025
db273e0
ALS-8899: Update Job to build bucket index files, etc (#147)
ramari16 Apr 25, 2025
e3e5385
[ALS-8534] Dump endpoint
Apr 22, 2025
c58a947
ALS-8837: Cleanup noisy logs (#148)
ramari16 Apr 29, 2025
d237721
ALS-9008: Update storage directory for BucketIndexBySample when loadi…
ramari16 May 7, 2025
2e56452
ALS-9007: Fix handling of SNP as category filter (#150)
ramari16 May 7, 2025
6780ccb
[ALS-8535] Local dump service
May 6, 2025
f908249
[ALS-8538] Devops for agg dict
May 8, 2025
4151d14
[ALS-8952] [ALS-8085] Reconsile docker networks + allow reupload when…
May 14, 2025
93c7fe3
Refactor to replace Float with Double for ContinuousConcept (#75)
Gcolon021 May 14, 2025
869ce85
[ALS-8583] Fix for networks, migrations
May 15, 2025
981109f
[ALS-8756] Support table / study logic for longer concepts
May 15, 2025
1e32711
[ALS-9020] Check db version before updating
May 16, 2025
df8ea75
[ALS-9113] Tree for concepts didnt work b/c sort was wrong
May 19, 2025
16c7c74
[ALS-8608] Missed break statement
Luke-Sikina May 21, 2025
2b5c5bd
[ALS-9114] getValuesForKeys did not work with unsorted sets
May 27, 2025
3482c82
Revert "[ALS-9114] getValuesForKeys did not work with unsorted sets"
May 27, 2025
45e89d0
[ALS-9114] getValuesForKeys did not work with unsorted sets
May 27, 2025
276af38
Update docker-compose.yml
Luke-Sikina Jun 3, 2025
0285908
ALS-9245: Fix exception being thrown getting cross counts with SNP fi…
ramari16 Jun 11, 2025
621a06b
"~/code/bch/picsure-dictionary/.git/COMMIT_EDITMSG" 33L, 1299B …
Jun 23, 2025
c287656
ALS-9092: Upgrade to Java 24 (#159)
ramari16 Jun 27, 2025
d813ca8
ALS-9386: Upgrade hpds-etl to java 24 (#161)
ramari16 Jul 8, 2025
03e6007
ALS-9289: Document PFB code (#162)
ramari16 Jul 9, 2025
6ffe42f
ALS-9088: Create initial query object for boolean filtering
ramari16 Jun 4, 2025
27449b5
ALS-9089: Mirror existing integration tests, add new test coverage to…
ramari16 Jun 9, 2025
28a3e0c
ALS-9090: Add old and new integration test coverage, initial implemen…
ramari16 Jun 18, 2025
3c0b192
ALS-9290: Map new Query entity to current genomic filtering (#157)
ramari16 Jun 27, 2025
ccbb0f7
ALS-9291: Re-implement all HpdsProcessors with new Query entity (#160)
ramari16 Jul 9, 2025
0d1bca2
[CHORE] Make tree endpoint for all datasets
Jul 7, 2025
bf23c2c
Update src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/Con…
Luke-Sikina Jul 8, 2025
4ad65e0
[ALS-9500] Facet endpoint performance fix
Jul 25, 2025
d398cb0
ALS-9303: Implement rest controller for new Query entity (#164)
ramari16 Jul 31, 2025
175bd38
ALS-9576: Fix maven tests by upgrading plugin versions, update a bunc…
ramari16 Aug 4, 2025
267fef4
ALS-9303: Refactoring and cleanup from previous PR (#166)
ramari16 Aug 6, 2025
1885809
ALS-9639: Revert CSV library upgrade (#167)
ramari16 Aug 13, 2025
4b54fbe
Make picsureId a UUID in new Query (#168)
ramari16 Sep 3, 2025
d9070bd
Create V5__add_cascade.sql
sharra44 Sep 15, 2025
1b6a4b9
Merge pull request #84 from hms-dbmi/cascade-flyway
sharra44 Sep 15, 2025
b519865
[ALS-9230] Findings from UTHSC prod: schema was altered
Sep 15, 2025
a5d0d01
ALS-9852: Add better error messaging for VcfIndex parsing (#169)
ramari16 Sep 17, 2025
aabfdcd
adding columnmeta csv generation for cases where sites do not have it…
sharra44 Sep 30, 2025
d0efac9
adding columnmeta csv generation for cases where sites do not have it…
sharra44 Sep 30, 2025
7872f88
Merge pull request #170 from hms-dbmi/columnmeta-csv
sharra44 Sep 30, 2025
604ba71
ALS-9868: Add test for cross counts (#171)
ramari16 Oct 23, 2025
15a8526
ALS-10129: Create endpoint to get concept hierarchy for a concept (#86)
ramari16 Oct 29, 2025
c39f5de
Release (#265)
Gcolon021 Nov 3, 2025
8e7efa5
Improve error handling and logging in FENCEAuthenticationService (#266)
Gcolon021 Nov 24, 2025
51b9fc8
ALS-10388: Move cache configuration to properties files (#89)
ramari16 Dec 2, 2025
c079127
[ALS-7748] Sort facet categories by metadata order then alphabeticall…
srpiatt Dec 3, 2025
4314512
Optimize Tomcat thread pool configuration for improved performance (#88)
TDeSain Dec 3, 2025
8ba1902
ALS-9955: Add tests to confirm handling of nulls in timestamp values …
ramari16 Dec 16, 2025
9270232
ALS-10113: Add swagger documentation for new query (#174)
ramari16 Dec 17, 2025
2e7fe38
Fix main branch name in github actions (#175)
ramari16 Jan 8, 2026
5061525
Fix java version in github actions (#176)
ramari16 Jan 8, 2026
c52629c
ALS-8744: Upgrade to java 24 (#267)
ramari16 Jan 13, 2026
7d972d8
Add httpcore5 dependency to pic-sure-auth-services pom file (#268)
Gcolon021 Jan 16, 2026
add10f7
ALS-10615: Add hpds base docker image to build (#269)
ramari16 Feb 3, 2026
2a09467
ALS-10615: Split docker build into build and application dockerfiles …
ramari16 Feb 3, 2026
cd450f3
init
JamesPeck Feb 13, 2026
50f3602
Create ci.yml
JamesPeck Feb 13, 2026
b8a724c
Update AuditLogService.java
JamesPeck Feb 13, 2026
0c5db81
Configure health port and add jenkinsfile (#1)
JamesPeck Feb 19, 2026
f46e1c4
[CHORE] Update docker build process (#2)
JamesPeck Feb 19, 2026
b038482
Update jenkinsfile (#3)
JamesPeck Feb 21, 2026
d8f60db
Fix jenkins (#4)
JamesPeck Feb 21, 2026
20e83f1
Update .dockerignore
JamesPeck Feb 21, 2026
0dbc811
Update jenkinsfile
JamesPeck Feb 21, 2026
22e1e02
Add debug logging for RAS Okta login introspection response
Gcolon021 Feb 23, 2026
d2dadb2
Use port 80
JamesPeck Feb 23, 2026
ee8f8c2
Remove session_id and logged_in from AppConfig
JamesPeck Feb 25, 2026
7dd8b7a
[ALS-10854] Update query to identify leaf nodes by returning null if …
srpiatt Mar 4, 2026
1ce05f2
[ALS-7018] Add uploader log output (#56)
srpiatt Mar 4, 2026
12059b9
[ALS-7018] Add aggdict and dictionary log outputs (#90)
srpiatt Mar 4, 2026
7f28807
add missing githash
JamesPeck Mar 4, 2026
f6538bf
update claims
JamesPeck Mar 10, 2026
0c32f18
ALS-9545: Support PSAMA changes (#183)
ramari16 Mar 10, 2026
1107840
Add timestamp fields and methods in ColumnMeta
TDeSain Mar 17, 2026
6658bc2
Add unit tests for ColumnMeta class
TDeSain Mar 17, 2026
ba3bdef
Improve ColumnMeta unit tests for timestamp fields
TDeSain Mar 17, 2026
0911d6f
Update `addConnection` to save UserMetadataMappings (#275)
Gcolon021 Mar 17, 2026
d31b69f
Simplify Dockerfiles by removing multi-stage builds and unused depend…
Gcolon021 Mar 20, 2026
1d72132
[ALS-10712] Update docker build process (#270)
Gcolon021 Mar 20, 2026
65d89a2
Add initial Dockerfile for `picsure-dictionary` and update `.dockerig…
Gcolon021 Mar 20, 2026
004c2a7
Merge pull request #184 from hms-dbmi/ALS-10763
TDeSain Mar 24, 2026
e542fe3
ALS-9545: Handle query encoded as string (#185)
ramari16 Mar 25, 2026
d12776b
Update Jenkinsfile: Fix workspace mount path and add --load flag to d…
Gcolon021 Mar 25, 2026
00bd3c7
ALS-11261: Pin github action versions to hashes (#186)
ramari16 Mar 25, 2026
c1dd5d8
Handle Session ids as first class
JamesPeck Mar 28, 2026
192ea39
Fix id batch size parameter (#188)
ramari16 Mar 30, 2026
ba0f573
[ALS-10849] Logging (#187)
JamesPeck Mar 31, 2026
faf5b18
[ALS-10848] Logging (#95)
JamesPeck Mar 31, 2026
784a3e2
[ALS-10851] Logging (#271)
JamesPeck Mar 31, 2026
d16929b
[bug] Add info endpoint (#5)
JamesPeck Apr 1, 2026
4e0cd60
ALS-9545: Add new Query entity authorization (#277)
ramari16 Apr 2, 2026
b331f7b
ALS-11340: Remove system.getproperty usages in favor of @Value (#189)
ramari16 Apr 2, 2026
8e4631b
ALS-11267: Pin versions in github actions (#278)
ramari16 Apr 2, 2026
a00a302
ALS-11368: Add configuration to require authorization filters for all…
ramari16 Apr 8, 2026
6e8a048
ALS-11390: Allow topmed and parent concepts to be used by everyone (#…
ramari16 Apr 9, 2026
03a45b5
[CHORE] Refactor key (#6)
JamesPeck Apr 10, 2026
7993c5b
[ALS-10712] Dockerize Build (#96)
JamesPeck Apr 13, 2026
a1bde1c
ALS-11513: Allow invalid concept paths to be exported as empty (#191)
ramari16 Apr 15, 2026
ec544dc
[ALS-11484] Fix null pointer exception in RASPassPortService and enha…
Gcolon021 Apr 15, 2026
4d7d0bd
Optimize SQL query structure and filtering logic (#97)
TDeSain Apr 15, 2026
e28d520
ALS-11397: Make defensive copy of variant filter array before sorting…
ramari16 Apr 15, 2026
e845092
ALS-11520: Fix bug where user consents were not getting updated (#281)
ramari16 Apr 19, 2026
373d277
Update searchable fields and language configuration in TSVector
TDeSain Apr 16, 2026
1a40e05
Require authorization filter by default (#193)
ramari16 Apr 27, 2026
f96139c
move logging location
JamesPeck Apr 28, 2026
4c464d6
[ALS-11555] Log query string (#194)
JamesPeck Apr 28, 2026
1e03371
[ALS-11555] Log query string (#101)
JamesPeck Apr 28, 2026
059a1ce
[ALS-11555] Log helpful things with inspect (#283)
JamesPeck May 4, 2026
b9cdc8a
ALS-11662: Add logging when query invalid for missing auth filter (#196)
ramari16 May 7, 2026
5ce717c
[ALS-11460] Meta config update (#102)
sharra44 May 27, 2026
6b7d53e
[ALS-11638] Handle required filters for V3 (#199)
JamesPeck May 27, 2026
92f68da
Rebuild visualization as a Spring Boot service
JamesPeck May 26, 2026
5a2e3e7
Add container and CI build support
JamesPeck May 26, 2026
3d45756
Split visualization endpoints by API responsibility
JamesPeck May 26, 2026
5dcf776
Implement HPDS-backed distribution processing
JamesPeck May 26, 2026
331fc7a
Add request audit logging and structured errors
JamesPeck May 26, 2026
70720f4
Update runtime configuration and Java baseline
JamesPeck May 26, 2026
0c4d569
Align visualization responses with frontend needs
JamesPeck May 26, 2026
5cd8afc
Bump org.apache.avro:avro from 1.12.0 to 1.12.1 (#181)
dependabot[bot] Jun 2, 2026
8434ecd
Bump org.apache.httpcomponents.client5:httpclient5 (#284)
dependabot[bot] Jun 3, 2026
05042f6
Bump com.fasterxml.jackson.core:jackson-core in /pic-sure-auth-servic…
dependabot[bot] Jun 3, 2026
0dd546e
Bump com.sun.mail:jakarta.mail in /pic-sure-auth-services (#282)
dependabot[bot] Jun 3, 2026
a190ace
Als 10196 fix roles (#286)
Gcolon021 Jun 5, 2026
3512bc0
ALS-11710: Enable v3 queries in aim-ahead (#288)
ramari16 Jun 9, 2026
a62543f
[ALS-11895] Fix v3 cross counts: merge duplicate filters and report o…
JamesPeck Jun 11, 2026
506170e
Add .sdkmanrc for SDK Man Java version pinning (#57)
Gcolon021 Jun 11, 2026
30fd819
Add .sdkmanrc for SDK Man Java version pinning (#104)
Gcolon021 Jun 11, 2026
87a4db2
Add .sdkmanrc for SDK Man Java version pinning (#7)
Gcolon021 Jun 11, 2026
e5a1474
Add .sdkmanrc for SDK Man Java version pinning (#289)
Gcolon021 Jun 11, 2026
0a30e28
Add .sdkmanrc for SDK Man Java version pinning (#201)
Gcolon021 Jun 11, 2026
14741a4
Add .sdkmanrc for SDK Man Java version pinning (#57)
Gcolon021 Jun 11, 2026
c8a182a
[ALS-10714] Pass thru the obfuscation #10
JamesPeck Jun 16, 2026
3c06de5
added documentation for the application properties file for dictionar…
sharra44 Jun 22, 2026
d8ffce0
[ALS-11493] Optimize query performance with parallel execution and in…
TDeSain Jun 23, 2026
c37015a
ALS-11850: Refactor common code into own library (#198)
ramari16 Jun 29, 2026
24edc50
ALS-11850: Move common code to common module (#292)
ramari16 Jun 29, 2026
726a290
ALS-11850: Use pic-sure-common for HPDS dependencies (#11)
ramari16 Jun 29, 2026
3190fe6
ALS-11788: Upgrade to java 25 (#107)
ramari16 Jun 29, 2026
68f9f5c
ALS-12219: Schema-qualify dict tables in flyway migrations V7 and V10…
Gcolon021 Jun 30, 2026
1bf29b4
Emit caller as a top-level audit field (#9)
Gcolon021 Jul 1, 2026
9b28bea
feat(health): expose Actuator /actuator/health with db indicator (Pha…
Gcolon021 Jul 3, 2026
e00a2ab
feat(health): expose Actuator /actuator/health with readiness indicat…
Gcolon021 Jul 3, 2026
8b678a0
feat(auth): segment-aware HPDS-v3 consent-skip (keep legacy /v3 until…
Gcolon021 Jul 3, 2026
ba8a5a2
feat(health): expose Actuator /actuator/health with db indicator (Pha…
Gcolon021 Jul 3, 2026
946c618
test(health): pin the native /health contract (Phase 3 Task 8)
Gcolon021 Jul 3, 2026
6a44fbc
fix(health): disable actuator mail indicator (SMTP-unreachable envs m…
Gcolon021 Jul 3, 2026
3d1e50f
WIP: Phase 3 — segment-aware HPDS-v3 consent-skip (#295)
Gcolon021 Jul 6, 2026
0d2c301
Merge pic_sure_api_rewrite_p3 into pic_sure_api_rewrite (Phase 3)
Gcolon021 Jul 6, 2026
50cfed3
Merge pic_sure_api_rewrite_p3 into pic_sure_api_rewrite (Phase 3)
Gcolon021 Jul 6, 2026
2c86261
Merge pic_sure_api_rewrite_p3 into pic_sure_api_rewrite (Phase 3)
Gcolon021 Jul 6, 2026
ceccefa
Merge pic_sure_api_rewrite_p3 into pic_sure_api_rewrite (Phase 3)
Gcolon021 Jul 6, 2026
a79e00c
feat: select AUTHORIZED vs OPEN from the gateway's X-User-Id header
Gcolon021 Jul 7, 2026
a5f1307
fix: tolerate null resourceUUID in distribution audit metadata
Gcolon021 Jul 7, 2026
af85ae9
fix: HpdsClient no longer requires a resource UUID
Gcolon021 Jul 7, 2026
0f149bc
chore(import): import PIC-SURE-Visualization at 1988897e2 as services…
Gcolon021 Jul 14, 2026
19f1f6b
chore(import): import pic-sure-auth-microapp at 114e56b77 as services…
Gcolon021 Jul 14, 2026
a7d019e
chore(import): import PIC-SURE-Logging at 0ed1c26c3 as services/pic-s…
Gcolon021 Jul 14, 2026
3483d00
chore(import): import pic-sure-hpds at 3f89e144c as services/pic-sure…
Gcolon021 Jul 14, 2026
276f0c3
chore(import): import pic-sure-services at c8620b323 as services/pic-…
Gcolon021 Jul 14, 2026
a83689f
chore(import): import picsure-dictionary at 84c788f58 as services/pic…
Gcolon021 Jul 14, 2026
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20 changes: 20 additions & 0 deletions services/pic-sure-auth-microapp/.github/release.yml
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changelog:
exclude:
labels:
- ignore-for-release
categories:
- title: Breaking Changes
labels:
- breaking-change
- title: Features
labels:
- feature
- title: Enhancements
labels:
- enhancement
- title: Bug Fixes
labels:
- bug
- title: Other Changes
labels:
- "*"
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name: Maven Run Tests

on:
push:
branches: [ "main", "release" ]
pull_request:
branches: [ "main", "release" ]

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2
- name: Set up JDK 25
uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0
with:
java-version: '25'
distribution: 'temurin'
- name: Test with Maven
run: mvn test
env:
GITHUB_TOKEN: ${{ github.token }}
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name: Label Checker
on:
pull_request:
types:
- opened
- synchronize
- reopened
- labeled
- unlabeled

jobs:

check_labels:
name: Check labels
runs-on: ubuntu-latest
steps:
- uses: agilepathway/label-checker@c3d16ad512e7cea5961df85ff2486bb774caf3c5 # v1.6.65
with:
one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies
repo_token: ${{ secrets.GITHUB_TOKEN }}

37 changes: 37 additions & 0 deletions services/pic-sure-auth-microapp/.gitignore
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target/
.idea/
.vscode/
*.iml
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
buildNumber.properties
.mvn/timing.properties

# Avoid ignoring Maven wrapper jar file (.jar files are usually ignored)
!/.mvn/wrapper/maven-wrapper.jar


httpd/pic-sure-auth-ui-webapp.zip

.project
.settings/
.classpath
.vscode/

.env
.DS_Store
.idea

.docker-compose.yml.swp
pic-sure-auth-services.war
pic-sure-auth-services.war.deployed
*.war
*.deployed
*.failed

.m2
!.m2/README.md
4 changes: 4 additions & 0 deletions services/pic-sure-auth-microapp/.m2/README.md
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The .m2 dir is used to pass proxy args to Jenkins
for environments that access the outside internet via
an HTTP proxy

1 change: 1 addition & 0 deletions services/pic-sure-auth-microapp/.sdkmanrc
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java=24.0.2-tem
128 changes: 128 additions & 0 deletions services/pic-sure-auth-microapp/CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the
overall community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or
advances of any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email
address, without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
avillach_lab_developers@googlegroups.com.
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series
of actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or
permanent ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within
the community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.

Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).

[homepage]: https://www.contributor-covenant.org

For answers to common questions about this code of conduct, see the FAQ at
https://www.contributor-covenant.org/faq. Translations are available at
https://www.contributor-covenant.org/translations.
55 changes: 55 additions & 0 deletions services/pic-sure-auth-microapp/Jenkinsfile.fence
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pipeline {
agent any

parameters {
string(name: 'DOCKER_REGISTRY', description: 'Docker registry URL (e.g., ECR URL)', defaultValue: 'hms-dbmi')
string(name: 'REPOSITORY_NAME', description: 'Docker repository name', defaultValue: 'psama')
string(name: 'DATASOURCE_URL', description: 'Datasource URL', defaultValue: '${database_host_address}')
string(name: 'DATASOURCE_USERNAME', description: 'Datasource username', defaultValue: '${database_app_user_secret_name}')
string(name: 'STACK_SPECIFIC_APPLICATION_ID', description: 'Application ID for base query', defaultValue: '${application_id_for_base_query}')
string(name: 'TARGET_STACK', description: 'Target stack for application deployment.')
string(name: 'STACK_S3_BUCKET', description: 'The s3 bucket', defaultValue: '${stack_s3_bucket}')
}

environment {
DOCKER_BUILD_ARGS = "-f ./pic-sure-auth-services/bdc.Dockerfile"
GIT_BRANCH_SHORT = sh(script: 'echo ${GIT_BRANCH} | cut -d "/" -f 2', returnStdout: true).trim()
GIT_COMMIT_SHORT = sh(script: 'echo ${GIT_COMMIT} | cut -c1-7', returnStdout: true).trim()
IMAGE_TAG = "${GIT_BRANCH_SHORT}_${GIT_COMMIT_SHORT}"
LATEST_TAG = "latest"
}

stages {
stage('Maven Build') {
steps {
sh '''docker run --rm \
-v "/var/jenkins_home/workspace/${JOB_NAME}/:/app:z" \
-v maven_m2_cache:/root/.m2 \
-w /app \
--platform=linux/amd64 \
maven:3.9-amazoncorretto-25 \
sh -lc "mvn clean install -DskipTests"'''
}
}

stage('Build Docker Image') {
steps {
script {
// Define the build args
def buildArgs = " --build-arg DATASOURCE_URL=${env.DATASOURCE_URL} " +
" --build-arg DATASOURCE_USERNAME=${env.DATASOURCE_USERNAME} " +
" --build-arg STACK_SPECIFIC_APPLICATION_ID=${env.STACK_SPECIFIC_APPLICATION_ID} "

sh "docker build --load ${DOCKER_BUILD_ARGS} ${buildArgs} -t ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${IMAGE_TAG} ."
sh "docker tag ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${IMAGE_TAG} ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${LATEST_TAG}"
}
}
}
stage('Deploy Docker Image') {
steps {
sh "docker save ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${LATEST_TAG} | gzip > psama.tar.gz"
sh "aws s3 --sse=AES256 cp psama.tar.gz s3://$STACK_S3_BUCKET/$TARGET_STACK/containers/psama.tar.gz"
}
}
}
}
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