Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MDACA 3.0.1 #2378

Open
wants to merge 155 commits into
base: mdaca-3.0.1
Choose a base branch
from
Open
Changes from 6 commits
Commits
Show all changes
155 commits
Select commit Hold shift + click to select a range
3f9e90c
Start version 2.15.0
chrisknoll Dec 11, 2023
f258186
Permission Performance Optimizations (#2341)
chrisknoll Feb 14, 2024
d90d653
Add Databricks profile (#2339)
anthonysena Feb 26, 2024
31b3332
MDACA Spring Boot 3 migration
May 16, 2024
38d62cb
MDACA Spring Boot 3 migration
May 17, 2024
ca031db
Updated for MDACA Migration to SB 3
spinsysmpeterson May 17, 2024
4053f4f
Updates for MDACA Migration to SB 3
spinsysmpeterson May 17, 2024
31a9da2
MDACA Spring boot 3 migration
May 17, 2024
7f04dd7
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
May 17, 2024
6faf8a8
changes for MDACA Migration to SB 3
spinsysmpeterson May 17, 2024
451f673
MDACA Spring boot 3 migration
May 17, 2024
c6ed67e
updates for MDACA migration to SB 3
spinsysmpeterson May 17, 2024
29f72e5
updates for MDACA Migration to SB 3
spinsysmpeterson May 17, 2024
6bb8336
changes for MDACA Migration to SB 3
spinsysmpeterson May 17, 2024
5786b7c
MDACA Spring Boot 3 migration, deprecated @TypeDefs & @TypeDef replaced
May 17, 2024
071015c
updates for MDACA migration to SB 3
spinsysmpeterson May 17, 2024
8c6b89b
MDACA Spring Boot 3 migration comment out jerey classes that need ref…
May 17, 2024
4fd9f03
MDACA Spring Boot 3 migration
May 17, 2024
c65bd97
Updates for MDACA Migration for SB 3
spinsysmpeterson May 17, 2024
a6a66d5
MDACA Spring Boot 3 migration
May 17, 2024
10cae96
MDACA Spring Boot 3 migration
May 20, 2024
bbbe90c
MDACA Spring Boot 3 migration
May 20, 2024
73a1e81
MDACA Spring Boot 3 migration
May 20, 2024
00039d9
MDACA Spring Boot 3 migration
May 20, 2024
b113d9a
MDACA Spring Boot 3 migration
May 20, 2024
915d697
Updates for MDACA Migration to SB 3
spinsysmpeterson May 20, 2024
7776ea0
MDACA Spring Boot 3 migration
May 20, 2024
8477431
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI.git
spinsysmpeterson May 20, 2024
70800ac
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI.git
spinsysmpeterson May 20, 2024
7e1b3cc
fix merge fix
spinsysmpeterson May 20, 2024
64e4be3
updates for MDACA Migration to SB3
spinsysmpeterson May 20, 2024
14b1111
MDACA Spring Boot 3 migration
May 20, 2024
66d7b03
MDACA Spring Boot 3 migration
May 20, 2024
54b69ee
increased log4j version for MDACA Migration to SB 3
spinsysmpeterson May 20, 2024
0a49a04
Updates for MDACA Migration to SB 3
spinsysmpeterson May 20, 2024
6a235a2
MDACA Spring Boot 3 migration
May 20, 2024
abc2a51
MDACA Spring Boot 3 migration
May 20, 2024
2e644c5
MDACA Spring Boot 3 migration compilation issue
May 20, 2024
90da66b
Updated config for MDACA Migration to SB 3
spinsysmpeterson May 20, 2024
f76526f
MDACA Spring Boot 3.2.5 migration, other recipes
May 20, 2024
ebf168a
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
May 20, 2024
f8519d0
MDACA Spring Boot 325 migration pom cleanup
May 20, 2024
5d2e4aa
MDACA Spring Boot 325 migration pom update security versions
May 20, 2024
26cb4f9
MDACA Spring Boot 3 migration
May 21, 2024
4324275
changes for MDACA Migration to SB 3
spinsysmpeterson May 21, 2024
450ce93
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI.g…
spinsysmpeterson May 21, 2024
cbd0980
updates for MDACA Migration to SB 3
spinsysmpeterson May 23, 2024
8b36d13
updates for MDACA Migration to SB 3
spinsysmpeterson May 23, 2024
678f040
docker workaround to upload to harbor
May 24, 2024
404676a
Updated paging for MDACA Upgrade to SB 3
spinsysmpeterson Jun 16, 2024
610fa0c
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
spinsysmpeterson Jun 16, 2024
add6419
security scan 2 dependency chnages
Jun 17, 2024
40fc510
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
Jun 17, 2024
3ec1e03
additional changes for MDACA migration to SB 3, shiro and pac4j changes
spinsysmpeterson Jun 21, 2024
2935355
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI.git
spinsysmpeterson Jun 21, 2024
ceae636
Fixed permissionIdx that was removed during upgrade
spinsysmpeterson Jun 24, 2024
db6812a
Added exlusion to Buji for Pac4j javaee, got it working with tomcat
spinsysmpeterson Jun 24, 2024
c221dc6
cleanup pre-pull request
spinsysmpeterson Jun 25, 2024
32ad9ad
Updated dockerfile & pom for MDACA containers
Jul 23, 2024
5353882
Updated job execution SQL for updated batch params table fields
Aug 12, 2024
44b6daa
Fixed Redshift dependency in pom
spinsysmpeterson Aug 15, 2024
a6699d1
patched pom for grype secuiryt scan
Aug 30, 2024
5bbe3da
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
Aug 30, 2024
8e02bc3
Updated dockerfile & adding WebAPI.war
Sep 16, 2024
683a07a
Track .war files with Git LFS
Sep 17, 2024
97bc021
removed war
Sep 18, 2024
b00cd25
Delete .github/workflows/release.yaml
stevensrtw Sep 18, 2024
7160afc
Update ci.yaml
stevensrtw Sep 18, 2024
9109a1b
Update pom.xml
stevensrtw Sep 18, 2024
ba96db9
Create settings.xml
stevensrtw Sep 18, 2024
8b9ca7e
Create Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
e2ba15c
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
6eb654d
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
3a082d7
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
2526f3b
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
ac67253
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
7801312
Update ci.yaml
stevensrtw Sep 18, 2024
a174948
Update ci.yaml
stevensrtw Sep 18, 2024
74363d9
Update ci.yaml
stevensrtw Sep 18, 2024
5a8f838
Update ci.yaml
stevensrtw Sep 18, 2024
5ee0140
Update ci.yaml
stevensrtw Sep 18, 2024
c5c0d36
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
b936eca
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
d21239b
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
843b8c3
Update Dockerfile-mvn-no-local
stevensrtw Sep 18, 2024
8c4c6c4
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
0f73208
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
fade004
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
4ce36a6
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
b302323
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
fbfdf5b
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
8193b05
Update ci.yaml
stevensrtw Sep 19, 2024
a2b6ba8
Update ci.yaml
stevensrtw Sep 19, 2024
bc153d0
Update ci.yaml
stevensrtw Sep 19, 2024
4a81413
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
d69f190
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
846f213
Update ci.yaml
stevensrtw Sep 19, 2024
50227d9
Update pom.xml
stevensrtw Sep 19, 2024
13c2b43
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
2b26c2d
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
649be12
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
22cc5ff
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
509bb69
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
043e7f0
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
6b2c19f
Update Dockerfile-mvn-no-local
stevensrtw Sep 19, 2024
582fcf8
updated telemetry version for security scan
Sep 19, 2024
f237fcd
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
Sep 19, 2024
6ef5daf
Update Dockerfile-mvn-no-local
stevensrtw Sep 20, 2024
7a8adbe
Update ci.yaml
stevensrtw Sep 20, 2024
a033b19
Update ci.yaml
stevensrtw Sep 22, 2024
3bee9c9
Update ci.yaml
stevensrtw Sep 22, 2024
7b007f2
Update ci.yaml
stevensrtw Sep 22, 2024
7b9cfa6
Update ci.yaml
stevensrtw Sep 22, 2024
c322b94
Update ci.yaml
stevensrtw Sep 22, 2024
e451e2b
Update Dockerfile-mvn-no-local
stevensrtw Nov 15, 2024
325e65e
Update ci.yaml
stevensrtw Nov 15, 2024
44994b8
Update Dockerfile-mvn-no-local
stevensrtw Nov 15, 2024
77afd2a
security scan version fix
Nov 21, 2024
884bba4
Update ci.yaml
stevensrtw Nov 25, 2024
684aa35
updated xmlsec dependency version for security scan. cleaned up pom o…
Nov 26, 2024
06a9ab1
update dependency for security scan
Nov 26, 2024
4bfeec1
remove bcprov 1.63 from cas-core dependency
Nov 27, 2024
013e6a5
Update ci.yaml
stevensrtw Dec 5, 2024
df210b4
Update ci.yaml
stevensrtw Dec 5, 2024
eeeb23b
add local mvn dockerfile
Dec 6, 2024
a84016e
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
Dec 6, 2024
f0de900
refactored commons after removing older spring batch admin mgr
Dec 17, 2024
9bbf929
Completed refactoring of jobs to Spring Batch 5, reverted changes to …
spinsysmpeterson Dec 18, 2024
9423548
Update ci.yaml
stevensrtw Dec 18, 2024
2af622e
fixed pom security setting
spinsysmpeterson Dec 19, 2024
4712777
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
spinsysmpeterson Dec 19, 2024
a1fc308
Fixed transactionManager on stepBuilders for tasklet, addresses cohor…
spinsysmpeterson Dec 21, 2024
e39de7c
updated DynamicEntityGraph paths
spinsysmpeterson Dec 23, 2024
016943b
Added missing transactionManagers
spinsysmpeterson Dec 23, 2024
9e71e01
Added missing transactionManagers
spinsysmpeterson Dec 23, 2024
7739165
fixes for FeAnalysisEntity to properly map design column, fixed enum …
spinsysmpeterson Dec 24, 2024
7cf9dcc
add transactionmanager, and jobrepository to fix delete cohort errors
Jan 3, 2025
7ca12af
added PlatformTransactionManager for previous fix not in previous commit
Jan 3, 2025
5f80745
updated tomcat version for cve-2024-56337
Feb 6, 2025
e3967ac
updated spring dependencies for security scans: CVE-2024-38816, CVE-2…
Feb 6, 2025
a6ca5db
updated spring dependencies for security scans: CVE-2024-47554
Feb 6, 2025
3a236dc
update dependencies for secuity scan: CVE-2024-47554
Feb 7, 2025
c360153
update for security scan: CVE-2022-24615 and CVE-2023-22899
Feb 7, 2025
d4fa9f2
update for security scan: CVE-2024-38829
Feb 7, 2025
9550aa5
update for security scan: CVE-2024-47554
Feb 7, 2025
c6d87b5
update for security scan: CVE-2024-47554
Feb 7, 2025
1435b0f
update for security scan: CVE-2024-47554
Feb 7, 2025
0665748
update for security scan: CVE-2024-47554
Feb 7, 2025
0defd00
update velocity-engine-core for security scan: CVE-2024-47554
Feb 10, 2025
cf58753
update velocity-engine-core for new CVEs
Feb 10, 2025
b09a84d
Updated tag from 3.20.3 to 3.20.6 for alpine patch and updated ci.yml…
stevensrtw Feb 22, 2025
cdbf5f3
Updated tag 3.0.2.2 to 3.0.2.3
stevensrtw Feb 22, 2025
29745c7
changed logging from debug to error
Feb 24, 2025
485f744
Merge branch 'mdaca-3.0.1' of https://github.com/mdaca/OHDSI-WebAPI i…
Feb 24, 2025
b25e7b5
update dependency version for security scan: cve-2024-57699
Feb 24, 2025
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions src/main/java/org/ohdsi/webapi/FlywayConfig.java
Original file line number Diff line number Diff line change
@@ -33,16 +33,16 @@ DataSource secondaryDataSource() {
@ConfigurationProperties(prefix = "flyway")
@DependsOnDatabaseInitialization
Flyway flyway() {
Flyway flyway = new Flyway();
flyway.setDataSource(secondaryDataSource());
Flyway flyway = null;/* new Flyway(); MDACA Spring Boot 3 migration compilation issue */
/* flyway.setDataSource(secondaryDataSource()); MDACA Spring Boot 3 migration compilation issue */
return flyway;
}

@Bean
FlywayMigrationInitializer flywayInitializer(ApplicationContext context, Flyway flyway) {

ApplicationContextAwareSpringJdbcMigrationResolver contextAwareResolver = new ApplicationContextAwareSpringJdbcMigrationResolver(context);
flyway.setResolvers(contextAwareResolver);
/* flyway.setResolvers(contextAwareResolver); MDACA Spring Boot 3 migration compilation issue */

return new FlywayMigrationInitializer(flyway, null);
}
Original file line number Diff line number Diff line change
@@ -182,10 +182,12 @@ public void saveRoleGroupMapping(LdapProviderType providerType, List<RoleGroupEn
List<RoleGroupEntity> deleted = RoleGroupUtils.findDeleted(exists, mappingEntities);
List<RoleGroupEntity> created = RoleGroupUtils.findCreated(exists, mappingEntities);
if (!deleted.isEmpty()) {
roleGroupMappingRepository.delete(deleted);
/* roleGroupMappingRepository.delete(deleted); MDACA Spring Boot 3 migration compilation issue */
roleGroupMappingRepository.deleteAll(deleted);
}
if (!created.isEmpty()) {
roleGroupMappingRepository.save(created);
/* roleGroupMappingRepository.saveAll(created); MDACA Spring Boot 3 migration compilation issue */
roleGroupMappingRepository.saveAll(created);
}
}