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ad5057b
Added: Request Variable annotation
djuarezgf Mar 4, 2025
901fa28
Merge pull request #24 from samply/feature/request-variable
djuarezgf Mar 5, 2025
6b3a787
Changed: Rename project state CREATED and ACCEPTED as REVIEW and APPR…
djuarezgf Mar 13, 2025
d1bd586
Bugfix
djuarezgf Mar 19, 2025
dc3ee16
Bugfix: RequestVariable in fetchRequestParamNames
djuarezgf Mar 19, 2025
99713b2
Added: Optimize JPA configuration
djuarezgf Mar 25, 2025
1890c9c
feat: compatibility with Authentik
djuarezgf Nov 18, 2025
f91809f
chore: update to maven 4
djuarezgf Nov 25, 2025
ef28f0a
chore: update to Java 25
djuarezgf Nov 25, 2025
db95189
chore: remove unnecessary comments in application.yaml
djuarezgf Nov 25, 2025
d458aab
chore: jwt decoder configuration
djuarezgf Nov 25, 2025
ed615cd
Merge pull request #25 from samply/feat/authentik
djuarezgf Nov 25, 2025
3e24ca7
test
djuarezgf Nov 25, 2025
8c8b139
chore: eclipse-temurin 25
djuarezgf Nov 26, 2025
60531da
fix: final name in pom
djuarezgf Nov 26, 2025
3776ae9
chore: ASP and ASP_DATA as query format
djuarezgf Nov 26, 2025
b6dc171
fix: AST and AST_DATA as query format
djuarezgf Nov 26, 2025
b55ec99
fix: init flyway migration in spring 4
djuarezgf Nov 26, 2025
df9623c
fix: jwt decoder configuration
djuarezgf Dec 5, 2025
c9a5f1b
fix: full name if first or last name is missing
djuarezgf Dec 19, 2025
eff6bd2
fix: only one user session at the same time
djuarezgf Dec 23, 2025
fefe7a4
chore: remove project bridgehead user with role creator
djuarezgf Jan 5, 2026
c1634e2
chore: view also own created projects even if they don't belong to ow…
djuarezgf Jan 5, 2026
fd6e004
chore: view all project bridgeheads for creator
djuarezgf Jan 5, 2026
9603ddb
Merge pull request #26 from samply/feat/not-own-bridgehead
djuarezgf Jan 5, 2026
70cea14
Added: Project Form
djuarezgf Apr 2, 2025
3320ed3
chore: title and label together identify a form field
djuarezgf Jan 7, 2026
7c23248
chore: project form services
djuarezgf Jan 7, 2026
6f9399b
chore: add language annotation
djuarezgf Jan 8, 2026
26855a3
chore: change RequestVariableMethodArgumentResolver for complexer dat…
djuarezgf Jan 12, 2026
a87d1bb
chore: add postman test collection
djuarezgf Jan 12, 2026
fdbdea5
chore: add form pdf service
djuarezgf Jan 13, 2026
0a35cd8
chore: add external execution not allowed profile
djuarezgf Jan 14, 2026
c16d1ec
chore: remove warnings (refactoring)
djuarezgf Jan 14, 2026
0da5246
chore: download form pdf
djuarezgf Jan 15, 2026
176fc81
chore: arrange form fields in right order in PDF
djuarezgf Jan 15, 2026
2d26802
chore: change form field priority sorting
djuarezgf Jan 15, 2026
a292e05
chore: add DataType in Form PDF
djuarezgf Jan 16, 2026
ae8e167
chore: add Form Variables Config
djuarezgf Jan 16, 2026
4570dbf
chore: refactoring form fields and form templates
djuarezgf Jan 19, 2026
db110b9
chore: add fetch form templates
djuarezgf Jan 20, 2026
4cc191b
chore: add fetch form template filename
djuarezgf Jan 20, 2026
96593f8
chore: add Current Date in Form Template
djuarezgf Jan 20, 2026
427bee6
chore: add project form fields
djuarezgf Jan 23, 2026
9011d8c
chore: add bridgehead affiliation
djuarezgf Jan 26, 2026
aad0049
chore: consider null project fields in a template
djuarezgf Jan 27, 2026
4369e08
chore: add Form Data Type Date and Timestamp
djuarezgf Jan 28, 2026
e4a0141
chore: refactoring in form service and form templates service
djuarezgf Jan 28, 2026
751fa2d
Merge pull request #27 from samply/feature/forms
djuarezgf Jan 29, 2026
d8407c0
chore: remove default template
djuarezgf Jan 29, 2026
7cc66ee
chore: HTTP Get methods fetch RequestParam and HTTP Post methods fetc…
djuarezgf Jan 30, 2026
4be58e0
chore: remove application form services
djuarezgf Jan 30, 2026
78fc1e6
chore: check organizational roles for any bridgehead
djuarezgf Feb 2, 2026
35d8bcf
chore: check organizational roles for any bridgehead (II)
djuarezgf Feb 2, 2026
2aadd84
chore: add form repository
djuarezgf Feb 3, 2026
20aa984
chore: update test collections
djuarezgf Feb 4, 2026
76762c8
chore: changed: edit form instead of just adding forms to project
djuarezgf Feb 4, 2026
0613448
chore: refactoring changelog
djuarezgf Feb 4, 2026
680af53
chore: change: add and rename forms instead of editing services
djuarezgf Feb 4, 2026
121a337
hotfix
djuarezgf Feb 5, 2026
e725f09
chore: add fetch all project states depending on project code
djuarezgf Feb 5, 2026
2da5b5e
hotfix
djuarezgf Feb 6, 2026
6645a9f
hotfix
djuarezgf Feb 9, 2026
9bc5e67
hotfix
djuarezgf Feb 9, 2026
4eed15d
refactoring
djuarezgf Feb 9, 2026
5cea150
refactoring
djuarezgf Feb 9, 2026
092c26f
refactoring
djuarezgf Feb 9, 2026
09ef3ce
refactoring
djuarezgf Feb 9, 2026
18f5e45
chore: make user role thread safe
djuarezgf Feb 9, 2026
c93b6fe
refactoring
djuarezgf Feb 9, 2026
2439221
chore: add Frontend Name
djuarezgf Feb 10, 2026
10d5629
chore: add Frontend Name test
djuarezgf Feb 10, 2026
a7fa2ae
chore: remove Frontend Name
djuarezgf Feb 10, 2026
c55f260
chore: log frontend config
djuarezgf Feb 10, 2026
95fd025
chore: add SAMPLES project type
djuarezgf Feb 10, 2026
fc6ae7f
chore: change: Notifications only for Project Manager Admin
djuarezgf Feb 10, 2026
267f146
chore: changed: filter templates by selected forms
djuarezgf Feb 10, 2026
3396515
chore: add project and forms configurations
djuarezgf Feb 12, 2026
819ea08
chore: samples project can generate exports not visible to researcher
djuarezgf Feb 12, 2026
2090d47
chore: use PUT and DELETE methods
djuarezgf Feb 13, 2026
7ce96eb
refactoring
djuarezgf Feb 13, 2026
7a4fb15
refactoring
djuarezgf Feb 13, 2026
8bb4cb8
hotfix: add PUT and DELETE methods to CORS
djuarezgf Feb 13, 2026
2cbc2df
feat: multiple types pro project
djuarezgf Feb 27, 2026
1a00011
chore: remove project output service
djuarezgf Feb 27, 2026
5e9a295
hotfix
djuarezgf Feb 27, 2026
32e3d23
chore: update postman test collection
djuarezgf Feb 27, 2026
062d64a
refactoring
djuarezgf Mar 5, 2026
b4b2d54
feat: multiple project types
djuarezgf Mar 20, 2026
968b632
chore: java 26
djuarezgf Mar 20, 2026
be67290
chore: project manager can edit project
djuarezgf Mar 20, 2026
d78d3c7
chore: back temporally to java 25 until available in github
djuarezgf Mar 23, 2026
46e2bb9
Merge pull request #28 from samply/feat/multiple-project-types
djuarezgf Mar 23, 2026
98e94d6
hotfix
djuarezgf Mar 24, 2026
42ef134
hotfix
djuarezgf Mar 24, 2026
f5898b8
hotfix
djuarezgf Mar 24, 2026
9719e2f
chore: isCustomConfig in Project as nullable
djuarezgf Mar 25, 2026
adb0779
chore: rename isCustomConfig as isCustomConfigSelected
djuarezgf Mar 25, 2026
d9776fd
hotfix
djuarezgf Mar 25, 2026
7223355
refactoring
djuarezgf Mar 26, 2026
28c8691
chore: generic fetch parameter annotation in aspect utils
djuarezgf Mar 27, 2026
bebb2b4
chore: use global conversion service of spring
djuarezgf Mar 27, 2026
99b648e
chore: improve convert value in resolve of request variable
djuarezgf Mar 27, 2026
5f1378b
chore: annotated Parameter Wrapper
djuarezgf Mar 27, 2026
f9cba82
chore: request Parameter
djuarezgf Mar 27, 2026
b3d2a98
hotfix
djuarezgf Apr 7, 2026
e7ededb
refactoring
djuarezgf Apr 7, 2026
f3ad15a
chore: synchronization between query outputs and bridgehead executions
djuarezgf Apr 9, 2026
aa1d7e1
Merge pull request #29 from samply/feat/reduce-db-resposability
djuarezgf Apr 9, 2026
d223522
chore: new test postman collection
djuarezgf Apr 10, 2026
71b7933
chore: ethical Approval in Project Context
djuarezgf Apr 13, 2026
6581387
hotfix
djuarezgf Apr 13, 2026
fe08720
chore: data type enum for form config
djuarezgf Apr 13, 2026
9b8d656
chore: add language to form field value
djuarezgf Apr 13, 2026
c3f61ba
chore: fetch selected forms returns also preconfigured titles
djuarezgf Apr 14, 2026
e4219ae
chore: fetch display value in form field for enums
djuarezgf Apr 14, 2026
f46bc19
refactoring
djuarezgf Apr 14, 2026
356952f
chore: project context in form template context
djuarezgf Apr 14, 2026
dd842ba
chore: template file
djuarezgf Apr 15, 2026
62f7973
chore: send a query with different project types to bridgehead
djuarezgf Apr 15, 2026
8b07f30
chore: list parameters in controller
djuarezgf Apr 16, 2026
9d3decf
chore: fetch best form templates
djuarezgf Apr 16, 2026
9e751c4
chore: simplify query label for bridgehead
djuarezgf Apr 16, 2026
00e18b3
fix: query output identified by project type, template id and output …
djuarezgf Apr 20, 2026
fe9df29
fix: update query outputs correctly
djuarezgf Apr 21, 2026
69f88de
chore: description document and related services
djuarezgf Apr 21, 2026
c60b0ec
chore: change description file constraints
djuarezgf Apr 22, 2026
4c67569
fix: update executions after query changes
djuarezgf Apr 23, 2026
d6b7632
refactoring
djuarezgf Apr 23, 2026
b47c918
chore: cohort definition in query
djuarezgf Apr 23, 2026
3e2b876
refactoring
djuarezgf Apr 23, 2026
4331f15
chore: pm-admin can edit project forms and configurations
djuarezgf Apr 23, 2026
c32ec7c
chore: send query to bridgehead event
djuarezgf Apr 24, 2026
6909b4a
hotfix
djuarezgf Apr 24, 2026
ed1a85f
chore: parameters for sending query to bridgehead
djuarezgf Apr 24, 2026
56ab8ac
fix: project description document for all bridgeheads
djuarezgf Apr 24, 2026
dcd22ee
fix: project description document for all bridgeheads (II)
djuarezgf Apr 24, 2026
eb4d786
chore: fetch project description
djuarezgf Apr 24, 2026
24af670
hotfix
djuarezgf Apr 24, 2026
3dc2c86
refactoring
djuarezgf Apr 24, 2026
5b4c969
refactoring
djuarezgf Apr 24, 2026
6c94491
chore: send Query To Bridgehead Event scheduled job
djuarezgf Apr 27, 2026
1950163
chore: query details
djuarezgf May 5, 2026
2fcee81
chore: exists publication service
djuarezgf May 6, 2026
932c2ac
hotfix
djuarezgf May 7, 2026
cc9b3b7
chore: send attachments in emails
djuarezgf May 26, 2026
3bc895b
chore: final report services
djuarezgf May 27, 2026
2e3cea5
refactoring
djuarezgf May 27, 2026
297c40e
fix: download documents
djuarezgf May 28, 2026
92e6cbb
Handle missing or null entries in fetchFormFieldOrder method
Jun 26, 2026
b5706c1
Add support for archived form fields and filter them from UI rendering
Jun 29, 2026
102a3e4
Add support for managing ethics approval documents (upload, download,…
Jun 29, 2026
cdcb29b
Support multiple project configurations and improve output matching l…
Jun 30, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ jobs:
uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '21'
java-version: '25'

- name: Check out Git repository
uses: actions/checkout@v3
Expand All @@ -47,7 +47,7 @@ jobs:
uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '21'
java-version: '25'

- name: Check out Git repository
uses: actions/checkout@v3
Expand Down
178 changes: 128 additions & 50 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,36 +4,36 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).

## [0.0.1 - 2025-02-11]
## [1.0.0 - 2026-05-27]
### Added
- First version of the project
- Spring Application
- State Machine for project
- State Machine for a project
- Project states and event states
- Project Service
- OAuth2 Security
- OIDC <> Organisation Roles Mapping
- OIDC <> Organization Roles Mapping
- Session User Info
- Session User Info email
- Multi bridgehead user
- Test user if security disabled
- Test user if security is disabled
- Bridgehead configuration
- User Service
- Project Role Constraints Aspect
- Extract path roles map for Security Configuration
- Project State Constraints Aspect
- Frontend service
- Set user as developer, pilot or final
- REST Services: Design and Create project
- REST Service: Accept, reject, archive, start develop, start pilot, start final, finish
- Set the user as a developer, pilot or final
- REST Services: Design and Create a project
- REST Service: Accept, reject, archive, start developer, start pilot, start final, finish
- Project Query and Query Format
- REST Services: Create Query and Create CQL DATA Query
- Document Service
- Upload and Download documents
- Project Type
- HTTP Method for every endpoint in Security Configuration
- IS_TEST_ENVIRONMENT variable disables CSRF
- Create CREATOR user after creating project
- Create CREATOR user after creating a project
- Send and execute query REST Services
- Label, description, template-id and output-format in Query
- Token Manager Service
Expand All @@ -42,7 +42,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Exporter Service implementation
- Bridgehead configuration with explorer and exporter mapping
- Bridgehead Operation
- Create query and draft project (Lens)
- Create a query and draft a project (Lens)
- humanReadable in Bridgehead Config
- Email Service
- Email Templates
Expand All @@ -55,29 +55,29 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Module names
- Http Method and Params for Actions
- Test endpoint
- Download application form
- Download the application form
- Edit project and query
- Fetch output format, query format and templates
- Query Context
- Download document rights to developer, pilot and final users
- Download document rights to a developer, pilot and final users
- Fetch Projects
- Modified Desc as parameter of fetch projects
- Modified Desc as a parameter of fetch projects
- Upload and download documents by document type
- Fetch publications and other documents
- Fetch project types
- Accept and reject project bridgehead
- Fetch project bridgeheads
- Accept, reject and request changes in script
- Accept, reject and request changes in a script
- Fetch all actions
- Accept, Reject and request changes in project results
- Notification Service
- Token Manager services
- Integration in Focus and Beam
- Frontend DTO
- Email as Mime message
- Email as a Mime message
- EmailSenderIfError annotation
- Frontend DTO converters
- Fetch all user visible notifications
- Fetch all user-visible notifications
- Accepted state requirement for setting user as developer or pilot
- Notification User Action
- Replace Bridgehead Operation through Notification
Expand All @@ -89,82 +89,82 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Add notifications for services: document, project bridgehead, project event, project, query, user
- DataSHIELD Token Manager Job
- Check Expired Active Projects Job
- Check if session scope is active before creating a notification for changing project state
- Fetch token status and project status of token manager
- New email if authentication script for DataSHIELD has changed
- Check if the session scope is active before creating a notification for changing the project state
- Fetch token status and project status of a token manager
- New email if an authentication script for DataSHIELD has changed
- Explorer URL in CORS
- Oauth2 Resource Server configuration
- Allow required headers
- Project Constraints: Project Type
- Email template for Accept/Reject/Request changes in project
- Email template for Accept/Reject/Request changes in a project
- User Autocomplete
- Explorer Ids to create and edit query
- Explorer Ids to create and edit a query
- Decode redirect explorer URL
- Fetch project users
- rejectProject state constraints
- Filter output formats for DataSHIELD
- Flag ENABLE_TOKEN_MANAGER
- Content Disposition in exposed headers
- Exists Votum and Application Form
- Exists Script
- Script exists
- Explorer Redirect URI
- User State in Frontend DTO
- Fetch project configurations
- Exists authentication script
- There exists an authentication script
- Remove inactive projects in Opal
- Project Bridgehead DataSHIELD info
- Set project bridgehead datashield removed to false while sending query of DATASHIELD project to exporter
- Set project bridgehead datashield removed to false while sending a query of a DATASHIELD project to exporter
- Fetch current project configuration
- Custom project configuration
- Fetch visible bridgeheads and fetch project bridgeheads
- Allow other documents of certain bridgeheads
- Fetch Project Roles
- Email Types: NEW_PROJECT_ACCEPTED, NEW_VOTUM, REQUEST_TECHNICAL_APPROVAL, NEW_PUBLICATION
- Email config for types NEW_PROJECT_ACCEPTED, NEW_VOTUM, REQUEST_TECHNICAL_APPROVAL, NEW_PUBLICATION
- Fetch label of application form, label and script
- Fetch label of an application form, label and script
- Service exist invited users
- R-Studio Group Manager
- Email Sender: ALL_DEVELOP, ALL_PILOT, ALL_FINAL
- Send email to all involved users after a publication has been uploaded
- Project and project view url in email context
- Create notification after sending an email
- Send message while requesting changes in script or project
- Send message while rejecting a project
- Create a notification after sending an email
- Send a message while requesting changes in a script or project
- Send a message while rejecting a project
- Exporter Job
- Check Queries in Exporter Job
- Max time to wait focus task in minutes
- Max time to wait a focus task in minutes
- Check export execution status
- Coder Service
- RStudio in Coder
- Research environment project type
- Upload file to Coder
- Delete Coder workspace job
- Resend export files to research environment
- Resend export files to a research environment
- Query Code in Explorer URL
- Decode human readable in base 64
- Log bridgeheads at start
- Replace hypen in bridgeheads
- Decode human-readable in base 64
- Log bridgeheads at the start
- Replace hype in bridgeheads
- Log bridgeheads sorted
- Replace hyphen in frontend sites
- Human Readable Bridgehead for frontend dto
- Http proxy configuration
- Email as HTML
- Provide also human readable by fetch all registered bridgeheads
- Provide also human-readable by fetching all registered bridgeheads
- DataSHIELD Project Status Error
- Catch token manager exceptions and return ERROR status
- Send emails in async execution pool
- Send emails in the async execution pool
- Notification async execution pool
- Exporter async execution pool
- Action explanations
- Integration of action explanatios in fetch Actions
- Integration of action examples in fetch Actions
- Action explanations templates
- Email Context
- Extend email context
- Thymeleaf Dialect for email context variables
- Combine first and last name in name
- Replace email context variables in email subject
- Default and Default var in html tags
- Fetch human readable bridgehead for emails
- Combine first and last name in a name
- Replace email context variables in the email subject
- Default and Default var in HTML tags
- Fetch human-readable bridgehead for emails
- Email context project bridgeheads variable
- Decode Base64 values of email context
- Enable minus in variables of email context
Expand All @@ -173,35 +173,35 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Process variables recursively in Thymeleaf
- Creator name in Frontend Project
- Action explanation priority
- Configurations as file
- Configurations as a file
- File Description for Frontend
- Fetch Project-States for dashboard site
- Fetch Project-States for the dashboard site
- Primary and Test Mail Server
- Email if project rejected
- Send email when the query has arrived to the exporter or it has been executed
- Email if a project is rejected
- Send email when the query has arrived to the exporter, or it has been executed
- Export dispatch counter
- Title and description in project configuration
- Annotation Ignore Project Configuration Match
- Send error email if error while sending query to bridgehead
- Mailing Black List
- Sort Mailing Black List by first and last name
- Send error email if error while sending a query to bridgehead
- Mailing Blacklist
- Sort Mailing Blacklist by first and last name
- Results
- DRN in exporter label
- DRN in the exporter label
- Final User State in results
- Create State in Frontend DTO's (for project and project bridgehead)
- Fetch email message and subject HTTP endpoint
- Send project results only if there are final users
- User Project State in State Constraints
- Bridgehead Admin info in the variables for the email templates
- Results URL in frontend dto
- Result URL in frontend dto
- EmailContextKey enum
- Votum for all
- Configuration Site
- REST Service: is project manager admin
- Research Environment URL key for Email Context
- REST Service: Fetch research environment URL
- REST Service: Exists research environment workspace for user
- View only last reseach environment workspace for a project
- REST Service: There exists a research environment workspace for user
- View only the last research environment workspace for a project
- Valid Email Aspect
- EncryptionConverter to encrypt results url
- Coder Configuration
Expand All @@ -217,3 +217,81 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Log App Register Service
- Removal conditions for ProjectBridgeheadDataShield
- Check message for HTTP requests to exporter
- Request Variable annotation
- Optimize JPA configuration
- Compatibility with Authentik
- JWT Decoder configuration
- AST and AST_DATA as query format
- Project Form
- Project Form Services
- Language annotation
- Form PDF Service
- External Execution Not Allowed Profile
- Download Form PDF
- Arrange form fields in the right order in PDF
- DataType in Form PDF
- Form Variables Config
- Fetch Form Templates
- Fetch Form Template Filename
- Current Date in Form Template
- Project Form Fields
- Bridgehead Affiliation
- Form Data Type Date and Timestamp
- HTTP Get methods fetch RequestParam and HTTP Post methods fetch RequestVariable except for uploading files
- Check organizational roles for any bridgehead
- Form Repository
- Fetch all project states depending on project code
- Make user role thread safe
- Log frontend config
- SAMPLES project type
- Project And Form Configuration
- Multiple types pro-project
- Remove the project output service
- Use global conversion service of spring
- Annotated Parameter Wrapper
- Request Parameter
- Synchronization between query outputs and bridgehead executions
- Project context in form template context
- Template Filename
- Send a query with different project types to bridgehead
- List parameters in a controller
- Fetch best form templates
- Description document and related services
- Cohort definition in a query
- Send Query To Bridgehead Event
- Send Query To Bridgehead Event scheduled job
- Send attachments in emails
- Final report services


### Changed
- Rename project state CREATED and ACCEPTED as REVIEW and APPROVAL
- Update to Maven 4
- Update to Java 25
- Remove project bridgehead user with role creator
- View also own-created projects even if they don't belong to own bridgeheads
- View all project bridgeheads for creator
- RequestVariableMethodArgumentResolver for complex datatypes
- Edit form instead of just adding forms to the project
- Add and rename forms instead of editing services
- Notifications only for Project Manager Admin
- Filter templates by selected forms
- Samples project can generate exports not visible to researcher
- there isCustomConfig in the Project as nullable
- Ethical Approval in Project Context
- Data Type Enum for Form Config
- Fetch selected forms returns also preconfigured titles
- Query Details
- There Exists Publication


### Removed
- RStudio Keycloak Groups
- Application Form Services

### Fixed
- Init flyway migration in spring 4
- Jwt decoder configuration
- Full name if the first or last name is missing
- Only one user session at the same time
- Update query outputs correctly
2 changes: 1 addition & 1 deletion Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM eclipse-temurin:21-jre
FROM eclipse-temurin:25-jre

COPY target/project-manager.jar /app/

Expand Down
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