chore: promote main changes

[brunopacheco1]

Summary by Sourcery

Promote changes from the main branch, including refactoring CKAN-related components, updating dependencies, and enhancing the build and deployment setup. Add new tests and remove obsolete code related to organization queries.

Enhancements:

• Refactor the CKAN filter builder and dataset repository to use builder pattern for constructing requests.
• Update the CKAN datasets repository to use a new mapper for dataset mapping.

Build:

• Upgrade dependencies in the pom.xml, including Lombok, Quarkus OpenAPI Generator, and MapStruct.
• Add MapStruct dependencies to the project for object mapping.

CI:

• Update Trivy vulnerability scanner version in GitHub workflows.
• Update reuse-action version in GitHub workflows.

Deployment:

• Add Dockerfile and docker-compose.yml for containerizing and running the application locally.
• Add start and stop scripts for managing the Docker-based local environment.

Tests:

• Add tests for CKAN datasets mapper and filter mapper.
• Add integration and unit tests for retrieving filter values.

Chores:

• Remove unused classes and files related to organization queries and CKAN utilities.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request implements significant refactoring to modernize the codebase, primarily focusing on introducing MapStruct for object mapping, reorganizing filter-related functionality, and cleaning up unused code. The changes improve code maintainability and introduce new filter value retrieval capabilities.

Class diagram for CkanDatasetsMapper and CkanFilterMapper

classDiagram
    class CkanDatasetsMapper {
        +RetrievedDataset map(CkanPackage ckanPackage)
        +ValueLabel map(CkanValueLabel ckanValueLabel)
        +ValueLabel map(CkanTag ckanTag)
        +RetrievedDistribution map(CkanResource ckanResource)
        +List<SearchedDataset> map(PackagesSearchResult result)
    }
    class CkanFilterMapper {
        +List<ValueLabel> map(PackagesSearchResponse packagesSearchResponse, String key)
        +List<ValueLabel> map(Map<String, CkanFacet> ckanFacets, String key)
        +List<ValueLabel> map(CkanFacet ckanFacet)
        +List<ValueLabel> map(List<CkanValueLabel> items)
        +ValueLabel map(CkanValueLabel valueLabel)
    }

Class diagram for RetrieveFiltersValuesQuery and CkanFiltersRepository

classDiagram
    class RetrieveFiltersValuesQuery {
        -FiltersRepository filtersRepository
        +List<ValueLabel> execute(String key)
    }
    class CkanFiltersRepository {
        -CkanQueryApi ckanQueryApi
        -CkanFilterMapper ckanFilterMapper
        +List<ValueLabel> getValuesForFilter(String key)
    }

File-Level Changes

Change	Details	Files
Introduced MapStruct for object mapping	Created CkanDatasetsMapper interface with MapStruct annotations for dataset mapping Added CkanFilterMapper for handling filter value mapping Implemented comprehensive unit tests for the new mappers	src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/ckan/mapper/CkanDatasetsMapper.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/mapper/CkanFilterMapper.java src/test/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/ckan/mapper/CkanDatasetsMapperTest.java src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/mapper/CkanFilterMapperTest.java
Added new filter values retrieval functionality	Created new endpoint for retrieving filter values Implemented FiltersRepository interface and CkanFiltersRepository Added RetrieveFiltersValuesQuery use case Created integration and unit tests for filter values retrieval	src/main/java/io/github/genomicdatainfrastructure/discovery/filters/application/ports/FiltersRepository.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/ckan/CkanFiltersRepository.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/application/usecases/RetrieveFiltersValuesQuery.java src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersValuesQueryTest.java
Removed deprecated organization-related code	Removed organization API implementation Deleted organization repository and related classes Removed organization query use case	src/main/java/io/github/genomicdatainfrastructure/discovery/api/OrganizationQueryApiImpl.java src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/application/ports/OrganizationsRepository.java src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/ckan/persistence/CkanOrganizationsRepository.java
Updated infrastructure configuration	Added Docker Compose setup for local development Created scripts for starting and stopping the application Updated GitHub workflow configurations Updated dependencies and Quarkus version	infra/docker-compose.yml infra/start.sh infra/stop.sh .github/workflows/main.yml .github/workflows/release.yml .github/workflows/test.yml pom.xml

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