Feat: alphanumeric + variant filters

[admy7]

Summary by Sourcery

Implement alphanumeric filters to enhance dataset querying capabilities, refactor the facet system to a filter-based approach, and update tests and documentation accordingly.

New Features:

• Introduce alphanumeric filters for querying datasets, allowing more flexible and precise data retrieval.

Enhancements:

• Refactor the existing facet system to a more generalized filter system, improving the structure and clarity of the codebase.
• Update the OpenAPI specifications to reflect the new filter system, replacing facets with filters.

Tests:

• Add new tests for the alphanumeric filter functionality to ensure correct implementation and behavior.
• Refactor existing tests to align with the new filter system, ensuring continued test coverage and reliability.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request implements significant changes to the filtering and facet handling in the discovery service, transitioning from a facet-based approach to a more flexible filter-based system. The changes include updates to the API, data models, and the introduction of new strategies for handling different types of filters, particularly for Beacon integration.

Sequence diagram for filter retrieval process

sequenceDiagram
    actor User
    participant Client
    participant FilterController
    participant RetrieveFiltersQuery
    participant FilterBuilder
    User->>Client: Request filters
    Client->>FilterController: GET /api/v1/filters
    FilterController->>RetrieveFiltersQuery: execute(accessToken)
    RetrieveFiltersQuery->>FilterBuilder: build(accessToken)
    FilterBuilder-->>RetrieveFiltersQuery: List of Filters
    RetrieveFiltersQuery-->>FilterController: List of Filters
    FilterController-->>Client: Response with Filters
    Client-->>User: Display Filters

ER diagram for updated filter data model

erDiagram
    DATASET_SEARCH_QUERY_FACET {
        STRING source
        STRING type
        STRING key
        STRING value
        STRING operator
        STRING entries
    }
    FILTER {
        STRING source
        STRING type
        STRING key
        STRING label
        STRING values
        STRING operators
        STRING entries
    }
    DATASET_SEARCH_QUERY_FACET ||--o{ FILTER : "maps to"
    FILTER ||--o{ VALUE_LABEL : "has"
    FILTER ||--o{ FILTER_ENTRY : "has"
    VALUE_LABEL {
        STRING label
        STRING value
    }
    FILTER_ENTRY {
        STRING id
        STRING label
    }

Updated class diagram for filter handling

classDiagram
    class DatasetSearchQueryFacet {
        - String source
        - FilterType type
        - String key
        - String value
        - Operator operator
        - List~QueryEntry~ entries
    }
    class FilterType {
        <<enumeration>>
        DROPDOWN
        FREE_TEXT
        ENTRIES
    }
    class Operator {
        <<enumeration>>
        EQUALS
        GREATER_THAN
        LESS_THAN
        DIFFERENT
        CONTAINS
    }
    class QueryEntry {
        - String label
        - String value
    }
    class Filter {
        - String source
        - FilterType type
        - String key
        - String label
        - List~ValueLabel~ values
        - List~Operator~ operators
        - List~FilterEntry~ entries
    }
    class ValueLabel {
        - String label
        - String value
    }
    class FilterEntry {
        - String id
        - String label
    }
    DatasetSearchQueryFacet --> FilterType
    DatasetSearchQueryFacet --> Operator
    DatasetSearchQueryFacet --> QueryEntry
    Filter --> FilterType
    Filter --> ValueLabel
    Filter --> Operator
    Filter --> FilterEntry

File-Level Changes

Change	Details	Files
Renamed and restructured facet-related components to filter-related components	Renamed 'Facet' to 'Filter' in various classes and interfaces Updated API endpoints from '/search-facets' to '/filters' Refactored 'FacetsBuilder' interface to 'FilterBuilder' Renamed 'RetrieveFacetsQuery' to 'RetrieveFiltersQuery'	src/main/openapi/discovery.yaml src/main/java/io/github/genomicdatainfrastructure/discovery/filters/application/ports/FilterBuilder.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/application/usecases/RetrieveFiltersQuery.java
Introduced new filter types and strategies for Beacon integration	Created 'FilterType' enum with DROPDOWN, FREE_TEXT, and ENTRIES types Implemented 'OntologyFilterStrategy' for handling ontology-based filters Implemented 'AlphanumericFilterStrategy' for free-text filters Implemented 'VariantFilterStrategy' for handling genetic variant filters Created 'FilterStrategyContext' to manage different filter strategies	src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/beacon/strategies/OntologyFilterStrategy.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/beacon/strategies/AlphanumericFilterStrategy.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/beacon/strategies/VariantFilterStrategy.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/beacon/strategies/FilterStrategyContext.java
Updated Beacon integration to support new filter system	Refactored 'BeaconIndividualsRequestMapper' to handle new filter types Updated 'BeaconFilterBuilder' to use new filter strategies Modified Beacon API models to support new filter structure	src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/beacon/persistence/BeaconIndividualsRequestMapper.java src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/beacon/BeaconFilterBuilder.java src/main/openapi/beacon.yaml
Updated CKAN integration to support new filter system	Refactored 'CkanFacetsQueryBuilder' to 'CkanFilterBuilder' Updated CKAN-related classes to use new filter structure	src/main/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/ckan/CkanFilterBuilder.java src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/ckan/persistence/CkanFacetsQueryBuilder.java
Updated and added tests for new filter system	Renamed and updated existing facet-related tests to filter-related tests Added new tests for filter strategies and builders Updated integration tests to reflect new API structure	src/test/java/io/github/genomicdatainfrastructure/discovery/filters/infrastructure/quarkus/RetrieveFiltersTest.java src/test/java/io/github/genomicdatainfrastructure/discovery/filters/application/usecases/RetrieveFiltersQueryTest.java src/test/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/ckan/CkanFacetsQueryBuilderTest.java

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[brunopacheco1]

@admy7 thanks for you patience. Let's wait the frontend change a bit and merge both at the same time.