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TASK-6565 Ensure the CellBase DB adaptors are updated to reflect the latest data releases #700

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TASK-6565 Ensure the CellBase DB adaptors are updated to reflect the latest data releases #700

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Commits on Jul 5, 2024

  1. Prepare next release 5.8.5-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Jul 5, 2024
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Commits on Jul 18, 2024

  1. lib: add DataReleaseSingleton and JUnit tests, #TASK-6565 

    On branch TASK-6565
Changes to be committed:
	new file:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java
	new file:   cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingletonTest.java
    @jtarraga
    jtarraga committed Jul 18, 2024
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  2. lib: update code to use the DataReleaseSingleton and rename some cons… 

    …tants, #TASK-6565

On branch TASK-6565
Changes to be committed:
	modified:   cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/CellBaseDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MissenseVariationFunctionalScoreMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/OntologyMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ProteinMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/PublicationMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/RegulationMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/RepeatsMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/SnpMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/SpliceScoreMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/TranscriptMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/XRefMongoDBAdaptor.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/CellBaseManagerFactory.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/DataReleaseManager.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
    @jtarraga
    jtarraga committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. server: check data release in URL in the GenericRestWSServer, #TASK-6565 

    On branch TASK-6565
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java
	modified:   cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
    @jtarraga
    jtarraga committed Jul 19, 2024
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  2. server: fix check data release in the GenericRestWSServer, #TASK-6565 

    On branch TASK-6565
Changes to be committed:
	modified:   cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
    @jtarraga
    jtarraga committed Jul 19, 2024
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  3. lib: fix check in the singlenton, #TASK-6565 

    On branch TASK-6565
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java
    @jtarraga
    jtarraga committed Jul 19, 2024
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  4. lib: fix checkstyle, #TASK-6565 

    On branch TASK-6565
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java
    @jtarraga
    jtarraga committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. lib: add MongoDB listener to check updates in the data_release collec… 

    …tion, #TASK-6565
    @jtarraga
    jtarraga committed Jul 22, 2024
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Commits on Aug 8, 2024

  1. lib: improve code and exception management in DataReleaseSingleton, #… 

    …TASK-6565
    @jtarraga
    jtarraga committed Aug 8, 2024
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Commits on Aug 13, 2024

  1. Merge branch 'release-6.2.x' into TASK-6565

    @jtarraga
    jtarraga committed Aug 13, 2024
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  2. lib: improve thread management in data release singleton, #TASK-6565

    @jtarraga
    jtarraga committed Aug 13, 2024
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  3. lib: fix checkstyle issue, #TASK-6565

    @jtarraga
    jtarraga committed Aug 13, 2024
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Commits on Sep 20, 2024

  1. Merge branch 'release-6.x.x' into TASK-6565

    @jtarraga
    jtarraga committed Sep 20, 2024
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Commits on Oct 1, 2024

  1. core: fix configuration file by removing 'conflicts' messages, #TASK-… 

    …6565
    @jtarraga
    jtarraga committed Oct 1, 2024
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