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.

Sign up for GitHub

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

Jump to bottom

TASK-6780 - Port Patch 6.2.1 -> 7.0.0 - Xetabase 2.2.1 -> 3.0.0 #711

Merged
merged 47 commits into from
Oct 14, 2024
Merged

TASK-6780 - Port Patch 6.2.1 -> 7.0.0 - Xetabase 2.2.1 -> 3.0.0 #711

merged 47 commits into from
Oct 14, 2024

Commits on Mar 4, 2024

  1. Merge branch 'release-6.0.x'

    @juanfeSanahuja
    juanfeSanahuja committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    72fd3ce View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. Prepare release 5.8.2

    @juanfeSanahuja
    juanfeSanahuja committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    08fd34a View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2024

  1. Prepare release 6.0.0

    @juanfeSanahuja
    juanfeSanahuja committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    8e79271 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'develop'

    @juanfeSanahuja
    juanfeSanahuja committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    d5c4959 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'release-6.0.x'

    @juanfeSanahuja
    juanfeSanahuja committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    2de3679 View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2024

  1. Prepare next release 5.8.4-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    4120c5c View commit details
    Browse the repository at this point in the history

Commits on May 21, 2024

  1. Merge branch 'release-6.1.x'

    @juanfeSanahuja
    juanfeSanahuja committed May 21, 2024
    Configuration menu
    Copy the full SHA
    8b1829b View commit details
    Browse the repository at this point in the history

Commits on May 30, 2024

  1. cicd: Update action version to test for compatibility with test and r… 

    …elease process #TASK-6264
    @juanfeSanahuja
    juanfeSanahuja committed May 30, 2024
    Configuration menu
    Copy the full SHA
    a618d75 View commit details
    Browse the repository at this point in the history

Commits on Jun 4, 2024

  1. lib: use the same OpenCGA normalization parameters in the "build" for… 

    … clinical variants, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalIndexer.java
    @jtarraga
    jtarraga committed Jun 4, 2024
    Configuration menu
    Copy the full SHA
    9ab2fe6 View commit details
    Browse the repository at this point in the history

  2. lib: update configuration file to download last versions of ClinVar a… 

    …nd Gwas, files to download; and update Cosmic version, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-core/src/main/resources/configuration.yml
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/ClinicalDownloadManager.java
    @jtarraga
    jtarraga committed Jun 4, 2024
    Configuration menu
    Copy the full SHA
    499407d View commit details
    Browse the repository at this point in the history

  3. core: update the configuration file to download the most recent versi… 

    …on of the GWAS Catalog, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-core/src/main/resources/configuration.yml
    @jtarraga
    jtarraga committed Jun 4, 2024
    Configuration menu
    Copy the full SHA
    45987b9 View commit details
    Browse the repository at this point in the history

  4. lib: update ClinVar filename, version and date to the most recent ver… 

    …sion, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
    @jtarraga
    jtarraga committed Jun 4, 2024
    Configuration menu
    Copy the full SHA
    9b4e446 View commit details
    Browse the repository at this point in the history

Commits on Jun 12, 2024

  1. lib: catch exceptions when parsing ClinVar file, #TASK-6347 

    On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
    @jtarraga
    jtarraga committed Jun 12, 2024
    Configuration menu
    Copy the full SHA
    9b91471 View commit details
    Browse the repository at this point in the history

Commits on Jun 18, 2024

  1. lib: add NCBI ID support for dbSNP file (and .tbi) when parsing GWAS … 

    …file; and fix some sonnar issues, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/GwasIndexer.java
    @jtarraga
    jtarraga committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    f11f507 View commit details
    Browse the repository at this point in the history

Commits on Jun 25, 2024

  1. cicd: Create branch and pull-reques-approved.yml #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jun 25, 2024
    Configuration menu
    Copy the full SHA
    547c8fe View commit details
    Browse the repository at this point in the history

  2. cicd: added script xetabase_branch #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jun 25, 2024
    Configuration menu
    Copy the full SHA
    d00ef5b View commit details
    Browse the repository at this point in the history

  3. lib: improve log messages for ClinVar indexer, #TASK-6347 

    On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
    @jtarraga
    jtarraga committed Jun 25, 2024
    Configuration menu
    Copy the full SHA
    f820260 View commit details
    Browse the repository at this point in the history

Commits on Jun 26, 2024

  1. Merge pull request #693 from opencb/TASK-6347 

    TASK-6347 Fix normalization issue in ClinVar
    @jtarraga
    jtarraga authored Jun 26, 2024
    Configuration menu
    Copy the full SHA
    dcbb95c View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2024

  1. cicd: added script get-xetabase-branch #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    60abe58 View commit details
    Browse the repository at this point in the history

Commits on Jul 5, 2024

  1. Prepare release 5.8.4

    @juanfeSanahuja
    juanfeSanahuja committed Jul 5, 2024
    Configuration menu
    Copy the full SHA
    73057b5 View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2024

  1. Merge branch 'release-6.2.x'

    @juanfeSanahuja
    juanfeSanahuja committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    6039f5d View commit details
    Browse the repository at this point in the history

  2. Prepare new development branch release-6.2.x

    @juanfeSanahuja
    juanfeSanahuja committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    386a510 View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2024

  1. Merge branch 'release-6.2.x' into TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    280bb79 View commit details
    Browse the repository at this point in the history

Commits on Jul 30, 2024

  1. Prepare Port patch #TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Jul 30, 2024
    Configuration menu
    Copy the full SHA
    b52c83d View commit details
    Browse the repository at this point in the history

  2. Merge branch 'release-6.2.x' into TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Jul 30, 2024
    Configuration menu
    Copy the full SHA
    1c1d8a2 View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2024

  1. Prepare Port Patch Cellbase 5.8.3 -> 6.2.1 #TASK-6647

    @juanfeSanahuja
    juanfeSanahuja committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    0f2a6d2 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'release-6.2.x' into TASK-6647

    @juanfeSanahuja
    juanfeSanahuja committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    bb51d33 View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2024

  1. Merge pull request #705 from opencb/TASK-6647-rel 

    TASK-6647 - Fix Port Patch 1.10.4 -> 2.2.1 - release
    @juanfeSanahuja
    juanfeSanahuja authored Aug 8, 2024
    Configuration menu
    Copy the full SHA
    70351e9 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'release-6.2.x' into TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Aug 8, 2024
    Configuration menu
    Copy the full SHA
    c63bafb View commit details
    Browse the repository at this point in the history

Commits on Aug 14, 2024

  1. Merge branch 'release-6.2.x' into TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    559ddb2 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #694 from opencb/TASK-6399 

    TASK-6399 - CI/CD: Include save reports option for tasks workflows
    @juanfeSanahuja
    juanfeSanahuja authored Aug 14, 2024
    Configuration menu
    Copy the full SHA
    9e3b773 View commit details
    Browse the repository at this point in the history

Commits on Aug 19, 2024

  1. Merge branch 'release-6.2.x' into TASK-6515

    @pfurio
    pfurio authored Aug 19, 2024
    Configuration menu
    Copy the full SHA
    4e09f2d View commit details
    Browse the repository at this point in the history

Commits on Aug 20, 2024

  1. Merge pull request #702 from opencb/TASK-6515 

    TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1
    @j-coll
    j-coll authored Aug 20, 2024
    Configuration menu
    Copy the full SHA
    a73579e View commit details
    Browse the repository at this point in the history

Commits on Sep 4, 2024

  1. cicd: Upload reference to develop branch in pull-request-approve to t… 

    …est-xetabase-workflow #TASK-6807
    @juanfeSanahuja
    juanfeSanahuja committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    8bde7d1 View commit details
    Browse the repository at this point in the history

Commits on Sep 9, 2024

  1. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 9, 2024
    Configuration menu
    Copy the full SHA
    2a0983a View commit details
    Browse the repository at this point in the history

Commits on Sep 10, 2024

  1. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    df4f83d View commit details
    Browse the repository at this point in the history

  2. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    7762ee8 View commit details
    Browse the repository at this point in the history

Commits on Sep 12, 2024

  1. Merge pull request #707 from opencb/TASK-6807 

    TASK-6807 - Pull request approve workflow Fail
    @juanfeSanahuja
    juanfeSanahuja authored Sep 12, 2024
    Configuration menu
    Copy the full SHA
    40f9b10 View commit details
    Browse the repository at this point in the history

Commits on Sep 13, 2024

  1. Prepare release 6.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    16a1eaa View commit details
    Browse the repository at this point in the history

  2. Prepare next release 6.2.2-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    44f8662 View commit details
    Browse the repository at this point in the history

  3. Prepare release 6.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    ae52617 View commit details
    Browse the repository at this point in the history

  4. Prepare release 6.2.0

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    b86ce69 View commit details
    Browse the repository at this point in the history

  5. Prepare release 6.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    67f14a0 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'release-6.2.x'

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    6b51c11 View commit details
    Browse the repository at this point in the history

  7. Prepare release 6.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    b7ce5b1 View commit details
    Browse the repository at this point in the history

Commits on Oct 3, 2024

  1. Port Patch 6.2.1 -> 7.0.0 XB 2.2.1 -> 3.0.0 #TASK-6780

    @juanfeSanahuja
    juanfeSanahuja committed Oct 3, 2024
    Configuration menu
    Copy the full SHA
    d3521cd View commit details
    Browse the repository at this point in the history

  2. Merge branch 'develop' into TASK-6780

    @juanfeSanahuja
    juanfeSanahuja committed Oct 3, 2024
    Configuration menu
    Copy the full SHA
    454c24a View commit details
    Browse the repository at this point in the history