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Add bug fixes from master to v1.2.0 #52

Merged
merged 19 commits into from
Apr 11, 2024
Merged

Add bug fixes from master to v1.2.0 #52

merged 19 commits into from
Apr 11, 2024

Commits on Feb 9, 2024

  1. Merge pull request #27 from CDCgov/final-merged 

    remove unwanted files
    @rchau88
    rchau88 committed Feb 9, 2024
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  2. Merge pull request #28 from CDCgov/final-merged 

    Final merged
    @rchau88
    rchau88 committed Feb 9, 2024
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  3. Create codeql-analysis.yml (#25)

    @dthoward96
    dthoward96 committed Feb 9, 2024
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  4. Create codeql.yml (#29)

    @dthoward96
    dthoward96 committed Feb 9, 2024
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Commits on Feb 12, 2024

  1. Dthoward96 workflow correction (#30) 

    * Delete .github/workflows/codeql-analysis.yml

* Delete .github/workflows/python-package-mamba.yml
    @dthoward96
    dthoward96 committed Feb 12, 2024
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  2. Add files via upload (#31)

    @dthoward96
    dthoward96 committed Feb 12, 2024
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Commits on Feb 16, 2024

  1. bug fix process.py (#32) 

    Missing a return for config file function and correcting a error message to print the correct df
    @dthoward96
    dthoward96 committed Feb 16, 2024
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Commits on Feb 22, 2024

  1. Create GHCR_docker.yml (#33) 

    * Create GHCR_docker.yml

* Update GHCR_docker.yml

Correct changes for master branch
    @dthoward96
    dthoward96 committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. FTP folder bug fix submit.py (#34) 

    Some FTP accounts have the folder structure /submit/Production/ instead of /Production/. This fix automatically corrects for this difference in folder structure.
    @dthoward96
    dthoward96 committed Feb 23, 2024
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  2. update template metadata required fields + check submitting databases… 

    … are valid
    @rchau88
    rchau88 committed Feb 23, 2024
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  3. Merge pull request #37 from CDCgov/fix_template_metadata 

    update template metadata with required fields for flu
    @rchau88
    rchau88 committed Feb 23, 2024
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Commits on Mar 6, 2024

  1. Update process.py 

    removed the gs-sequence_name specified for flu
    @rchau88
    rchau88 committed Mar 6, 2024
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  2. Merge pull request #39 from CDCgov/rchau88-patch-1 

    Update process.py
    @rchau88
    rchau88 committed Mar 6, 2024
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Commits on Mar 8, 2024

  1. Create docker_test_build.yml (#41) 

    automatic test builds dockerfile on pull request. This will prevent merging to master if Dockerfile fails to build correctly.
    @dthoward96
    dthoward96 committed Mar 8, 2024
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  2. Dthoward96 org id patch (#42) 

    * Update cov_config.yaml

remove org_id from examples

* Update flu_config.yaml

remove org_id from examples

* Update create.py

remove org_id from xml creation
    @dthoward96
    dthoward96 committed Mar 8, 2024
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Commits on Mar 12, 2024

  1. Dthoward96 bugfix (#45) 

    * Update report.py

Bug fix to allow for other submit folders in FTP of ncbi

* Update process.py

bug fix for capitalization of folder name
    @dthoward96
    dthoward96 committed Mar 12, 2024
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Commits on Apr 3, 2024

  1. Add files via upload (#49) 

    Changes requirement from only isolate to require either strain or isolate for BioSample and GenBank
    @dthoward96
    dthoward96 committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. create.py duplicate strain name bug (#50) 

    Fixes issue that creates duplicate strain columns when using src-strain
    @dthoward96
    dthoward96 committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. Bug fix process.py (#51) 

    Bug fix for upload log. When only one database was submitted it, it would convert the database name into a list and error out.
    @dthoward96
    dthoward96 committed Apr 5, 2024
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