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feat: add ensembl mysql table wrapper #3103

Merged
merged 26 commits into from
Aug 14, 2024
Merged

feat: add ensembl mysql table wrapper #3103

merged 26 commits into from
Aug 14, 2024

Commits on Jul 26, 2024

  1. feat: create ensembl-mysql-table wrapper, start with copy of ensembl-… 

    …biomart-table wrapper
    @dlaehnemann
    dlaehnemann committed Jul 26, 2024
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  2. feat: set up packages / environment defintion for ensembl-mysql-table

    @dlaehnemann
    dlaehnemann committed Jul 26, 2024
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  3. docs: update description of ensembl-mysql-table wrapper

    @dlaehnemann
    dlaehnemann committed Jul 26, 2024
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  4. chore: snakedeploy pin-conda-envs environment.yaml

    @dlaehnemann
    dlaehnemann committed Jul 26, 2024
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Commits on Aug 7, 2024

  1. feat: add completed version of ensembl-mysql-table wrapper (not yet t… 

    …ested)
    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  2. fix: add timeout to initial database connection (for getting database… 

    … names)
    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  3. fix: missing comma

    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  4. fix: consistent renaming of main_table to main_tables where necessary

    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  5. fix: correct str_c syntax

    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  6. fix: clean up the database and table selection, make it clearer to read

    @dlaehnemann
    dlaehnemann committed Aug 7, 2024
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  7. Merge branch 'master' into feat/add-ensembl-mysql-table-wrapper

    @dlaehnemann
    dlaehnemann authored Aug 7, 2024
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Commits on Aug 8, 2024

  1. Merge branch 'master' into feat/add-ensembl-mysql-table-wrapper

    @dlaehnemann
    dlaehnemann authored Aug 8, 2024
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  2. fix: switch to proper dbplyr syntax

    @dlaehnemann
    dlaehnemann committed Aug 8, 2024
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  3. docs: add comment about potential spot for filtering before downloadi… 

    …ng a table
    @dlaehnemann
    dlaehnemann committed Aug 8, 2024
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Commits on Aug 12, 2024

  1. feat: improve test for correct build (start with meta table entry che… 

    …cking, do previously created options as fallback), structure error messages better
    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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  2. Merge branch 'master' into feat/add-ensembl-mysql-table-wrapper

    @dlaehnemann
    dlaehnemann authored Aug 12, 2024
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  3. fix: add url field

    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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  4. Merge branch 'feat/add-ensembl-mysql-table-wrapper' of github.com:sna… 

    …kemake/snakemake-wrappers into feat/add-ensembl-mysql-table-wrapper
    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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  5. docs: attempt at a better description of the ensembl mysql wrapper

    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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  6. docs: clean up species params description

    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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  7. fix: clean up accidental paste...

    @dlaehnemann
    dlaehnemann committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. chore: coderabbit nitpicking

    @dlaehnemann
    dlaehnemann committed Aug 13, 2024
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  2. chore: fix typo 

    Co-authored-by: Till Hartmann <[email protected]>
    @dlaehnemann @tedil
    dlaehnemann and tedil authored Aug 13, 2024
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  3. feat: make table-syntax in params: consistent

    @dlaehnemann
    dlaehnemann committed Aug 13, 2024
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  4. Merge branch 'feat/add-ensembl-mysql-table-wrapper' of github.com:sna… 

    …kemake/snakemake-wrappers into feat/add-ensembl-mysql-table-wrapper
    @dlaehnemann
    dlaehnemann committed Aug 13, 2024
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  5. chore: fix typo 

    Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
    @dlaehnemann @coderabbitai
    dlaehnemann and coderabbitai[bot] authored Aug 13, 2024
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