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Rename functions/variables to remove references to delta lake format
* allow bucket-only ls with s3 cli * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * add s3 cli helper tests * and changes missing from last commit * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Update src/cdm_data_loaders/utils/s3.py Co-authored-by: i alarmed alien <ialarmedalien@users.noreply.github.com> * address review comments --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: i alarmed alien <ialarmedalien@users.noreply.github.com>
Renaming spark_delta => spark
Use berdl_notebook_utils on spark_notebook image
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
* add ncbi promote cli and update docs * remove notebook; update tests * clear notebook output * add promote pipeline tests * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * address review comments --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Update CEPH health check
* add xsv-validator to Dockerfile * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * workaround for potential ceph service race condition --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
* Moving the settings objects to cdm_data_loaders.core * Apply suggestions from code review Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> * fixing missing import * another incorrect import * Another infernal import error * remove -l alias; use generate_aliases where possible * minor rearrangement * fix uniref alias --------- Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
* add xsv module * formatting * Potential fix for pull request finding 'Unused global variable' Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * fix copilot mod * exclude xsv tests from spark test action * use pydantic for validation * formatting --------- Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
* draft pdb manifest pipeline and tests * add tests; fix bug in transfer manifest logic * write walkthrough doc and debug * clean up paths * add missing tests * address reviewer comments * create holdings file parser * remove unused variables * increase trivy timeout
* Move utils.s3 to utils.file_transfer.s3.* * convert new modules to using relocated s3 functions
* Move cli commands to their own module * Removing tests from old module, cleaning up some cruft * remove the cli functions... duh
* Updating checksum module to provide a generic interface to calculate checksums * Updated version of tests
* Adding in missing tests and an interface to upload_fileobj * missing moon
* Minor reorg: - function renaming - use the same mock s3 client for tests where AWS is mocked - centralise values in a DEFAULT config
* Adding new xsv validator mode plus support, with tests. * adding vital fixtures * adding qsv check cmd; updating dockerfile with new qsv version * fix failing tests
Housekeeping
Convert the xsv import pipeline to using the filesystem resource
* Introduce PipelineCli, run_cli cli_args, and non-fatal _save_load_info * Fix failing tests and apply ruff lint/format fixes * Restore stream_to_s3 re-export in streamer.py
Field reorg
…rce LocalInputOutputSettings
Remove destination
update dockerfile and entry point
Adding extra codecov coverage uploads
Removing commented-out code
Adding pipeline report file to output
Bump version from 0.1.10 to 0.1.11
remove infernal spark-based annoyances
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