Releases | Open Source Science

ena-upload-cli - 0.9.0 - Unencrypted checksum support

What's Changed

Add unencrypted checksum support by @cgirardot in https://github.com/usegalaxy-eu/ena-upload-cli/pull/107
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/113
removed the auth=ENA from URL by @cgirardot in https://github.com/usegalaxy-eu/ena-upload-cli/pull/112

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.8.0...0.9.0

- Python
Published by bedroesb 10 months ago

ena-upload-cli - 0.8.0 - Custom attributes and read info support

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/105
Allow for custom attributes and read type description of fastq by @cgirardot in https://github.com/usegalaxy-eu/ena-upload-cli/pull/102

New Contributors

@cgirardot made their first contribution in https://github.com/usegalaxy-eu/ena-upload-cli/pull/102

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.7.5...0.8.0

- Python
Published by bedroesb about 1 year ago

ena-upload-cli - 0.7.5 - Resolved compatibility issues

What's Changed

Improved use of GitHub Actions + pandas warning fix by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/101
Bugfix paired end reads throwing type error by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/103

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.7.4...0.7.5

- Python
Published by bedroesb about 1 year ago

What's Changed

pyyaml 5.4.* is giving problems upon installation by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/97

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.7.3...0.7.4

- Python
Published by bedroesb over 1 year ago

ena-upload-cli - 0.7.3 - Trigger new release

This release is an attempt to trigger the automatic BioConda recipe updating process.

- Python
Published by bedroesb almost 2 years ago

ena-upload-cli - 0.7.2 - Support for latest checklists + timeout fix

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/91
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/92
Increase timeouts and improve handling of high-latency connections by @nuwang in https://github.com/usegalaxy-eu/ena-upload-cli/pull/93
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/94

New Contributors

@nuwang made their first contribution in https://github.com/usegalaxy-eu/ena-upload-cli/pull/93

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.7.1...0.7.2

- Python
Published by bedroesb almost 2 years ago

ena-upload-cli - 0.7.1 - ISA-json support fix

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/89
Bugfix: isa-json not working when tool is not launched in the ENA-upload-cli directory by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/90

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.7.0...0.7.1

- Python
Published by bedroesb about 2 years ago

ena-upload-cli - 0.7.0 - ISA-JSON support + better validation

What's Changed

Bug fix: mandatory fields are handled better when not filled in by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/71
Adding ISA-JSON support as input file. by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/88

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.6.3...0.7.0

- Python
Published by bedroesb about 2 years ago

ena-upload-cli - 0.6.3 - Add support for pandas 2.0

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/81
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/82
Add support for pandas 2.0 support + lock versions by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/84

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.6.2...0.6.3

- Python
Published by bedroesb over 2 years ago

ena-upload-cli - 0.6.2 - Updated checklists

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/74
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/76
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/77
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/78
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/79
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/80

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.6.1...0.6.2

- Python
Published by bedroesb almost 3 years ago

ena-upload-cli - 0.6.1 - Updated checklists

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/72
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/73

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.6.0...0.6.1

- Python
Published by bedroesb over 3 years ago

ena-upload-cli - 0.6.0 - Better and new templates + bugfix

What's Changed

Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/63
Automatic update of ENA Sample Checklists by @github-actions in https://github.com/usegalaxy-eu/ena-upload-cli/pull/64
Adding units to templates by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/67
Bug fix for the remote check by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/69

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.5.3...0.6.0

- Python
Published by bedroesb almost 4 years ago

What's Changed

Fixing float giving error when parsed in the xml by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/61

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.5.2...0.5.3

- Python
Published by bedroesb about 4 years ago

What's Changed

Automatic check if an object already exists on ENA by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/60

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.5.1...0.5.2

- Python
Published by bedroesb about 4 years ago

What's Changed

Hotfix for release/cancel to not require files by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/57
Adding support for old sheet names + error handling when sheet is missing in xlsx template by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/58
Hotfix by @bedroesb in https://github.com/usegalaxy-eu/ena-upload-cli/pull/59

Full Changelog: https://github.com/usegalaxy-eu/ena-upload-cli/compare/0.5.0...0.5.1

- Python
Published by bedroesb about 4 years ago

With this release we would like to highlight a new feature: using xlsx templates as input file for the metadata instead of the usual (1-4) tsv tables. For every sample checklist you can find an example of such a xlsx template on this repo. Read more about in our readme!

- Python
Published by bedroesb about 4 years ago

ena-upload-cli - 0.4.5

Implemented enhancements:

Supporting all optional fields in the run/experiment and study xml #37

Closed issues:

Empty rows give error #52
Support FTPS connection to protect account credidentials #48
Add GitHub Action to check if new xsd templates are added to ENA #14

Merged pull requests:

FTPS stability and speed improvements #55 (bedroesb)
Drop empty rows #54 (bedroesb)
Updating introduction #51 (bedroesb)
Correct use of optional attributes in run/experiment and study tables #46 (bedroesb)

- Python
Published by bedroesb about 4 years ago

ena-upload-cli - 0.4.4

Implemented enhancements:

Changing release date through API #36
If table is given without action values, an error is thrown #34

Merged pull requests:

Adding TLS to the ftp connection #50 (bedroesb)
Create CITATION.cff #49 (bedroesb)
Adding release and cancel as an action #41 (bedroesb)

- Python
Published by bedroesb about 4 years ago

ena-upload-cli - 0.4.3

Implemented enhancements:

Adding flag to not do a submission but just to generate the XMLs #43
If table is given without action values, an error is thrown #34

Merged pull requests:

Handling tables that have no actions in the status column #45 (bedroesb)
Adding draft flag to not perform a submission #44 (bedroesb)
Automatic update of ENA Sample Checklists #42 (github-actions[bot])

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.4.2

Merged pull requests:

Adding back tool name to sample metadata #39 (bedroesb)

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.4.1

This new version includes especially bug fixes.

Fixed bugs:

--no_upload parameter not working #33
Most minimal example not working #29

Closed issues:

Possible values for file_format are not clear #30

Merged pull requests:

Generating md5 hash when not given with -no_upload flag #35 (bedroesb)
Updating documentation about modify #32 (bedroesb)
Fixing template to allow no filled in optional fields #31 (bedroesb)
Fixing bug if empty cell for file_checksum column #28 (bedroesb)

IMPORTANT: the no_upload flag is changed to a more understanding flag: --no_data_upload

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.4.0

Implemented enhancements:

Dropping unnecessary columns #21
Adding support for all official ENA checklists #20
Possibility to give the taxon_id through the table #6

Closed issues:

Library name generation #23

Merged pull requests:

Taxon ID parsing improvements #27 (bedroesb)
Adding support for all official sample checklists on ENA #26 (bedroesb)
Taking away the need to give columns that are automatically filled in by the tool #25 (bedroesb)
Allow to skip file upload and provide a file of filenames as source for data files #24 (mobilegenome)
Adding support for multiple checklists #19 (bedroesb)
Read md5sum from table, and only generate if missing #18 (mobilegenome)
Add ENA_template_ERC000011_sample.xml #17 (rabuono)
Small fixes based on #15 #16 (bedroesb)

NOTE: This release is not backwards compatible with previous release! Check following things if you update from 0.3.1 or earlier: - Headers in the sample table will now follow the exact vocabulary as on ENA - The --vir parameter is not supported anymore and is replaced by --checklist ERC000033 + support for all official checklists - The scientific_name column in the sample table is not mandatory anymore + the taxon_id column is recommended instead - Sample columns accession,submission_date, status are not needed anymore

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.3.1

Support for all optional and recommended fields for viral submissions based on the ERC000033 checklist
Support for empty values in optional and recommended fields (these will not be included in the final XML)

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.3.0

This release includes: - Updated the XSD templates from ENA enabling correct local validations of the tables - Updated XML templates to support new fields - Replacing the curl dependency with the requests library from python (thank you @mobilegenome!) - --version option to print out the version of the tool

- Python
Published by bedroesb over 4 years ago

ena-upload-cli - 0.2.8

Support for non mandatory columns in the viral sample table (Thanks @tpall !)

- Python
Published by bedroesb almost 5 years ago

ena-upload-cli - 0.2.7

Better parsing of accession numbers and outputted in stdout in a tab separated manner
Receipt is outputted as a receipt.xml file in the working directory
Better handling of errors that do not produce a receipt
Dropping support for python v2.X

- Python
Published by bedroesb almost 5 years ago

ena-upload-cli - Zenodo release

- Python
Published by bgruening about 5 years ago

ena-upload-cli - 0.2.5

--tool option split in two: --tool TOOLNAME default='ena-upload-cli' and `--toolversion` TOOL_VERSION default='0.2.5'
--tool is not a mandatory option anymore
toolname and toolversion used for extra metadata fields in run, experiment, study and sample tables: <RUN_ATTRIBUTES> <RUN_ATTRIBUTE> <TAG>SUBMISSION_TOOL</TAG> <VALUE>${tool_name}</VALUE> </RUN_ATTRIBUTE> <RUN_ATTRIBUTE> <TAG>SUBMISSION_TOOL_VERSION</TAG> <VALUE>${tool_version}</VALUE> </RUN_ATTRIBUTE> </RUN_ATTRIBUTES>

- Python
Published by bedroesb about 5 years ago