0.5.2

What's Changed

• Automatic check if an object already exists on ENA by @bedroesb in #60

Full Changelog: 0.5.1...0.5.2

0.5.1

What's Changed

• Hotfix for release/cancel to not require files by @bedroesb in #57
• Adding support for old sheet names + error handling when sheet is missing in xlsx template by @bedroesb in #58
• Hotfix by @bedroesb in #59

Full Changelog: 0.5.0...0.5.1

0.5.0

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!

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)

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)

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])

0.4.2

Merged pull requests:

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

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

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

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)