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Standardize CLI #96

Merged
merged 21 commits into from
Oct 13, 2022
Merged

Standardize CLI #96

merged 21 commits into from
Oct 13, 2022

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ielis
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@ielis ielis commented Oct 6, 2022

Improve CLI structure, work on documentation and improve format sniffing.

ielis and others added 20 commits October 5, 2022 12:53
@ielis
Simplify CLI commands.
4bd2c04 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Draft CLI documentation.
2b7751c 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Improve format sniffing and extract the code into util module.
57a5a29 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add Gender constants.
bc3401e 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Setup common CLI options and I/O workflow.
2444e62 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Write to STDOUT only, improve CLI documentation, logging. Add banner.
baffdb2 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Improve Javadocs, improve logging.
c0d151b 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Separate functions for reading and writing within the base command.
c72e440 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Draft validation command and output formatting.
4028674 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Print banner in examples command.
d3ab396 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Support multiple inputs as well as STDIN for validate and convert.
91459f7 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Group CLI arguments into sections.
b278157 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Work on documentation.
4aeff6e 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@pnrobinson
fixing vcf record JSON Schema ($ref)
844a0aa
@pnrobinson
Adding functions for unknown/not provided ACMG and actionability
e978326
@pnrobinson
Moving example to supplement
78fd2e3
@pnrobinson
removing -o option
e694f72
@pnrobinson
don't print empty disease onset. Fix inexistant ACMG/Actionability co…
d8ee811 
…nversion bug
@pnrobinson
documentation
b98b3e4
@pnrobinson
documentation update
d3b4f03
@ielis ielis marked this pull request as ready for review October 13, 2022 15:53
@ielis ielis merged commit afaddc7 into phenopackets:develop Oct 13, 2022
@ielis ielis deleted the standardize_cli branch October 13, 2022 15:58
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@ielis @pnrobinson