Update for the ena upload tool: added ISA json support, changed phrasings, moved macro's,... #5802
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@bgruening This pull request brings some improvements to the interface + adds the new feature that was brought to ENA-upload-cli, ISA-JSON support. I think we can close #5691 . |
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Thanks @B0r1sD for all the improvements! |
tools/ena_upload/ena_upload.xml
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| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
| <has_n_columns n="17"/> | ||
| <!-- <has_line_matching expression="alias\tstudy_alias\tsample_alias\tlibrary_name\ttitle\taccession\tsubmission date\tstatus\tdesign_description\tlibrary_source\tlibrary_strategy\tlibrary_selection\tlibrary_layout\tinsert_size\tplatform\tinstrument_model\tsubmission_date"/> --> |
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should this go in again? some more assertions?
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We had some problems with letting it match for some weird reason. Although we where using the exact same "correct" output as matching expression, the test kept complaining :(
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Ok I was able to bring 3 out of 4 back in without problems!
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Ok I think the feedback is implemented, let me know if we should improve something else! |
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@bgruening Anything that should still be done? |
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Attention: deployment failure! https://github.com/galaxyproject/tools-iuc/actions/runs/8404730682 |
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Restarted |
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Thanks :) |
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@bgruening or @bernt-matthias thank a lot for merging this! How long does it take on average for a tool to be available in the toolshed? |
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Should be already there. |
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https://toolshed.g2.bx.psu.edu/repository?repository_id=0db04aa13ef9d2f8 shows me that there is a more resent revision but the dropdown itself does not visualize it, and neither does it in de galaxy instance if I have to believe our admins .. :/ |
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Hmm. Odd. All looks good (also here) except for the dropdown. |
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Weirdly the latest tool that has been updated on this repo compleasm, did get a correct new version in the toolshed. So it is a problem specific to this one. Could the failed action have caused a problem? and should I trigger a ne version? |
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Can you report the issue here: https://github.com/galaxyproject/usegalaxy-playbook/issues and ask if bumping might be an option? |
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What do you mean by bumping ? The usegalaxy playbook is for deploying playbooks, that's not a good place to report anything. Here or the galaxy repo are good places. |
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Looks like the first upload timed out but succeeded without creating the repository metadata, the second upload didn't do anything. @bernt-matthias try uploading manually with some whitespace change ? |
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I updated manually. |
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Thanks a lot everyone! |
FOR CONTRIBUTOR: