Closed jwokaty closed 3 years ago
lwaldron
commented
3 years ago Thanks @jwokaty. @paolinomanghi, we should touch base next week about metadata cleanup, and enlist some additional help if needed to fix everything that's due to be released in cMD 3.0. I see some other issues on the gh-pages site too (https://waldronlab.io/curatedMetagenomicDataCuration).
paolinomanghi
commented
3 years ago The errors appear because I merged the pull request you asked me to merge. I told you there would have been several errors. I suggest to delete these files for now, as including them in the current release would mean restart the manuscript from scratch.
On Fri, Apr 2, 2021 at 9:30 PM Levi Waldron @.***> wrote:
Thanks @jwokaty https://github.com/jwokaty. @paolinomanghi https://github.com/paolinomanghi, we should touch base next week about metadata cleanup, and enlist some additional help if needed to fix everything that's due to be released in cMD 3.0. I see some other issues on the gh-pages site too ( https://waldronlab.io/curatedMetagenomicDataCuration).
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/46#issuecomment-812677952, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGZXSV3CENKPN54M5C2UZ53TGYLNLANCNFSM42HYYDSA .
lwaldron
commented
3 years ago @paolinomanghi you shouldn't update your analysis and these don't have to be merged immediately, I just didn't want the PRs going stale. I put these files in a new branch https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/smk508 only, which can be merged after fixing syntax. @jwokaty is this issue resolved now with these files gone?
lwaldron
commented
3 years ago Yes it looks like the GHA is passing again, so I will close (open again if I'm wrong). Closed by 78bb441ede2b1682f8417529bd1c5b830d0714ba
lwaldron
commented
3 years ago Actually maybe I was premature since GHA was passing after these merges too. @jwokaty is the problem still here?
https://github.com/waldronlab/curatedMetagenomicDataCuration/actions/runs/712129628
jwokaty
commented
3 years ago The problems still exist. I see them with https://github.com/waldronlab/curatedMetagenomicData/runs/2258353419?check_suite_focus=true#step:5:52 when creating and checking the curation. I want to try to look at these a little more to see why the warnings are happening.
The third issue appears to be from ZhuF_2020. There's one Xian with an apostrophe https://github.com/waldronlab/curatedMetagenomicDataCuration/blob/master/inst/curated/ZhuF_2020/ZhuF_2020_metadata.tsv#L88. (Were the others stripped?) I think if we strip that one too that it will be parsed correctly by makeCombinedMetadata().
jwokaty
commented
3 years ago Removing the apostrophe from ZhuF_2020_metadata.tsv will avoid the warnings when calling makeCombinedMetadata().
For the second issue, "dataset_name" isn't in /inst/extdata/template.csv. It gets prepended in makeCombinedMetadata(). Should it be added to template.csv?
paolinomanghi
commented
3 years ago Thanks, @jwokaty. I substituted Xi'an with Xi_an (I guess is a different place wrt Xian).
On Mon, Apr 5, 2021 at 5:10 PM jwokaty @.***> wrote:
Removing the apostrophe from ZhuF_2020_metadata.tsv will avoid the warnings when calling makeCombinedMetadata().
For the second issue, "dataset_name" isn't in /inst/extdata/template.csv https://github.com/waldronlab/curatedMetagenomicDataCuration/blob/master/inst/extdata/template.csv. It gets prepended in makeCombinedMetadata(). Should it be added to template.csv?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/46#issuecomment-813444590, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGZXSV3ZOGKF3IBLEZDJIWLTHHHFBANCNFSM42HYYDSA .
When creating combined_metadata, I get the following warnings:
Calling checkCuration on it, I get another warning:
While looking at combined_metadata, I noticed a large chunk of text with tab separated values and wanted to include it here in case this was also an issue: