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Fix #149: Missing or mis-reported resistances #173
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microSALT/utils/scraper.py
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@@ -438,6 +438,7 @@ def scrape_blast(self, type="", file_list=[]): | |||
self.name, str(e) | |||
) | |||
) | |||
return hypo |
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This hypo variable is something extra
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This return was added here in order to be able to check the outcome of the scraping in tests. Optimally one would have refactored the code more, so as not to save to the database inside the scraping function at all like is done now, but this was the smallest change I could find that would do the trick.
pixi.lock
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we should include this in the git ignore
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Yes, well, I wasn't even sure if I wanted to keep the pixi stuff here at all, (after moving out of draft status). Will probably just get outdated as compared with the original config, so probably better to avoid.
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Looks good, I have made som comments, but I think all that is left is to check the differences of these two on validation data
pixi.toml
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this one as well. So probably just add a pixi.*
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This fixes #149
The same change might need to be done for other matching as well.
Description
##Remove elements in cursive as needed.##
The features of this PR primarily concerns end-users/bioinformaticians/internals
Summary of the changes made:
If not self-evident, mention what prompted the change.
Primary function of PR
Testing
If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.
Test routine to verify the stability of the PR:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME
us
source activate S_microSALT
export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
microSALT analyse project MIC3109
microSALT analyse project MIC4107
microSALT analyse project MIC4109
microSALT analyse project ACC5551
Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx
Test results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
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