Fix parsing of experiment IDs and names #38
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| @@ -91,7 +91,7 @@ echo -e "\n#### Selected differential experiments\n" >> $releaseNotesFile | |||
| ## parse list of new differential studies to get write experiment titles | |||
| curl 'https://wwwdev.ebi.ac.uk/gxa/json/experiments' | \ | |||
| jq -r '.experiments | .[] | select(.loadDate | strptime("%d-%m-%Y") | mktime > '$last_release_epoch_time') | select(.rawExperimentType | test("DIFFERENTIAL"; "i")) | [.experimentAccession, .experimentDescription] | @csv' | \ | |||
| awk -v FS="," '{ printf "- [%s](https://www.ebi.ac.uk/gxa/experiments/%s)\n", $2, $1}' | sed s/\"//g >> $releaseNotesFile | |||
| awk -v FPAT="^([^,]+)|(\"[^\"]+\")$" '{ printf "- [%s](https://www.ebi.ac.uk/gxa/experiments/%s)\n", $2, $1}' | sed s/\"//g >> $releaseNotesFile | |||
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| awk -v FPAT="^([^,]+)|(\"[^\"]+\")$" '{ printf "- [%s](https://www.ebi.ac.uk/gxa/experiments/%s)\n", $2, $1}' | sed s/\"//g >> $releaseNotesFile |
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Done in edd0bde, thanks!
Co-authored-by: Jonathan Manning <[email protected]>
irisdianauy
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The previous parser uses
,as a field separator, which does not behave as planned when an experiment name string uses a comma, as reported here. This fix replaces the field separator with a regular expresion for the desired field patterns. It also only accepts,when inside the second/last element (the experiment name) of the parsed string.This, as far as tested, works using
gawk(the default awk in codon as fg_atlas or fg_atlas_sc), but not in other awk versions, likemawkor the originalawk.