Re: Typo in edam scopes or new format

[Steffen Möller <steffen_moeller@gmx.de>]

Hi again,

On 08.04.19 12:05, Steffen Möller wrote:
> Hi Andreas,
>
> On 08.04.19 09:49, Andreas Tille wrote:
> > Hi,
> >
> > when inspecting UDD import logs I realised the following warnings:
> >
> >   $ grep "Unknown Edam scope in file" blends_prospective_gatherer.log
> > 2019-04-07 23:46:18,355 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie.edam' of
> > source 'bowtie' of debian-med: input.
> > 2019-04-07 23:46:18,355 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie.edam' of
> > source 'bowtie' of debian-med: output.
> > 2019-04-07 23:46:18,355 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie.edam' of
> > source 'bowtie' of debian-med: input.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: input.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: output.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: input.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: output.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: input.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: output.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: input.
> > 2019-04-07 23:46:18,441 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/b/bowtie2.edam' of
> > source 'bowtie2' of debian-med: output.
> > 2019-04-07 23:46:26,636 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/c/cd-hit.edam' of
> > source 'cd-hit' of debian-med: input.
> > 2019-04-07 23:46:26,636 - WARNING - (539): Unknown Edam scope in file
> > '/srv/udd.debian.org/mirrors/machine-readable/c/cd-hit.edam' of
> > source 'cd-hit' of debian-med: output.
> >
> >
> > Are these just typos in bowtie, bowtie2 and cd-hit or did you droped the
> > plural in the scope filed (the importer expects inputs and outputs with
> > plural 's' at the end).
>
> Many thanks for spotting this. I have no reply from Matúš, yet. My
> favorite solution would be to accept it either way. Otherwise, the
> plural form should win since there are typically more than one scope
> that a tool can be used for.
I missread this. It is about input(s)/output(s), not about scope(s). I
like the singular form much better. Would not want to change that, really.

Matúš?

Steffen