Re: Typo in edam scopes or new format

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Andreas,

On 11.04.19 16:13, Andreas Tille wrote:
> On Mon, Apr 08, 2019 at 11:13:18PM +0200, Steffen Möller wrote:
> > On 08.04.19 22:34, Andreas Tille wrote:
> > > > 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.
> > > Please settle with **one** form, **change** it to the prefered form and
> > > **stick** to this.  The importer is checking for typos and either
> > > singular or plural is a typo (whatever you decide).
> > It shall be singular for both input and output. Please kindly adjust the
> > parser
> > and all other EDAM files then need to be adjusted.
> Are you **really** sure, you just want to edit at least 70 files
> instead of 7?
>
> .../salsa/med-team $ grep -w input */debian/upstream/edam | wc -l
> 7
> .../salsa/med-team $ grep -w output */debian/upstream/edam | wc -l
> 7
>
> .../salsa/med-team $ grep -w outputs */debian/upstream/edam | wc -l
> 73
> .../salsa/med-team $ grep -w inputs */debian/upstream/edam | wc -l
> 70
>
> > >    I'd love if we make
> > > scientific decisions in biology and not linguistics.
> > ;)
> Since I have not seen any commits tackling this I simply hesitate to
> edit the parser which would reduce the valid data set by one order of
> magnitude.  Are you *really* sure that you want this?

You are cordially invited to change the parser to accept both singular
_and_ plural forms - and to raise an error when the plural form is given
for a single input/output only. Linguistics aside, the singular form is
how bio.tools has it. And one of the design goals was to remain
compatible with how they are expecting EDAM annotation.

I don't have all the packages checked out, which would make it much like
a "sed -i 's/   inputs:/   input:/' */debian/upstream/edam" kind of
thing. No worries. This can be dealt with quickly.

Best,

Steffen