Typo in edam scopes or new format

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Typo in edam scopes or new format

Andreas Tille-5
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).

Kind regards

       Andreas.

--
http://fam-tille.de

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Re: Typo in edam scopes or new format

Steffen Möller
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'll correct the three entries.

Cheers,

Steffen


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Re: Typo in edam scopes or new format

Steffen Möller
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

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Re: Typo in edam scopes or new format

Andreas Tille-5
On Mon, Apr 08, 2019 at 12:10:23PM +0200, Steffen Möller wrote:
> > 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.

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).  I'd love if we make
scientific decisions in biology and not linguistics.

Kind regards

       Andreas.

--
http://fam-tille.de

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Re: Typo in edam scopes or new format

Steffen Möller

On 08.04.19 22:34, Andreas Tille wrote:

> On Mon, Apr 08, 2019 at 12:10:23PM +0200, Steffen Möller wrote:
>>> 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.
> 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.
>   I'd love if we make
> scientific decisions in biology and not linguistics.
;)

Best,
Steffen


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Re: Typo in edam scopes or new format

Andreas Tille-5
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?

Kind regards

       Andreas.

--
http://fam-tille.de

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Re: Typo in edam scopes or new format

Steffen Möller
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




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Re: Typo in edam scopes or new format

Andreas Tille-5
On Thu, Apr 11, 2019 at 05:24:55PM +0200, Steffen Möller wrote:
>
> 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.

I was running

curdir=$(pwd)
for edam in $(grep -wl outputs */debian/upstream/edam) ; do
  cd $(dirname $edam)
  sed -i -e 's/outputs *:/output:/' -e 's/inputs *:/input:/' edam
  git commit -am"Fix edam syntax input+output is singular"
  git push
  cd "$curdir"
done


So this should be solved for most edam files now.

Kind regards

      Andreas.

--
http://fam-tille.de

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Re: Typo in edam scopes or new format

Steffen Möller
Hi Andreas,

On 11.04.19 21:34, Andreas Tille wrote:

> On Thu, Apr 11, 2019 at 05:24:55PM +0200, Steffen Möller wrote:
>> 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.
> I was running
>
> curdir=$(pwd)
> for edam in $(grep -wl outputs */debian/upstream/edam) ; do
>    cd $(dirname $edam)
>    sed -i -e 's/outputs *:/output:/' -e 's/inputs *:/input:/' edam
>    git commit -am"Fix edam syntax input+output is singular"
>    git push
>    cd "$curdir"
> done
>
Thank you tons! This is so nice!

Steffen