Re: Status bibref gatherer (Was: Tasks pages (close to) fixed; Bibref does not seem to be updated automatically)
Le Sun, Mar 11, 2012 at 03:04:49PM +0100, Andreas Tille a écrit :
> Hi Charles,
>
> I'm very sorry that my work caused frustration on your side. This was
> absolutely not intended. I strongly believed I would work on the same
> goal as you and following your plan. Obviosely e-mails do not work
> out as deescalation means and so I'm for the moment delaying my answer.
Hi Andreas,
thanks for your answer. I am sure that we have the same goal, and it seems
that we have isolated the core of our misunderstanding: the syntax of the
debian/upstream files.
According to http://wiki.debian.org/UpstreamMetadata, the two following
files would be equivalent:
---
Reference-PMID: 19854763
Contact: Manolo Gouy <mgouy@biomserv.univ-lyon1.fr>
Reference-journal: Mol Biol Evol
Name: SeaView
Homepage: http://pbil.univ-lyon1.fr/software/seaview
Reference-author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
...
---
Contact: Manolo Gouy <mgouy@biomserv.univ-lyon1.fr>
Reference:
journal: Mol Biol Evol
PMID: 19854763
author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
Name: SeaView
Homepage: http://pbil.univ-lyon1.fr/software/seaview
Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
...
For good or bad, there is no "Reference" field in the spec. There
is just a hack saying that if there is a "Reference" hash, the fields
it contains have to be consered prefixed by "Reference-".
This can be changed or clarified, and I think that the sooner we do
it the better it is.
Also, all the fields in the spec are "scalar": they just contain text. So
things like the following are bogus.
Screenshots:
- http://pbil.univ-lyon1.fr/binaries/seaview4.png
- http://pbil.univ-lyon1.fr/binaries/seaview-tree.png
The problem here is that if we allow arrays, one can not in advance
expect if the content of a field is its value or an array of values.
This is difficult to parse.
Back to the references, it means that the following two are not
equivalent:
---
Reference:
journal: Mol Biol Evol
PMID: 19854763
author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
...
---
Reference:
- journal: Mol Biol Evol
PMID: 19854763
author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
...
Regardless about what I wrote about the non-existence of a "Reference" field,
having the co-existence of some upstream file where there is an array, and some
upstream files where there is not, is likely to cause trouble.
According to the point of view, these are bugs or features of the spec, but
they will be difficult to change after we start to use it seriously. We
therefore need make good choice here. The more complex the data structure we
use, the less this file will be used directly. And "direct use" also includes
Lintian tests and helper integration.
Cheers,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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