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Re: Gathering package upstream meta-data in the UDD. (was: Re: more formally indicating the registration URL)

Le Tue, Jan 19, 2010 at 08:58:04AM +0100, Andreas Tille a écrit :
> On Tue, Jan 19, 2010 at 08:08:19AM +0900, Charles Plessy wrote:
> > This is more or less what I meant by ???long??? format (in the sense of R???s
> > reshape() function). In order to fit this information in a SQL table, I was
> > more thinking about:
> > 
> > package	title	text
> > package	authors	text
> > package	published-in	text
> > package	year	text
> > etc.
> Hmmm, I'm not comfortable enough with R's reshape function, but I can
> tell that the 'package' stuff you was putting in front of the column
> definitions are not SQL conform.  I was thinking of the package name
> as kind of a primary key.

Are you sure we need a primary key… For instance, to retreive a publication
year, I have the impression that the following paraphrasing the python code of
blends’ blendstasktools.py would be enough:

# Obtain the year of publication of an article describing the software contained in the package:
query = """PREPARE query_get_publication_year (text) AS
           SELECT value FROM biblio WHERE package = $1 AND key = "Reference-Year";"""


query = "EXECUTE query_get_publication_year ('%s')" % (self.pkg)
if curs.rowcount > 0:
    self.publication_year = curs.fetchone()[0]

With a table like:

CREATE TABLE "biblio" (package, key, value);
INSERT INTO "bib" VALUES('kalign','DOI','10.1093/nar/gkn1006');
INSERT INTO "bib" VALUES('seaview','DOI','10.1093/molbev/msp259');
INSERT INTO "bib" VALUES('ballview','DOI','10.1093/bioinformatics/bti818');
INSERT INTO "bib" VALUES('kalign','PMID','19103665');
INSERT INTO "bib" VALUES('seaview','PMID','19854763');
INSERT INTO "bib" VALUES('ballview','Reference-Year','2006');
INSERT INTO "bib" VALUES('kalign','Reference-Year','2009');
INSERT INTO "bib" VALUES('seaview','Reference-Year','2009');

Note that this is the first time I deal with Python code, so please be indulgent :)


Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan

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