[BioSQL-l] python

[Yves Bastide]

[kept bioSQL cc'ed, f'up to biopython-dev at biopython.org]

christen wrote:
> Hi there
> 
> I am a new comer to python and biosql
> 
> I have tried to get working biosql under mysql and python as ewplained in
> Basic BioSQL with Biopoython

OK, mysql vs. postgresql issues.

> I have donwloaded the latest version of both, and tried the example with
> cor6_6.gb
> 
> then I got numerous problems
> 
> I fixed the first one by changing line 104 in cursors from
>             if args is None:
> to :
>             if args is None or args=='':
> 

Where's this line? "args is None" looks like something done to allow the 
empty string; the usual way (to mean what you're using) would be "if not 
args:"

> then in Loader, in def _load_reference(self, reference, rank, bioentry_id):,
> i made the following changes (in particular replaced JOIN by INNER JOIN)
> if reference.medline_id:
>             sql="SELECT reference_id" \
>                 "  FROM reference INNER JOIN dbxref ON reference .dbxref_id
> = dbxref.dbxref_id" \
>                 " WHERE ((dbname = 'MEDLINE') AND (accession = %s))"
>             refs =
> self.adaptor.execute_and_fetch_col0(sql,reference.medline_id)
> 

JOIN -> INNER JOIN: ok
using (field) -> on t1.field = t2.field: *sigh* ok
But are the extraneous parentheses really needed?

> 
> Now, I have one more pb:
> 
> Traceback (most recent call last):
>   File "C:\Python23\RC_databases\rc_BioSQL_GenBank.py", line 21,
> in -toplevel-
>     db.load(iterator)
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 343,
> in load
>     db_loader.load_seqrecord(cur_record)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 46, in
> load_seqrecord
>     self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 366, in
> _load_seqfeature
>     self._load_seqfeature_locations(feature, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 409, in
> _load_seqfeature_locations
>     self._insert_seqfeature_location(feature, 1, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 430, in
> _insert_seqfeature_location
>     self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank))
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 223,
> in execute
>     self.cursor.execute(sql, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 95, in
> execute
>     return self._execute(query, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 119, in
> _execute
>     self.errorhandler(self, exc, value)
>   File "C:\Python23\Lib\site-packages\MySQLdb\connections.py", line 33, in
> defaulterrorhandler
>     raise errorclass, errorvalue
> OperationalError: (1048, "Le champ 'strand' ne peut \xeatre vide (null)")


Hilmar: seems like there's a buglet in biosqldb-pg.sql: strand is 
missing the NOT NULL.

Richard:
Loader.py, line 424
-         strand = feature.strand
+         strand = feature.strand or 0
should do the trick

> 
> 
> I am for the time being only trying some quick and dirty (like modification
> of cursor instead of loader I guess...) changes  to try to get it working
> My questions are :
> Is there somebody else having trouble, or do you I miss something ?
> If I did it right, Is there somebody else trying to fix these problems ?

It seems like you're the first trying these things with MySQL since they 
were last changed. Thanks for the report!

> If things need some help, it would be very nice to have some clear
> description of biosql structure. I have not been able to find it. Somebody
> could help ?
> 
> thanks in advance

De rien,

> 
> Richard CHRISTEN
> Champion de saut en largeur
> UMR6543 CNRS - Université de Nice Sophia Antipolis
> 
> Centre de Biochimie
> Parc Valrose
> 06108 Nice cedex2
> 
> tel  33 - 492 076 947
> fax 33 - 492 076 408
> 

yves