[Bioperl-l] bioperl-db: posqgresql adaptor

[Hilmar Lapp]

It will work so long as the input doesn't specify things which are 
already in the database and which the adaptors don't cache. By 
default, only taxa, namespaces, ontology terms, and dbxrefs are 
cached. Therefore, a reference that exists already will make the 
whole entry fail. You can enable caching for references by

	$radp = $db->get_object_adaptor("Bio::Annotation::Reference");
	$radp->caching_mode(1);

before any entry is loaded. (adaptor instances are cached, hence 
every subsequent call to obtain an adaptor for references will 
return the instance you just manipulated - which is what you want)

Associations are generally not cached. Most associations are ranked, 
however, so as long as you only insert and don't update you should 
be fine for those. Unfortunately, dbxref associations are not 
ranked, so if the same dbxref occurs twice in the entry (believe it 
or not, swissprot and some others have this once in a while), that 
entry will fail.

So, for inserts most things will work if you enable caching for 
references or your input doesn't have references. Those entries with 
redundant dbxrefs will fail to load, but shouldn't bail out the 
script (supply --safe; the failure will cause a rollback for that 
entry which terminates the transaction - after that Pg should be 
happy again. I haven't tested this though.). Updating deserialized 
entries should be fine, too (those will immediately result in an 
UPDATE). Loading the same entry twice (second time from an updated 
datasource) will fail with Pg at this time (however, you could 
provide --remove to load_seqdatabase.pl - that should work too).

	-hilmar

On Monday, November 25, 2002, at 04:09 AM, AUnderwood@PHLS.org.uk wrote:

>
> Also do I understand correctly from your later postings that the 
> problems
> with the postgres database adaptor mean that the load_seqdatabase 
> script
> won't work for the time being?
>
>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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