[Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Nov 23 14:07:52 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2337





------- Comment #5 from cjfields at bioperl.org  2008-11-23 14:07 EST -------
(In reply to comment #4)
> Whoops. Naohisa didn't read the entire spec, and neither did I. He focused on
> one sentence, "There is no other data in this file", but this sentence is
> contradicted later in the spec. Check these excerpts:

Can we clarify that (i.e. do we still have CVS commit access for OBDA)?

Also (separate issue), I don't think OBDA has migrated over to svn, so maybe we
should go ahead and set that up.

> 2) The subdirectory contains a file named "config.dat" containing tab
> separated key/value pairs.  The first line contains the key "index"
> and value "index\tBerkeleyDB/1".  This means the first few characters
> of the config.dat file is "index\tBerkeleyDB/1\n".
> 
> There is no other data in this file.
> 
> 3) Global configuration data is stored in the database named "config".
> At present there are only two entries in the config database:
> 
>    "primary_namespace" - contains the primary namespace name
> 
>    "secondary_namespaces" - contains the tab separated list of
>       secondary namespaces.  If there are no secondary namespaces
>       then this entry exists but contains the empty string as the
>       value.
> 
> 
> 5) The primary identifier namespace is stored in config.dat under the
> key named 'primary_namespace'.  For example, if the dbname is
> "swissprot" which uses the "ID" as the primary identifier then the
> file "swissprot/config.dat" will contain the following line somewhere
> in the file:
> 
>  "primary_namespace" "\t" "ID" "\n"
> 
> 
> 7) The list of secondary namespaces is stored in config.dat under the
> key "secondary_namespaces".  Mutiple terms are separated by a tab
> character.  If there are no secondary namespaces then this entry must
> exist but the value is the empty string.
> 
> Lincoln's config.dat does 5) and 7) correctly, as requested by the spec.
> 
> I can add the "primary_namespace" and "secondary_namespace" names to the
> "config" database, then we'll have exactly the same info. in 2 places. That's
> what they want?

I say go ahead and implement the above changes. At that point we should be
compliant with everything but the ambiguous (2).  Beyond that I think we have
to go with whatever the spec states.  

We'll also need to notify BioRuby (or post a bug report) indicating the
clarification, as they don't appear to comply with the full spec either.


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