[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 12:33:39 EST 2008


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





------- Comment #4 from bosborne at alum.mit.edu  2008-11-23 12:33 EST -------
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:

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?


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