[pygr-notify] [pygr commit] r29 - wiki

[codesite-noreply at google.com]

Author: jqian.ubc
Date: Mon Jun 16 01:54:37 2008
New Revision: 29

Modified:
   wiki/PygrOnEnsembl.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/PygrOnEnsembl.wiki
==============================================================================
--- wiki/PygrOnEnsembl.wiki	(original)
+++ wiki/PygrOnEnsembl.wiki	Mon Jun 16 01:54:37 2008
@@ -36,4 +36,26 @@

  Currently, we are in the process of trying pygr to access the dna and 
exon tables of the ensembl core database and build bi-directional 
mappings between the genome and the annotation.  For more information, 
please refer to the following thread [http://groups.google.com/group/pygr-dev/browse_thread/thread/5d55fd9d071fbf4d?hl=en].

-Stay tuned for further progress reports from us :)
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+Stay tuned for further progress reports from us :)
+
+= Design Decisions =
+
+*Scope*
+For the time being, the primary focus of this API is to provide means 
to retrieve information from the ensembl core databases.
+
+*Framework*
+
+*1.* the datamodel module (datamodel.py): a BaseModel super class and 
its subclasses.  Each subclass represents a biological entity.
+
+*2.* the adaptor module (adaptor.py): a driver class, a generic 
adaptor class (super class) and many specialized adaptor classes (sub 
classes).  Each specialized adaptor class employs pygr modules (mainly 
the sqlgraph module) and provides access to its corresponding sql table 
in an ensembl core database.
+
+*3.* the supporting module (seqregion.py): extensions of the pygr core 
modules, used by the adaptor module.
+
+*Design Pattern*
+The Driver class in the adaptor module is implemented as a singleton 
class, since making a connection to the database is expensive.
+
+= updates =
+
+*1.* mini-release v0.01: (running environment: the latest pygr)
+
+*2.* output file from running the sample code in datamodel.py, which 
gives a preliminary test results for implemented functions in each 
specialized datamodel class.
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