[pygr-notify] [pygr commit] r105 - wiki

[codesite-noreply at google.com]

Author: titus at idyll.org
Date: Mon Sep 15 21:04:06 2008
New Revision: 105

Modified:
    wiki/DevelopmentRoadmap.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/DevelopmentRoadmap.wiki
==============================================================================
--- wiki/DevelopmentRoadmap.wiki	(original)
+++ wiki/DevelopmentRoadmap.wiki	Mon Sep 15 21:04:06 2008
@@ -25,18 +25,18 @@


  New features:
-  * pygr.Data auto-download capabilities (download=True mode)
-  * simple browsing / searching HTTP interface for pygr.Data server
-  * simple management functions over SSL XMLRPC
-  * XMLRPC annotation services
-  * classes supporting Ensembl annotation (in support of Jenny & Rob's  
project)
-  * additional UCSC alignment format(s), e.g. supporting hg18/hg17 mapping
+  * pygr.Data auto-download capabilities (download=True mode) - _done_
+  * simple browsing / searching HTTP interface for pygr.Data server -  
_deferred_
+  * simple management functions over SSL XMLRPC - *not done*
+  * XMLRPC annotation services - _done_
+  * classes supporting Ensembl annotation (in support of Jenny & Rob's  
project) - _done_
+  * additional UCSC alignment format(s), e.g. supporting hg18/hg17 mapping  
- _done_

  API Clean-up:
-  * define an "alignment parser API" that makes it simple to add a parser  
for an arbitrary alignment format, and have the results automatically  
loaded into an NLMSA.
-  * ensure that dict-like interfaces in Pygr properly support all the  
standard Mapping Protocol methods
-  * greatly expanded test suites courtesy of Rachel, Alex and Titus
-  * other clean-up and bug fixes
+  * define an "alignment parser API" that makes it simple to add a parser  
for an arbitrary alignment format, and have the results automatically  
loaded into an NLMSA. - *not done*
+  * ensure that dict-like interfaces in Pygr properly support all the  
standard Mapping Protocol methods - *in progress*
+  * greatly expanded test suites courtesy of Rachel, Alex and Titus - *in  
progress*
+  * other clean-up and bug fixes - *in progress*

  == v0.9: NLMSA Joins ==
  In a  
[http://groups.google.com/group/pygr-dev/browse_thread/thread/0d4d02149022e5a6?hl=en  
number of discussions], we have already gone into some detail about new  
possible features for NLMSA.  The main idea is to define general purpose  
JOIN operations that execute in a high-speed, scalable way, obviating the  
need for researchers to write their own Python code (slow and possibly  
buggy) every time they need to find some intersection between two or more  
datasets.  The result of an NLMSA join will of course just be another  
NLMSA.  The goal is to make alignment and annotation query a killer app in  
terms of speed, query capabilities and ease of use.
@@ -55,4 +55,4 @@
    * pygr.Data makerules: initially this could be implemented as simple  
construction rules a la SCons for building some type of resource from some  
types of dependencies.
    * pygr.Data security via Signed Pickles: Python pickles create potential  
security vulnerabilities.  One simple and general solution is to create  
digitally signed pickles using OpenPGP that can be verified with the  
author's public key.  This would then integrate with standard tools (e.g.  
GnuPG) for listing sets of people whose content you trust.
    * Pygr.Data management tools for viewing, copying, organizing, deleting  
resource and schema entries between pygr.Data resource databases.  These  
should work transparently with local resource databases, MySQL resource  
databases, and remote XMLRPC resource databases (all using authentication).
-  * DNS-like framework for servers to share name lookup info with each  
other
+  * DNS-like framework for servers to share name lookup info with each  
other
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