[pygr-notify] Issue 127 in pygr: no default annotationType for AnnotationDBs served by XMLRPC

pygr at googlecode.com pygr at googlecode.com
Thu Feb 25 21:46:58 PST 2010 

Status: New
Owner: pygr-bug... at googlegroups.com
Labels: Type-Defect Priority-Medium

New issue 127 by kmdaily: no default annotationType for AnnotationDBs  
served by XMLRPC
http://code.google.com/p/pygr/issues/detail?id=127

Starting an XMLRPC server, serving AnnotationDB objects (exactly as in the
tutorial). There doesn't seem to be a default annotationType (should be
None).

In [5]: m =
worldbase.Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID80492
21_en_db()
In [9]: from pygr import worldbase
In [10]: m
Out[10]: <pygr.annotation.AnnotationClient object at 0x1028910>
In [11]: m.seqDB
Out[11]: <XMLRPCSequenceDB 'type'>
In [13]: m.url
Out[13]: 'http://mine-16.ics.uci.edu:3542'
In [14]: m.itemClass
Out[14]: <class 'pygr.annotation.AnnotationSeq'>
In [15]: x = m[1]
In [16]: x
Out[16]: ------------------------------------------------------------------
---------
AttributeError                            Traceback (most recent call last)

/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/sit
e-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/annotation.pyc in
annotation_repr(self)
      12
      13 def annotation_repr(self):
---> 14     if self.annotationType is not None:
      15         title = self.annotationType
      16     else:

/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/sit
e-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/annotation.pyc in
getAnnotationAttr(self, attr)
       8 def getAnnotationAttr(self, attr):
       9     'forward attributes from slice object if available'
---> 10     return self.db.getSliceAttr(self.db.sliceDB[self.id], attr)
      11
      12

/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/sit
e-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/annotation.pyc in
getSliceAttr(self, sliceInfo, attr)
     512         else:
     513             v = self.server.get_annotation_attr(sliceInfo[0], attr)
     514             if v=='':
--> 515                 raise AttributeError('this annotation has no attr:
' + attr)
     516             return v

In [21]: m.annotationType = None
In [22]: m
Out[22]: <pygr.annotation.AnnotationClient object at 0x1028910>
In [23]: x = m[167528]
In [24]: x
Out[24]: annot167528[0:6]
In [26]: x.sequence
Out[26]: -chr3L[9396999:9397005]

Log of server follows:

In [39]: server.serve_forever(daemonize=False)
Serving on interface "mine-16.ics.uci.edu", port 3542
START_SERVER:/tmp/worldbase-server.log 2010-02-25 21:27:22.834144

XMLRPC: objectInfo ('index',) 2010-02-25 21:28:12.733800
XMLRPC: methodCall ('index', 'getName', []) 2010-02-25 21:28:12.738848
XMLRPC: methodCall ('index', 'dir', ['', False, 'p']) 2010-02-25
21:28:12.741079
XMLRPC: methodCall ('index', 'dir', ['', False, 'p']) 2010-02-25
21:28:18.989647
XMLRPC: objectInfo ('index',) 2010-02-25 21:28:23.767680
XMLRPC: methodCall ('index', 'getName', []) 2010-02-25 21:28:23.783641
XMLRPC: methodCall ('index', 'dir', ['Bio', False, 'p']) 2010-02-25
21:28:23.785981
XMLRPC: methodCall ('index', 'dir', ['Bio.SCHEMA', False, 'p']) 2010-02-25
21:28:23.793780
XMLRPC: methodCall ('index', 'getName', []) 2010-02-25 21:28:23.796145
XMLRPC: methodCall ('index', 'getResource',
['Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
']) 2010-02-25 21:30:57.705041
XMLRPC: methodCall ('index', 'getResource', ['Bio.Seq.Genome.DROME.dm3'])
2010-02-25 21:30:57.722184
XMLRPC: objectInfo ('Bio.Seq.Genome.DROME.dm3',) 2010-02-25 21:30:57.731047
XMLRPC: methodCall ('Bio.Seq.Genome.DROME.dm3', 'get_seqtype', []) 2010-02-
25 21:30:57.733799
XMLRPC: methodCall ('index', 'getResource',
['SCHEMA.Bio.Seq.Genome.DROME.dm3']) 2010-02-25 21:30:57.736141
XMLRPC: objectInfo
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
',) 2010-02-25 21:30:57.738662
XMLRPC: methodCall ('index', 'getResource',
['SCHEMA.Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID804922
1_en_db']) 2010-02-25 21:30:57.741432
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_slice_tuple', [167528]) 2010-02-25 21:31:02.154026
XMLRPC: methodCall ('Bio.Seq.Genome.DROME.dm3', 'getSeqLen', ['chr3L'])
2010-02-25 21:31:02.168680
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'tonylong']) 2010-02-25 21:31:04.698285
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'tonylong']) 2010-02-25 21:31:04.703970
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'annotationType']) 2010-02-25
21:31:07.077661
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'annotationType']) 2010-02-25
21:31:13.788887
pv141097.reshsg.uci.edu - - [25/Feb/2010 21:32:50] code 501, message
Unsupported method ('GET')
pv141097.reshsg.uci.edu - - [25/Feb/2010 21:32:50] code 501, message
Unsupported method ('GET')
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'annotationType']) 2010-02-25
21:34:13.175572
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '__members__']) 2010-02-25
21:34:14.015452
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '__methods__']) 2010-02-25
21:34:14.019716
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'trait_names']) 2010-02-25
21:34:14.023576
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '_getAttributeNames']) 2010-02-25
21:34:14.027735
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '__members__']) 2010-02-25
21:34:17.727636
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '__methods__']) 2010-02-25
21:34:17.731959
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'trait_names']) 2010-02-25
21:34:17.735799
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', '_getAttributeNames']) 2010-02-25
21:34:17.739154
XMLRPC: methodCall
('Bio.Annotation.MotifMap.DROME.dm3.multiz15way_fliesonly.PMID8049221_en_db
', 'get_annotation_attr', ['chr3L', 'annotationType']) 2010-02-25
21:34:31.345408



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