def test_schema(self):
"Test schema"
sp_hbb1 = testutil.datafile('sp_hbb1')
sp2 = seqdb.BlastDB(sp_hbb1)
sp2.__doc__ = 'another sp'
worldbase.Bio.Seq.sp2 = sp2
sp = worldbase.Bio.Seq.Swissprot.sp42()
m = mapping.Mapping(sourceDB=sp,targetDB=sp2)
m.__doc__ = 'sp -> sp2'
worldbase.Bio.Seq.testmap = m
worldbaseSchema.Bio.Seq.testmap = metabase.OneToManyRelation(sp, sp2)
worldbase.commit()
worldbase.clear_cache()
sp3 = seqdb.BlastDB(sp_hbb1)
sp3.__doc__ = 'sp number 3'
worldbase.Bio.Seq.sp3 = sp3
sp2 = worldbase.Bio.Seq.sp2()
m = mapping.Mapping(sourceDB=sp3,targetDB=sp2)
m.__doc__ = 'sp3 -> sp2'
worldbase.Bio.Seq.testmap2 = m
worldbaseSchema.Bio.Seq.testmap2 = metabase.OneToManyRelation(sp3, sp2)
l = worldbase._mdb.resourceCache.keys()
l.sort()
assert l == ['Bio.Seq.sp2', 'Bio.Seq.sp3', 'Bio.Seq.testmap2']
worldbase.commit()
g = worldbase._mdb.writer.storage.graph
expected = set(['Bio.Annotation.annoDB',
'Bio.Seq.Swissprot.sp42', 'Bio.Seq.sp2', 'Bio.Seq.sp3'])
found = set(g.keys())
self.EQ(len(expected - found), 0)
def setUp(self,**kwargs):
TestBase.setUp(self)
dnaseq = testutil.datafile('dnaseq.fasta')
tryannot = testutil.tempdatafile('tryannot')
db = seqdb.BlastDB(dnaseq)
try:
db.__doc__ = 'little dna'
worldbase.Bio.Test.dna = db
annoDB = seqdb.AnnotationDB({1:('seq1',5,10,'fred'),
2:('seq1',-60,-50,'bob'),
3:('seq2',-20,-10,'mary')},
db,
sliceAttrDict=dict(id=0, start=1, stop=2,
name=3))
annoDB.__doc__ = 'trivial annotation'
worldbase.Bio.Test.annoDB = annoDB
nlmsa = cnestedlist.NLMSA(tryannot,'w',pairwiseMode=True,
bidirectional=False)
try:
for annID in annoDB:
nlmsa.addAnnotation(annoDB[annID])
nlmsa.build(verbose=False)
nlmsa.__doc__ = 'trivial map'
worldbase.Bio.Test.map = nlmsa
worldbaseSchema.Bio.Test.map = metabase.ManyToManyRelation(db,
annoDB,bindAttrs=('exons',))
worldbase.commit()
worldbase.clear_cache()
finally:
nlmsa.close()
finally:
db.close()
def test_schema(self):
"Test schema"
sp_hbb1 = testutil.datafile('sp_hbb1')
sp2 = seqdb.BlastDB(sp_hbb1)
sp2.__doc__ = 'another sp'
worldbase.Bio.Seq.sp2 = sp2
sp = worldbase.Bio.Seq.Swissprot.sp42()
m = mapping.Mapping(sourceDB=sp, targetDB=sp2)
m.__doc__ = 'sp -> sp2'
worldbase.Bio.Seq.testmap = m
worldbase.schema.Bio.Seq.testmap = metabase.OneToManyRelation(sp, sp2)
worldbase.commit()
worldbase.clear_cache()
sp3 = seqdb.BlastDB(sp_hbb1)
sp3.__doc__ = 'sp number 3'
worldbase.Bio.Seq.sp3 = sp3
sp2 = worldbase.Bio.Seq.sp2()
m = mapping.Mapping(sourceDB=sp3, targetDB=sp2)
m.__doc__ = 'sp3 -> sp2'
worldbase.Bio.Seq.testmap2 = m
worldbase.schema.Bio.Seq.testmap2 = metabase.OneToManyRelation(
sp3, sp2)
l = worldbase._mdb.resourceCache.keys()
l.sort()
assert l == ['Bio.Seq.sp2', 'Bio.Seq.sp3', 'Bio.Seq.testmap2']
worldbase.commit()
g = worldbase._mdb.writer.storage.graph
expected = set([
'Bio.Annotation.annoDB', 'Bio.Seq.Swissprot.sp42', 'Bio.Seq.sp2',
'Bio.Seq.sp3'
])
found = set(g.keys())
self.EQ(len(expected - found), 0)
def test_mapping_FR(self):
"""Test the forward mapping.
>>> from pygr import worldbase
>>> adb = worldbase('Test.Annotations.annodb1_db')
>>> a1 = adb['A1']
>>> adb2 = worldbase('Test.Annotations.annodb2_db')
>>> a2 = adb2['E2']
>>> a1 == a2.annotdb1[0]
True
"""
print '# Create mapping'
M = PygrUtils.AnnotationDBMapping(self.annodb1,self.annodb2,'test.mapping','test.mapping','annotdb2','annotdb1',mode='nr')
M[self.annot1]=self.annot10
M.close(commitData=True)
print '# Reload recently committed data, eg, mapping'
worldbase.clear_cache()
print '# Test forward mapping'
annodb2 = worldbase('Test.Annotations.annodb2_db')
a10 = annodb2['E2']
self.assertEqual(repr(self.annot1), repr(a10.annotdb1[0]))
print '# Test reverse mapping'
annodb1 = worldbase('Test.Annotations.annodb1_db')
a1 = annodb1['A1']
self.assertEqual(repr(self.annot10), repr(a1.annotdb2[0]))
def setUp(self):
TestBase.setUp(self)
populate_swissprot() # save some data
worldbase.commit() # finally save everything to metabase
worldbase.clear_cache() # force all requests to reload
res = [ 'Bio.Seq.Swissprot.sp42', 'Bio.Seq.frag', 'Bio.Seq.spmap',
'Bio.Annotation.annoDB', 'Bio.Annotation.map' ]
self.server = testutil.TestXMLRPCServer(res, self.tempdir.path)
def setUp(self):
TestBase.setUp(self)
populate_swissprot() # save some data
worldbase.commit() # finally save everything to metabase
worldbase.clear_cache() # force all requests to reload
res = [
'Bio.Seq.Swissprot.sp42', 'Bio.Seq.frag', 'Bio.Seq.spmap',
'Bio.Annotation.annoDB', 'Bio.Annotation.map'
]
self.server = testutil.TestXMLRPCServer(res, self.tempdir.path)
def setUp(self, **kwargs):
TestBase.setUp(self)
dnaseq = testutil.datafile('dnaseq.fasta')
tryannot = testutil.tempdatafile('tryannot')
db = seqdb.BlastDB(dnaseq)
try:
db.__doc__ = 'little dna'
worldbase.Bio.Test.dna = db
annoDB = seqdb.AnnotationDB(
{
1: ('seq1', 5, 10, 'fred'),
2: ('seq1', -60, -50, 'bob'),
3: ('seq2', -20, -10, 'mary')
},
db,
sliceAttrDict=dict(id=0, start=1, stop=2, name=3))
annoDB.__doc__ = 'trivial annotation'
worldbase.Bio.Test.annoDB = annoDB
nlmsa = cnestedlist.NLMSA(tryannot,
'w',
pairwiseMode=True,
bidirectional=False)
try:
for annID in annoDB:
nlmsa.addAnnotation(annoDB[annID])
nlmsa.build()
nlmsa.__doc__ = 'trivial map'
worldbase.Bio.Test.map = nlmsa
worldbase.schema.Bio.Test.map = metabase.ManyToManyRelation(
db, annoDB, bindAttrs=('exons', ))
worldbase.commit()
worldbase.clear_cache()
finally:
nlmsa.close()
finally:
db.close()
def test_xmlrpc(self):
"Test XMLRPC"
worldbase.clear_cache() # force all future requests to reload
worldbase.update("http://localhost:%s" % self.server.port) # from XMLRPC
check_match(self) # run all our tests
check_dir(self)
check_dir_noargs(self)
check_dir_download(self)
check_dir_re(self)
check_bind(self)
check_bind2(self)
sb_hbb1 = testutil.datafile('sp_hbb1') # test readonly checks
sp2 = seqdb.BlastDB(sb_hbb1)
sp2.__doc__ = 'another sp'
try:
worldbase.Bio.Seq.sp2 = sp2
worldbase.commit()
msg = 'failed to catch bad attempt to write to XMLRPC server'
raise KeyError(msg)
except ValueError:
pass
def test_xmlrpc(self):
"Test XMLRPC"
worldbase.clear_cache() # force all future requests to reload
# Add our test XMLRPC resource.
worldbase.update("http://localhost:%s" % self.server.port)
check_match(self) # run all our tests
check_dir(self)
check_dir_noargs(self)
check_dir_download(self)
check_dir_re(self)
check_bind(self)
check_bind2(self)
sb_hbb1 = testutil.datafile('sp_hbb1') # test readonly checks
sp2 = seqdb.BlastDB(sb_hbb1)
sp2.__doc__ = 'another sp'
try:
worldbase.Bio.Seq.sp2 = sp2
worldbase.commit()
msg = 'failed to catch bad attempt to write to XMLRPC server'
raise KeyError(msg)
except ValueError:
pass
def setUp(self, *args, **kwargs):
TestBase.setUp(self, *args, **kwargs)
populate_swissprot()
worldbase.commit() # finally save everything
worldbase.clear_cache() # force all requests to reload
def setUp(self, *args, **kwargs):
TestBase.setUp(self, *args, **kwargs)
populate_swissprot()
worldbase.commit() # finally save everything
worldbase.clear_cache() # force all requests to reload
