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'
pygrData.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'
pygrData.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'
pygrData.Bio.Test.map = nlmsa
pygrSchema.Bio.Test.map = metabase.ManyToManyRelation(db,
annoDB,bindAttrs=('exons',))
pygrData.commit()
pygrData.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'
pygrData.Bio.Seq.sp2 = sp2
sp = pygrData.Bio.Seq.Swissprot.sp42()
m = mapping.Mapping(sourceDB=sp,targetDB=sp2)
m.__doc__ = 'sp -> sp2'
pygrData.Bio.Seq.testmap = m
pygrSchema.Bio.Seq.testmap = metabase.OneToManyRelation(sp, sp2)
pygrData.commit()
pygrData.clear_cache()
sp3 = seqdb.BlastDB(sp_hbb1)
sp3.__doc__ = 'sp number 3'
pygrData.Bio.Seq.sp3 = sp3
sp2 = pygrData.Bio.Seq.sp2()
m = mapping.Mapping(sourceDB=sp3,targetDB=sp2)
m.__doc__ = 'sp3 -> sp2'
pygrData.Bio.Seq.testmap2 = m
pygrSchema.Bio.Seq.testmap2 = metabase.OneToManyRelation(sp3, sp2)
l = pygrData._mdb.resourceCache.keys()
l.sort()
assert l == ['Bio.Seq.sp2', 'Bio.Seq.sp3', 'Bio.Seq.testmap2']
pygrData.commit()
g = pygrData._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):
TestBase.setUp(self)
populate_swissprot() # save some data
pygrData.commit() # finally save everything to metabase
pygrData.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 test_download(self):
"Downloading of gzipped file using pygr.Data"
url = SourceURL('http://www.doe-mbi.ucla.edu/~leec/test.gz')
url.__doc__ = 'test download'
pygrData.add_resource('Bio.Test.Download1', url)
pygrData.commit()
# performs the download
fpath = pygrData.Bio.Test.Download1()
h = testutil.get_file_md5(fpath)
self.assertEqual(h.hexdigest(), 'f95656496c5182d6cff9a56153c9db73')
os.remove(fpath)
def test_xmlrpc(self):
"Test XMLRPC"
pygrData.clear_cache() # force all future requests to reload
pygrData.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:
pygrData.Bio.Seq.sp2 = sp2
pygrData.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()
pygrData.commit() # finally save everything
pygrData.clear_cache() # force all requests to reload
