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_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