def test_schema(self):
"Test schema"
sp_hbb1 = testutil.datafile('sp_hbb1')
sp2 = seqdb.BlastDB(sp_hbb1)
sp2.__doc__ = 'another sp'
pygr.Data.Bio.Seq.sp2 = sp2
sp = pygr.Data.Bio.Seq.Swissprot.sp42()
m = mapping.Mapping(sourceDB=sp, targetDB=sp2)
m.__doc__ = 'sp -> sp2'
pygr.Data.Bio.Seq.testmap = m
pygr.Data.schema.Bio.Seq.testmap = pygr.Data.OneToManyRelation(sp, sp2)
pygr.Data.save()
pygr.Data.clear_cache()
sp3 = seqdb.BlastDB(sp_hbb1)
sp3.__doc__ = 'sp number 3'
pygr.Data.Bio.Seq.sp3 = sp3
sp2 = pygr.Data.Bio.Seq.sp2()
m = mapping.Mapping(sourceDB=sp3, targetDB=sp2)
m.__doc__ = 'sp3 -> sp2'
pygr.Data.Bio.Seq.testmap2 = m
pygr.Data.schema.Bio.Seq.testmap2 = pygr.Data.OneToManyRelation(sp3,
sp2)
# List all cached resources.
l = pygr.Data.getResource.resourceCache.keys()
l.sort()
assert l == ['Bio.Seq.sp2', 'Bio.Seq.sp3', 'Bio.Seq.testmap2']
pygr.Data.save()
g = pygr.Data.getResource.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_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 setUp(self, testDir=None):
'''restrict megatest to an initially empty directory, need
large space to perform'''
import random
tmpList = [c for c in 'PygrBuildNLMSAMegabase']
random.shuffle(tmpList)
# Comment out the next line to run in current directory.
testDir = os.path.join(testOutputBaseDir, 'TEST_' + ''.join(tmpList))
if testDir is None:
testDir = 'TEST_' + ''.join(tmpList)
try:
os.mkdir(testDir)
testDir = os.path.realpath(testDir)
except:
raise IOError
self.path = testDir
try:
tmpFileName = os.path.join(testDir, 'DELETE_THIS_TEMP_FILE')
open(tmpFileName, 'w').write('A' * 1024 * 1024)
except:
raise IOError
pygr.Data.update(self.path)
from pygr import seqdb
for orgstr in msaSpeciesList:
genome = seqdb.BlastDB(os.path.join(seqDir, orgstr))
genome.__doc__ = docStringDict[orgstr]
pygr.Data.addResource('TEST.Seq.Genome.' + orgstr, genome)
pygr.Data.save()
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'
self.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'
self.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()
nlmsa.__doc__ = 'trivial map'
self.pygrData.Bio.Test.map = nlmsa
self.schema.Bio.Test.map = metabase.ManyToManyRelation(db,
annoDB, bindAttrs=('exons', ))
self.metabase.commit()
self.metabase.clear_cache()
finally:
nlmsa.close()
finally:
db.close()
def populate_swissprot():
"Populate the current worldbase with swissprot data"
# build BlastDB out of the sequences
sp_hbb1 = testutil.datafile('sp_hbb1')
sp = seqdb.BlastDB(sp_hbb1)
sp.__doc__ = 'little swissprot'
worldbase.Bio.Seq.Swissprot.sp42 = sp
# also store a fragment
hbb = sp['HBB1_TORMA']
ival = hbb[10:35]
ival.__doc__ = 'fragment'
worldbase.Bio.Seq.frag = ival
# build a mapping to itself
m = mapping.Mapping(sourceDB=sp, targetDB=sp)
trypsin = sp['PRCA_ANAVA']
m[hbb] = trypsin
m.__doc__ = 'map sp to itself'
worldbase.Bio.Seq.spmap = m
# create an annotation database and bind as exons attribute
worldbase.schema.Bio.Seq.spmap = metabase.OneToManyRelation(
sp, sp, bindAttrs=('buddy', ))
annoDB = seqdb.AnnotationDB({1: ('HBB1_TORMA', 10, 50)},
sp,
sliceAttrDict=dict(id=0, start=1, stop=2))
exon = annoDB[1]
# generate the names where these will be stored
tempdir = testutil.TempDir('exonAnnot')
filename = tempdir.subfile('cnested')
nlmsa = cnestedlist.NLMSA(filename,
'w',
pairwiseMode=True,
bidirectional=False)
nlmsa.addAnnotation(exon)
nlmsa.build()
annoDB.__doc__ = 'a little annotation db'
nlmsa.__doc__ = 'a little map'
worldbase.Bio.Annotation.annoDB = annoDB
worldbase.Bio.Annotation.map = nlmsa
worldbase.schema.Bio.Annotation.map = \
metabase.ManyToManyRelation(sp, annoDB, bindAttrs=('exons', ))
def test_xmlrpc(self):
"Test XMLRPC"
pygr.Data.clear_cache() # force all requests to reload
pygr.Data.update("http://localhost:%s" % self.server.port)
check_match(self)
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')
sp2 = seqdb.BlastDB(sb_hbb1)
sp2.__doc__ = 'another sp'
try:
pygr.Data.Bio.Seq.sp2 = sp2
pygr.Data.save()
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