def reset(self):
"Resets the root temporary directory"
logger.debug('resetting path %s' % self.tempdir)
shutil.rmtree(self.path, ignore_errors=True)
shutil.rmtree(self.tempdir, ignore_errors=True)
self.path = self.get_path()
def run_server(self):
'this method blocks, so run it in a separate thread'
cmdArgs = (sys.executable, self.server_script) + tuple(sys.argv) \
+ ('--port-file=' + self.port_file,
'--pygrdatapath=' + self.pygrDataPath,
'--downloadDB=' + self.downloadDB,
'--resources=' + ':'.join(self.pygrDataNames))
if self.port: # only add port argument if set
cmdArgs += ('--port=' + str(self.port), )
p = classutil.FilePopen(cmdArgs,
stdout=classutil.PIPE,
stderr=classutil.PIPE)
try:
logger.debug('Starting XML-RPC server: ')
logger.debug(repr(cmdArgs))
if p.wait():
logger.warn('XML-RPC server command failed!')
output = p.stdout.read()
errout = p.stderr.read()
logger.debug('XML-RPC server output: %s' % output)
logger.debug('XML-RPC server error out: %s' % errout)
finally:
p.close()
logger.debug('server stopped')
def setUp(self):
TestBase.setUp(self)
logger.debug('accessing ensembldb.ensembl.org')
conn = sqlgraph.DBServerInfo(host='ensembldb.ensembl.org',
user='******', passwd='')
try:
translationDB = sqlgraph.SQLTable(
'homo_sapiens_core_47_36i.translation', serverInfo=conn)
exonDB = sqlgraph.SQLTable('homo_sapiens_core_47_36i.exon',
serverInfo=conn)
sql_statement = '''SELECT t3.exon_id FROM
homo_sapiens_core_47_36i.translation AS tr,
homo_sapiens_core_47_36i.exon_transcript AS t1,
homo_sapiens_core_47_36i.exon_transcript AS t2,
homo_sapiens_core_47_36i.exon_transcript AS t3 WHERE tr.translation_id = %s
AND tr.transcript_id = t1.transcript_id AND t1.transcript_id =
t2.transcript_id AND t2.transcript_id = t3.transcript_id AND t1.exon_id =
tr.start_exon_id AND t2.exon_id = tr.end_exon_id AND t3.rank >= t1.rank AND
t3.rank <= t2.rank ORDER BY t3.rank
'''
translationExons = sqlgraph.GraphView(translationDB, exonDB,
sql_statement,
serverInfo=conn)
except ImportError:
raise SkipTest('missing MySQLdb module?')
translationExons.__doc__ = 'test saving exon graph'
self.pygrData.Bio.Ensembl.TranslationExons = translationExons
self.metabase.commit()
self.metabase.clear_cache()
def reset(self):
"Resets the root temporary directory"
logger.debug('resetting path %s' % self.tempdir)
shutil.rmtree(self.path, ignore_errors=True)
shutil.rmtree(self.tempdir, ignore_errors=True)
self.path = self.get_path()
def setUp(self):
# test will be skipped if mysql module or ensembldb server unavailable
logger.debug('accessing ensembldb.ensembl.org')
conn = DBServerInfo(host='ensembldb.ensembl.org', user='******',
passwd='')
try:
translationDB = SQLTable('homo_sapiens_core_47_36i.translation',
serverInfo=conn)
exonDB = SQLTable('homo_sapiens_core_47_36i.exon', serverInfo=conn)
except ImportError,e:
raise SkipTest(e)
def setUp(self):
# test will be skipped if mysql module or ensembldb server unavailable
logger.debug('accessing ensembldb.ensembl.org')
conn = DBServerInfo(host='ensembldb.ensembl.org',
user='******',
passwd='')
try:
translationDB = \
SQLTableCatcher('homo_sapiens_core_47_36i.translation',
serverInfo=conn)
translationDB.catchIter = True # should not iter in this test!
exonDB = SQLTable('homo_sapiens_core_47_36i.exon', serverInfo=conn)
except ImportError, e:
raise SkipTest(e)
def run_server(self):
'this method blocks, so run it in a separate thread'
cmdArgs = (sys.executable, self.server_script) + tuple(sys.argv) \
+ ('--port=' + str(self.port),
'--port-file=' + self.port_file,
'--pygrdatapath=' + self.pygrDataPath,
'--downloadDB=' + self.downloadDB,
'--resources=' + ':'.join(self.pygrDataNames))
p = classutil.FilePopen(cmdArgs, stdout=classutil.PIPE,
stderr=classutil.PIPE)
try:
logger.debug('Starting XML-RPC server: ')
logger.debug(repr(cmdArgs))
if p.wait():
logger.warn('XML-RPC server command failed!')
output = p.stdout.read()
errout = p.stderr.read()
logger.debug('XML-RPC server output: %s' % output)
logger.debug('XML-RPC server error out: %s' % errout)
finally:
p.close()
logger.debug('server stopped')
