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 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')