def __init__(self, *args, **kwargs): # pylint: disable=unused-argument self._raiseExceptions = kwargs.get("raiseExceptions", False) self._siteId = kwargs.get("siteId", getSiteId()) self._serverId = kwargs.get("serverId", None) self.__cI = ConfigInfo(siteId=getSiteId()) # cD = self.__cI.get(self._serverId, {}) self._hostName = cD.get("HOST_NAME", None) self._userName = cD.get("HOST_USERNAME", None) self._password = cD.get("HOST_PASSWORD", None) self._hostPort = int(cD.get("HOST_PORT", 22)) self._protocol = cD.get("HOST_PROTOCOL", None) self._rootPath = cD.get("HOST_ROOT_PATH", None) self._keyFilePath = cD.get("HOST_KEY_FILE_PATH", None) self._keyFileType = cD.get("HOST_KEY_FILE_TYPE", None)
def __init__(self, log=sys.stderr, verbose=False): """ """ self.__lfh = log self.__verbose = verbose self.__debug = True self.__siteId = getSiteId() cI = ConfigInfo() cIcommon = ConfigInfoAppCommon(self.__siteId) self.__schemaPath = cIcommon.get_site_da_internal_schema_path() self.__dbHost = cI.get("SITE_DB_HOST_NAME") self.__dbUser = cI.get("SITE_DB_USER_NAME") self.__dbPw = cI.get("SITE_DB_PASSWORD") self.__dbPort = str(cI.get("SITE_DB_PORT_NUMBER")) self.__dbSocket = cI.get("SITE_DB_SOCKET") self.__archivePath = cI.get("SITE_ARCHIVE_STORAGE_PATH") self.__dbName = "da_internal" self.__workPath = os.path.join(self.__archivePath, "archive") self.__mysql = "mysql " self.__dbLoader = cIcommon.get_db_loader_path() self.__mapping = self.__schemaPath self.__workDir = "dbdata" self._dbCon = None
def setUp(self): # self.__verbose = True self.__siteId = getSiteId(defaultSiteId=None) self.__startTime = time.time() logger.debug("Starting %s at %s" % (self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())))
def __setup(self, defSiteId=None, sessionId=None): """Simulate the web application environment for managing session storage of temporaty data files.""" self.__siteId = getSiteId(defaultSiteId=defSiteId) # self.__cI = ConfigInfo(self.__siteId) self.__topPath = self.__cI.get("SITE_WEB_APPS_TOP_PATH") self.__topSessionPath = self.__cI.get( "SITE_WEB_APPS_TOP_SESSIONS_PATH") # self.__reqObj = InputRequest({}, verbose=self.__verbose, log=self.__lfh) self.__reqObj.setValue("TopSessionPath", self.__topSessionPath) self.__reqObj.setValue("TopPath", self.__topPath) self.__reqObj.setValue("WWPDB_SITE_ID", self.__siteId) # self.__reqObj.setValue("SITE_DA_INTERNAL_DB_USER", os.environ["SITE_DA_INTERNAL_DB_USER"]) self.__reqObj.setValue("SITE_DA_INTERNAL_DB_PASSWORD", os.environ["SITE_DA_INTERNAL_DB_PASSWORD"]) os.environ["WWPDB_SITE_ID"] = self.__siteId if sessionId is not None: self.__reqObj.setValue("sessionid", sessionId) # retained due to side effects _sessionObj = self.__reqObj.newSessionObj() # noqa: F841 self.__reqObj.printIt(ofh=self.__lfh)
def __init__(self): self.__site_id = getSiteId() self.__cI = ConfigInfo(siteId=self.__site_id) self.__packagePath = self.__cI.get('SITE_PACKAGES_PATH') self.node_path = os.path.join(self.__packagePath, 'node', 'bin', 'node') self.volume_server_pack = self.__cI.get('VOLUME_SERVER_PACK') self.volume_server_query = self.__cI.get('VOLUME_SERVER_QUERY')
def setUp(self): self.__tmpPath = TESTOUTPUT # self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n", self.__siteId) # self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") self.__testFileCif = "1xbb.cif"
def setUp(self): # self.__verbose = True self.__lfh = sys.stdout self.__testFile1 = "./tests/D_1000200183_model-annotate_P1.cif.V1" self.__testFile2 = "./tests/D_1000200183_model-release_P1.cif.V1" self.__siteId = getSiteId(defaultSiteId="WWPDB_DEPLOY_TEST") self.__sessionPath = "."
def setUp(self): self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n", self.__siteId) # # self.__tmpPath = TESTOUTPUT self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") # self.__testFileCif = '1xbb.cif' self.__testFileAnnotSS = "4deq.cif" self.__testFileAnnotSSTop = "topology.txt" # self.__testFileAnnotLink = "3rij.cif" self.__testFileAnnotCisPeptide = "5hoh.cif" self.__testFileAnnotSolvent = "4ec0.cif" self.__testFileAnnotValidate = "3rij.cif" self.__testFileAnnotNA = "1o3q.cif" self.__testFileAnnotSite = "1xbb.cif" self.__testIdAnnotSite = "1xbb" # self.__testFileAnnotSiteAlt = "4p00.cif" self.__testIdAnnotSiteAlt = "4P00" # OK JDW self.__testFileAnnotRcsb = "3of4.cif" # # self.__testFilePdbPisa = '1xbb.pdb' # self.__testFileCifPisa = '1xbb.cif' # # self.__testFileStarCs = "2MMZ-cs.str" # self.__testFileCsRelatedCif = "cor_16703_test.cif" # self.__testFileValidateXyz = "1cbs.cif" self.__testFileValidateSf = "1cbs-sf.cif" # self.__testValidateIdList = ["1cbs", "3of4", "3oqp"] # self.__testFileMtzBad = "mtz-bad.mtz" self.__testFileMtzGood = "mtz-good.mtz" self.__testFileMtzRunaway = "bad-runaway.mtz" # self.__testFileXyzRunaway = "bad-runaway.cif" self.__testMapNormal = "normal.map" self.__testMapSpider = "testmap.spi" # OK JDW self.__testFilePrdSearch = "D_1200000237_model_P1.cif.V1" self.__testValidateXrayIdList = ["1cbs"] self.__testValidateNmrIdList = ["2MM4", "2MMZ"] self.__testDccModelId = "4wpo" self.__testSpecialPosition = "5uee.cif" self.__testDepAssembly = "1cbs.cif"
def setUp(self): self.__lfh = sys.stderr self.__verbose = True # Get siteId from the environment - self.__siteId = getSiteId() self.__cI = ConfigInfo(siteId=self.__siteId) # In test mode, no deletions are performed - self.__testMode = True # # An data set ID list must be set -- self.__idListPath = "RELEASED.LIST" # self.__milestoneL = [] self.__milestoneL.append(None) self.__milestoneL.extend(self.__cI.get("CONTENT_MILESTONE_LIST")) self.__cTBD = self.__cI.get("CONTENT_TYPE_BASE_DICTIONARY") self.__cTD = self.__cI.get("CONTENT_TYPE_DICTIONARY") self.__cTL = sorted(self.__cTBD.keys()) # Example list of candidate content types for purging -- this is based on system V15x for X-ray content types self.__cTypesOtherL = [ "assembly-assign", "assembly-model", "assembly-model-xyz", "assembly-report", "chem-comp-assign", "chem-comp-assign-details", "chem-comp-assign-final", "chem-comp-depositor-info", "chem-comp-link", "component-image", "dcc-report", "dict-check-report", "dict-check-report-r4", "format-check-report", "geometry-check-report", "merge-xyz-report", "misc-check-report", "notes-from-annotator", "polymer-linkage-distances", "polymer-linkage-report", "secondary-structure-topology", "seq-align-data", "seq-assign", "seq-data-stats", "seqdb-match", "sequence-fasta", "sf-convert-report", "site-assign", "special-position-report", "validation-data", "validation-report", "validation-report-depositor", "validation-report-full", "validation-report-slider", ] # # Test snapshot directory required for recovery tests - self.__snapShotPath = "/net/wwpdb_da_data_archive/.snapshot/nightly.1/data"
def setUp(self): self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) # self.__tmpPath = TESTOUTPUT self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__testFileCif = '1xbb.cif' self.__testFileAnnotSS = '4deq.cif' self.__testFileAnnotSSTop = 'topology.txt' # self.__testFileAnnotLink = '3rij.cif' self.__testFileAnnotCisPeptide = '5hoh.cif' self.__testFileAnnotSolvent = '4ec0.cif' self.__testFileAnnotValidate = '3rij.cif' self.__testFileAnnotNA = '1o3q.cif' self.__testFileAnnotSite = '1xbb.cif' self.__testIdAnnotSite = '1xbb' # self.__testFileAnnotSiteAlt = '4p00.cif' self.__testIdAnnotSiteAlt = '4P00' ## OK JDW self.__testFileAnnotRcsb = '3of4.cif' # self.__testFilePdbPisa = '1xbb.pdb' self.__testFileCifPisa = '1xbb.cif' # self.__testFileStarCs = "2MMZ-cs.str" self.__testFileCsRelatedCif = "cor_16703_test.cif" # self.__testFileValidateXyz = "1cbs.cif" self.__testFileValidateSf = "1cbs-sf.cif" self.__testValidateIdList = ["1cbs", "3of4", "3oqp"] # self.__testFileMtzBad = "mtz-bad.mtz" self.__testFileMtzGood = "mtz-good.mtz" self.__testFileMtzRunaway = "bad-runaway.mtz" self.__testFileXyzRunaway = "bad-runaway.cif" self.__testMapNormal = "normal.map" self.__testMapSpider = "testmap.spi" ## OK JDW self.__testFilePrdSearch = 'D_1200000237_model_P1.cif.V1' self.__testValidateXrayIdList = ['1cbs'] self.__testValidateNmrIdList = ['2MM4', '2MMZ'] self.__testDccModelId = '4wpo' self.__testSpecialPosition = '5uee.cif' self.__testDepAssembly = "1cbs.cif"
def get_model_file(depid, version_id, mileStone=None, siteId=None): if siteId is None: siteId = getSiteId() pi = PathInfo(siteId, sessionPath=".", verbose=True, log=sys.stderr) mmcif = pi.getModelPdbxFilePath(dataSetId=depid, fileSource="archive", versionId=version_id, mileStone=mileStone) logging.debug("mmcif file path: %s", mmcif) return mmcif
def testWrapper(self): """Tests wrapper""" modelfile = os.path.join(mockTopPath, 'dp-utils', '1cbs.cif') sffile = os.path.join(mockTopPath, 'dp-utils', '1cbs-sf.cif') foout = os.path.join(TESTOUTPUT, '1cbs-fo.cif') twofoout = os.path.join(TESTOUTPUT, '1cbs-2fo.cif') pdf = os.path.join(TESTOUTPUT, '1cbs-val.pdf') fullpdf = os.path.join(TESTOUTPUT, '1cbs-full-val.pdf') xml = os.path.join(TESTOUTPUT, '1cbs-val.xml') svg = os.path.join(TESTOUTPUT, '1cbs-val.svg') png = os.path.join(TESTOUTPUT, '1cbs-val.png') oflog = os.path.join(TESTOUTPUT, '1cbs-val.log') #ofpdf, ofxml, offullpdf, ofpng, ofsvg, ofmtz if os.path.exists(foout): os.unlink(foout) if os.path.exists(twofoout): os.unlink(twofoout) import sys sys.stderr.write("CKP1\n") siteid = getSiteId() sys.stderr.write("SITEID %s\n" % siteid) vw = ValidationWrapper(tmpPath=TESTOUTPUT, siteId=getSiteId()) vw.imp(modelfile) vw.addInput(name="sf_file_path", value=sffile) vw.addInput(name='step_list', value='mogul,percentiles,writexml,writepdf,eds') vw.addInput(name='run_dir', value=os.path.join(TESTOUTPUT, 'validation_run')) vw.addInput(name="request_annotation_context", value="yes") vw.addInput(name="always_clear_calcs", value="yes") vw.op("annot-wwpdb-validate-all-sf") vw.expLog(oflog) ret = vw.expList(dstPathList=[pdf, xml, fullpdf, png, svg, foout, twofoout]) self.assertTrue(ret, "Writing SF file") self.assertTrue(os.path.exists(foout)) self.assertTrue(os.path.exists(twofoout))
def setUp(self): self.__tmpPath = TESTOUTPUT # self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__testFileCif = '1xbb.cif'
def __init__(self, siteId=None, sessionPath=".", verbose=False, log=None): """""" self.__verbose = verbose self.__lfh = log # self.__debug = False # pylint: disable=unused-private-member self.__siteId = siteId if siteId is not None else getSiteId(defaultSiteId=siteId) self.__sessionPath = sessionPath self.__sessionDownloadPath = None if self.__sessionPath is not None: self.__sessionDownloadPath = os.path.join(self.__sessionPath, "downloads") # self.__cI = ConfigInfo(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
def __init__(self, schemaDefObj, verbose=False, log=sys.stderr): self.__verbose = verbose self.__lfh = log self.__debug = False # self.__siteId = getSiteId(defaultSiteId="WWPDB_DEPLOY_MACOSX") self.__cI = ConfigInfo(self.__siteId) # self.__sd = schemaDefObj self.__databaseName = self.__sd.getDatabaseName() self.__dbCon = None self.__defaultD = {} self.__attributeParameterMap = {} self.__attributeConstraintParameterMap = {}
def setUp(self): self.__siteId = getSiteId(defaultSiteId="WWPDB_DEPLOY_TEST") logger.info("\nTesting with site environment for: %s", self.__siteId) # self.__tmpPath = TESTOUTPUT # self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") self.__testFileFastaP = os.path.join(self.__testFilePath, "1KIP.fasta") self.__testFileFastaN = os.path.join(self.__testFilePath, "2WDK.fasta") # logger.info("\nTest fasta protein file path %s", self.__testFileFastaP) logger.info("\nTest fasta RNA file path %s", self.__testFileFastaN)
def setUp(self): # Pick up site information from the environment or failover to the development site id. self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__tmpPath = TESTOUTPUT # self.__testFilePdbPisa = '3rer.pdb' self.__testFileCifPisa = '3rer.cif' # logger.info("\nTest file path %s\n" % (self.__testFilePath)) logger.info("\nCIF file path %s\n" % (self.__testFileCifPisa))
def setUp(self): # Pick up site information from the environment or failover to the development site id. self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n", self.__siteId) # self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") self.__tmpPath = TESTOUTPUT # self.__testFilePdbPisa = "3rer.pdb" self.__testFileCifPisa = "3rer.cif" # logger.info("\nTest file path %s\n", self.__testFilePath) logger.info("\nCIF file path %s\n", self.__testFileCifPisa)
def setUp(self): self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n", self.__siteId) # self.__tmpPath = TESTOUTPUT self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") # self.__testFileValidateXyz = "1cbs.cif" self.__testFileValidateSf = "1cbs-sf.cif" self.__testValidateIdList = ["1cbs", "3of4", "3oqp"] # self.__testFileMtzBad = "mtz-bad.mtz" self.__testFileMtzGood = "mtz-good.mtz" self.__testFileMtzRunaway = "bad-runaway.mtz"
def setUp(self): self.__lfh = sys.stderr self.__verbose = True # Pick up site information from the environment or failover to the development site id. self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n", self.__siteId) # self.__testFilePath = os.path.join(TOPDIR, "wwpdb", "mock-data", "dp-utils") self.__tmpPath = TESTOUTPUT # self.__testFileStarCs = "2MMZ-cs.str" self.__testFileNmrModel = "2MMZ.cif" self.__testFileNmrModelAlt = "1MM0.cif" self.__testConcatCS = "2mmz-cs-file-full-2.cif"
def __init__(self, verbose=False, log=sys.stderr): # pylint: disable=unused-argument self.__verbose = verbose self.__debug = True self.__cI = ConfigInfo(siteId=None, verbose=self.__verbose) self.__cIDepUI = ConfigInfoAppDepUI(siteId=getSiteId()) # Default data set id range assignments self.__depIdAssignments = self.__cI.get( "SITE_DATASET_ID_ASSIGNMENT_DICTIONARY") self.__depTestIdAssignments = self.__cI.get( "SITE_DATASET_TEST_ID_ASSIGNMENT_DICTIONARY") self.__siteBackupD = self.__cI.get("SITE_BACKUP_DICT", default={}) self.__dsLocD = None # self.__lockDirPath = self.__cI.get( "SITE_SERVICE_REGISTRATION_LOCKDIR_PATH", "/tmp") lockutils.set_defaults(self.__lockDirPath)
def setUp(self): self.__lfh = sys.stderr self.__verbose = True # Pick up site information from the environment or failover to the development site id. self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__tmpPath = TESTOUTPUT # self.__testFileStarCs = '2MMZ-cs.str' self.__testFileNmrModel = '2MMZ.cif' self.__testFileNmrModelAlt = '1MM0.cif' self.__testFileNmrMr = '2MMZ.mr' self.__testConcatCS = '2mmz-cs-file-full-2.cif'
def setUp(self): self.__siteId = getSiteId(defaultSiteId='WWPDB_DEPLOY_TEST') logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) self.__tmpPath = TESTOUTPUT # self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__testFileFastaP = os.path.join(self.__testFilePath, '1KIP.fasta') self.__testFileFastaN = os.path.join(self.__testFilePath, '2WDK.fasta') # logger.info("\nTest fasta protein file path %s\n" % (self.__testFileFastaP)) logger.info("\nTest fasta RNA file path %s\n" % (self.__testFileFastaN))
def setUp(self): self.__siteId = getSiteId(defaultSiteId=None) logger.info("\nTesting with site environment for: %s\n" % self.__siteId) # self.__cI = ConfigInfo(self.__siteId) # self.__tmpPath = TESTOUTPUT self.__testFilePath = os.path.join(TOPDIR, 'wwpdb', 'mock-data', 'dp-utils') self.__testMapSpider = "testmap.spi" # # Brian's protein dna complex 3IYD self.__testMapEmd = 'emd_5127.map' self.__testMapNormal = self.__testMapEmd # XML header self.__testXMLHeader = 'emd_8137_v2.xml'
def setUp(self): self.__lfh = sys.stderr self.__verbose = False # self.__serverId = "BACKUP_SERVER_RDI2" self.__cI = ConfigInfo(siteId=getSiteId(), verbose=self.__verbose, log=self.__lfh) cD = self.__cI.get(self.__serverId, {}) self.__hostName = cD.get("HOST_NAME") self.__userName = cD.get("HOST_USERNAME") self.__hostPort = int(cD.get("HOST_PORT")) # self.__protocol = cD.get("HOST_PROTOCOL") self.__rootPath = cD.get("HOST_ROOT_PATH") self.__keyFilePath = cD.get("HOST_KEY_FILE_PATH") self.__keyFileType = cD.get("HOST_KEY_FILE_TYPE") # self.__testLocalFilePath = "./data/TEST-FILE.DAT" self.__testLocalOutputFilePath = "./JUNK.JUNK" # self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
def __init__(self, command, job_name, log_dir, timeout=5600, memory_limit=0, number_of_processors=1, add_site_config=False, add_site_config_database=False): self.command = self.escape_substitution(command) if timeout: self.timeout = timeout else: self.timeout = 5600 self.memory_limit = memory_limit self.number_of_processors = number_of_processors self.job_name = job_name self.log_dir = log_dir self.memory_used = 0 self.memory_unit = 'MB' self.bsub_exit_status = 0 self.siteId = getSiteId() self.cI = ConfigInfo(self.siteId) self.bsub_source_command = self.cI.get('BSUB_SOURCE') self.bsub_run_command = self.cI.get('BSUB_COMMAND') self.pdbe_cluster_queue = self.cI.get('PDBE_CLUSTER_QUEUE') self.pdbe_memory_limit = 100000 self.bsub_login_node = self.cI.get('BSUB_LOGIN_NODE') self.bsub_timeout = self.cI.get('BSUB_TIMEOUT') self.bsub_retry_delay = self.cI.get('BSUB_RETRY_DELAY') self.bsub_log_file = os.path.join(self.log_dir, self.job_name + '.log') self.bsub_out_file = os.path.join(self.log_dir, self.job_name + '.out') self.add_site_config = add_site_config self.add_site_config_database = add_site_config_database self.out = None self.err = None
def testGetSiteId(self): self.assertEqual(getSiteId(), "WWPDB_DEPLOY_TEST")
def main(): # adding a conservative permission mask for this # os.umask(0o022) # siteId = getSiteId(defaultSiteId=None) cI = ConfigInfo(siteId) # topPath = cI.get('SITE_WEB_APPS_TOP_PATH') topSessionPath = cI.get("SITE_WEB_APPS_TOP_SESSIONS_PATH") # myFullHostName = platform.uname()[1] myHostName = str(myFullHostName.split(".")[0]).lower() # wsLogDirPath = os.path.join(topSessionPath, "ws-logs") # Setup logging -- now = time.strftime("%Y-%m-%d", time.localtime()) usage = "usage: %prog [options]" parser = OptionParser(usage) parser.add_option("--start", default=False, action="store_true", dest="startOp", help="Start consumer client process") parser.add_option("--stop", default=False, action="store_true", dest="stopOp", help="Stop consumer client process") parser.add_option("--restart", default=False, action="store_true", dest="restartOp", help="Restart consumer client process") parser.add_option("--status", default=False, action="store_true", dest="statusOp", help="Report consumer client process status") # parser.add_option("-v", "--verbose", default=False, action="store_true", dest="verbose", help="Enable verbose output") parser.add_option("--debug", default=1, type="int", dest="debugLevel", help="Debug level (default=1) [0-3]") parser.add_option("--instance", default=1, type="int", dest="instanceNo", help="Instance number [1-n]") # (options, _args) = parser.parse_args() # pidFilePath = os.path.join( wsLogDirPath, myHostName + "_" + str(options.instanceNo) + ".pid") stdoutFilePath = os.path.join( wsLogDirPath, myHostName + "_" + str(options.instanceNo) + "_stdout.log") stderrFilePath = os.path.join( wsLogDirPath, myHostName + "_" + str(options.instanceNo) + "_stderr.log") wfLogFilePath = os.path.join( wsLogDirPath, myHostName + "_" + str(options.instanceNo) + "_" + now + ".log") # logger = logging.getLogger(name="root") # pylint: disable=redefined-outer-name logging.captureWarnings(True) formatter = logging.Formatter( "%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s") handler = logging.FileHandler(wfLogFilePath) handler.setFormatter(formatter) logger.addHandler(handler) # lt = time.strftime("%Y %m %d %H:%M:%S", time.localtime()) # if options.debugLevel > 2: logger.setLevel(logging.DEBUG) elif options.debugLevel > 0: logger.setLevel(logging.INFO) else: logger.setLevel(logging.ERROR) # # myDP = MyDetachedProcess(pidFile=pidFilePath, stdout=stdoutFilePath, stderr=stderrFilePath, wrkDir=wsLogDirPath) if options.startOp: sys.stdout.write( "+DetachedMessageConsumer() starting consumer service at %s\n" % lt) logger.info( "DetachedMessageConsumer() starting consumer service at %s", lt) myDP.start() elif options.stopOp: sys.stdout.write( "+DetachedMessageConsumer() stopping consumer service at %s\n" % lt) logger.info( "DetachedMessageConsumer() stopping consumer service at %s", lt) myDP.stop() elif options.restartOp: sys.stdout.write( "+DetachedMessageConsumer() restarting consumer service at %s\n" % lt) logger.info( "DetachedMessageConsumer() restarting consumer service at %s", lt) myDP.restart() elif options.statusOp: sys.stdout.write( "+DetachedMessageConsumer() reporting status for consumer service at %s\n" % lt) sys.stdout.write(myDP.status()) else: pass
def setUp(self): self.__lfh = sys.stderr # Pick up site information from the environment or failover to the development site id. self.__siteId = getSiteId(defaultSiteId='WWPDB_DEPLOY_TEST') self.__lfh.write("\nTesting with site environment for: %s\n" % self.__siteId) # self.FILE_ROOT = os.path.dirname(os.path.realpath(__file__)) self.__cI = ConfigInfo(self.__siteId) self.__siteWebAppsSessionsPath = self.__cI.get( 'SITE_WEB_APPS_SESSIONS_PATH') self.__tmpPath = tempfile.mkdtemp(dir=self.__siteWebAppsSessionsPath) self.__testFilePath = os.path.join(self.FILE_ROOT, 'data') self.__testFileAnnotSS = 'rcsb070236.cif' self.__testFileAnnotSSTop = 'topology.txt' # self.__testFileAnnotLink = '3rij.cif' self.__testFileAnnotCisPeptide = '5hoh.cif' self.__testFileAnnotSolvent = 'D_900002_model_P1.cif' self.__testFileAnnotValidate = '3rij.cif' self.__testFileAnnotNA = '1o3q.cif' self.__testFileAnnotSite = '1xbb.cif' self.__testIdAnnotSite = '1xbb' # self.__testFileAnnotSiteAlt = 'D_1000200391_model_P1.cif.V27' self.__testIdAnnotSiteAlt = 'D_1000200391' # self.__testFileAnnotRcsb = 'rcsb033781.cif' self.__testFileAnnotRcsbEps = 'rcsb013067.cifeps' # self.__testFilePdbPisa = self.__cI.get('DP_TEST_FILE_PDB_PISA') self.__testFileCifPisa = self.__cI.get('DP_TEST_FILE_CIF_PISA') # self.__testFileStarCs = "star_16703_test_2.str" self.__testFileCsRelatedCif = "cor_16703_test.cif" # self.__testFileValidateXyz = "1cbs.cif" self.__testFileValidateSf = "1cbs-sf.cif" self.__testValidateIdList = ["1cbs", "3of4", "3oqp"] self.__testArchiveIdList = [("D_900002", "4EC0"), ("D_600000", "4F3R")] # self.__testFileCifSeq = "RCSB095269_model_P1.cif.V1" self.__testFileSeqAssign = "RCSB095269_seq-assign_P1.cif.V1" self.__testFileMtzBad = "mtz-bad.mtz" self.__testFileMtzGood = "mtz-good.mtz" self.__testFileMtzRunaway = "bad-runaway.mtz" self.__testFileXyzRunaway = "bad-runaway.cif" self.__testMapNormal = "normal.map" self.__testMapSpider = "testmap.spi" self.__testMapLarge = "large.map" # self.__testFilePrdSearch = '3RUN.cif' self.__testFilePrdSearch = 'D_1200000237_model_P1.cif.V1' self.__testValidateXrayIdList = ['1cbs', '4hea', '4u4r'] self.__testValidateNmrIdList = ['2MM4', '2MMZ'] self.__testValidateXrayNeutronModel = 'D_1200007116_model-upload_P1.cif.V1' self.__testValidateXrayNeutronSF = 'D_1200007116_sf-upload_P1.cif.V1' #self.__testValidateXrayLargeIdList = ['4u4r'] #self.__testValidateNmrIdList = ['2MM4'] #self.__testValidateNmrLargeIdList = ['2MMZ'] self.__testDccModelId = '4wpo' self.__testSpecialPosition = 'D_1000225739_model_P1.cif.V4' self.__testDepAssembly = "testassem.cif"
def testImport(self): vw = ValidationWrapper(tmpPath=TESTOUTPUT, siteId=getSiteId())