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())
