def injectTestFile(self, srcFiles, dstDir, timeout):
"""
Copy test file and wait for import to complete.
"""
try:
destFiles = []
for src in srcFiles:
ext = pathModule.path(src).ext
dstFile = os.path.join(dstDir, str(uuid.uuid1())+ext)
destFiles.append((src, dstFile))
except:
log.exception("Error source files:")
return -1
try:
for filePair in destFiles:
shutil.copy(filePair[0],filePair[1])
except:
log.exception("Error copying file:")
return -1
self.importCount = len(srcFiles)
self.event.wait(timeout)
if not self.event.isSet():
log.error("notifyTestFile not called enough times (%s/%s)", len(srcFiles)-self.importCount, len(srcFiles))
else:
log.info("All imports completed.")
try:
sf = omero.util.internal_service_factory(
self.communicator(), "root", "system",
retries=self.maxRetries, interval=self.retryInterval)
except:
log.exception("Failed to get Session: \n")
return -1
p = omero.sys.Parameters()
retVal = 0
for i in self.imageIds:
query = "select i from Image i where i.id = " + "'" + i + "'"
out = sf.getQueryService().findAllByQuery(query, p)
if len(out) > 0:
for item in out:
fname = item._name._val
log.info("Query on id=%s returned file %s", i, fname)
else:
log.error("No items found.")
retVal = -1
try:
sf.destroy()
except:
log.exception("Failed to get close session: \n")
return retVal
def testListOrphans(self, gatewaywrapper):
gatewaywrapper.loginAsUser()
eid = gatewaywrapper.gateway.getUserId()
imageList = list()
for i in range(0, 5):
imageList.append(
gatewaywrapper.createTestImage(
imageName=(str(uuid.uuid1()))).getName())
findImages = list(gatewaywrapper.gateway.listOrphans("Image"))
assert len(findImages) == 5, "Did not find orphaned images"
for p in findImages:
assert p.getName(
) in imageList, "All images should have queried name"
params = omero.sys.ParametersI()
params.page(1, 3)
findImagesInPage = list(
gatewaywrapper.gateway.listOrphans("Image", eid=eid,
params=params))
assert len(
findImagesInPage) == 3, "Did not find orphaned images in page"
for p in findImages:
client = p._conn
handle = client.deleteObjects('Image', [p.getId()],
deleteAnns=True)
try:
client._waitOnCmd(handle)
finally:
handle.close()
def testListOrphans(self, gatewaywrapper):
gatewaywrapper.loginAsUser()
eid = gatewaywrapper.gateway.getUserId()
imageList = list()
for i in range(0,5):
imageList.append(gatewaywrapper.createTestImage(imageName=(str(uuid.uuid1()))).getName())
findImages = list(gatewaywrapper.gateway.listOrphans("Image"))
assert len(findImages) == 5, "Did not find orphaned images"
for p in findImages:
assert p.getName() in imageList, "All images should have queried name"
params = omero.sys.ParametersI()
params.page(1, 3)
findImagesInPage = list(gatewaywrapper.gateway.listOrphans("Image", eid=eid, params=params))
assert len(findImagesInPage) == 3, "Did not find orphaned images in page"
for p in findImages:
client = p._conn
handle = client.deleteObjects('Image', [p.getId()], deleteAnns=True)
try:
client._waitOnCmd(handle)
finally:
handle.close()
def _getNextMonitorId(self):
"""
Return next monitor ID and increment.
The monitorID is a unique key to identify a monitor on the
file system. In the present implementation this is a string
generated by uuid.uuid1()
:return: Next monitor Id
:rtype: string
"""
return str(uuid.uuid1())
def __init__(self, eventTypes, pathMode, pathString, whitelist, blacklist, ignoreSysFiles, ignoreDirEvents, proxy):
"""
Set-up Monitor thread.
After initialising the superclass and some instance variables
try to create an FSEventStream. Throw an exeption if this fails.
:Parameters:
eventTypes :
A list of the event types to be monitored.
pathMode :
The mode of directory monitoring: flat, recursive or following.
pathString : string
A string representing a path to be monitored.
whitelist : list<string>
A list of files and extensions of interest.
blacklist : list<string>
A list of subdirectories to be excluded.
ignoreSysFiles :
If true platform dependent sys files should be ignored.
monitorId :
Unique id for the monitor included in callbacks.
proxy :
A proxy to be informed of events
"""
AbstractPlatformMonitor.__init__(self, eventTypes, pathMode, pathString, whitelist, blacklist, ignoreSysFiles, ignoreDirEvents, proxy)
self.log = logging.getLogger("fsserver."+__name__)
#: an FSEvents.FSEventStream StreamRef object reference.
self.streamRef = None
#: FSEvents.CFRunLoop object reference.
self.runLoopRef = None
self.clientInfo = str(uuid.uuid1())
#
# Without using the mutable array, ie using the Python list directly,
# the code works but throws up a couple of horrible warnings:
# "Oject of class OC_PythonArray autoreleased with no pool in place
# - just leaking"
# With the array there are still warnings about the strings whether
# Python native strings are used or NSStrings.
#
# All of these warnings are eliminated by using a pool for the lifetime
# of the NSMutableArray.
#
pool = NSAutoreleasePool.alloc().init()
pathsToMonitor = NSMutableArray.alloc().init()
ms = NSString.stringWithString_(self.pathsToMonitor)
pathsToMonitor.insertObject_atIndex_(ms, 0)
self.directory = fsDirectory.Directory(pathString=self.pathsToMonitor,
whitelist=self.whitelist,
pathMode=self.pathMode)
self.streamRef = FSEvents.FSEventStreamCreate(FSEvents.kCFAllocatorDefault,
self.callback,
self.clientInfo,
pathsToMonitor,
FSEvents.kFSEventStreamEventIdSinceNow,
1,
FSEvents.kFSEventStreamCreateFlagWatchRoot)
#
# Release the pool now that the NSMutableArray has been used.
#
del pool
if self.streamRef == None:
raise Exception('Failed to create FSEvent Stream')
self.log.info('Monitor set-up on %s', str(self.pathsToMonitor))
self.log.info('Monitoring %s events', str(self.eTypes))
# set up mpi world recover number of nodes and rank of each process
# Process of rank=0 acts as co-ordinating process and does the latex generation
comm = mpi.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
name = mpi.Get_processor_name()
# get the command line arguments
try:
opts, args = gop.getopt(argv, "h:u:p:c:e:r:o", [
"host", "user", "password", "control", "experiment", "rfid",
"outputfilename"
])
except gop.error, msg:
print >> sys.stderr, msg
return 2
s_dir = str(uuid.uuid1()) + '/'
d_args = {}
d_args['d'] = s_dir
for opt, arg in opts:
if opt in ("-h", "--host"):
host = arg.strip()
d_args['host'] = host
if opt in ("-u", "--user"):
user = arg.strip()
d_args['user'] = user
if opt in ("-p", "--password"):
password = arg.strip()
d_args['password'] = password
if opt in ("-c", "--control"):
control = arg.strip()
d_args['control'] = control
def mpi_run(argv):
texfilename = 'test_n.tex';
# set up mpi world recover number of nodes and rank of each process
# Process of rank=0 acts as co-ordinating process and does the latex generation
comm = mpi.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
name= mpi.Get_processor_name()
# get the command line arguments
try:
opts, args = gop.getopt(argv, "h:u:p:c:e:r:o", ["host","user","password","control","experiment", "rfid", "outputfilename"])
except gop.error, msg:
print >>sys.stderr, msg
return 2
s_dir = str(uuid.uuid1())+'/';
d_args={}
d_args['d'] = s_dir;
for opt, arg in opts:
if opt in ("-h", "--host"):
host=arg.strip()
d_args['host']=host
if opt in ("-u", "--user"):
user=arg.strip()
d_args['user']=user
if opt in ("-p", "--password"):
password=arg.strip()
d_args['password']=password
if opt in ("-c", "--control"):
control=arg.strip()
d_args['control']=control
def injectTestFile(self, srcFiles, dstDir, timeout):
"""
Copy test file and wait for import to complete.
"""
try:
destFiles = []
for src in srcFiles:
ext = pathModule.path(src).ext
dstFile = os.path.join(dstDir, str(uuid.uuid1()) + ext)
destFiles.append((src, dstFile))
except:
log.exception("Error source files:")
return -1
try:
for filePair in destFiles:
shutil.copy(filePair[0], filePair[1])
except:
log.exception("Error copying file:")
return -1
self.importCount = len(srcFiles)
self.event.wait(timeout)
if not self.event.isSet():
log.error("notifyTestFile not called enough times (%s/%s)",
len(srcFiles) - self.importCount, len(srcFiles))
else:
log.info("All imports completed.")
try:
sf = omero.util.internal_service_factory(
self.communicator(),
"root",
"system",
retries=self.maxRetries,
interval=self.retryInterval)
except:
log.exception("Failed to get Session: \n")
return -1
p = omero.sys.Parameters()
retVal = 0
for i in self.imageIds:
query = "select i from Image i where i.id = " + "'" + i + "'"
out = sf.getQueryService().findAllByQuery(query, p)
if len(out) > 0:
for item in out:
fname = item._name._val
log.info("Query on id=%s returned file %s", i, fname)
else:
log.error("No items found.")
retVal = -1
try:
sf.destroy()
except:
log.exception("Failed to get close session: \n")
return retVal
texfilename = "test_n.tex"
# set up mpi world recover number of nodes and rank of each process
# Process of rank=0 acts as co-ordinating process and does the latex generation
comm = mpi.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
name = mpi.Get_processor_name()
# get the command line arguments
try:
opts, args = gop.getopt(
argv, "h:u:p:c:e:r:o", ["host", "user", "password", "control", "experiment", "rfid", "outputfilename"]
)
except gop.error, msg:
print >>sys.stderr, msg
return 2
s_dir = str(uuid.uuid1()) + "/"
d_args = {}
d_args["d"] = s_dir
for opt, arg in opts:
if opt in ("-h", "--host"):
host = arg.strip()
d_args["host"] = host
if opt in ("-u", "--user"):
user = arg.strip()
d_args["user"] = user
if opt in ("-p", "--password"):
password = arg.strip()
d_args["password"] = password
if opt in ("-c", "--control"):
control = arg.strip()
d_args["control"] = control
