Hi Josh
ulimit -n
2560
Thanks for the reply. Today I've had less issues with this script due to a couple of changes to the way I'm doing things. However there has been some different errors and I would guess I'm not doing things the most efficient way (although it does seem to be using a single session and not creating new ones).
At the moment it fails a few times with this error that I'll paste in after the code. I'm using the same user credentials for all requests and only uploading about 800 files total from different directories - into only 3 projects and about 1 or 2 datasets under each.
- Code: Select all
#!/usr/bin/python
import os
import requests
import json
from xml.dom.minidom import parseString
import glob
import shutil
import sys
import os.path
import sys, getopt
import mysql.connector
from mysql.connector import errorcode
import omero.rtypes
import omero
import omero.cli
from omero.gateway import BlitzGateway
from omero.rtypes import wrap
from omero.model import DatasetI, ProjectI
from common import splitString
responseFailed=0
numberOfImageDownloadAttemps=0
totalNumberOfImagesWeHave=0
numFoundInSolr=0
cli=None
group='system'
uniqueUris=set()
def main(argv):
solrUrl="""http://wwwdev.ebi.ac.uk/mi/impc/dev/solr/experiment/select?q=observation_type:image_record&fq=(download_file_path:*mousephenotype.org*%20AND%20!download_file_path:*.pdf)&fl=id,download_file_path,phenotyping_center,pipeline_stable_id,procedure_stable_id,datasource_name,parameter_stable_id&wt=json&indent=on&rows=10000000"""
#below url for testing one paremeter only
#solrUrl="""http://wwwdev.ebi.ac.uk/mi/impc/dev/solr/experiment/select?q=observation_type:image_record&fq=(download_file_path:*mousephenotype.org*%20AND%20parameter_stable_id:IMPC_XRY_034_001)&fl=id,download_file_path,phenotyping_center,pipeline_stable_id,procedure_stable_id,datasource_name,parameter_stable_id&wt=json&indent=on&rows=1000000"""
#note cant split this url over a few lines as puts in newlines into url which doesn't work
rootDestinationDir='myimagesdir'
omeroHost = ''localhost'
omeroPort = 4064
omeroUser = 'user'
omeroPass = 'userpass''
print("running python image download script for impc images")
try:
opts, args = getopt.getopt(argv,"d:s:h:p:u::db:pass:ohost:oport:ouser:opass",[])
except getopt.GetoptError:
print 'upload_to_omero2.py -d <rootDestinationDir> -s <solrUrl> -h <komp2host> -p <komp2Port> -db <komp2db> -u <komp2User> -pass <komp2Pass> -ohost <omerohost> -oport <omero port> -ouser <omero user> -opass <omero pass>'
sys.exit(2)
for opt, arg in opts:
print 'upload_to_omero2.py -d <rootDestinationDir> -s <solrUrl> -h <komp2host> -p <komp2Port> -db <komp2db> -u <komp2User> -pass <komp2Pass> -ohost <omerohost> -oport <omero port> -ouser <omero user> -opass <omero pass>'
if opt in ("-d", "--rootDestinationDir"):
rootDestinationDir = arg
elif opt in ("-s", "--solrUrl"):
solrUrl = arg
print 'rootDestinationDir is "', rootDestinationDir
print 'solrUrl', solrUrl
#deleteImagesAlreadyInOmero(omeroHost, omeroPort, omeroUser, omeroPass)
alreadyInOmero=getImagesAlreadyInOmero(omeroHost, omeroPort, omeroUser, omeroPass)
runWithSolrAsDataSource(solrUrl, rootDestinationDir, alreadyInOmero, omeroUser, omeroPass, omeroHost, omeroPort)
def getImagesAlreadyInOmero( omeroHost, omeroPort, omeroUsername, omeroPass ):
alreadyInOmero=set()
from omero.gateway import BlitzGateway
# Connect to the Python Blitz Gateway
# =============================================================
# Make a simple connection to OMERO, printing details of the
# connection. See OmeroPy/Gateway for more info
conn = BlitzGateway(omeroUsername, omeroPass, host=omeroHost, port=omeroPort)
connected = conn.connect()
# Check if you are connected.
# =============================================================
if not connected:
import sys
sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
sys.exit(1)
# Using secure connection.
# =============================================================
# By default, once we have logged in, data transfer is not encrypted (faster)
# To use a secure connection, call setSecure(True):
# conn.setSecure(True) # <--------- Uncomment this
# Current session details
# =============================================================
# By default, you will have logged into your 'current' group in OMERO. This
# can be changed by switching group in the OMERO.insight or OMERO.web clients.
user = conn.getUser()
print "Current user:"
print " ID:", user.getId()
print " Username:", user.getName()
print " Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
print "Other Members of current group:"
for exp in conn.listColleagues():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
print "Owner of:"
for g in conn.listOwnedGroups():
print " ID:", g.getName(), " Name:", g.getId()
# New in OMERO 5
print "Admins:"
for exp in conn.getAdministrators():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
# The 'context' of our current session
ctx = conn.getEventContext()
# print ctx # for more info
print ctx
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is False, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
print_obj(project)
for dataset in project.listChildren():
print_obj(dataset, 2)
for image in dataset.listChildren():
#print_obj(image, 4)
fileset = image.getFileset()
if fileset is not None:
print image.getId()
filesetId=fileset.getId()
query = 'SELECT clientPath FROM FilesetEntry WHERE fileset.id = :id'
params = omero.sys.ParametersI()
params.addId(omero.rtypes.rlong(filesetId))
for path in conn.getQueryService().projection(query, params):
fullPath=path[0].val
if splitString in fullPath:
print 'path in omero=' +fullPath
relativeOmeroUrl=fullPath.split(splitString,1)[1]
print "adding to hash relative omero url="+relativeOmeroUrl
alreadyInOmero.add(relativeOmeroUrl)
# Close connection:
# =================================================================
# When you are done, close the session to free up server resources.
conn._closeSession()
return alreadyInOmero
def print_obj(obj, indent=0):
"""
Helper method to display info about OMERO objects.
Not all objects will have a "name" or owner field.
"""
print """%s%s:%s Name:"%s" (owner=%s)""" % (\
" " * indent,
obj.OMERO_CLASS,\
obj.getId(),\
obj.getName(),\
obj.getOwnerOmeName())
def runWithSolrAsDataSource(solrUrl, rootDestinationDir, alreadyInOmero, omeroUser, omeroPass, omeroHost, omeroPort):
#need to get these passed in as arguments - the host and db name etc for jenkins to run
#first get the list of download urls and the data source, experiment, procdure and parameter and observation id for the images
v = json.loads(requests.get(solrUrl).text)
docs=v['response']['docs']
numFoundInSolr=v['response']['numFound']
for doc in docs:
download_file_path=doc['download_file_path']
datasource_id=doc['datasource_name']
phenotyping_center=doc['phenotyping_center']
#experiment=doc['experiment']
pipeline_stable_id=doc['pipeline_stable_id']
observation_id=doc['id']
procedure_stable_id=doc['procedure_stable_id']
parameter_stable_id=doc['parameter_stable_id']
processFile(alreadyInOmero,observation_id, rootDestinationDir,phenotyping_center,pipeline_stable_id, procedure_stable_id, parameter_stable_id, download_file_path, omeroUser, omeroPass, omeroHost, omeroPort)
print 'number found in solr='+str(numFoundInSolr)+' number of failed responses='+str(responseFailed)+' number of requests='+str(numberOfImageDownloadAttemps)+' total totalNumberOfImagesWeHave='+str(totalNumberOfImagesWeHave)
def createDestinationFilePath(rootDestinationDir, phenotyping_center, pipeline_stable_id, procedure, parameter, download_file_path):
directory="/".join([rootDestinationDir,phenotyping_center, pipeline_stable_id,procedure,parameter])
return directory
def processFile(alreadyInOmero, observation_id, rootDestinationDir, phenotyping_center,pipeline_stable_id, procedure, parameter, downloadFilePath, omeroUser, omeroPass, omeroHost, omeroPort):
global totalNumberOfImagesWeHave
global responseFailed
global numberOfImageDownloadAttemps
directory = createDestinationFilePath(rootDestinationDir, phenotyping_center, pipeline_stable_id, procedure,parameter, downloadFilePath)
print 'directory='+directory
print 'downloadFilePath='+downloadFilePath
dstfilename=directory+"/"+str(downloadFilePath.split('/')[-1])
print 'dstfilename='+dstfilename
calculatedFilePath=dstfilename.split(splitString,1)[1]
#print 'calculatedFilePath='+calculatedFilePath
if calculatedFilePath in alreadyInOmero:
print 'calculatedFilePath is already in Omero '+calculatedFilePath
else:
print 'should load into omero '+calculatedFilePath
slashSplit=calculatedFilePath.split("/")
project=slashSplit[0]
print 'project='+project
dataset=slashSplit[3]
print 'dataset='+dataset
loadIntoOmero(dstfilename, project, dataset, omeroUser, omeroPass, omeroHost, omeroPort)
if dstfilename in uniqueUris:
print '---------------------!!!!!!!!!!error the filePath is not unique and has been specified before:'+dstfilename
uniqueUris.add(dstfilename)
print 'dstfilename '+dstfilename
def loadIntoOmero(fullNfsUrl, project, dataset, omeroUser, omeroPass, omeroHost, omeroPort):
print 'need to load into omero here'
do_import(omeroUser, omeroPass, omeroHost, omeroPort, fullNfsUrl, dataset, project, omeroPass)
print "import finished"
def do_import(omeroUser, omeroPass, omeroHost, omeroPort, filename, dataset=None, project=None, passw=None):
#print "printing user info"+user, group, filename
global cli
print "-"*100
if cli is None:
print "cli is none!!!!!"
cli = omero.cli.CLI()
cli.loadplugins()
cli.invoke(["login", omeroUser+'@'+omeroHost, "-w", passw, "-C"], strict=True)
#cli.invoke(["login", "%s@localhost" % user, "-w", passw, "-C"], strict=True)
cli.invoke(["sessions", "group", group], strict=True)
import_args = ["import"]
if dataset is not None:
dsId = create_containers(cli, dataset,omeroHost, project)
print "dsId="+str(dsId)
import_args.extend(["-d", str(dsId),"--debug", "DEBUG"])#,"--debug", "ALL"])
else:
print "dataset is None!!!!!!!!!!!!!!!!!!!!"
import_args.append(filename)
print " import args="
print import_args
cli.invoke(import_args, strict=True)
def create_containers(cli, dataset, omeroHost, project=None):
"""
Creates containers with names provided if they don't exist already.
Returns Dataset ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host=omeroHost)
conn.connect(sUuid = sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
#print "ownerId="+conn.getUser().getId()
#project=None
from omero.rtypes import rstring
d = None
prId = None
if project is not None:
p = conn.getObject("Project", attributes={'name': project}, params=params)
if p is None:
print "Creating Project:", project
p = omero.model.ProjectI()
p.name = wrap(str(project))
prId = conn.getUpdateService().saveAndReturnObject(p).id.val
else:
print "Using Project:", project, p
prId = p.getId()
# Since Project already exists, check children for Dataset
for c in p.listChildren():
if c.getName() == dataset:
d = c
if d is None:
d = conn.getObject("Dataset", attributes={'name': dataset}, params=params)
if d is None:
print "Creating Dataset:", dataset
d = omero.model.DatasetI()
d.name = wrap(str(dataset))
dsId = conn.getUpdateService().saveAndReturnObject(d).id.val
if prId is not None:
print "Linking Project-Dataset..."
link = omero.model.ProjectDatasetLinkI()
link.child = omero.model.DatasetI(dsId, False)
link.parent = omero.model.ProjectI(prId, False)
conn.getUpdateService().saveObject(link)
else:
print "Using Dataset:", dataset, d
dsId = d.getId()
return dsId
def deleteImagesAlreadyInOmero( omeroHost, omeroPort, omeroUsername, omeroPass ):
from omero.gateway import BlitzGateway
# Connect to the Python Blitz Gateway
# =============================================================
# Make a simple connection to OMERO, printing details of the
# connection. See OmeroPy/Gateway for more info
conn = BlitzGateway(omeroUsername, omeroPass, host=omeroHost, port=omeroPort)
connected = conn.connect()
# Check if you are connected.
# =============================================================
if not connected:
import sys
sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
sys.exit(1)
# Using secure connection.
# =============================================================
# By default, once we have logged in, data transfer is not encrypted (faster)
# To use a secure connection, call setSecure(True):
# conn.setSecure(True) # <--------- Uncomment this
# Current session details
# =============================================================
# By default, you will have logged into your 'current' group in OMERO. This
# can be changed by switching group in the OMERO.insight or OMERO.web clients.
user = conn.getUser()
print "Current user:"
print " ID:", user.getId()
print " Username:", user.getName()
print " Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
print "Other Members of current group:"
for exp in conn.listColleagues():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
print "Owner of:"
for g in conn.listOwnedGroups():
print " ID:", g.getName(), " Name:", g.getId()
# New in OMERO 5
print "Admins:"
for exp in conn.getAdministrators():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
# The 'context' of our current session
ctx = conn.getEventContext()
# print ctx # for more info
print ctx
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is False, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
print_obj(project)
object_ids=[project.getId()]
deleteChildren = True
handle = conn.deleteObjects("Project", object_ids,\
deleteAnns=True, deleteChildren=deleteChildren)
# Close connection:
# =================================================================
# When you are done, close the session to free up server resources.
conn._closeSession()
if __name__ == "__main__":
main(sys.argv[1:])
errors:
- Code: Select all
import finished
dstfilename /Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_034_001/30971.bmp
directory=/Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001
downloadFilePath=http://images.mousephenotype.org/src/6/10/1182/35/91/2172/30982.bmp
dstfilename=/Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp
calculatedFilePath=ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp
should load into omero ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp
project=ICS
dataset=IMPC_XRY_048_001
need to load into omero here
----------------------------------------------------------------------------------------------------
Using Project: ICS <_ProjectWrapper id=102>
Using Dataset: IMPC_XRY_048_001 <_DatasetWrapper id=103>
dsId=103
import args=
['import', '-d', '103', '--debug', 'DEBUG', u'/Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp']
Using session 77096529-6faa-43e7-be22-fec671760dbe (root@172.22.68.222:4064). Idle timeout: 10.0 min. Current group: system
2014-07-22 12:41:35,709 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.0.2-ice35-b26
2014-07-22 12:41:35,730 262 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 5.0.2-ice35-b26 revision: 0c4215a date: 27 May 2014
2014-07-22 12:41:35,743 275 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: DEBUG OMERO.importer: DEBUG
2014-07-22 12:41:35,744 276 [ main] DEBUG ome.formats.importer.ImportConfig - Loaded savedDirectory from ome.formats.importer.util.IniFileLoader@13e7f00e
2014-07-22 12:41:35,744 276 [ main] DEBUG ome.formats.importer.ImportConfig - Loaded savedDirectory from default
2014-07-22 12:41:36,029 561 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-07-22 12:41:36,031 563 [ main] DEBUG ome.formats.importer.cli.ErrorHandler - SCANNING: Depth:0 Num: 1 Tot: n/a File: 48_001/30982.bmp
2014-07-22 12:41:36,033 565 [ main] DEBUG loci.common.Location - Location.mapFile: embedded-stream.raw -> null
2014-07-22 12:41:36,036 568 [ main] DEBUG loci.formats.Memoizer - skipping memo: no directory given
2014-07-22 12:41:36,043 575 [ main] DEBUG loci.common.NIOByteBufferProvider - Using mapped byte buffer? false
2014-07-22 12:41:36,048 580 [ main] INFO loci.formats.ImageReader - BMPReader initializing /Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp
2014-07-22 12:41:36,048 580 [ main] DEBUG loci.formats.FormatHandler - BMPReader initializing /Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp
2014-07-22 12:41:36,048 580 [ main] DEBUG loci.formats.FormatHandler - loci.formats.in.BMPReader.initFile(/Users/jwarren/images/impc/ICS/ICS_001/IMPC_XRY_001/IMPC_XRY_048_001/30982.bmp)
2014-07-22 12:41:36,050 582 [ main] INFO loci.formats.FormatHandler - Reading bitmap header
2014-07-22 12:41:36,051 583 [ main] INFO loci.formats.FormatHandler - Populating metadata
2014-07-22 12:41:36,131 663 [ main] DEBUG loci.common.services.ServiceFactory - Loaded properties from: services.properties
2014-07-22 12:41:36,133 665 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.POIService and implementation class loci.formats.services.POIServiceImpl
2014-07-22 12:41:36,133 665 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MDBService and implementation class loci.formats.services.MDBServiceImpl
2014-07-22 12:41:36,133 665 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JPEGTurboService and implementation class loci.formats.services.JPEGTurboServiceImpl
2014-07-22 12:41:36,134 666 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JAIIIOService and implementation class loci.formats.services.JAIIIOServiceImpl
2014-07-22 12:41:36,135 667 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.WlzService and implementation class loci.formats.services.WlzServiceImpl
2014-07-22 12:41:36,136 668 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.NetCDFService and implementation class loci.formats.services.NetCDFServiceImpl
2014-07-22 12:41:36,136 668 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MetakitService and implementation class loci.formats.services.MetakitServiceImpl
2014-07-22 12:41:36,137 669 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.LuraWaveService and implementation class loci.formats.services.LuraWaveServiceImpl
2014-07-22 12:41:36,138 670 [ main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.OMEXMLService and implementation class loci.formats.services.OMEXMLServiceImpl
2014-07-22 12:41:36,154 686 [ main] DEBUG loci.formats.Memoizer - start[1406029296036] time[118] tag[loci.formats.Memoizer.setId]
2014-07-22 12:41:36,163 695 [ main] DEBUG loci.common.Location - Location.mapFile: embedded-stream.raw -> null
2014-07-22 12:41:36,164 696 [ main] DEBUG ome.formats.importer.cli.ErrorHandler - SCANNING: Depth:0 Num: 1 Tot: 1 File: 48_001/30982.bmp
2014-07-22 12:41:36,165 697 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 132ms. (136ms total) [0 unknowns]
2014-07-22 12:41:36,506 1038 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to 172.22.68.222:4064
2014-07-22 12:41:37,029 1561 [ main] ERROR formats.importer.cli.CommandLineImporter - Error during import process.
Ice.SecurityException: javax.net.ssl.SSLException: Received fatal alert: bad_record_mac
at IceInternal.ConnectRequestHandler.getConnection(ConnectRequestHandler.java:244) ~[ice.jar:na]
at IceInternal.ConnectRequestHandler.sendRequest(ConnectRequestHandler.java:141) ~[ice.jar:na]
at IceInternal.Outgoing.invoke(Outgoing.java:77) ~[ice.jar:na]
at Ice._ObjectDelM.ice_isA(_ObjectDelM.java:33) ~[ice.jar:na]
at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:98) ~[ice.jar:na]
at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:61) ~[ice.jar:na]
at Glacier2.RouterPrxHelper.checkedCast(RouterPrxHelper.java:2262) ~[ice-glacier2.jar:na]
at omero.client.getRouter(client.java:770) ~[blitz.jar:na]
at omero.client.createSession(client.java:693) ~[blitz.jar:na]
at omero.client.joinSession(client.java:623) ~[blitz.jar:na]
at ome.formats.OMEROMetadataStoreClient.initialize(OMEROMetadataStoreClient.java:674) ~[blitz.jar:na]
at ome.formats.importer.ImportConfig.createStore(ImportConfig.java:303) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:125) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:719) ~[blitz.jar:na]
Caused by: javax.net.ssl.SSLException: Received fatal alert: bad_record_mac
at sun.security.ssl.Alerts.getSSLException(Alerts.java:208) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.fatal(SSLEngineImpl.java:1619) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.fatal(SSLEngineImpl.java:1587) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.recvAlert(SSLEngineImpl.java:1756) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.readRecord(SSLEngineImpl.java:1060) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.readNetRecord(SSLEngineImpl.java:884) ~[na:1.7.0_25]
at sun.security.ssl.SSLEngineImpl.unwrap(SSLEngineImpl.java:758) ~[na:1.7.0_25]
at javax.net.ssl.SSLEngine.unwrap(SSLEngine.java:624) ~[na:1.7.0_25]
at IceSSL.TransceiverI.handshakeNonBlocking(TransceiverI.java:543) ~[ice.jar:na]
at IceSSL.TransceiverI.initialize(TransceiverI.java:109) ~[ice.jar:na]
at Ice.ConnectionI.initialize(ConnectionI.java:1933) ~[ice.jar:na]
at Ice.ConnectionI.message(ConnectionI.java:1084) ~[ice.jar:na]
at IceInternal.ThreadPool.run(ThreadPool.java:321) ~[ice.jar:na]
at IceInternal.ThreadPool.access$300(ThreadPool.java:12) ~[ice.jar:na]
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) ~[ice.jar:na]
at java.lang.Thread.run(Thread.java:724) ~[na:1.7.0_25]
Traceback (most recent call last):
File "upload_to_omero2.py", line 382, in <module>
main(sys.argv[1:])
File "upload_to_omero2.py", line 60, in main
runWithSolrAsDataSource(solrUrl, rootDestinationDir, alreadyInOmero, omeroUser, omeroPass, omeroHost, omeroPort)
File "upload_to_omero2.py", line 186, in runWithSolrAsDataSource
processFile(alreadyInOmero,observation_id, rootDestinationDir,phenotyping_center,pipeline_stable_id, procedure_stable_id, parameter_stable_id, download_file_path, omeroUser, omeroPass, omeroHost, omeroPort)
File "upload_to_omero2.py", line 214, in processFile
loadIntoOmero(dstfilename, project, dataset, omeroUser, omeroPass, omeroHost, omeroPort)
File "upload_to_omero2.py", line 224, in loadIntoOmero
do_import(omeroUser, omeroPass, omeroHost, omeroPort, fullNfsUrl, dataset, project, omeroPass)
File "upload_to_omero2.py", line 247, in do_import
cli.invoke(import_args, strict=True)
File "/Users/jwarren/Documents/omerolibs/OMERO.server-5.0-1.2-ice35-b26/lib/python/omero/cli.py", line 794, in invoke
self.assertRC()
File "/Users/jwarren/Documents/omerolibs/OMERO.server-5.0-1.2-ice35-b26/lib/python/omero/cli.py", line 783, in assertRC
raise NonZeroReturnCode(self.rv, "assert failed")
omero.cli.NonZeroReturnCode: assert failed
