- Code: Select all
Log files: Tables-0.log 3.0 KB
Could you attach it to the thread?
~Josh
Log files: Tables-0.log 3.0 KB
2012-05-07 13:18:59,646 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2012-05-07 13:18:59,647 INFO [ omero.util.Server] (MainThread) Starting
2012-05-07 13:18:59,647 INFO [ omero.util.Server] (MainThread) Loaded dependency numpy (1.6.2rc1)
2012-05-07 13:18:59,647 INFO [ omero.util.Server] (MainThread) Loaded dependency tables (2.3.1, hdf=1.8.8)
2012-05-07 13:18:59,648 INFO [ omero.util.Resources] (Thread-2 ) Starting
2012-05-07 13:19:17,209 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2012-05-07 13:19:27,428 INFO [ omero.util.Server] (MainThread) Entering main loop
2012-05-07 13:21:19,417 INFO [ omero.remote] (Dummy-3 ) Meth: TablesI.getTable
2012-05-07 13:21:19,417 INFO [ omero.tables.TablesI] (Dummy-3 ) getTable: 251 {}
2012-05-07 13:21:19,549 INFO [ omero.tables.HdfStorage] (Dummy-3 ) Size: 0 - Attaching Table-11D7C028-826A-495F-AF11-94ED0323B486 to /OMERO/Files/251
2012-05-07 13:21:19,550 INFO [ omero.remote] (Dummy-3 ) Rslt: 11D7C028-826A-495F-AF11-94ED0323B486 -t @ Tables-0.TablesAdapter
2012-05-07 13:21:19,579 INFO [ omero.remote] (Dummy-4 ) Meth: TableI.initialize
2012-05-07 13:21:19,595 INFO [ omero.tables.TableI] (Dummy-4 ) Initialized Table-11D7C028-826A-495F-AF11-94ED0323B486 with 2 col(s)
2012-05-07 13:21:19,595 INFO [ omero.remote] (Dummy-4 ) Rslt: None
2012-05-07 13:21:19,596 INFO [ omero.remote] (Dummy-5 ) Meth: TableI.addData
2012-05-07 13:21:19,597 INFO [ omero.tables.TableI] (Dummy-5 ) Added 10 row(s) of data to Table-11D7C028-826A-495F-AF11-94ED0323B486
2012-05-07 13:21:19,598 INFO [ omero.remote] (Dummy-5 ) Rslt: None
2012-05-07 13:21:19,598 INFO [ omero.remote] (Dummy-6 ) Meth: TableI.close
2012-05-07 13:21:19,599 INFO [ omero.tables.HdfStorage] (Dummy-6 ) Size: 1 - Detaching Table-11D7C028-826A-495F-AF11-94ED0323B486 from /OMERO/Files/251
2012-05-07 13:21:19,599 INFO [ omero.tables.HdfStorage] (Dummy-6 ) Cleaning storage: /OMERO/Files/251
2012-05-07 13:21:19,600 INFO [ omero.tables.TableI] (Dummy-6 ) Closed Table-11D7C028-826A-495F-AF11-94ED0323B486
2012-05-07 13:21:19,772 INFO [ omero.tables.TableI] (Dummy-6 ) Updated file object 251 to sha1=f48b6e69ebc9a55f01c9fcefc60f6eb4802e86ad (73792 bytes)
2012-05-07 13:21:19,772 INFO [ omero.remote] (Dummy-6 ) Rslt: None
2012-05-07 13:21:19,773 INFO [ omero.remote] (Dummy-7 ) Meth: TableI.getOriginalFile
2012-05-07 13:21:19,774 INFO [ omero.tables.TableI] (Dummy-7 ) Table-11D7C028-826A-495F-AF11-94ED0323B486.getOriginalFile() => id=251
2012-05-07 13:21:19,774 INFO [ omero.remote] (Dummy-7 ) Rslt: object #0 (::omero::model::OriginalFile)
{
_id = object #1 (::omero::RLong)
{
_val = 251
}
_deta
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2011 University of Dundee & Open Microscopy Environment.
# All Rights Reserved.
# Use is subject to license terms supplied in LICENSE.txt
#
"""
FOR TRAINING PURPOSES ONLY!
"""
import omero
import omero.grid
from omero.gateway import BlitzGateway
#from Connect_To_OMERO import USERNAME, PASSWORD, HOST, PORT
USERNAME = "*******"
PASSWORD = "********"
HOST = "localhost"
PORT = "4064"
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
print conn.connect()
# Configuration
# =================================================================
datasetId = 33
# Create a name for the Original File (should be unique)
# =================================================================
from random import random
tablename = "TablesDemo:%s" % str(random())
col1 = omero.grid.LongColumn('Uid', 'testLong', [])
col2 = omero.grid.StringColumn('MyStringColumnInit', '', 64, [])
columns = [col1, col2]
# Create and initialize a new table.
# =================================================================
repositoryId = 1
table = conn.c.sf.sharedResources().newTable(repositoryId, tablename)
table.initialize(columns)
#table.initialzis(WellColumn)
# Add data to the table.
# =================================================================
ids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
strings = ["one", "two", "three", "four", "five",\
"six", "seven", "eight", "nine", "ten"]
data1 = omero.grid.LongColumn('Uid', 'test Long', ids)
data2 = omero.grid.StringColumn('MyStringColumn', '', 64, strings)
data = [data1, data2]
table.addData(data)
table.close() # when we're done, close.
# Get the table as an original file...
# =================================================================
orig_file = table.getOriginalFile()
orig_file_id = orig_file.id.val
# ...so you can attach this data to an object. E.g. Dataset
fileAnn = omero.model.FileAnnotationI()
fileAnn.setFile(omero.model.OriginalFileI(orig_file_id, False)) # use unloaded OriginalFileI
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = omero.model.DatasetAnnotationLinkI()
link.setParent(omero.model.DatasetI(datasetId, False))
link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))
conn.getUpdateService().saveAndReturnObject(link)
# Table API
# =================================================================
# See: http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/slice2html/omero/grid/Table.html
openTable = conn.c.sf.sharedResources().openTable(orig_file)
print "Table Columns:"
for col in openTable.getHeaders():
print " ", col.name
rowCount = openTable.getNumberOfRows()
print "Row count:", rowCount
# Get data from every column of the specified rows
# =================================================================
rowNumbers = [3, 5, 7]
print "\nGet All Data for rows: ", rowNumbers
data = openTable.readCoordinates(range(rowCount))
for col in data.columns:
print "Data for Column: ", col.name
for v in col.values:
print " ", v
# Get data from specified columns of specified rows
# =================================================================
colNumbers = [1]
start = 3
stop = 7
print "\nGet Data for cols: ", colNumbers,\
" and between rows: ", start, "-", stop
data = openTable.read(colNumbers, start, stop)
for col in data.columns:
print "Data for Column: ", col.name
for v in col.values:
print " ", v
# Query the table for rows where the 'Uid' is in a particular range
# =================================================================
queryRows = openTable.getWhereList("(Uid > 2) & (Uid <= 8)",\
variables={}, start=0, stop=rowCount, step=0)
data = openTable.readCoordinates(queryRows)
for col in data.columns:
print "Query Results for Column: ", col.name
for v in col.values:
print " ", v
openTable.close() # we're done
# In future, to get the table back from Original File
# =================================================================
orig_table_file = conn.getObject("OriginalFile", attributes={'name': tablename}) # if name is unique
savedTable = conn.c.sf.sharedResources().openTable(orig_table_file._obj)
print "Opened table with row-count:", savedTable.getNumberOfRows()
# Close connection:
# =================================================================
# When you're done, close the session to free up server resources.
conn._closeSession()
# Configuration
# =================================================================
datasetId = 33
python tables.py
No handlers could be found for logger "blitz_gateway"
True
Table Columns:
Uid
MyStringColumnInit
Row count: 10
Get All Data for rows: [3, 5, 7]
Data for Column: Uid
1
2
3
4
5
6
7
8
9
10
Data for Column: MyStringColumnInit
one
two
three
four
five
six
seven
eight
nine
ten
Get Data for cols: [1] and between rows: 3 - 7
Data for Column: MyStringColumnInit
four
five
six
seven
Traceback (most recent call last):
File "tables.py", line 127, in ?
variables={}, start=0, stop=rowCount, step=0)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero_Tables_ice.py", line 687, in getWhereList
return _M_omero.grid.Table._op_getWhereList.invoke(self, ((condition, variables, start, stop, step), _ctx))
omero.InternalException: exception ::omero::InternalException
{
serverStackTrace = Traceback (most recent call last):
File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/util/decorators.py", line 61, in exc_handler
File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/util/decorators.py", line 28, in handler
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 601, in getWhereList
rv = self.storage.getWhereList(self.stamp, condition, variables, None, start, stop, step)
File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/util/decorators.py", line 81, in with_lock
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 65, in check_and_update_stamp
return func(*args, **kwargs)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 394, in getWhereList
return self.__mea.getWhereList(condition, variables, None, start, stop, step).tolist()
File "/usr/lib64/python2.4/site-packages/tables/table.py", line 1541, in getWhereList
coords = [ p.nrow for p in
File "/usr/lib64/python2.4/site-packages/tables/table.py", line 1437, in _where
compiled = self._compileCondition(condition, condvars)
File "/usr/lib64/python2.4/site-packages/tables/table.py", line 1316, in _compileCondition
compiled = compile_condition(condition, typemap, indexedcols, copycols)
File "/usr/lib64/python2.4/site-packages/tables/conditions.py", line 391, in compile_condition
func = NumExpr(expr, signature, copy_args=copycols)
File "/usr/lib64/python2.4/site-packages/numexpr-1.4.2-py2.4-linux-x86_64.egg/numexpr/necompiler.py", line 518, in NumExpr
input_names)
RuntimeError: invalid program: reduction operations must occur last
serverExceptionClass =
message = Internal exception
}
2012-05-07 15:25:25,126 INFO [ omero.util.Server] (MainThread) Loaded dependency numpy (1.3.0)
2012-05-07 15:25:25,126 INFO [ omero.util.Server] (MainThread) Loaded dependency tables (2.1.2, hdf=1.8.4)
python -c "import numexpr; print numexpr.__file__"
python -c "import numexpr.version; print numexpr.version.version"
import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/numpy/__init__.py", line 128, in ?
from version import git_revision as __git_revision__
Thorondor wrote:now I tired to install a older numpy version and I get:
trying to fix that, what numexp version would you recommend?
the newest one?
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