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combining TIFF and CSV file with metadata

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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Thu May 03, 2012 9:17 am

after reinstall I get this md5sum:

Code: Select all
md5sum /lib64/libexpat.so.0
8f010448ab2d49152c3af1e283402191  /lib64/libexpat.so.0

still different to yours.

and still the same error:

Code: Select all
./omero admin start
Traceback (most recent call last):
  File "./omero", line 123, in ?
    rv = omero.cli.argv()
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/cli.py", line 1172, in argv
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/cli.py", line 722, in invoke
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/cli.py", line 791, in onecmd
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/cli.py", line 871, in execute
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/plugins/prefs.py", line 64, in open_and_close_config
  File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/plugins/admin.py", line 887, in open_config
    config = omero.config.ConfigXml(str(cfg_xml))
  File "/omero/OMERO.server-Beta-4.3.4/lib/python/omero/config.py", line 68, in __init__
  File "/usr/lib/python2.4/site-packages/elementtree/ElementTree.py", line 959, in XML
    parser = XMLTreeBuilder()
  File "/usr/lib/python2.4/site-packages/elementtree/ElementTree.py", line 1114, in __init__
    raise ImportError(
ImportError: No module named expat; use SimpleXMLTreeBuilder instea


edit:
the expat version is the one out of the repository:
einstalling:
expat x86_64 1.95.8-8.3.el5_5.3 base 76 k

online available there is:
expat 2.1.0, which do you use?
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining TIFF and CSV file with metadata

Postby cxallan » Thu May 03, 2012 9:53 am

How are you reinstalling it?
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am

Re: combining TIFF and CSV file with metadata

Postby Thorondor » Thu May 03, 2012 9:57 am

like that:
yum reinstall expat.x86_64
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining TIFF and CSV file with metadata

Postby cxallan » Thu May 03, 2012 10:59 am

Okay, that's the latest version which matches up with what I have:

Code: Select all
$ md5sum /lib64/libexpat.so.0
8f010448ab2d49152c3af1e283402191  /lib64/libexpat.so.0
$ rpm -qf /lib64/libexpat.so.0
expat-1.95.8-8.3.el5_5.3
$ rpm -qi expat
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 11:37:47 AM EDT
Install Date: Thu 03 May 2012 06:48:48 AM EDT      Build Host: builder10.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 172126                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 12:34:21 PM EDT, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 11:38:04 AM EDT
Install Date: Thu 03 May 2012 06:48:55 AM EDT      Build Host: builder17.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 161650                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 12:34:21 PM EDT, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.


What are you getting when you import xml.parsers.expat now?
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am

Re: combining TIFF and CSV file with metadata

Postby Thorondor » Thu May 03, 2012 11:19 am

still the same error, so its not expat. :-/

Code: Select all
import xml.parsers.expat
import xml # directory /usr/lib64/python2.4/xml
# /usr/lib64/python2.4/xml/__init__.pyc matches /usr/lib64/python2.4/xml/__init__.py
import xml # precompiled from /usr/lib64/python2.4/xml/__init__.pyc
import xml.parsers # directory /usr/lib64/python2.4/xml/parsers
# /usr/lib64/python2.4/xml/parsers/__init__.pyc matches /usr/lib64/python2.4/xml/parsers/__init__.py
import xml.parsers # precompiled from /usr/lib64/python2.4/xml/parsers/__init__.pyc
# /usr/lib64/python2.4/xml/parsers/expat.pyc matches /usr/lib64/python2.4/xml/parsers/expat.py
import xml.parsers.expat # precompiled from /usr/lib64/python2.4/xml/parsers/expat.pyc
dlopen("/usr/lib64/python2.4/lib-dynload/pyexpat.so", 2);
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib64/python2.4/xml/parsers/expat.py", line 4, in ?
    from pyexpat import *
ImportError: /usr/lib64/python2.4/lib-dynload/pyexpat.so: undefined symbol: XML_StopParser

Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining TIFF and CSV file with metadata

Postby cxallan » Thu May 03, 2012 12:53 pm

Oh it's definitely expat, that's the library that provides the XML_StopParser symbol. Okay, let's summarise where we are then from the top:

Code: Select all
$ ls -al /usr/lib64/python2.4/lib-dynload/pyexpat.so
-rwxr-xr-x 1 root root 46448 Feb 22 16:06 /usr/lib64/python2.4/lib-dynload/pyexpat.so
$ rpm -qf /usr/lib64/python2.4/lib-dynload/pyexpat.so
python-libs-2.4.3-46.el5
$ md5sum /usr/lib64/python2.4/lib-dynload/pyexpat.so
27a2d7cf584450e8bba4b313d8d3170d  /usr/lib64/python2.4/lib-dynload/pyexpat.so
$ ldd /usr/lib64/python2.4/lib-dynload/pyexpat.so
   libexpat.so.0 => /lib64/libexpat.so.0 (0x00002b40d9525000)
   libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b40d9747000)
   libc.so.6 => /lib64/libc.so.6 (0x00002b40d9962000)
   /lib64/ld-linux-x86-64.so.2 (0x0000003bf4000000)
$ ls -al /lib64/libexpat.so.0
lrwxrwxrwx 1 root root 17 May  3 06:48 /lib64/libexpat.so.0 -> libexpat.so.0.5.0
$ rpm -qf /lib64/libexpat.so.0
expat-1.95.8-8.3.el5_5.3
$ md5sum /lib64/libexpat.so.0
8f010448ab2d49152c3af1e283402191  /lib64/libexpat.so.0
$ ldd /lib64/libexpat.so.0
   libc.so.6 => /lib64/libc.so.6 (0x00002aee2d774000)
   /lib64/ld-linux-x86-64.so.2 (0x0000003bf4000000)
$ rpm -qi python-libs expat
Name        : python-libs                  Relocations: (not relocatable)
Version     : 2.4.3                             Vendor: CentOS
Release     : 46.el5                        Build Date: Wed 22 Feb 2012 04:10:34 PM EST
Install Date: Fri 27 Apr 2012 01:09:35 PM EDT      Build Host: builder10.centos.org
Group       : Applications/System           Source RPM: python-2.4.3-46.el5.src.rpm
Size        : 22010716                         License: PSF - see LICENSE
Signature   : DSA/SHA1, Wed 22 Feb 2012 04:29:17 PM EST, Key ID a8a447dce8562897
URL         : http://www.python.org/
Summary     : The libraries for python runtime
Description :
The python interpreter can be embedded into applications wanting to
use python as an embedded scripting language.  The python-libs package
provides the libraries needed for this.
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 11:37:47 AM EDT
Install Date: Thu 03 May 2012 06:48:48 AM EDT      Build Host: builder10.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 172126                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 12:34:21 PM EDT, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 11:38:04 AM EDT
Install Date: Thu 03 May 2012 06:48:55 AM EDT      Build Host: builder17.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 161650                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 12:34:21 PM EDT, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.


So basically I need you to run and paste the output of the following:

Code: Select all
ls -al /usr/lib64/python2.4/lib-dynload/pyexpat.so
rpm -qf /usr/lib64/python2.4/lib-dynload/pyexpat.so
md5sum /usr/lib64/python2.4/lib-dynload/pyexpat.so
ldd /usr/lib64/python2.4/lib-dynload/pyexpat.so
ls -al /lib64/libexpat.so.0
rpm -qf /lib64/libexpat.so.0
md5sum /lib64/libexpat.so.0
ldd /lib64/libexpat.so.0
rpm -qi python-libs expat
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am

Re: combining TIFF and CSV file with metadata

Postby Thorondor » Thu May 03, 2012 12:58 pm

Code: Select all
[omero@bqichipdb1 ~]$ ls -al /usr/lib64/python2.4/lib-dynload/pyexpat.so
-rwxr-xr-x 1 root root 46448 Feb 22 22:06 /usr/lib64/python2.4/lib-dynload/pyexpat.so
[omero@bqichipdb1 ~]$ rpm -qf /usr/lib64/python2.4/lib-dynload/pyexpat.so
python-libs-2.4.3-46.el5
[omero@bqichipdb1 ~]$ md5sum /usr/lib64/python2.4/lib-dynload/pyexpat.so
27a2d7cf584450e8bba4b313d8d3170d  /usr/lib64/python2.4/lib-dynload/pyexpat.so
[omero@bqichipdb1 ~]$ ldd /usr/lib64/python2.4/lib-dynload/pyexpat.so
        libexpat.so.0 => /data/oracle/product/11g/db_1/lib/libexpat.so.0 (0x00002b3d735e5000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b3d7371b000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b3d73936000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003b20600000)
[omero@bqichipdb1 ~]$ ls -al /lib64/libexpat.so.0
lrwxrwxrwx 1 root root 17 May  3 11:15 /lib64/libexpat.so.0 -> libexpat.so.0.5.0
[omero@bqichipdb1 ~]$ rpm -qf /lib64/libexpat.so.0
expat-1.95.8-8.3.el5_5.3
[omero@bqichipdb1 ~]$ md5sum /lib64/libexpat.so.0
8f010448ab2d49152c3af1e283402191  /lib64/libexpat.so.0
[omero@bqichipdb1 ~]$ ldd /lib64/libexpat.so.0
        libc.so.6 => /lib64/libc.so.6 (0x00002b47aa00c000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003b20600000)
[omero@bqichipdb1 ~]$ rpm -qi python-libs expat
Name        : python-libs                  Relocations: (not relocatable)
Version     : 2.4.3                             Vendor: CentOS
Release     : 46.el5                        Build Date: Wed 22 Feb 2012 10:10:34 PM CET
Install Date: Tue 17 Apr 2012 10:08:01 AM CEST      Build Host: builder10.centos.org
Group       : Applications/System           Source RPM: python-2.4.3-46.el5.src.rpm
Size        : 22010716                         License: PSF - see LICENSE
Signature   : DSA/SHA1, Wed 22 Feb 2012 10:29:17 PM CET, Key ID a8a447dce8562897
URL         : http://www.python.org/
Summary     : The libraries for python runtime
Description :
The python interpreter can be embedded into applications wanting to
use python as an embedded scripting language.  The python-libs package
provides the libraries needed for this.
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 05:38:04 PM CEST
Install Date: Fri 27 Apr 2012 01:49:01 PM CEST      Build Host: builder17.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 161650                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 06:34:21 PM CEST, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.
Name        : expat                        Relocations: (not relocatable)
Version     : 1.95.8                            Vendor: CentOS
Release     : 8.3.el5_5.3                   Build Date: Tue 07 Sep 2010 05:37:47 PM CEST
Install Date: Thu 03 May 2012 11:15:08 AM CEST      Build Host: builder10.centos.org
Group       : System Environment/Libraries   Source RPM: expat-1.95.8-8.3.el5_5.3.src.rpm
Size        : 172126                           License: BSD
Signature   : DSA/SHA1, Sun 12 Sep 2010 06:34:21 PM CEST, Key ID a8a447dce8562897
URL         : http://www.libexpat.org/
Summary     : A library for parsing XML.
Description :
This is expat, the C library for parsing XML, written by James Clark. Expat
is a stream oriented XML parser. This means that you register handlers with
the parser prior to starting the parse. These handlers are called when the
parser discovers the associated structures in the document being parsed. A
start tag is an example of the kind of structures for which you may
register handlers.


here it is. I hope it helps.
I really appreciate your support.
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining TIFF and CSV file with metadata

Postby cxallan » Thu May 03, 2012 1:29 pm

A ha! There we go...

Code: Select all
...
[omero@bqichipdb1 ~]$ ldd /usr/lib64/python2.4/lib-dynload/pyexpat.so
        libexpat.so.0 => /data/oracle/product/11g/db_1/lib/libexpat.so.0 (0x00002b3d735e5000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b3d7371b000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b3d73936000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003b20600000)
...


You have Oracle installed on your system and its manipulation of LD_LIBRARY_PATH when you are logged in as omero results in an incompatible version of expat being loaded on to the dynamic library path. You'll need to unset LD_LIBRARY_PATH to get anywhere with Python.
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am

Re: combining TIFF and CSV file with metadata

Postby Thorondor » Fri May 04, 2012 8:14 am

nice, so I did set the LD_LIBRARY_PAHT like that in my .bashrc: LD_LIBRARY_PATH=/usr/share/java:/usr/lib

and finally it works again. :-)

thanks for figuring that out with me!
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

Re: combining TIFF and CSV file with metadata

Postby Thorondor » Fri May 04, 2012 8:52 am

ok, back to the real problems with Omero.tables

I still try to get the sample script working (see: viewtopic.php?f=4&t=1101&start=10#p4082)

I get:
Code: Select all
./tables.py
No handlers could be found for logger "blitz_gateway"
True
Traceback (most recent call last):
  File "./tables.py", line 55, in ?
    table.initialize(columns)
AttributeError: 'NoneType' object has no attribute 'initialize'

the True is from: print conn.connect()

running omero admin diagnostics gives:
Code: Select all
================================================================================
OMERO Diagnostics 4.3.4-dbcbce5a-b4
================================================================================
       
Commands:   java -version                  1.6.0     (/data/applications/jdk1.6.0_31/bin/java -- 2 others)
Commands:   python -V                      2.4.3     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.1.3     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2556, enabled)
Server:     DropBox                        active (pid = 2579, enabled)
Server:     FileServer                     active (pid = 2582, enabled)
Server:     Indexer-0                      active (pid = 2587, enabled)
Server:     MonitorServer                  active (pid = 2591, enabled)
Server:     OMERO.Glacier2                 active (pid = 2610, enabled)
Server:     OMERO.IceStorm                 active (pid = 2592, enabled)
Server:     PixelData-0                    active (pid = 2606, enabled)
Server:     Processor-0                    active (pid = 2608, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /data/applications/OMERO.server-Beta-4.3.4/var/log exists

Log files:  Blitz-0.log                    236.0 MB      errors=28   warnings=20 
Log files:  DropBox.log                    8.0 KB        errors=8    warnings=3   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  223.0 KB      errors=6    warnings=9   
Log files:  MonitorServer.log              5.0 KB        errors=5    warnings=0   
Log files:  OMEROweb.log                   167.0 KB      errors=327  warnings=0   
Log files:  PixelData-0.log                147.0 KB      errors=6    warnings=9   
Log files:  Processor-0.log                1.0 MB        errors=0    warnings=1   
Log files:  Processor-0.log.1              4.0 MB       
Log files:  Processor-0.log.2              4.0 MB       
Log files:  Processor-0.log.3              4.0 MB       
Log files:  Processor-0.log.4              4.0 MB       
Log files:  Processor-0.log.5              4.0 MB       
Log files:  Processor-0.log.6              4.0 MB       
Log files:  Processor-0.log.7              4.0 MB       
Log files:  Processor-0.log.8              4.0 MB        errors=1467 warnings=8805
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     277.94 MB

Parsing Blitz-0.log:[line:863] => Server restarted <=
Parsing Blitz-0.log:[line:2047] => Server restarted <=
Parsing Blitz-0.log:[line:1534950] => Server restarted <=

Environment:OMERO_HOME=/data/applications/OMERO.server-Beta-4.3.4
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/data/applications/apache-ant-1.8.3/bin:/data/applications/jdk1.6.0_31/bin:/root/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin
Environment:ICE_HOME=/usr/share/Ice-3.3.1 
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib
Environment:DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:

OMERO data dir: '/OMERO'        Exists? True    Is writable? True
OMERO.web status... [RUNNING] (PID 27118)


so where is the problem? :D
Thorondor
 
Posts: 58
Joined: Thu Apr 12, 2012 8:10 am

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