Open Microscopy Environment

Dear all,
I try to include the omero.gateway module into a python script. When I load the module with

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from omero.gateway import BlitzGateway

I get the error:

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    from omero.gateway import BlitzGateway

  File "omero/gateway/__init__.py", line 37, in <module>
    import omero.scripts as scripts

  File "omero/scripts.py", line 28, in <module>
    import omero.util.temp_files

  File "omero/util/temp_files.py", line 343, in <module>
    manager = TempFileManager()

  File "omero/util/temp_files.py", line 52, in __init__
    self.userdir = self.tmpdir() / ("%s_%s" %

  File "omero/util/temp_files.py", line 153, in tmpdir
    targets.append(path(tempfile.gettempdir()) / "omero" / "tmp")

NameError: global name 'path' is not defined


Any help is appreciated.
Thanks
Alex

Hi Alex,

can you give us details about what version of OMERO this is and how you installed it?

Thanks,
~Josh

Hi Josh
the server is a OMERO 5.4.10 with ice 3.6.4. I am running python 2.7 an a client and want to connect to the server. The error occurs on the client, when I try to load the BlitzGateway from the omero.gateway module.
The local library is from the same version as the server (5.4.10, ice 3.6)
Thanks Alex

Hi Alex,

do use the Python libraries from the OMERO.server or from the OMERO.py package? Both should work by the way, I'm just trying to replicate the issue.
Could you try to set the PYTHONPATH to only this directory before running the script, e. g. something like

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export PYTHONPATH=/home/user/libs/OMERO.py-5.4.10-ice36-b105/lib/python

Regards,
Dominik

Hi Dominik,
I am using the python libraries from the downloaded server. I have the path to the library added in my pythonpath and to make sure it is working I also tried

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sys.path.append("/Users/alexrapp/Documents/OMERO.server-5.4.10-ice36-b105/lib/python")


Nevertheless this still resulted in the path error.
I then went on and generated a new environment, where I placed again only the libraries for Omero and then it works. I think by having other libraries activated it might choose path from a different library with incompatible versions?
See here: https://github.com/pickleshare/pickleshare/issues/8
How can I check or specify which version of path I am loading?
Best wishes
Alex

Hi Alex,

I think I'm still missing something. Can you run the following code before you call sys.append?

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import sys
for p in sys.path:
    print "-->", p
import os
for x in os.environ.keys():
    if x.startswith("OMERO_"):
        print "env:", x, "=", os.environ.get(x, "Missing?")
import path
print "path.py is: ", path.__file__


I get:

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--> /private/tmp/OMERO.py-5.4.10-ice36-b105/lib/python
...
--> /opt/anaconda/lib/python2.7/site-packages/yaclifw-0.2.0-py2.7.egg
path.py is:  /private/tmp/OMERO.py-5.4.10-ice36-b105/lib/python/path.pyc


~Josh

Dear josh,
thanks for the help.
I tested this in the spyder /anaconda editor:
With this:

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import sys
for p in sys.path:
    print "-->", p


print('OMERO:')   
import os
for x in os.environ.keys():
    if x.startswith("OMERO_"):
        print "env:", x, "=", os.environ.get(x, "Missing?")

print('path:')
import path
print "path.py is: ", path.__file__


I get that:

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--> /Users/alexrapp/Documents/INPLACE/env
--> /Users/alexrapp/anaconda2/lib/python27.zip
--> /Users/alexrapp/anaconda2/lib/python2.7
--> /Users/alexrapp/anaconda2/lib/python2.7/plat-darwin
--> /Users/alexrapp/anaconda2/lib/python2.7/plat-mac
--> /Users/alexrapp/anaconda2/lib/python2.7/plat-mac/lib-scriptpackages
--> /Users/alexrapp/anaconda2/lib/python2.7/lib-tk
--> /Users/alexrapp/anaconda2/lib/python2.7/lib-old
--> /Users/alexrapp/anaconda2/lib/python2.7/lib-dynload
--> /Users/alexrapp/anaconda2/lib/python2.7/site-packages
--> /Users/alexrapp/anaconda2/lib/python2.7/site-packages/aeosa
--> /Users/alexrapp/anaconda2/lib/python2.7/site-packages
--> /Users/alexrapp/anaconda2/lib/python2.7/site-packages/IPython/extensions
--> /Users/alexrapp/.ipython
--> /Users/alexrapp/Documents/OMERO.server-5.4.10-ice36-b105/lib/python
--> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
OMERO:
path:
path.py is:  /Users/alexrapp/anaconda2/lib/python2.7/site-packages/path.pyc


But when I add:

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from omero.gateway import BlitzGateway


I get:

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File "/Users/alexrapp/Documents/test_modules.py", line 24, in <module>
    from omero.gateway import BlitzGateway

  File "omero/gateway/__init__.py", line 37, in <module>
    import omero.scripts as scripts

  File "omero/scripts.py", line 28, in <module>
    import omero.util.temp_files

  File "omero/util/temp_files.py", line 343, in <module>
    manager = TempFileManager()

  File "omero/util/temp_files.py", line 52, in __init__
    self.userdir = self.tmpdir() / ("%s_%s" %

  File "omero/util/temp_files.py", line 152, in tmpdir
    targets.append(get_omero_userdir() / "tmp")

  File "omero/util/__init__.py", line 834, in get_omero_userdir
    return path.path(get_user_dir()) / "omero"

AttributeError: 'module' object has no attribute 'path'


Thanks for your help.
Alex

Thanks for the output. That explains it. Your anaconda installation includes (I assume) https://pypi.org/project/path.py/. Can you try again and insert OMERO's "lib/python" at the front of your sys.path?

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sys.path.insert(0, ...)


This isn't necessarily a full fix, but it will hopefully let us test if your installation can work without path.py.

~Josh.

Hi josh,
thanks, that helped. Now the blitzgateway is working with now error thrown up by the path import.
Alex

Glad to hear it! We'll look into putting a permanent fix in place, most likely by removing our copy of `path.py` when we move to Python 3.

Cheers,
~Josh