Hi, I was trying to setup a galaxy server and connect to our UGE cluster. If I setup the default job runner as "local", our galaxy server works properly. But if I change the default job runner as "drmaa", our galaxy server throws out the following error message. It looks like drmaa.py has unicode decoding issue. I wonder does someone have the same problem before and how can I fix it. The python version we are using is 2.7.10. Thank you. galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception calling queue_job Traceback (most recent call last): File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line 103, in run_next method(arg) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in queue_job job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in <lambda> job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: ordinal not in range(128) Best LW
On Thu, Feb 4, 2016 at 1:21 PM, Le-shin Wu <leshin@gmail.com> wrote:
Hi,
I was trying to setup a galaxy server and connect to our UGE cluster. If I setup the default job runner as "local", our galaxy server works properly. But if I change the default job runner as "drmaa", our galaxy server throws out the following error message. It looks like drmaa.py has unicode decoding issue. I wonder does someone have the same problem before and how can I fix it. The python version we are using is 2.7.10. Thank you.
galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception calling queue_job Traceback (most recent call last): File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line 103, in run_next method(arg) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in queue_job job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in <lambda> job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: ordinal not in range(128)
Hi, Does your tool ID or user email address contain a unicode character? Regardless, this is a bug and we can fix it, I just want to verify the problem. Thanks, --nate
Best
LW
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Hi Nate, The tool ID is simply as "upload1" (I just tried to upload a file) and user email address is simply as "leshin@gmail.com". The original job name before applying the lambda function is something like "g6_upload1_leshin@gmail.com". I am not sure why this job_name will create the problem. But after I removing the job_wrapper.user out of the job_name in __init__.py and dramm.py, I can run jobs on our UGE with problems. The only issue for this approach is that there is no actual user information inside the UGE job name anymore. Thanks LW On Fri, Feb 5, 2016 at 1:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Thu, Feb 4, 2016 at 1:21 PM, Le-shin Wu <leshin@gmail.com> wrote:
Hi,
I was trying to setup a galaxy server and connect to our UGE cluster. If I setup the default job runner as "local", our galaxy server works properly. But if I change the default job runner as "drmaa", our galaxy server throws out the following error message. It looks like drmaa.py has unicode decoding issue. I wonder does someone have the same problem before and how can I fix it. The python version we are using is 2.7.10. Thank you.
galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception calling queue_job Traceback (most recent call last): File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line 103, in run_next method(arg) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in queue_job job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in <lambda> job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: ordinal not in range(128)
Hi,
Does your tool ID or user email address contain a unicode character?
Regardless, this is a bug and we can fix it, I just want to verify the problem.
Thanks, --nate
Best
LW
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participants (2)
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Le-shin Wu -
Nate Coraor