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Question: Tool produces output, but leads to ERROR state
0
gravatar for letawjohn
2.6 years ago by
letawjohn • 0
United States
letawjohn • 0 wrote:

Having trouble resolving this behavior in a Galaxy wrapper I'm working on. The tool runs to completion, and I can view the output file via shell. The problem is, the tool continues to go in to an ERROR state, thus the workflow does not continue. No errors from the tools, or from my wrapper, just the following in one of the logs.

Blockquote File "/home/groups/clinical/Galaxy/galaxy-dist/eggs/SQLAlchemy-1.0.0-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", line 1226, in _safe_close_cursor cursor.close() InternalError: current transaction is aborted, commands ignored until end of transaction block

This error message is a little vague for me to determine the problem, though I'm sure the root cause must be something in my wrapper. All other tools continue to behave normally. I'm hoping perhaps someone has come across this in the past and might save me from the headache.

Thanks!
galaxy • 698 views
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modified 2.6 years ago • written 2.6 years ago by letawjohn • 0
3
gravatar for Martin Čech
2.6 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The dataset will end in an error state if the tool writes into stderr. To get better help could you share your wrapper please?
ADD COMMENT • link written 2.6 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for letawjohn
2.6 years ago by
letawjohn • 0
United States
letawjohn • 0 wrote:

See, this is why I asked the question as opposed to spending the next several hours beating my head against the wall for such a simple fix! The tool I was wrapping was indeed writing some output to stderr instead of stdout. For people that may run in to this, and happen to be writing tools in Python, you can simply adjust your call to subprocess.Popen and instruct it as to where you would like stderr to be written. You can tell it to send it the same place as stdout if you'd like.

Thanks so much Martin!
ADD COMMENT • link written 2.6 years ago by letawjohn • 0

Great - glad to help, do not ever hesitate to ask us anything and thanks for using Galaxy.

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k
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