Dear Galaxy mailing-list,
I did some more tests in order to find out what might be causing this issue and it appears that we are facing this problem on two of our local Galaxy instances, which makes me think of a possible Galaxy bug rather than a database issue (both Galaxy instances using a different database). Does anybody else is facing this issue?
As a reminder, the issue we are currently facing is the "Dataset generation error" page displaying the wrong information (the information related to a completely different dataset) when clicking on the bug icon. (This is happening about half the time a tool ends in error).
Note that every time this issue occurs: The stdout and stderr (displayed in the dataset peek window) are correct. The information displayed when clicking on "stdout" and "stderr" in the "view details" window is also correct. (It pertains to the actual dataset) The information displayed in the "Dataset generation errors" (the window displayed after clicking the bug icon) is incorrect. It relates to a completely different dataset.
I have attached a screenshot for better understanding (see dataset_generation_errors.jpg). In this picture, you can see a brand new history having only one dataset produced by my test tool (which only output a simple text to both stdout and stderr, which makes the dataset ends in error). In this picture, I have clicked on the bug icon of dataset 1 (the one and only dataset in the history), and you can see that the "Dataset generation error" page displays information about some Dataset 64: Compute sequence length on data 1, which makes no sense at all.
I've also looked in Galaxy database to see if the information was correctly recorded with the creation of my new dataset. Everything seems ok to me, the job is recorded with its proper stdout and stderr and all the IDs seems ok (I've looked at tables job, history, history_dataset_association, dataset).
My hypothesis regarding this issue, is that sometime, when clicking the bug icon, the wrong hda is sent to the "Dataset generation errors" page, hence the retrieval of information pertaining to a different dataset. I don't know why this happens but it is really frustrating because it makes debugging tools really difficult, having to refer to the database to have the complete and accurate error message.
We have 3 different instances of Galaxy running locally and we are experiencing this issue on two of them (both of them are now at the latest release, Feb 8th, 2013). The third instance has not been updated for a while (Sept. 7 2012 distribution) and does not have this problem.
I've tried to look into some Galaxy files and I found out that the function calling the "Dataset generation errors" page ("dataset/errors.mako") had some changes between the latest release and the Sept. 7th 2012 distribution. Maybe this have nothing to do at all with the bug, but just in case I thought I would mention it.
def errors( self, trans, id ): try: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) except: hda = None if not hda: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( trans.security.decode_id( id ) ) if not hda or not self._can_access_dataset( trans, hda ): return trans.show_error_message( "Either this dataset does not exist or you do not have permission to access it." ) return trans.fill_template( "dataset/errors.mako", hda=hda )
Sept. 7 2012 distribution:
def errors( self, trans, id ): hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) return trans.fill_template( "dataset/errors.mako", hda=hda )
If someone else is facing this issue or might have an idea of what's going on, please let me know.
Thank you, Jean-François
From: Jean-Francois Payotte email@example.com To: firstname.lastname@example.org Date: 27/02/2013 09:45 AM Subject: [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset Sent by: email@example.com
Dear Galaxy mailing-list,
We are currently facing a strange issue with our local Galaxy installation (distribution from Jan. 11 2013). I'm going to try to describe the problem as much as I can, and feel free to ask for more details if it can help in solving this issue.
So basically, we have a situation where (about half the time), when a job ends in error, the error message (shown when clicking on the bug icon), doesn't seem to be related to the dataset in error. As this particular problem seem to be present only when datasets ends in error, I created a simple python script which simply does 2 things: 1. It outputs the hostname to stdout (in order to investigate if the problem is node-dependant) 2. It outputs the following message "This is an error message printed to stderr", to stderr. (This is done in order to get only error datasets and to investigate the before-mentioned issue.)
Here is the code of my python script:
import sys import socket
def main(): print socket.gethostname() sys.stderr.write('This is an error message printed to stderr\n')
if __name__ == '__main__': main()
I ran this tool about 50 times and I looked at the error messages displayed both in the preview section of the dataset (in the history), and the error message displayed when clicking on the bug icon "view or report this error".
About half the time, the results were as expected: the dataset stdout would read the name of the node where the job was executed the dataset stderr would read: "This is an error message printed to stderr" and the error message displayed when clicking on the bug icon would be:
Dataset generation errors Dataset 54: Test error Tool execution generated the following error message: This is an error message printed to stderr
The tool produced the following additional output: some.server.name
However, the other half of the time, the error message shown in stderr doesn't correspond to the error message displayed when clicking on the bug icon: the dataset stdout is still reading the name of the node the dataset stderr is still reading "This is an error message printed to stderr" but the error message displayed when clicking on the bug icon would be something like:
Dataset generation errors
Dataset 3: chrM.bed Tool execution did not generate any error messages.
We can clearly see a discrepancy between the error message in stderr and the error message of the bug report. Actually, the bug report is saying that there is not any error and it makes reference to some "Dataset 3: chrM.bed", even when the actual dataset is "Dataset 53: Test error". There is absolutely no .bed file in my history and the dataset 3 actually reads "Dataset 3: Test error". Some of the datasets mentioned in the faulty bug reports seems to be really old datasets (like one year old).
So my question to you is, could this be related to some mix-up between datasets ID? And how can I look this up. I must say that at the moment, I have absolutely no idea how to solve this issue.
Many thanks for your help!
Best regards, Jean-François ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: