Dear Dannon, John and Carl, Thank you for your answers and for taking the time to help me solve this issue. Here are my answers to your questions:
I don't think our number of HDAs is large enough to cause an overflow.
>From what I can see, the HDAs number in our two faulty galaxy instances
are:
galaxy_prod : 263,163 HDAs
galaxy_dev : 14,119 HDAs
Here is a list of hashed IDs for HDAs where I'm seeing this behaviour:
(None of them are of 16-digit integers)
I've also tried applying John's patch on our development Galaxy instance
and so far, it seems to do the trick.
I've run my test tool (wich output a message to stderr) about 50 times,
and the bug report always displayed the correct dataset. Yay!!
I would have two question though before applying the patch to our
production Galaxy instance:
If I run the below "hg diff -r f25f3fee4da7
lib/galaxy/webapps/galaxy/controllers/dataset.py" command, I receive the
following error:
abort: unknown revision 'f25f3fee4da7'!
Is this a normal behaviour? Are we missing something important?
Also, out of curiosity, is there a particular way to "apply" a patch (like
the one you sent me), or if I simply have to manually edit the file?
(That's what I did.)
Thanks again for your help! This is greatly appreciated!
Jean-Francois
From: Carl Eberhard <carlfeberh...@gmail.com>
To: John Chilton <chil...@msi.umn.edu>
Cc: Jean-Francois Payotte <jean-francois.payo...@dnalandmarks.ca>,
"galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Date: 08/03/2013 06:07 PM
Subject: Re: [galaxy-dev] Strange issue where the dataset reported
in the bug report doesn't correspond to the current dataset
Hello,
We explored this for quite a while this afternoon and believe John is
correct about the location as well as the design decision.
It may be that the hashes generated in some instances will correctly parse
as 16 digit integers and, since an integer lookup is tried first (and you
may either have an extraordinary large number of HDAs or there is some
integer roll over/overflow - at a guess), the incorrect dataset is being
returned without attempting to decode the hash into the proper dataset.
This may also explain why it is consistent but intermittent.
I would be curious to see the hashed ids of the HDAs where you're seeing
this behavior. Can you provide some?
If the hash produces fully integer strings as we're (tentatively)
guessing, the if not str( id ).isdigit() may still branch improperly
unfortunately.
In any event and to John's last point, from what we can tell,
dataset.errors is only called from the new history panel and only encoded
ids are used there - so the backwards compatibility may not be needed at
this point.*
I will thoroughly check that that controller method isn't called elsewhere
with a raw id, but, in the meantime: Jean-Francois, can you apply the
patch below (and attached) to your more updated installation and (when
convenient) see if that helps?
*PS. if user's are still using the older history panel - please, do not
apply this patch as it relies on the older, raw ids for this function.
diff -r f25f3fee4da7 lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 16:01:25
2013 -0500
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 17:41:46
2013 -0500
@@ -171,14 +171,17 @@
@web.expose
def errors( self, trans, id ):
+ hda = None
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 ) )
+ # only sent from the history panel (which uses encoded ids)
+ decoded_id = trans.security.decode_id( id )
+ hda = trans.sa_session.query( model.HistoryDatasetAssociation
).get( decoded_id )
+ except Exception, exc:
+ log.error( 'Could not retrieve hda with id "%s": %s', id,
str( exc ), exc_info=True )
+
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.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 )
@web.expose
On Fri, Mar 8, 2013 at 3:49 PM, John Chilton <chil...@msi.umn.edu> wrote:
Does rewriting this:
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 )
to say this:
def errors( self, trans, id ):
if not str(id).isdigit():
id = trans.security.decode_id( id )
hda = trans.sa_session.query( model.HistoryDatasetAssociation
).get( 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 )
help the problem? Neither of these are particularly good design
decisions. errors should either take in an id or an encoded id, or at
least take them in as different parameters.
-John
-John
On Tue, Mar 5, 2013 at 12:38 PM, Jean-Francois Payotte
<jean-francois.payo...@dnalandmarks.ca> wrote:
> 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.
>
>
> Latest release:
>
> 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 <
jean-francois.payo...@dnalandmarks.ca>
> To: galaxy-dev@lists.bx.psu.edu
> 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: galaxy-dev-boun...@lists.bx.psu.edu
> ________________________________
>
>
>
> 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
> ___________________________________________________________
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>
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>
>
> ___________________________________________________________
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>
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[attachment "dataset.errors_id.patch" deleted by Jean-Francois
Payotte/NA/BASF]
<<image/gif>>
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