Dear Carl,

I forgot to ask you something.
In one of your previous mails, you said:

*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. 

So, before applying the patch to our production Galaxy instance, I would 
like to know what you meant by "if users are still using the older history 
panel"?
What exactly is the "older history panel"?  Our galaxy instance is up to 
date with the latest revision (Feb 08, 2013), does that mean that I don't 
have to worry about the "older history panel"?

Thanks,

Jean-Francois




From:   Jean-Francois Payotte <jean-francois.payo...@dnalandmarks.ca>
To:     carlfeberh...@gmail.com
Cc:     "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Date:   12/03/2013 12:40 PM
Subject:        Re: [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



Hi Carl, 

We are using a mysql database backend as well. 
Thank you for your help and do not hesitate if I can sen you any other 
useful information about our local Galaxy instance. 

Thanks, 

Jean-Francois 




From:        Carl Eberhard <carlfeberh...@gmail.com> 
To:        Jean-Francois Payotte <jean-francois.payo...@dnalandmarks.ca> 
Cc:        John Chilton <chil...@msi.umn.edu>, 
"galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> 
Date:        12/03/2013 09:18 AM 
Subject:        Re: [galaxy-dev] Strange issue where the dataset reported 
in the bug report doesn't correspond to the current dataset 



1 & 2: Very interesting then. I'll do some more digging as to why a query 
would succeed (with the wrong record) with those ids. 

3: Good! 

4.1: That first line is just the beginning of the diff/patch file and not 
something you have to enter. It records the command used to generate the 
diff file. That revision was the revision I was updated to when generating 
the patch and, since I was using a development version more recently 
updated than your machine, your hg can't find it. There's no need to run 
that line, tho (see 4.2). 

4.2: If you want to import a patch in the future, I've had good luck with 
'hg import --no-commit <mypatchfile.patch>'. This will make the changes in 
the patch file without committing them ('--no-commit'). If you want to 
remove the changes later (and assuming you haven't made any other changes 
you want to keep in that file) you can use 'hg revert 
<thefilethatwaschanged.py>' and that will return the file to the previous 
state. Keep in mind, of course, that patches (like any changes) may make 
updating, and/or merging your instance later more difficult. 

A question I forgot to ask: what database backend are you using 
(postgresql, mysql, etc.)? 

Carl 



On Mon, Mar 11, 2013 at 12:34 PM, Jean-Francois Payotte <
jean-francois.payo...@dnalandmarks.ca> wrote: 
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: 

1.        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 
2.        Here is a list of hashed IDs for HDAs where I'm seeing this 
behaviour:
(None of them are of 16-digit integers)


3.        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!!

4.        I would have two question though before applying the patch to 
our production Galaxy instance: 
1.        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?

2.        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-Fran├žois
>
>
>
>
>
> 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-Fran├žois
> ___________________________________________________________
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>
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>
>
> ___________________________________________________________
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>
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Payotte/NA/BASF] 
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