Hello, Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help?

If not, we can diagnose further. Thanks, Carl

On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte < jean-francois.payotte@dnalandmarks.ca> wrote:

Dear Eric,

I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;)

I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue.

You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-i...

Best regards,

*Jean-Francois*

From: Eric Enns eric.enns@phac-aspc.gc.ca To: galaxy-dev@bx.psu.edu Date: 08/03/2013 03:14 PM Subject: [galaxy-dev] Error Report contains STDERR from different job Sent by: galaxy-dev-bounces@lists.bx.psu.edu

---

Hey,

When clicking the "View or report this error button" the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history.

-Eric___________________________________________________________ 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:

http://lists.bx.psu.edu/

---

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:

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Can you post the stack trace from the error, please?

Thanks for the info, Carl

On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

Hey,

I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend.

-Eric

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/08/2013 05:10PM Cc: eric.enns@phac-aspc.gc.ca, "galaxy-dev@bx.psu.edu" < galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Hello, Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help?

If not, we can diagnose further. Thanks, Carl

On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte < jean-francois.payotte@dnalandmarks.ca> wrote:

...

Dear Eric,

I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;)

I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue.

You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-i...

Best regards,

*Jean-Francois*

From: Eric Enns eric.enns@phac-aspc.gc.ca To: galaxy-dev@bx.psu.edu Date: 08/03/2013 03:14 PM Subject: [galaxy-dev] Error Report contains STDERR from different job Sent by: galaxy-dev-bounces@lists.bx.psu.edu

---

Hey,

When clicking the "View or report this error button" the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history.

-Eric____________________________________________ _______________ 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:

http://lists.bx.psu.edu/

---

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:

http://lists.bx.psu.edu/

Thanks, Eric

Since the HDA is None, the if statement should be sending you the trans.show_error_message.

Just to make sure we're on the same page, could you please attach or post the errors method from the dataset controller in your installation. It can be found at lib/galaxy/webapps/galaxy/controllers/dataset.py?

Carl

On Tue, Mar 12, 2013 at 10:59 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

The following is the stack trace I got when I applied the patch and clicked the bug icon.

"GET /dataset/errors?id=c39bc73d0eae67dd HTTP/1.0" 500 - " http://galaxy/history" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'hid' URL: http://galaxy/dataset/errors?id=c39bc73d0eae67dd File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call_ _ app_iter = self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 175 in errors return trans.fill_template( "dataset/errors.mako", hda=hda ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data ) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec _template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/galaxy-dist/database/compiled_templates/dataset/errors.mako.py', line 27 in render_body __M_writer(unicode(hda.hid)) AttributeError: 'NoneType' object has no attribute 'hid'

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Eric Enns eric.enns@phac-aspc.gc.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/12/2013 09:47AM Cc: "galaxy-dev@bx.psu.edu" galaxy-dev@bx.psu.edu, Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca

Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Can you post the stack trace from the error, please?

Thanks for the info, Carl

On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

...

Hey,

I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend.

-Eric

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/08/2013 05:10PM Cc: eric.enns@phac-aspc.gc.ca, "galaxy-dev@bx.psu.edu" < galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Hello, Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help?

If not, we can diagnose further. Thanks, Carl

On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte < jean-francois.payotte@dnalandmarks.ca> wrote:

...

Dear Eric,

I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;)

I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue.

You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-i...

Best regards,

*Jean-Francois*

From: Eric Enns eric.enns@phac-aspc.gc.ca To: galaxy-dev@bx.psu.edu Date: 08/03/2013 03:14 PM Subject: [galaxy-dev] Error Report contains STDERR from different job Sent by: galaxy-dev-bounces@lists.bx.psu.edu

---

Hey,

When clicking the "View or report this error button" the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history.

-Eric___________________________ _________________ _______ ________ 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:

http://lists.bx.psu.edu/

---

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:

http://lists.bx.psu.edu/

Glad to hear it's working, Carl

On Tue, Mar 12, 2013 at 11:47 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

Hey,

My bad I didn't see the patch and thought you had wanted me to revert to the Sept 12 release for that function. I now applied the patch, and am seeing the correct error when clicking the bug button. If I encounter any issue I will post back.

-Eric

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Eric Enns eric.enns@phac-aspc.gc.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/12/2013 10:15AM

Cc: "galaxy-dev@bx.psu.edu" galaxy-dev@bx.psu.edu, Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Thanks, Eric

Since the HDA is None, the if statement should be sending you the trans.show_error_message.

Just to make sure we're on the same page, could you please attach or post the errors method from the dataset controller in your installation. It can be found at lib/galaxy/webapps/galaxy/controllers/dataset.py?

Carl

On Tue, Mar 12, 2013 at 10:59 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

...

The following is the stack trace I got when I applied the patch and clicked the bug icon.

"GET /dataset/errors?id=c39bc73d0eae67dd HTTP/1.0" 500 - " http://galaxy/history" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'hid' URL: http://galaxy/dataset/errors?id=c39bc73d0eae67dd File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call_ _ app_iter = self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 175 in errors return trans.fill_template( "dataset/errors.mako", hda=hda ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data ) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec _template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable _(context, *args, **kwargs)

File '/galaxy-dist/database/compiled_templates/dataset/errors.mako.py', line 27 in render_body __M_writer(unicode(hda.hid)) AttributeError: 'NoneType' object has no attribute 'hid'

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Eric Enns eric.enns@phac-aspc.gc.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/12/2013 09:47AM Cc: "galaxy-dev@bx.psu.edu" galaxy-dev@bx.psu.edu, Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca

Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Can you post the stack trace from the error, please?

Thanks for the info, Carl

On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.enns@phac-aspc.gc.cawrote:

...

Hey,

I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend.

-Eric

-----Carl Eberhard carlfeberhard@gmail.com wrote: ----- To: Jean-Francois Payotte jean-francois.payotte@dnalandmarks.ca From: Carl Eberhard carlfeberhard@gmail.com Date: 03/08/2013 05:10PM Cc: eric.enns@phac-aspc.gc.ca, "galaxy-dev@bx.psu.edu" < galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Error Report contains STDERR from different job

Hello, Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help?

If not, we can diagnose further. Thanks, Carl

On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte < jean-francois.payotte@dnalandmarks.ca> wrote:

...

Dear Eric,

I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;)

I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue.

You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-i...

Best regards,

*Jean-Francois*

From: Eric Enns eric.enns@phac-aspc.gc.ca To: galaxy-dev@bx.psu.edu Date: 08/03/2013 03:14 PM Subject: [galaxy-dev] Error Report contains STDERR from different job Sent by: galaxy-dev-bounces@lists.bx.psu.edu

---

Hey,

When clicking the "View or report this error button" the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history.

-Eric_____________________ ______ _________________ _______ ________

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:

http://lists.bx.psu.edu/

---

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:

http://lists.bx.psu.edu/