Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html.

Thanks, Liisa

Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca.

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

This functionality works fine in some instances, e.g. for this history:

http://main.g2.bx.psu.edu/u/cartman/h/repeats

I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history?

Thanks, J.

On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote:

Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following.

Error - <type 'exceptions.NameError'>: global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 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 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined

If I import the history into my own history pane I can click on the eye and see the data with no errors.

Any ideas how I can see the data from the published histories?

Thanks, Liisa

Liisa Koski Bioinformatics Programmer ___________________________________________________________ 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/

Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference.

Thanks, Liisa

Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca.

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 14:46 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly:

http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2

(Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.)

Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way?

J.

On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote:

Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html.

Thanks, Liisa

Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca.

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

This functionality works fine in some instances, e.g. for this history:

http://main.g2.bx.psu.edu/u/cartman/h/repeats

I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history?

Thanks, J.

On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote:

Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following.

Error - <type 'exceptions.NameError'>: global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 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 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined

If I import the history into my own history pane I can click on the eye and see the data with no errors.

Any ideas how I can see the data from the published histories?

Thanks, Liisa

Liisa Koski Bioinformatics Programmer ___________________________________________________________ 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 Jeremy, that changeset fixed the issue :)

Cheers, Liisa

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-30 18:07 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

Updating FastQC won't solve this issue. You'll need to manually update galaxy-dist with this changeset to see the graphs:

https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea

Otherwise, you can wait until the next galaxy-dist to get this changeset.

Best, J.

On Nov 30, 2011, at 2:39 PM, Liisa Koski wrote:

Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference.

Thanks, Liisa

Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca.

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 14:46 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly:

http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2

(Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.)

Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way?

J.

On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote:

Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html.

Thanks, Liisa

Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca.

From: Jeremy Goecks jeremy.goecks@emory.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa,

This functionality works fine in some instances, e.g. for this history:

http://main.g2.bx.psu.edu/u/cartman/h/repeats

I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history?

Thanks, J.

On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote:

Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following.

Error - <type 'exceptions.NameError'>: global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 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 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined

If I import the history into my own history pane I can click on the eye and see the data with no errors.

Any ideas how I can see the data from the published histories?

Thanks, Liisa

Liisa Koski Bioinformatics Programmer ___________________________________________________________ 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/