Bug in galaxy-dist/latest_15.05 for "Share history with user" function
Hello I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05. To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting"). The following patch appears to fix the problem: diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories def _get_users( self, trans, user, emails_or_ids ): also available via this gist: https://gist.github.com/pjbriggs/65c29a87e094d4d257f6 Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know) Best wishes Peter -- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hey Peter, this was indeed reported and fixed in https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9..., which should already be available in the release_15.05 branch of the repository if you update. Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch! -Dannon On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello Dannon Thanks for the quick response - glad to hear it's already been detected and fixed. Just to confirm though - am I right in thinking that the fix hasn't propagated through to bitbucket/galaxy-dist yet? Our production instance is still based off this and the change didn't seem to come up when I did "hg update" to the tip. Should we be considering migrating our deployment to github at some point? Thanks again, best wishes Peter On 17/06/15 14:12, Dannon Baker wrote:
Hey Peter, this was indeed reported and fixed in https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9..., which should already be available in the release_15.05 branch of the repository if you update.
Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch!
-Dannon
On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi Peter, it seems that bugfixes are not backported to bitbucket. We had the same trouble here and I migrated to git real quick. It is pretty easy. Check out 15.05 in bitbucket and clone one github repo with the same branch. Now you can swap the .hg and .git folders. Make a backup of everything before :) And do not forget to copy the .gitignore over :) Hope this hleps! Bjoern
Hello Dannon
Thanks for the quick response - glad to hear it's already been detected and fixed.
Just to confirm though - am I right in thinking that the fix hasn't propagated through to bitbucket/galaxy-dist yet? Our production instance is still based off this and the change didn't seem to come up when I did "hg update" to the tip.
Should we be considering migrating our deployment to github at some point?
Thanks again, best wishes
Peter
On 17/06/15 14:12, Dannon Baker wrote:
Hey Peter, this was indeed reported and fixed in
https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9...,
which should already be available in the release_15.05 branch of the
repository if you update.
Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch!
-Dannon
On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello Bjoern Thanks for that - it doesn't sound too difficult so I'll take a look at doing it when time allows. Much appreciated, best wishes Peter On 17/06/15 15:06, Bjoern Gruening wrote:
Hi Peter,
it seems that bugfixes are not backported to bitbucket. We had the same trouble here and I migrated to git real quick.
It is pretty easy. Check out 15.05 in bitbucket and clone one github repo with the same branch. Now you can swap the .hg and .git folders. Make a backup of everything before :)
And do not forget to copy the .gitignore over :) Hope this hleps! Bjoern
Hello Dannon
Thanks for the quick response - glad to hear it's already been detected and fixed.
Just to confirm though - am I right in thinking that the fix hasn't propagated through to bitbucket/galaxy-dist yet? Our production instance is still based off this and the change didn't seem to come up when I did "hg update" to the tip.
Should we be considering migrating our deployment to github at some point?
Thanks again, best wishes
Peter
On 17/06/15 14:12, Dannon Baker wrote:
Hey Peter, this was indeed reported and fixed in
https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9...,
which should already be available in the release_15.05 branch of the
repository if you update.
Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch!
-Dannon
On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Yeah - moving to git is great if it is an option. For the record though - bitbucket will be updated eventually to include this fix - but it does lag behind github some. -John On Wed, Jun 17, 2015 at 10:06 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Peter,
it seems that bugfixes are not backported to bitbucket. We had the same trouble here and I migrated to git real quick.
It is pretty easy. Check out 15.05 in bitbucket and clone one github repo with the same branch. Now you can swap the .hg and .git folders. Make a backup of everything before :)
And do not forget to copy the .gitignore over :) Hope this hleps! Bjoern
Hello Dannon
Thanks for the quick response - glad to hear it's already been detected and fixed.
Just to confirm though - am I right in thinking that the fix hasn't propagated through to bitbucket/galaxy-dist yet? Our production instance is still based off this and the change didn't seem to come up when I did "hg update" to the tip.
Should we be considering migrating our deployment to github at some point?
Thanks again, best wishes
Peter
On 17/06/15 14:12, Dannon Baker wrote:
Hey Peter, this was indeed reported and fixed in
https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9...,
which should already be available in the release_15.05 branch of the
repository if you update.
Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch!
-Dannon
On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello John Thanks for the clarification, also useful to know! Best wishes Peter On 17/06/15 15:30, John Chilton wrote:
Yeah - moving to git is great if it is an option. For the record though - bitbucket will be updated eventually to include this fix - but it does lag behind github some.
-John
On Wed, Jun 17, 2015 at 10:06 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Peter,
it seems that bugfixes are not backported to bitbucket. We had the same trouble here and I migrated to git real quick.
It is pretty easy. Check out 15.05 in bitbucket and clone one github repo with the same branch. Now you can swap the .hg and .git folders. Make a backup of everything before :)
And do not forget to copy the .gitignore over :) Hope this hleps! Bjoern
Hello Dannon
Thanks for the quick response - glad to hear it's already been detected and fixed.
Just to confirm though - am I right in thinking that the fix hasn't propagated through to bitbucket/galaxy-dist yet? Our production instance is still based off this and the change didn't seem to come up when I did "hg update" to the tip.
Should we be considering migrating our deployment to github at some point?
Thanks again, best wishes
Peter
On 17/06/15 14:12, Dannon Baker wrote:
Hey Peter, this was indeed reported and fixed in
https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e9...,
which should already be available in the release_15.05 branch of the
repository if you update.
Sorry for the trouble, and even though it's resolved now, thanks for taking the time to debug this and write such a detailed error report including a patch!
-Dannon
On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hello
I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05.
To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know)
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
participants (4)
-
Bjoern Gruening -
Dannon Baker -
John Chilton -
Peter Briggs