Nice 'citable' URLs for Galaxy Tool Shed repositories
Dear all, Something I am conscious of every time I have directed someone to a tool or wrapper on the Galaxy Tool Shed is the lack of nice stable URLs. The current frame based design hinders this - and as a result I usually just have to give the ToolShed URL and tell them what to search for. This problem is particularly acute for citing a tool shed entry, where a nice URL would be far better. I appreciate moving away from the current frame interface is a lot of work - although what Jeremy Goecks wrote last week suggests that is a long term goal: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-January/012792.html I would like something similar to the repository URL, but for the ToolShed interface. e.g. The repository view for my MIRA wrapper: http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler Perhaps is the short-term what could be done is to enhance the repository view, and include links between this and the current "Tool Shed" frame based page? That way we can share a nice URL like http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler to direct someone to a resource in the Tool Shed? e.g. (1) When viewing an entry on the "Tool Shed", include a prominent link to the repository URL (perhaps even with social media links like tweet or share this to emphasise this is the best URL to share). (2) In the header for each repo (perhaps in place of the current Mercuiral logo?) have a link to the "Tool Shed" frameset for the tool being viewed. Thanks, Peter
Hi Peter, Thanks for your request, having citable tool shed URLs is definitely important. I've got this on my list (which is maxed out as usual). I will look into this in a timely manner and keep you posted appropriately. Greg Von Kuster On Jan 28, 2013, at 8:41 AM, Peter Cock wrote:
Dear all,
Something I am conscious of every time I have directed someone to a tool or wrapper on the Galaxy Tool Shed is the lack of nice stable URLs. The current frame based design hinders this - and as a result I usually just have to give the ToolShed URL and tell them what to search for. This problem is particularly acute for citing a tool shed entry, where a nice URL would be far better.
I appreciate moving away from the current frame interface is a lot of work - although what Jeremy Goecks wrote last week suggests that is a long term goal: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-January/012792.html
I would like something similar to the repository URL, but for the ToolShed interface. e.g. The repository view for my MIRA wrapper: http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler
Perhaps is the short-term what could be done is to enhance the repository view, and include links between this and the current "Tool Shed" frame based page? That way we can share a nice URL like http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler to direct someone to a resource in the Tool Shed? e.g.
(1) When viewing an entry on the "Tool Shed", include a prominent link to the repository URL (perhaps even with social media links like tweet or share this to emphasise this is the best URL to share).
(2) In the header for each repo (perhaps in place of the current Mercuiral logo?) have a link to the "Tool Shed" frameset for the tool being viewed.
Thanks,
Peter ___________________________________________________________ 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:
On Mon, Jan 28, 2013 at 6:49 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
Thanks for your request, having citable tool shed URLs is definitely important. I've got this on my list (which is maxed out as usual). I will look into this in a timely manner and keep you posted appropriately.
Greg Von Kuster
Sounds like my to do list too :( Is there a Trello issue on this, or should I file one? Thanks, Peter P.S. Citable Tool Shed URLs would also be good for the @GalaxyProject tweets, as pointed out by John Chilton: https://twitter.com/jmchilton/status/295890843372515328
I've opened a Trello card, but it's in the Galaxy development project, so not sure if you can see it or not. Here's the link to the card just in case... https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/... On Jan 28, 2013, at 2:28 PM, Peter Cock wrote:
On Mon, Jan 28, 2013 at 6:49 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
Thanks for your request, having citable tool shed URLs is definitely important. I've got this on my list (which is maxed out as usual). I will look into this in a timely manner and keep you posted appropriately.
Greg Von Kuster
Sounds like my to do list too :(
Is there a Trello issue on this, or should I file one?
Thanks,
Peter
P.S. Citable Tool Shed URLs would also be good for the @GalaxyProject tweets, as pointed out by John Chilton: https://twitter.com/jmchilton/status/295890843372515328
On Mon, Jan 28, 2013 at 7:56 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
I've opened a Trello card, but it's in the Galaxy development project, so not sure if you can see it or not. Here's the link to the card just in case...
https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/...
I can't see that :( I was wondering about taking a look at this to see how hard it would be - but my first query is where is the ToolShed source code? My plan is/was to use this pattern: http://toolshed.g2.bx.psu.edu/repository/username/ --> All tools by that username http://toolshed.g2.bx.psu.edu/repository/username/toolname --> The given tool from that author This would match the pattern for the the underlying hg repository, http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler That would become this for the ToolShed entry: http://toolshed.g2.bx.psu.edu/repository/peterjc/mira_assembler Thanks, Peter
On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I was wondering about taking a look at this to see how hard it would be - but my first query is where is the ToolShed source code?
I think I've found it, in the main repository under the slightly misleading name of community: lib/galaxy/webapps/community https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/c... Browsing the files it isn't immediately clear to me how to start... but I'll spend a bit more time on this today. Peter
Yes, the tool shed used to be named the Galaxy Community Space. On Jan 29, 2013, at 11:14 AM, Peter Cock wrote:
On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I was wondering about taking a look at this to see how hard it would be - but my first query is where is the ToolShed source code?
I think I've found it, in the main repository under the slightly misleading name of community: lib/galaxy/webapps/community
https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/c...
Browsing the files it isn't immediately clear to me how to start... but I'll spend a bit more time on this today.
Peter
On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
The tool shed source is mostly in the following places.
~/lib/galaxy/webapps/community/ /lib/galaxy/tool_shed/ /lib/galaxy/util/shed_util_common.py /lib/galaxy/util/shed_util.py /template/webapps/community/
I'll get to this as soon as I can, but glad you're willing to take a look.
And according to http://wiki.galaxyproject.org/HostingALocalToolShed it gets launched via run_community.sh and is configured via community_wsgi.ini - that makes sense. This is looking to be a bigger job than I had hoped (given the learning curve to first understand the way the ToolShed webapp works). On Tue, Jan 29, 2013 at 4:18 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Yes, the tool shed used to be named the Galaxy Community Space.
Presumably at this point changing the name in the code would break too many things? Thanks, Peter
On Tue, Jan 29, 2013 at 11:44 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Presumably at this point changing the name in the code would break too many things?
Actually, changing the package name would probably be a pretty clean refactoring, just some changes in buildapp. But given how many people ar actively working on that code it might be best to wait, merging lots of code on top of renames can get messy. -- James Taylor, Assistant Professor, Biology/CS, Emory University
Thanks for your request Peter, I've added a Trello card for this and I'll get to it as soon as possible - the restriction is simply a bandwidth issue as my plate is maxed out and the code renaming work just hasn't been a high priority. Here's the link to the trello card - I believe the plan is to soon make the development view public. https://trello.com/card/change-the-references-to-community-in-the-galaxy-cod... Greg Von Kuster On Jan 30, 2013, at 1:00 PM, James Taylor wrote:
On Tue, Jan 29, 2013 at 11:44 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Presumably at this point changing the name in the code would break too many things?
Actually, changing the package name would probably be a pretty clean refactoring, just some changes in buildapp. But given how many people ar actively working on that code it might be best to wait, merging lots of code on top of renames can get messy.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 29, 2013 at 4:44 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
The tool shed source is mostly in the following places.
~/lib/galaxy/webapps/community/ /lib/galaxy/tool_shed/ /lib/galaxy/util/shed_util_common.py /lib/galaxy/util/shed_util.py /template/webapps/community/
I'll get to this as soon as I can, but glad you're willing to take a look.
And according to http://wiki.galaxyproject.org/HostingALocalToolShed it gets launched via run_community.sh and is configured via community_wsgi.ini - that makes sense.
This is looking to be a bigger job than I had hoped (given the learning curve to first understand the way the ToolShed webapp works).
I do have some progress to report :) I could get http://example.org/repositoties/owner/name to work, but http://example.org/repositoties/owner would conflict with the other URLs used as actions by the repository controller. Perhaps there is an elegant solution in the routing? For now, I am using http://example.org/view/owner/name and http://example.org/view/owner instead. I haven't worked out how to show a full frame set, rather than just the content frame - but the following is close to what I want to do. Also, I'm using a redirect (rather than staying at the citable URL) as some of the URLs in the displayed page. Peter $ hg diff diff -r 04e221996871 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/buildapp.py Thu Jan 31 16:42:52 2013 +0000 @@ -63,6 +63,8 @@ # Create the universe WSGI application webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="community" ) add_ui_controllers( webapp, app ) + webapp.add_route( '/view/{owner}/', controller='repository', action='citable_owner' ) + webapp.add_route( '/view/{owner}/{name}/', controller='repository', action='citable_repository' ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) diff -r 04e221996871 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jan 31 16:42:52 2013 +0000 @@ -688,6 +688,60 @@ id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) return self.repository_grid( trans, **kwd ) + + @web.expose + def citable_owner( self, trans, owner): + """Support for citeable URL for each contributor's tools, e.g. http://example.org/view/owner""" + try: + user = suc.get_user_by_username( trans, owner ) + except: + user = None + if user is None: + #Would a specific 404 error page be better? + message = "Unknown repository owner %s" % owner + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + id = trans.security.encode_id( user.id ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation="repositories_by_user", + user_id=id) ) + + @web.expose + def citable_repository( self, trans, owner, name): + """Support for citeable URL for each tool, e.g. http://example.org/view/owner/name""" + try: + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + except: + repository = None + if repository is None: + #TODO - If the owner is OK, show their repositories? + #Would a specific 404 error page be better? + message = "Unknown repository %s/%s" % (owner, name) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #Good, found the repository + id = trans.security.encode_id( repository.id ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + #return self.view_repository(trans, id) + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + id=id) ) + + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd )
Hi Peter, Thanks for the update and your contributions. Would you like me to continue with the work you've started, or would you like to continue yourself? I'll try to fit this in this week if you want to hand it off to me. Please let me know. Thanks! Greg Von Kuster On Jan 31, 2013, at 11:49 AM, Peter Cock wrote:
On Tue, Jan 29, 2013 at 4:44 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
The tool shed source is mostly in the following places.
~/lib/galaxy/webapps/community/ /lib/galaxy/tool_shed/ /lib/galaxy/util/shed_util_common.py /lib/galaxy/util/shed_util.py /template/webapps/community/
I'll get to this as soon as I can, but glad you're willing to take a look.
And according to http://wiki.galaxyproject.org/HostingALocalToolShed it gets launched via run_community.sh and is configured via community_wsgi.ini - that makes sense.
This is looking to be a bigger job than I had hoped (given the learning curve to first understand the way the ToolShed webapp works).
I do have some progress to report :)
I could get http://example.org/repositoties/owner/name to work, but http://example.org/repositoties/owner would conflict with the other URLs used as actions by the repository controller. Perhaps there is an elegant solution in the routing? For now, I am using http://example.org/view/owner/name and http://example.org/view/owner instead.
I haven't worked out how to show a full frame set, rather than just the content frame - but the following is close to what I want to do. Also, I'm using a redirect (rather than staying at the citable URL) as some of the URLs in the displayed page.
Peter
$ hg diff diff -r 04e221996871 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/buildapp.py Thu Jan 31 16:42:52 2013 +0000 @@ -63,6 +63,8 @@ # Create the universe WSGI application webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="community" ) add_ui_controllers( webapp, app ) + webapp.add_route( '/view/{owner}/', controller='repository', action='citable_owner' ) + webapp.add_route( '/view/{owner}/{name}/', controller='repository', action='citable_repository' ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) diff -r 04e221996871 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jan 31 16:42:52 2013 +0000 @@ -688,6 +688,60 @@
id=trans.security.encode_id( repository.id ),
changeset_revision=v ) ) return self.repository_grid( trans, **kwd ) + + @web.expose + def citable_owner( self, trans, owner): + """Support for citeable URL for each contributor's tools, e.g. http://example.org/view/owner""" + try: + user = suc.get_user_by_username( trans, owner ) + except: + user = None + if user is None: + #Would a specific 404 error page be better? + message = "Unknown repository owner %s" % owner + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + id = trans.security.encode_id( user.id ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation="repositories_by_user", + user_id=id) ) + + @web.expose + def citable_repository( self, trans, owner, name): + """Support for citeable URL for each tool, e.g. http://example.org/view/owner/name""" + try: + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + except: + repository = None + if repository is None: + #TODO - If the owner is OK, show their repositories? + #Would a specific 404 error page be better? + message = "Unknown repository %s/%s" % (owner, name) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #Good, found the repository + id = trans.security.encode_id( repository.id ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + #return self.view_repository(trans, id) + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + id=id) ) + + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) ___________________________________________________________ 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:
On Thursday, January 31, 2013, Greg Von Kuster wrote:
Hi Peter,
Thanks for the update and your contributions. Would you like me to continue with the work you've started, or would you like to continue yourself? I'll try to fit this in this week if you want to hand it off to me. Please let me know.
Thanks!
Greg Von Kuster
If you're happy to take a look this week that would be great - at this point I think I still need to learn more about the Galaxy web framework before I can get much further. Thanks, Peter
Hello Peter, I've added an enhanced version of your implementation for citable URLS in the tool shed to change set revision 8720:e27d0dd12752. This is currently running on the test tool shed, and viewing repositories now displays a link like this: I've used the same routes you set up, so both of the following work: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler http://testtoolshed.g2.bx.psu.edu/view/peterjc/ i was under a rush to get this in before the next release cutoff. There is still some work to do on this (e.g., we can add additions routes for citing a specific repository revision, etc) but this should be a good start and it will be in the next Galaxy release currently scheduled for next week. Thanks very much for your contribution on this and please let me know if you encounter any issues or have any additional suggestions. Greg Von Kuster On Jan 31, 2013, at 11:49 AM, Peter Cock wrote:
On Tue, Jan 29, 2013 at 4:44 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I do have some progress to report :)
I could get http://example.org/repositoties/owner/name to work, but http://example.org/repositoties/owner would conflict with the other URLs used as actions by the repository controller. Perhaps there is an elegant solution in the routing? For now, I am using http://example.org/view/owner/name and http://example.org/view/owner instead.
I haven't worked out how to show a full frame set, rather than just the content frame - but the following is close to what I want to do. Also, I'm using a redirect (rather than staying at the citable URL) as some of the URLs in the displayed page.
Peter
$ hg diff diff -r 04e221996871 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/buildapp.py Thu Jan 31 16:42:52 2013 +0000 @@ -63,6 +63,8 @@ # Create the universe WSGI application webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="community" ) add_ui_controllers( webapp, app ) + webapp.add_route( '/view/{owner}/', controller='repository', action='citable_owner' ) + webapp.add_route( '/view/{owner}/{name}/', controller='repository', action='citable_repository' ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) diff -r 04e221996871 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Jan 30 16:47:20 2013 -0500 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jan 31 16:42:52 2013 +0000 @@ -688,6 +688,60 @@
id=trans.security.encode_id( repository.id ),
changeset_revision=v ) ) return self.repository_grid( trans, **kwd ) + + @web.expose + def citable_owner( self, trans, owner): + """Support for citeable URL for each contributor's tools, e.g. http://example.org/view/owner""" + try: + user = suc.get_user_by_username( trans, owner ) + except: + user = None + if user is None: + #Would a specific 404 error page be better? + message = "Unknown repository owner %s" % owner + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + id = trans.security.encode_id( user.id ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation="repositories_by_user", + user_id=id) ) + + @web.expose + def citable_repository( self, trans, owner, name): + """Support for citeable URL for each tool, e.g. http://example.org/view/owner/name""" + try: + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + except: + repository = None + if repository is None: + #TODO - If the owner is OK, show their repositories? + #Would a specific 404 error page be better? + message = "Unknown repository %s/%s" % (owner, name) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_categories', + id=None, + name=None, + owner=None, + message=message, + status='error' ) ) + #Good, found the repository + id = trans.security.encode_id( repository.id ) + #TODO - Ideally this would load the frameset, not just the frame! + #TODO - Remove the redirect (assuming the links on the page OK) + #return self.view_repository(trans, id) + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + id=id) ) + + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) ___________________________________________________________ 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:
On Sat, Feb 2, 2013 at 12:46 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Peter,
I've added an enhanced version of your implementation for citable URLS in the tool shed to change set revision 8720:e27d0dd12752. This is currently running on the test tool shed, and viewing repositories now displays a link like this:
I've used the same routes you set up, so both of the following work:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler http://testtoolshed.g2.bx.psu.edu/view/peterjc/
i was under a rush to get this in before the next release cutoff. There is still some work to do on this (e.g., we can add additions routes for citing a specific repository revision, etc) but this should be a good start and it will be in the next Galaxy release currently scheduled for next week.
Thanks very much for your contribution on this and please let me know if you encounter any issues or have any additional suggestions.
Greg Von Kuster
Quick work :) I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to another section/repository/etc the URL in the browser's address bar does not update. You can be looking at repository B, but the address bar URL still says repository A. (This was one reason I stuck a redirect in my prototype). Separately, but perhaps related, it would be nice if via the search or otherwise, the new URLs were automatically used - that would be slightly easier than copying it from the text of the page. However, this is already functional enough to start sharing direct links. Once this goes live, you'll have to brief the whoever writes the new tool alerts for Twitter to use it :) Thanks, Peter
On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sat, Feb 2, 2013 at 12:46 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Peter,
I've added an enhanced version of your implementation for citable URLS in the tool shed to change set revision 8720:e27d0dd12752. This is currently running on the test tool shed, and viewing repositories now displays a link like this:
I've used the same routes you set up, so both of the following work:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler http://testtoolshed.g2.bx.psu.edu/view/peterjc/
i was under a rush to get this in before the next release cutoff. There is still some work to do on this (e.g., we can add additions routes for citing a specific repository revision, etc) but this should be a good start and it will be in the next Galaxy release currently scheduled for next week.
Thanks very much for your contribution on this and please let me know if you encounter any issues or have any additional suggestions.
Greg Von Kuster
Quick work :)
I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to another section/repository/etc the URL in the browser's address bar does not update. You can be looking at repository B, but the address bar URL still says repository A.
(This was one reason I stuck a redirect in my prototype).
Do you think this going to be easy to fix, or should we revert to the redirect trick to avoid this 'stale' URL problem?
Separately, but perhaps related, it would be nice if via the search or otherwise, the new URLs were automatically used - that would be slightly easier than copying it from the text of the page.
However, this is already functional enough to start sharing direct links. Once this goes live, you'll have to brief the whoever writes the new tool alerts for Twitter to use it :)
I see the new citable URLs are already in use on the wiki (but not yet working as the live ToolShed doesn't have this update yet): http://wiki.galaxyproject.org/ToolShedToolFeatures#Example_repositories_in_t... Regards, Peter
Hi Peter, On Feb 8, 2013, at 5:26 AM, Peter Cock wrote:
On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to another section/repository/etc the URL in the browser's address bar does not update. You can be looking at repository B, but the address bar URL still says repository A.
(This was one reason I stuck a redirect in my prototype).
Do you think this going to be easy to fix, or should we revert to the redirect trick to avoid this 'stale' URL problem?
This shouldn't be too difficult to fix. There actually is still a redirect, but it comes after the panel layout. I'll take a look at this today.
I see the new citable URLs are already in use on the wiki (but not yet working as the live ToolShed doesn't have this update yet):
There is a release scheduled for today, so the main Galaxy tool shed will include this new feature. I always have the wiki updated just before the release.
http://wiki.galaxyproject.org/ToolShedToolFeatures#Example_repositories_in_t...
Regards,
Peter
Hello Peter, In addition to the fixes I've commented on inline below, I've also added a new rout for specified repository revisions. So the following citable URLs are now supported in the test tool shed. These fixes and enhancements will not be available on the main Galaxy tool shed until the next Galaxy release. http://testtoolshed.g2.bx.psu.edu/view/peterjc/ http://testtoolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id http://testtoolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id/66e2e0f16c... On Feb 8, 2013, at 5:26 AM, Peter Cock wrote:
On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to another section/repository/etc the URL in the browser's address bar does not update. You can be looking at repository B, but the address bar URL still says repository A.
(This was one reason I stuck a redirect in my prototype).
Do you think this going to be easy to fix, or should we revert to the redirect trick to avoid this 'stale' URL problem?
This behavior has been fixed in change set revision 8802:7ccddea80a25 which is currently running on the test Galaxy tool shed.
Separately, but perhaps related, it would be nice if via the search or otherwise, the new URLs were automatically used - that would be slightly easier than copying it from the text of the page.
This one is tricky and may have to wait until we eliminate the Galaxy iframes. If I can figure out a way to make this work before that, i certainly will. I've created a separate Trello card for this. https://trello.com/card/toolshed-nice-citable-urls-for-galaxy-tool-shed-repo...
However, this is already functional enough to start sharing direct links. Once this goes live, you'll have to brief the whoever writes the new tool alerts for Twitter to use it :)
I see the new citable URLs are already in use on the wiki (but not yet working as the live ToolShed doesn't have this update yet):
http://wiki.galaxyproject.org/ToolShedToolFeatures#Example_repositories_in_t...
These are now working since the Galaxy release last Friday. Thanks! Greg Von Kuster
On Mon, Feb 11, 2013 at 5:01 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Peter,
In addition to the fixes I've commented on inline below, I've also added a new rout for specified repository revisions. So the following citable URLs are now supported in the test tool shed. These fixes and enhancements will not be available on the main Galaxy tool shed until the next Galaxy release.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ http://testtoolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id http://testtoolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id/66e2e0f16c...
Lovely - by the way the fasta_filter_by_id tool was replaced by this more general tool: http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id or in the main shed: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to another section/repository/etc the URL in the browser's address bar does not update. You can be looking at repository B, but the address bar URL still says repository A. (This was one reason I stuck a redirect in my prototype).
Do you think this going to be easy to fix, or should we revert to the redirect trick to avoid this 'stale' URL problem?
This behavior has been fixed in change set revision 8802:7ccddea80a25 which is currently running on the test Galaxy tool shed.
Thanks
Separately, but perhaps related, it would be nice if via the search or otherwise, the new URLs were automatically used - that would be slightly easier than copying it from the text of the page.
This one is tricky and may have to wait until we eliminate the Galaxy iframes. If I can figure out a way to make this work before that, i certainly will. I've created a separate Trello card for this.
https://trello.com/card/toolshed-nice-citable-urls-for-galaxy-tool-shed-repo...
Great.
However, this is already functional enough to start sharing direct links. Once this goes live, you'll have to brief the whoever writes the new tool alerts for Twitter to use it :)
I look forward to seeing the first tweets links straight to a tool shed repository :) In fact we can start using these URLs in links to dependencies on other repositories as well. Thanks Greg for doing this so promptly, Peter
On Mon, Feb 11, 2013 at 5:16 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
However, this is already functional enough to start sharing direct links. Once this goes live, you'll have to brief the whoever writes the new tool alerts for Twitter to use it :)
I look forward to seeing the first tweets links straight to a tool shed repository :)
I should have checked Twitter while writing that email, first examples are out (note I have expanded the Twitter short URLs): https://twitter.com/galaxyproject/status/301011276711211008 Now in Galaxy Tool Shed: blastxml_to_top_descr: Make table of top BLAST match descriptions http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr #usegalaxy https://twitter.com/galaxyproject/status/301011636578316290 Galaxy Tool Shed now supports direct linking to tools, e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr http://toolshed.g2.bx.psu.edu/ #usegalaxy Nice :) Peter
Hi all, I am using galaxy on the cloud and I keep getting the following error: "An error occurred running this job: Job output not returned from cluster" Any clues? thanks Alfonso
Hi Alfonso, Is this any particular tool that's failing? What does the state of your cloud cluster look like, are there any failures in the log? (in the cloudman interface) And lastly, when writing a new issue to the mailing list, please create a new email instead of replying to an unrelated thread. This will help us assist you and keep track of your individual issue instead of associating it with someone else. -Dannon On Feb 11, 2013, at 12:40 PM, Alfonso Garrido-Lecca <Alfonso.Garrido-lecca@colorado.edu> wrote:
Hi all, I am using galaxy on the cloud and I keep getting the following error: "An error occurred running this job: Job output not returned from cluster" Any clues? thanks Alfonso ___________________________________________________________ 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:
Hi Peter, The tool shed source is mostly in the following places. ~/lib/galaxy/webapps/community/ /lib/galaxy/tool_shed/ /lib/galaxy/util/shed_util_common.py /lib/galaxy/util/shed_util.py /template/webapps/community/ I'll get to this as soon as I can, but glad you're willing to take a look. Greg Von Kuster On Jan 29, 2013, at 11:04 AM, Peter Cock wrote:
On Mon, Jan 28, 2013 at 7:56 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
I've opened a Trello card, but it's in the Galaxy development project, so not sure if you can see it or not. Here's the link to the card just in case...
https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/...
I can't see that :(
I was wondering about taking a look at this to see how hard it would be - but my first query is where is the ToolShed source code?
My plan is/was to use this pattern:
http://toolshed.g2.bx.psu.edu/repository/username/ --> All tools by that username
http://toolshed.g2.bx.psu.edu/repository/username/toolname --> The given tool from that author
This would match the pattern for the the underlying hg repository, http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler
That would become this for the ToolShed entry: http://toolshed.g2.bx.psu.edu/repository/peterjc/mira_assembler
Thanks,
Peter ___________________________________________________________ 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:
participants (5)
-
Alfonso Garrido-Lecca -
Dannon Baker -
Greg Von Kuster -
James Taylor -
Peter Cock