[galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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/
Re: [galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
To add some information to my earlier post - It seems that the remote repository is updated, but the commandline returns a confusing abort message. Trying on a private test toolshed, I see the following in the community-webapp.log: 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=capabilities HTTP/1.1 200 130 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=batch HTTP/1.1 200 43 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - testjorrit [13/Mar/2013:22:08:23 +] POST /repos/testjorrit/testrepo?cmd=unbundle HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 58 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] POST /repos/testjorrit/testrepo?cmd=pushkey HTTP/1.1 401 - - mercurial/proto-1.0 Which seems to indicate that most http get/post succeed, but the last one, pushkey, fails to authenticate. I am wondering whether I am the only one seeing this confusing behaviour and what I can do to stop this from happening. thx, -jorrit On Mar 13, 2013, at 2:37 PM, jorrit poelen wrote: Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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/
Re: [galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
Thanks Dave for your super-quick response! Works like a charm. -jorrit On Mar 15, 2013, at 12:16 PM, Dave Bouvier wrote: Jorrit, Thank you for reporting this issue, I've committed a fix in the default branch at 9077:62bd6fe0e9aa, and it will be updated in stable at our next release. --Dave B. On 3/13/13 18:11:27.000, jorrit poelen wrote: To add some information to my earlier post - It seems that the remote repository is updated, but the commandline returns a confusing abort message. Trying on a private test toolshed, I see the following in the community-webapp.log: 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=capabilities HTTP/1.1 200 130 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=batch HTTP/1.1 200 43 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - testjorrit [13/Mar/2013:22:08:23 +] POST /repos/testjorrit/testrepo?cmd=unbundle HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 58 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] POST /repos/testjorrit/testrepo?cmd=pushkey HTTP/1.1 401 - - mercurial/proto-1.0 Which seems to indicate that most http get/post succeed, but the last one, pushkey, fails to authenticate. I am wondering whether I am the only one seeing this confusing behaviour and what I can do to stop this from happening. thx, -jorrit On Mar 13, 2013, at 2:37 PM, jorrit poelen wrote: Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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/ ___ 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/
[galaxy-dev] galaxy not picking up updates from test toolshed
Hey y'all, I noticed that my local galaxy instance doens't pickup latest updates from test toolshed. Steps to reproduce: 1. install obotools from test toolshed using hg clone http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotools , revision 45:bb20766df19c 2. hg push new change of obotools of galaxy tool to testtoolshed , creating revision 46:532808477800 3. update obotools in galaxy admin expected result: galaxy admin detects new version and give an option to update. actual result: galaxy admin does not detect new version. I've attached some galaxy logging below. One thing I noticed that the reported commit time in testtoolshed seems 7 hours off - just minutes after I pushed the change, testtoolshed says the change was commit ~ 7 hours ago. Workaround I am using to do update is to deactivate and remove the tool all together, and re-install straight from test-toolshed. What should I do to make the tool version update work? I am probably missing something. Thanks! -jorrit Galaxy logging on looking for updates in test toolshed: --- 24.130.122.217 - - [26/Mar/2013:01:12:46 +] GET /admin_toolshed/browse_repositories HTTP/1.1 200 - http://galaxy:7474/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:51 +] GET /admin_toolshed/browse_repositories?operation=get+updatesid=a799d38679e985db HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:51 +] GET /admin_toolshed/check_for_updates?id=a799d38679e985db HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:52 +] GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/name=obotoolsowner=jorritchangeset_revision=bb20766df19clatest_changeset_revision=bb20766df19clatest_ctx_rev=45 HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:52 +] GET /admin_toolshed/manage_repository?status=donemessage=The+installed+repository+named+%27obotools%27+is+current%2C+there+are+no+updates+available.++id=a799d38679e985db HTTP/1.1 200 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy not picking up updates from test toolshed
Hey Dave, Thanks against for your quick response! I checked my universe_wsgi.ini file and can confirm that the enabled_tool_shed_check was *commented*. I've uncommented the settings and changed them to: enable_tool_shed_check = True hours_between_check = 1 Then I followed the steps outlined in my initial email and the observed the same (unexpected) behavior. Perhaps I am describing a feature request rather than a bug: My expectation is that whenever I explicitly request to update a tool, a immediate check is performed against the relevant tool shed. To make sure that I correctly understand the existing tool update feature, please confirm that the following describes the currently expected tool update behavior: 0. admin of galaxy instance Z enables the feature to check for tool updates in toolsheds every hour 1. tool X revision 1.0 is installed from tool shed Y into galaxy instance Z by tool developer using hg push 2. tool X is current revision is updated to revision 1.1 in tool shed Y 3. immediately after, admin of galaxy instance Z attempts to (manually) upgrade tool X to version 1.1 using the admin web interface 4. galaxy instance Z reports that no new version of tool X are available, even though a new version exists in the toolshed 5. galaxy instance Z detects version 1.1 of tool X at most one hour after the update was made 6. admin of galaxy instance Z tries again Thanks for your patience and efforts, -jorrit On Mar 26, 2013, at 8:19 AM, Dave Bouvier wrote: Jorrit, Just to eliminate one possible cause of this behavior, could you confirm that your local Galaxy instance's universe_wsgi.ini file's enable_tool_shed_check setting is uncommented and set to True, and the hours_between_check is also uncommented and set to a value between 1 and 12? --Dave B. On 3/25/13 21:26:07.000, jorrit poelen wrote: Hey y'all, I noticed that my local galaxy instance doens't pickup latest updates from test toolshed. Steps to reproduce: 1. install obotools from test toolshed using hg clone http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotools , revision 45:bb20766df19c 2. hg push new change of obotools of galaxy tool to testtoolshed , creating revision 46:532808477800 3. update obotools in galaxy admin expected result: galaxy admin detects new version and give an option to update. actual result: galaxy admin does not detect new version. I've attached some galaxy logging below. One thing I noticed that the reported commit time in testtoolshed seems 7 hours off - just minutes after I pushed the change, testtoolshed says the change was commit ~ 7 hours ago. Workaround I am using to do update is to deactivate and remove the tool all together, and re-install straight from test-toolshed. What should I do to make the tool version update work? I am probably missing something. Thanks! -jorrit Galaxy logging on looking for updates in test toolshed: --- 24.130.122.217 - - [26/Mar/2013:01:12:46 +] GET /admin_toolshed/browse_repositories HTTP/1.1 200 - http://galaxy:7474/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:51 +] GET /admin_toolshed/browse_repositories?operation=get+updatesid=a799d38679e985db HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:51 +] GET /admin_toolshed/check_for_updates?id=a799d38679e985db HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:52 +] GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/name=obotoolsowner=jorritchangeset_revision=bb20766df19clatest_changeset_revision=bb20766df19clatest_ctx_rev=45 HTTP/1.1 302 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 24.130.122.217 - - [26/Mar/2013:01:12:52 +] GET /admin_toolshed/manage_repository?status=donemessage=The+installed+repository+named+%27obotools%27+is+current%2C+there+are+no+updates+available.++id=a799d38679e985db HTTP/1.1 200 - http://galaxy:7474/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10 ___ 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
[galaxy-dev] inable to login to testtoolshed login because of Server Error: AttributeError: 'GalaxySession' object has no attribute 'current_history'
Hey y'all galaxiers, Today, I tried to login using the testtoolshed web ui. To make sure that it wasn't just isolated to an existing account, I created a new account, and still I encountered the Server Error attached below. This error is not shown when entering an invalid password. I was able to login and push hg changes a couple of days ago. Was the test toolshed recently upgraded? Please let me know what I can do to login to testtoolshed at http://testtoolshed.g2.bx.psu.edu thx, -jorrit PS Please find attached stack trace on login with valid password through toolshed web ui at around 2pm PST. URL: http://testtoolshed.g2.bx.psu.edu/user/login?use_panels=True File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 128 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/galaxy/controllers/user.py', line 466 in login active_view=user ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 863 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 874 in fill_template_mako return template.render( **data ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/database/compiled_templates/community/base/base_panels.mako.py', line 85 in render_body __M_writer(unicode(self.masthead())) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/database/compiled_templates/community/webapps/galaxy/base_panels.mako.py', line 337 in render_masthead usage = trans.app.quota_agent.get_usage( trans=trans ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/quota/__init__.py', line 26 in get_usage history = trans.history File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 741 in get_history history = self.galaxy_session.current_history AttributeError: 'GalaxySession' object has no attribute 'current_history' ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
