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://jorrit@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 +0000] "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 +0000] "GET /admin_toolshed/browse_repositories?operation=get+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/2013:01:12:51 +0000] "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 +0000] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&name=obotools&owner=jorrit&changeset_revision=bb20766df19c&latest_changeset_revision=bb20766df19c&latest_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 +0000] "GET /admin_toolshed/manage_repository?status=done&message=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"
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://jorrit@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 +0000] "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 +0000] "GET /admin_toolshed/browse_repositories?operation=get+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/2013:01:12:51 +0000] "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 +0000] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&name=obotools&owner=jorrit&changeset_revision=bb20766df19c&latest_changeset_revision=bb20766df19c&latest_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 +0000] "GET /admin_toolshed/manage_repository?status=done&message=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/
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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://jorrit@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 +0000] "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 +0000] "GET /admin_toolshed/browse_repositories?operation=get+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/2013:01:12:51 +0000] "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 +0000] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&name=obotools&owner=jorrit&changeset_revision=bb20766df19c&latest_changeset_revision=bb20766df19c&latest_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 +0000] "GET /admin_toolshed/manage_repository?status=done&message=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/
___________________________________________________________ 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/
Jorrit, First, allow me to clarify a point of naming: It's not quite right to say "tools" in this situation, as tools are only one of several utilities that a tool shed repository can contain, along with datatypes, workflows, repository dependencies, and so on. This is an important distinction, because some repositories can (and do) contain no tools, and only datatypes and/or other Galaxy utilities. In your process description for the current behavior, the tool shed will not report updates to a repository if the tool version has changed. For more details on how and why this happens, see the following wiki page: http://wiki.galaxyproject.org/RepositoryRevisions#Adding_additional_change_s... Where the behavior is detailed in these sections: Adding additional change sets to the initial change set in a repository • What is repository metadata? • What does it mean when repository metadata is associated with a change set in the repository change log? • Adding a change set that does not generate a new repository metadata record • Adding a change set that generates a new repository metadata record • More examples of installable repository change set revisions --Dave B. On 3/26/13 12:45:41.000, jorrit poelen wrote:
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://jorrit@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 +0000] "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 +0000] "GET /admin_toolshed/browse_repositories?operation=get+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/2013:01:12:51 +0000] "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 +0000] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&name=obotools&owner=jorrit&changeset_revision=bb20766df19c&latest_changeset_revision=bb20766df19c&latest_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 +0000] "GET /admin_toolshed/manage_repository?status=done&message=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/
___________________________________________________________ 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/
participants (2)
-
Dave Bouvier -
jorrit poelen