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_sets_to_the_initial_change_set_in_a_repository
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://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 +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"
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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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___________________________________________________________
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:
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