Hi Folks,

I've done a bit more work on this problem that I posted about on Friday.
 I'm working on streamlining the installation of two tools, one of which
has a complex repository dependency on the other.  FWIW, both tools are in
the test tool shed, under visualization: xena_import has a complex
repository dependency on start_xena.

I know that it should not be necessary to specify the toolshed and
changeset revision in tool_dependencies.xml when indicating the complex
repository dependency.  But here is what I observed.  When I specified the
changeset_revision and toolshed, the installation worked fine.  When I
removed the changeset_revision tag and reinstalled the tool, I experienced
the bug detailed below, where a Google Chrome pop-up window told me that
the repository installation failed, and after I clicked OK on the pop-up
window, Galaxy seemed to go into an infinite state of indicating that the
tool was "Cloning" and showing the same repeated POST commands in
paster.log.  When I put the changeset_revision tag back again, the tool
installation worked just fine.

Just to make sure that this wasn't all from some cruft hiding somewhere in
my Galaxy installation, I started with a clean install today (including an
'hg update stable') and a clean shed_tools subdirectory.

I hope this helps.  In the meantime, thanks, everyone for all of your help!

Melissa


On Fri, Sep 12, 2014 at 12:02 PM, Melissa Cline <cl...@soe.ucsc.edu> wrote:

> Thanks, folks!  Everything you've said has clarified many things, and I'm
> working on putting them into practice.  But in the meantime, I've got a new
> error condition, with the same repositories (and complex repository
> dependencies), and could use some guidance.
>
> I started to see this error condition when I removed the toolshed and
> changeset_revision tags in the tool_dependencies.xml for the dependent
> repository xena_install.  It now reads:
>
> <?xml version="1.0"?>
>
> <tool_dependency>
>
>   <package name="installXena" version="1.0">
>
>     <repository name="start_xena" owner="melissacline"/>
>
>   </package>
>
> </tool_dependency>
>
> Short and simple.  But lately, when I try to install this repository from
> the test toolshed, I get a pop-up window from Chrome (my web browser) that
> says "The page at 127.0.0.1:8080 says:", "Initializing repository
> installation failed", with an OK button.  There is no error message visible
> in paster.log.  Here is what I do see:
>
> 127.0.0.1 - - [12/Sep/2014:11:45:57 -0700] "GET
> /admin_toolshed/prepare_for_ins\
>
> tall?tool_shed_url=
> https://testtoolshed.g2.bx.psu.edu/&repository_ids=4ab1d3705\
>
> ad0de2d&changeset_revisions=fe95cf1ae864 HTTP/1.1" 200 - "-" "Mozilla/5.0
> (Maci\
>
> ntosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/37.\
>
> 0.2062.94 Safari/537.36"
>
> tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
> \
>
> DEBUG 2014-09-12 11:46:05,937 Creating repository dependency objects...
>
> tool_shed.util.shed_util_common DEBUG 2014-09-12 11:46:07,214 Updating an
> exist\
>
> ing row for repository 'xena_import' in the tool_shed_repository table,
> status \
>
> set to 'New'.
>
> tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
> \
>
> DEBUG 2014-09-12 11:46:07,241 Skipping installation of revision
> 75c7d80df9c1 of\
>
>  repository 'start_xena' because it was installed with the (possibly
> updated) r\
>
> evision 75c7d80df9c1 and its current installation status is 'Installed'.
>
> tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
> \
>
> DEBUG 2014-09-12 11:46:07,241 Building repository dependency
> relationships...
>
> 127.0.0.1 - - [12/Sep/2014:11:46:05 -0700] "POST
> /admin_toolshed/prepare_for_in\
>
> stall HTTP/1.1" 200 - "
> http://127.0.0.1:8080/admin_toolshed/prepare_for_install\
>
> ?tool_shed_url=
> https://testtoolshed.g2.bx.psu.edu/&repository_ids=4ab1d3705ad0d\
>
> e2d&changeset_revisions=fe95cf1ae864" "Mozilla/5.0 (Macintosh; Intel Mac
> OS X 1\
>
> 0_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94
> Safari/537.36\
>
> "
>
> warning: testtoolshed.g2.bx.psu.edu certificate with fingerprint
> 79:94:82:1f:74\
>
> :e6:f8:5c:1c:b8:3e:8d:89:f0:0e:88:9a:ac:2b:61 not verified (check
> hostfingerpri\
>
> nts or web.cacerts config setting)
>
> 127.0.0.1 - - [12/Sep/2014:11:46:07 -0700] "POST
> /admin_toolshed/manage_reposit\
>
> ories HTTP/1.1" 500 - "
> http://127.0.0.1:8080/admin_toolshed/prepare_for_install\
>
> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36
> (KHTML, li\
>
> ke Gecko) Chrome/37.0.2062.94 Safari/537.36"
>
> Debug at: http://127.0.0.1:8080/_debug/view/1410547505
>
>
> Then when I click OK, the status of the tool changes to "Cloning", and
> stays in that state indefinitely while paster.log keeps logging a repeat of
> this message:
>
> 127.0.0.1 - - [12/Sep/2014:11:55:28 -0700] "POST
> /admin_toolshed/repository_ins\
>
> tallation_status_updates HTTP/1.1" 200 - "
> http://127.0.0.1:8080/admin_toolshed/\
>
> prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4)
> AppleWebKi\
>
> t/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94 Safari/537.36"
>
> Just in case this is from some cruft from a previous installation, I tried
> starting over with a brand new galaxy-dist directory.  It doesn't look like
> that changed anything.
>
>
> Any ideas?  Many thanks in advance!
>
>
> Melissa
>
>
>
>
>
> On Fri, Sep 12, 2014 at 10:30 AM, Dave Bouvier <d...@bx.psu.edu> wrote:
>
>> Melissa,
>>
>> The revision recorded in the filesystem path can seem odd at first
>> glance. My inline responses should hopefully clarify that.
>>
>>    --Dave B.
>>
>> On 09/10/2014 05:49 PM, Melissa Cline wrote:
>>
>>> Hi Folks,
>>>
>>> Okay, I really need debugging ideas on this one.
>>>
>>> I have three repositories I'm developing under the test toolshed.
>>>   They're named start_xena, xena_import and xena_find_datasets (they're
>>> all under visualization).  start_xena contains a simple tool dependency
>>> to a package named installXena.  xena_import and xena_find_datasets
>>> contain complex dependencies to installXena.  I've installed these tools
>>> on two computers.  On one, everything works great - amazingly well, in
>>> fact!  Kudos, Development Team!  On the other computer, the env.sh files
>>> associated with the complex dependencies keep referencing the wrong
>>> version of start_xena/installXena.
>>>
>>> Here are the gory details.
>>>
>>> The start_xena tool is installed in
>>> testtoolshed.g2.bx.psu.edu/repos/melissacline/start_xena/
>>> 82755b0ee5a5/start_xena
>>> <http://testtoolshed.g2.bx.psu.edu/repos/melissacline/
>>> start_xena/82755b0ee5a5/start_xena>.
>>>   I'm a bit confused about the revision part of the path, because the
>>> latest revision is different (75c7d80df9c1), and I have uninstalled and
>>> re-installed the tool since its last update.  Its package, installXena,
>>> is installed under tool_dependencies at
>>> tool_dependencies/installXena/1.0/melissacline/start_xena/82755b0ee5a5/.
>>>   That directory contains all the files I'd expect to be there, and its
>>> env.sh file contains all the environment variables I'd intended to set.
>>>    So far, so good.
>>>
>>> xena_import is installed on my computer at
>>> testtoolshed.g2.bx.psu.edu/repos/melissacline/xena_
>>> import/dc42b6bbc22b/xena_import
>>> <http://testtoolshed.g2.bx.psu.edu/repos/melissacline/
>>> xena_import/dc42b6bbc22b/xena_import>.
>>>   Its tool_dependencies.xml reference installXena under start_xena as:
>>>
>>> <?xml version="1.0"?>
>>>
>>> <tool_dependency>
>>>
>>>    <package name="installXena" version="1.0">
>>>
>>>      <repository toolshed="http://testtoolshed.g2.bx.psu.edu";
>>> name="start_xena" owner="melissacline" changeset_revision="
>>> 82755b0ee5a5"/>
>>>
>>>    </package>
>>>
>>> </tool_dependency>
>>>
>>> (Aside: is it necessary to have the changeset_revision in there?  I'm a
>>> bit worried about the maintenance task of updating it for all of my
>>> dependent tools every time I update start_xena, but as I'll explain,
>>> it's not clear that this revision info is getting used).
>>>
>>
>> It is not necessary to populate the changeset_revision or toolshed
>> attributes. If you omit them, they will be automatically filled in based on
>> the most recent matching repository.
>>
>>
>>> The tool dependency dir for xena_import is at
>>> tool_dependencies/installXena/1.0/melissacline/xena_import/dc42b6bbc22b/.
>>> Its
>>> env.sh reads:
>>>
>>> if [ -f
>>> /Users/melissacline/src/galaxy-dist/tool_dependencies/
>>> installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
>>> ] ; then .
>>> /Users/melissacline/src/galaxy-dist/tool_dependencies/
>>> installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
>>> ; fi
>>>
>>> Notice that the wrong revision number is in there.  The 06 revision was
>>> an older one.  Needless to say, the files and environment variables I
>>> need aren't in the 06 directory.
>>>
>>> Where does this incorrect revision number come from?  I've deleted all
>>> the 06 directories, repeatedly.  I've deleted and reinstalled the tools,
>>> and verified that after deletion, the directories in question were in
>>> fact gone.  I've tried resetting the metadata for these tools under the
>>> Galaxy Admin menu.  Now I need new ideas.  As I mentioned, all of this
>>> works beautifully on a second computer.  It's as if the first Galaxy
>>> installation, on the first computer, got stuck with some outdated
>>> information, and I haven't figured out how to clear it out.
>>>
>>
>> The 0676 revision number is based on the revision that was first
>> installed, and should never change. When you update the repository, the
>> database will record the new revision in a separate field, but the original
>> revision id needs to be recorded in order to find the env.sh file on the
>> filesystem.
>>
>>
>>
>>> Thanks!
>>>
>>> Melissa
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
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>>>
>
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