On Mon, May 13, 2013 at 10:34 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Fri, May 10, 2013 at 8:11 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>> Hi Dave,
>> that was fast.
>> Thanks a lot!
>> Björn
> Thanks Dave,
> I see this also should fix handling of JAR files in download_by_url :)
> https://bitbucket.org/galaxy/galaxy-central/commits/b4733e42a2c98c42401bca5e0643fc4d4dcf2db6
> Could I suggest an enhancement to abort on undefined action types,
> rough patch below (untested)? This will help give a clear error if a new
> command is used but the Galaxy host is too old to implement it (which
> is exactly the situation we'd see right now on the main Tool Shed if
> the new download_file action is used).
> Regards,
> Peter

Another data point, with my old wget based tool_wrapper.xml file:

>From the test failure of the previous commit I suspected this, but this
revision checks specifically for the 'module' subdirectory and confirms
it is not being created:

Effective T3 module folder not found:

I infer the 'install script' is failing silently after setting the environment
variable but before or when creating the sub-directory $INSTALL_DIR/module,

                <!-- Set environment variable so Python script knows
where to look -->
                <action type="set_environment">
                    <environment_variable name="EFFECTIVET3"
                <!-- Main JAR file -->
                <action type="shell_command">wget
                <!-- Three model JAR files -->
                <action type="make_directory">$INSTALL_DIR/module</action>
                <action type="shell_command">wget
                <action type="shell_command">wget
                <action type="shell_command">wget

The first possible cause of failure is the set_environment action,
but from the limited information from the failing test that worked.

The second possible causes of failure is the wget call, perhaps that
command line tool isn't even installed? However, from the limited
information reported via the failing test I know the JAR file was
downloaded (and moved into place).

The third possible failure is the move_file action, and again I know
from the limited information reported via the failing test that
the TTSS_GUI-1.0.1.jar file was moved into place.

My suspicion therefore falls on the make_directory action - my
debug output from the failing test indicates the expected directory
was not created.

However, any exception within fabric_util.install_and_build_package
should be caught by install_util.install_and_build_package_via_fabric
and recorded in the tool_dependency object.

Tracing up the call tree, I found this puzzling bit in the
common_install_util.py file:


def handle_tool_dependencies( app, tool_shed_repository,
tool_dependencies_config, tool_dependencies ):
                if tool_dependency.can_install:
                        tool_dependency = install_package( app, elem,
tool_shed_repository, tool_dependencies=tool_dependencies )
                    except Exception, e:
                        error_message = "Error installing tool
dependency %s version %s: %s" % ( str( package_name ), str(
package_version ), str( e ) )
                        log.debug( error_message )
                        if tool_dependency:
                            tool_dependency.status =
                            tool_dependency.error_message = error_message
                            sa_session.add( tool_dependency )
                    if tool_dependency and tool_dependency.status in [

app.model.ToolDependency.installation_status.ERROR ]:
                        installed_tool_dependencies.append( tool_dependency )

It seems even if install_package fails, the tool_dependency is still
considered to be installed? If so, why?

This would explain the behaviour I am seeing with effectivet3 and
other tools on the Tool Shed - despite the tool_dependencies.xml
seeming to fail part way though, the tests are run anyway.

(I would instead expect the Tool Shed to tell me the install failed,
and not bother trying to run the tests, which are probably going to
fail anyway).



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