ToolShed dependencies KeyError: 'invalid_repository_dependencies'

8 Jul 2013

      Hi Greg,

Previously my workflows had hard coded dependencies on the main
Tool Shed, which currently is a bit of a problem on the Test Tool Shed.

Therefore I'm update my Tool Shed workflows using a
repository_dependencies.xml with implicit repository and revision fields
(i.e. the latest revision within the current ToolShed).

It worked for one example but not the other - this turned out to be my
own error, but the Tool Shed did not handle it gracefully. Perhaps
this class of error could be caught instead? Thanks!

----------------------------------------------------------------

This worked, secreted_protein_workflow, Revision: 2:aecb871dfe4c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow

Input:

<?xml version="1.0"?>
<repositories description="This requires my SignalP and TMHMM wrapers,
and my FASTA filtering tool.">
    <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the
current latest - but older should be OK -->
    <repository name="tmhmm_and_signalp" owner="peterjc" />
    <!-- Revision 2:abdd608c869b on the main tool shed is v0.0.5, the
current latest - but older should be OK -->
    <repository name="seq_filter_by_id" owner="peterjc" />
</repositories>

----------------------------------------------------------------

This failed, rxlr_venn_workflow, Revision: 3:65d174589251
http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow

On uploading the tar-ball I got this error in the browser:

<quote>
Internal Server Error
Galaxy was unable to sucessfully complete your request

URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=20a9f7389ced56...
Module galaxy.web.framework.middleware.error:149 in __call__
...
...
app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
 environ, self.app)
Module paste.wsgilib:543 in intercept_output
 app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
 return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
 return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
 return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
 body = method( trans, **kwargs )
Module galaxy.web.framework:98 in decorator
 return func( self, trans, *args, **kwargs )
Module galaxy.webapps.tool_shed.controllers.upload:219 in upload
 invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict )
Module tool_shed.util.repository_dependency_util:252 in
generate_message_for_invalid_repository_dependencies
 invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'invalid_repository_dependencies' ]
KeyError: 'invalid_repository_dependencies'
extra data
full traceback

text version

This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
</quote>

Input repository_dependencies.xml where for the tmhmm_and_signalp entry
I am missing the 'n' in name:

<?xml version="1.0"?>
<repositories description="This requires my SignalP and TMHMM wrapers,
and my FASTA filtering tool.">
    <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the
current latest - but older should be OK -->
    <repository ame="tmhmm_and_signalp" owner="peterjc" />
    <!-- Revision 2:abdd608c869b on the main tool shed is v0.0.5, the
current latest - but older should be OK -->
    <repository name="seq_filter_by_id" owner="peterjc" />
    <!-- Revisiion 2:c96bef0643dc on the main tool shed is v0.0.3, the
current latest -->
    <repository name="venn_list" owner="peterjc" />
</repositories>

Output repository_dependencies.xml with mangled tmhmm_and_signalp entry:

<?xml version="1.0"?>
<repositories description="This requires my SignalP and TMHMM wrapers,
and my FASTA filtering tool.">
    <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the
current latest - but older should be OK -->
    <repository ame="tmhmm_and_signalp" owner="peterjc"
toolshed="http://testtoolshed.g2.bx.psu.edu" />
    <!-- Revision 2:abdd608c869b on the main tool shed is v0.0.5, the
current latest - but older should be OK -->
    <repository changeset_revision="66d1ca92fb38"
name="seq_filter_by_id" owner="peterjc"
toolshed="http://testtoolshed.g2.bx.psu.edu" />
    <!-- Revisiion 2:c96bef0643dc on the main tool shed is v0.0.3, the
current latest -->
    <repository changeset_revision="51fe47a5a803" name="venn_list"
owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
</repositories>

I corrected the ame/name error, and re-uploaded a fresh tar-ball which worked,
Revision: 4:25e0ffd4f762

Peter

Peter Cock

Greg Von Kuster

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