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!
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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>
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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