Hello Peter, Thanks for reporting this - I have committed a fix in changeset 10206:86efa5ac1fae, which is currently running on the test tool shed.
Greg Von Kuster On Jul 8, 2013, at 11:35 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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=20a9f7389ced5696 > 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 > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
