Hi Greg, We have now pulled the lastest revision 8359:c08a5d0d2a4f but the problem persists. The stack trace remains the same... Any ideas on what could be happening? Ideally we would like to be able to fix the problem through the galaxy interface, but in case we find no solution, do galaxy devs have some repo for MySQL scripts to ³clean² the DB?? (ex. Complete delete of a toolshed tool)..
Thanks, On 5/12/12 9:10 PM, "Greg Von Kuster" <g...@bx.psu.edu> wrote: > If you have not yet updated your Galaxy instance to the revision from the > galaxy-dist repository in bitbucket, then that is most likely the cause of the > behavior you are seeing. > > Greg Von Kuster > > On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote: > >> Re-installing error persists >> >> >> Hi Greg, >> >> I have now modified the tool_dependencies.xml thank you for that.. >> >> I still have problems re-installing the tool... (need to reinstall to update >> the tool dependency and test it correctly) >> >> Is the reinstalling failure related to my galaxy version?? >> >> Here is the error: >> Server Error >> URL: >> http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or >> +reinstall&id=88ee2d7021e4dc1a >> Module paste.exceptions.errormiddleware:143 in __call__ >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter = self.application(environ, >>>> start_response) >> Module paste.debug.prints:98 in __call__ >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) >> Module paste.wsgilib:539 in intercept_output >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter = application(environ, >>>> replacement_start_response) >> Module paste.recursive:80 in __call__ >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, >>>> start_response) >> Module paste.httpexceptions:632 in __call__ >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, >>>> start_response) >> Module galaxy.web.framework.base:160 in __call__ >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) >> Module galaxy.web.framework:184 in decorator >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, >>>> **kwargs ) >> Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return >>>> self.reselect_tool_panel_section( trans, **kwd ) >> Module galaxy.web.framework:184 in decorator >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, >>>> **kwargs ) >> Module galaxy.web.controllers.admin_toolshed:1352 in >> reselect_tool_panel_section >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> status=status ) >> Module galaxy.web.framework:746 in fill_template >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return self.fill_template_mako( >>>> filename, **kwargs ) >> Module galaxy.web.framework:757 in fill_template_mako >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) >> Module mako.template:296 in render >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> return runtime._render(self, >>>> self.callable_, args, data) >> Module mako.runtime:660 in _render >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> **_kwargs_for_callable(callable_, >>>> data)) >> Module mako.runtime:692 in _render_context >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> _exec_template(inherit, lclcontext, >>>> args=args, kwargs=kwargs) >> Module mako.runtime:718 in _exec_template >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) >> Module _base_mako:42 in render_body >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> __M_writer(unicode(next.body())) >> Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in >> render_body >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> >>>> __M_writer(unicode(render_tool_dependency_section( >>>> install_tool_dependencies_check_box, [ repo_info_dict ] ))) >> Module _admin_tool_shed_repository_common_mako:204 in >> render_render_tool_dependency_section >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) >> Module posixpath:67 in join >>>> >> >>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ >>>> ate+or+reinstall&id=88ee2d7021e4dc1a#> elif path == '' or >>>> path.endswith('/'): >> AttributeError: 'NoneType' object has no attribute 'endswith' >> >> Thanks, >> >> Franco >> >> >> This email (including any attachments or links) may contain confidential >> and/or legally privileged information and is intended only to be read or used >> by the addressee. If you are not the intended addressee, any use, >> distribution, disclosure or copying of this email is strictly prohibited. >> Confidentiality and legal privilege attached to this email (including any >> attachments) are not waived or lost by reason of its mistaken delivery to >> you. If you have received this email in error, please delete it and notify us >> immediately by telephone or email. Peter MacCallum Cancer Centre provides no >> guarantee that this transmission is free of virus or that it has not been >> intercepted or altered and will not be liable for any delay in its receipt. > > This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
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