Wiki Addition: Site Map and Site Index
Everyone, Bitbucket (our code and wiki host) does not offer any way to search the wiki, so there are now two new pages to fill the void: SiteMap and SiteIndex. These are both generated automatically. The idea is that the pages should be generated by a script that is scheduled to run each night, but I'm still getting that going--in the meantime, I'll be running the script manually. SiteMap is a simple listing of all the pages found under the base wiki directory. You can get a pretty good idea what the page is about just by the name of it, which is all that's included in this list. You can see SiteMap at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap. SiteIndex is more complicated. It is a traditional index, which means that (almost) every word that appears in the wiki is included with a list of the pages on which it appears following it. A stoplist was used to remove useless or meaningless words, but there is still some junk that has made it past this filter. The index involves multiple pages, divided up alphabetically. It's available at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteIndex . Regards, Kelly
Hi, I have a large number of files in a Galaxy library that are stored externally using the upload from file path and setting copy to galaxy to no. A few times it has been necessary to rename or remove these files. I find that if the file was associated with a Galaxy history then that history is no longer accessible and produces a server error. I realise the best option is to keep copies of these files so that Galaxy histories remain consistent. However, it might be more user friendly if the particular history dataset displayed an appropriate error message and the rest of the history was still accessible. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
SHAUN WEBB wrote:
Hi, I have a large number of files in a Galaxy library that are stored externally using the upload from file path and setting copy to galaxy to no.
A few times it has been necessary to rename or remove these files. I find that if the file was associated with a Galaxy history then that history is no longer accessible and produces a server error. I realise the best option is to keep copies of these files so that Galaxy histories remain consistent. However, it might be more user friendly if the particular history dataset displayed an appropriate error message and the rest of the history was still accessible.
Thanks Shaun Webb
Hi Shaun, This is not intentional. The history should still display, and the only noticeable difference is that the 'eye' and file save links would result in an error. Could you provide the error that's generated when this history display problem happens? Thanks, --nate
Thanks Nate, I have pasted the full traceback below. Shaun -------- URL: http://bifx3.bio.ed.ac.uk:8080/history Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred >> environ, self.app) Module paste.wsgilib:539 in intercept_output << data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ << environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ << []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> return self.application(environ, start_response) Module galaxy.web.framework.base:134 in __call__ << if callable( body ): # Assume the callable is another WSGI application to run return body( environ, start_response ) elif isinstance( body, types.FileType ): # Stream the file back to the browser >> return body( environ, start_response ) Module galaxy.web.framework:630 in render << buffer = StreamBuffer() context = mako.runtime.Context( buffer, **data ) template.render_context( context ) return [] return render>> template.render_context( context ) Module mako.template:146 in render_context << if getattr(context, '_with_template', None) is None: context._with_template = self runtime._render_context(self, self.callable_, context, *args, **kwargs) def has_def(self, name):>> runtime._render_context(self, self.callable_, context, *args, **kwargs) Module mako.runtime:381 in _render_context << # if main render method, call from the base of the inheritance stack (inherit, lclcontext) = _populate_self_namespace(context, tmpl) _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) else: # otherwise, call the actual rendering method specified>> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:414 in _exec_template << error_template.render_context(context, error=error) else: callable_(context, *args, **kwargs)>> callable_(context, *args, **kwargs) Module root_history_mako:203 in render_body << __M_writer(u'">\n ') # SOURCE LINE 458 __M_writer(unicode(render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = True ))) __M_writer(u'\n </div>\n') # SOURCE LINE 462 >> __M_writer(unicode(render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = True ))) Module mako.runtime:255 in <lambda> << if self.template and self.template.has_def(key): callable_ = self.template._get_def_callable(key) return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) if self._module and hasattr(self._module, key):>> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) Module root_history_common_mako:259 in render_render_dataset << # SOURCE LINE 112 __M_writer(u' ') target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) __M_writer(u'\n')>> target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) ValueError: need more than 0 values to unpack Quoting Nate Coraor <nate@bx.psu.edu>:
SHAUN WEBB wrote:
Hi, I have a large number of files in a Galaxy library that are stored externally using the upload from file path and setting copy to galaxy to no.
A few times it has been necessary to rename or remove these files. I find that if the file was associated with a Galaxy history then that history is no longer accessible and produces a server error. I realise the best option is to keep copies of these files so that Galaxy histories remain consistent. However, it might be more user friendly if the particular history dataset displayed an appropriate error message and the rest of the history was still accessible.
Thanks Shaun Webb
Hi Shaun,
This is not intentional. The history should still display, and the only noticeable difference is that the 'eye' and file save links would result in an error. Could you provide the error that's generated when this history display problem happens?
Thanks, --nate
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
participants (3)
-
Kelly Vincent -
Nate Coraor -
SHAUN WEBB