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vloux / ProteoRE

GNU General Public License v3.0
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Feedback session Grenoble : extract workflow doesn't work when an history has a special character in its name #195

Open vloux opened 5 years ago

vloux commented 5 years ago

To reproduce : Put an "é" or "è" in tyhe anme of a dataset, extract the workflow. Try to edit the workflow -> error ("Loading workflow failed")

`193.49.216.158 - - [08/Feb/2019:09:36:46 +0200] "GET /api/webhooks HTTP/1.1" 200 - "http://www.proteore.org/workflow/editor?id=bf0806da5b28c6d9" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_3) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/12.0.3 Safari/605.1.15" Error - <type 'exceptions.UnicodeEncodeError'>: 'ascii' codec can't encode character u'\xe9' in position 16: ordinal not in range(128) URL: http://www.proteore.org/workflow/load_workflow?id=bf0806da5b28c6d9&_=1549615005764 File '/home/proteore/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in call app_iter = self.application(environ, sr_checker) File '/home/proteore/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in call return self.application(environ, start_response) File '/home/proteore/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in call return self.application(environ, start_response) File '/home/proteore/galaxy/lib/galaxy/web/framework/base.py', line 143 in call return self.handle_request(environ, start_response) File '/home/proteore/galaxy/lib/galaxy/web/framework/base.py', line 222 in handle_request body = method(trans, *kwargs) File '/home/proteore/galaxy/lib/galaxy/web/framework/decorators.py', line 57 in call_and_format rval = func(self, trans, args, **kwargs) File '/home/proteore/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 676 in load_workflow return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor", version=version) File '/home/proteore/galaxy/lib/galaxy/managers/workflows.py', line 386 in workflow_to_dict wf_dict = self._workflow_to_dict_editor(trans, stored, workflow) File '/home/proteore/galaxy/lib/galaxy/managers/workflows.py', line 501 in _workflow_to_dict_editor self.__set_default_label(step, module, step.tool_inputs) File '/home/proteore/galaxy/lib/galaxy/managers/workflows.py', line 1014 in __set_default_label if str(default_label).lower() not in ['input dataset', 'input dataset collection']: UnicodeEncodeError: 'ascii' codec can't encode character u'\xe9' in position 16: ordinal not in range(128)

CGI Variables

CONTENT_LENGTH: '0' HTTP_ACCEPT: 'application/json, text/javascript, /; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'fr-fr' HTTP_CONNECTION: 'close' HTTP_COOKIE: '_ga=GA1.2.801910372.1525422310; _gat_gtag_UA_88179_2=1; _gid=GA1.2.1327099447.1549465398; galaxysession=c6ca0ddb55be603a7f1cc6280a362cf4d7d4af614c36239ad8bea1f53a572fa80b531babd619fcc9' HTTP_DNT: '1' HTTP_HOST: 'www.proteore.org' HTTP_REFERER: 'http://www.proteore.org/workflow/editor?id=bf0806da5b28c6d9' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_3) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/12.0.3 Safari/605.1.15' HTTP_X_FORWARDED_FOR: '193.49.216.158' HTTP_X_FORWARDED_HOST: 'www.proteore.org' HTTP_X_FORWARDED_SERVER: '138.102.144.54' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' ORGINAL_HTTP_HOST: '138.102.144.54:8080' ORGINAL_REMOTE_ADDR: '138.102.144.54' PATH_INFO: '/workflow/load_workflow' QUERYSTRING: 'id=bf0806da5b28c6d9&=1549615005764' REMOTE_ADDR: '193.49.216.158' REQUEST_METHOD: 'GET' SERVER_NAME: '138.102.144.54' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1'

WSGI Variables

application: <paste.recursive.RecursiveMiddleware object at 0xe0e4e10> controller_action_key: u'web.workflow.load_workflow' is_api_request: False paste.cookies: (, '_ga=GA1.2.801910372.1525422310; _gat_gtag_UA_88179_2=1; _gid=GA1.2.1327099447.1549465398; galaxysession=c6ca0ddb55be603a7f1cc6280a362cf4d7d4af614c36239ad8bea1f53a572fa80b531babd619fcc9') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xe0da910> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xe20fc50> paste.parsedquerystring: ([('id', 'bf0806da5b28c6d9'), ('', '1549615005764')], 'id=bf0806da5b28c6d9&_=1549615005764') paste.recursive.forward: paste.recursive.include: paste.recursive.include_app_iter: paste.recursive.script_name: '' paste.throw_errors: True request_id: 'ab4737702b7c11e99aedea1fc2ab5f0c' webob._parsed_queryvars: (GET([(u'id', u'bf0806da5b28c6d9'), (u'', u'1549615005764')]), 'id=bf0806da5b28c6d9&_=1549615005764') wsgi process: 'Multithreaded' ------------------------------------------------------------`

vloux commented 5 years ago

TODO : open an issue in galaxyProject

vloux commented 5 years ago

https://github.com/galaxyproject/galaxy/issues/7421