I’ve been trying to get the nxinx upload stuff working…
I think i have the nginx config is working properly (files are present in the
right spot with correct ownership and have correct content),
but I see a traceback in the log (see below).
I don’t see anything in the mail list search about this, so maybe I’ve done
something wrong...
— here’s are the relevant bits of my galaxy config file ---
# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
# Configuration for this is complex and explained in detail in the
# documentation linked above. The upload store is a temporary directory in
# which files uploaded by the upload module will be placed.
nginx_upload_store = /mnt/galaxy/data/galaxy/tmp/upload_store
# This value overrides the action set on the file upload form, e.g. the web
# path where the nginx_upload_module has been configured to intercept upload
# requests.
nginx_upload_path = /_upload
——nginx config ——
#direct file uploads
location /_upload {
upload_store /mnt/galaxy/data/galaxy/tmp/upload_store;
upload_pass_form_field "";
upload_set_form_field "__${upload_field_name}__is_composite" "true";
upload_set_form_field "__${upload_field_name}__keys" "name path";
upload_set_form_field "${upload_field_name}_name"
"$upload_file_name";
upload_set_form_field "${upload_field_name}_path"
"$upload_tmp_path";
upload_pass_args on;
upload_pass /_upload_done;
}
location /_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
Any ideas?
Brad
File
'/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 92 in __call__
return self.app( environ, start_response )
File
'/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 84 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line
1869 in handle_input
self.update_state( trans, self.inputs_by_page[state.page], state.inputs,
incoming, old_errors=old_errors or {}, source=source )
File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line
2263 in update_state
current_case = input.get_current_case( value, trans )
File
'/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py',
line 462 in get_current_case
raise Exception( "No case matched value:", self.name, str_value )
Exception: ('No case matched value:', 'files_metadata', None)
CGI Variables
-------------
CONTENT_LENGTH: '-1'
CONTENT_TYPE: 'multipart/form-data;
boundary=----WebKitFormBoundaryfTsa16a7MJyYSF0i'
HTTP_ACCEPT: 'application/json'
HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8'
HTTP_AUTHORIZATION: 'Basic bGFuZ2hvcnN0Om1pZWRoaWRsc2hhZmRv'
HTTP_CACHE_CONTROL: 'no-cache'
HTTP_CONNECTION: 'close'
HTTP_COOKIE:
'galaxysession=dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be;
__utma=171448127.504006193.1380078797.1392
167382.1394500277.13; __utmc=171448127;
__utmz=171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/'
HTTP_DNT: '1'
HTTP_HOST: 'galaxy.neb.com<http://galaxy.neb.com>'
HTTP_ORIGIN: 'http://galaxy.neb.com'
HTTP_REFERER: 'http://galaxy.neb.com/'
HTTP_REMOTE_USER: 'langho...@neb.com<mailto:langho...@neb.com>'
HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.117 Safari/537.36'
HTTP_X_FORWARDED_FOR: '172.17.1.252'
HTTP_X_FORWARDED_HOST: 'galaxy.neb.com<http://galaxy.neb.com>'
HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
ORGINAL_HTTP_HOST: 'galaxy_app'
ORGINAL_REMOTE_ADDR: '127.0.0.1'
PATH_INFO: '/tool_runner/index'
REMOTE_ADDR: '172.17.1.252'
REQUEST_METHOD: 'POST'
SERVER_NAME: '127.0.0.1'
SERVER_PORT: '8080'
SERVER_PROTOCOL: 'HTTP/1.0'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x98d8cd0>
is_api_request: False
paste.cookies: (<SimpleCookie:
__utma='171448127.504006193.1380078797.1392167382.1394500277.13'
__utmc='171448127'
__utmz='171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/'
galaxysession='dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be'>,
'galaxysession=dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be;
__utma=171448127.504006193.1380078797.1392167382.1394500277.13;
__utmc=171448127;
__utmz=171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
0x98d8ad0>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0x9c3ed50>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: '6193e9a2a9db11e388e10050568436c1'
webob._parsed_post_vars: (MultiDict([('history_id', '792704c2cfd232ef'),
('tool_id', 'upload1'), ('inputs',
'{"dbkey":"?","file_type":"auto","files_0|type":"upload_dataset","files_0|url_paste":"","space_to_tabs":false}'),
('__files_0|file_data__is_composite', 'true'), ('__files_0|file_data__keys',
'name path'), ('files_0|file_data_name', 'seq_elements2.txt'),
('files_0|file_data_path',
'/mnt/galaxy/data/galaxy/tmp/upload_store/0000000004')]), <FakeCGIBody at
7f4f001a8c90 viewing MultiDict([('hi...4')])>)
webob._parsed_query_vars: (MultiDict([]), '')
wsgi process: 'Multithreaded'
------------------------------------------------------------
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist
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