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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
4 stars 2 forks source link

better way to handle option parsing in post routes #241

Open kevinkle opened 6 years ago

kevinkle commented 6 years ago

eg. so if an older ver of the frontend sends a post w/o the required keys, it doesnt fail. ex:

webserver_1              | [pid: 18|app: 0|req: 1/1] 192.168.5.18 () {50 vars in 789 bytes} [Sun Nov  5 16:18:13 2017] OPTIONS /api/v0/upload => generated 0 bytes in 7 msecs (HTTP/1.1 200) 6 headers in 245 bytes (0 switches on core 0)
webserver_1              | 192.168.5.18 - - [05/Nov/2017:16:18:13 +0000] "OPTIONS /api/v0/upload HTTP/1.1" 200 0 "http://192.168.5.19:8090/subtyping" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36" "-"
webserver_1              | 2017/11/05 16:18:13 [warn] 12#12: *1 a client request body is buffered to a temporary file /var/cache/nginx/client_temp/0000000001, client: 192.168.5.18, server: , request: "POST /api/v0/upload HTTP/1.1", host: "192.168.5.19:8000", referrer: "http://192.168.5.19:8090/subtyping"
webserver_1              | [<FileStorage: u'ESC_AA7854AA_AS.fasta' ('application/octet-stream')>]
webserver_1              | upload(): about to enqueue files
webserver_1              | Uploaded File Saved at /datastore/2017-11-05-16-18-17-627480-ESC_AA7854AA_AS.fasta
webserver_1              | [2017-11-05 16:18:17,663] ERROR in app: Exception on /api/v0/upload [POST]
webserver_1              | Traceback (most recent call last):
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
webserver_1              |     response = self.full_dispatch_request()
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
webserver_1              |     rv = self.handle_user_exception(e)
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask_cors/extension.py", line 161, in wrapped_function
webserver_1              |     return cors_after_request(app.make_response(f(*args, **kwargs)))
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
webserver_1              |     reraise(exc_type, exc_value, tb)
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
webserver_1              |     rv = self.dispatch_request()
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
webserver_1              |     return self.view_functions[rule.endpoint](**req.view_args)
webserver_1              |   File "./routes/ra_posts.py", line 244, in upload
webserver_1              |     {'i': filename, 'pi':options['pi'], 'options':options})
webserver_1              |   File "./modules/spfy.py", line 268, in spfy
webserver_1              |     jobs_dict = blob_savvy(args_dict)
webserver_1              |   File "./modules/spfy.py", line 255, in blob_savvy
webserver_1              |     d.update(blob_savvy_enqueue(args_dict))
webserver_1              |   File "./modules/spfy.py", line 182, in blob_savvy_enqueue
webserver_1              |     if single_dict['options']['stx1']:
webserver_1              | KeyError: 'stx1'
webserver_1              | [pid: 17|app: 0|req: 1/2] 192.168.5.18 () {52 vars in 968 bytes} [Sun Nov  5 16:18:17 2017] POST /api/v0/upload => generated 291 bytes in 81 msecs (HTTP/1.1 500) 4 headers in 153 bytes (19 switches on core 0)
webserver_1              | 192.168.5.18 - - [05/Nov/2017:16:18:17 +0000] "POST /api/v0/upload HTTP/1.1" 500 291 "http://192.168.5.19:8090/subtyping" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36" "-"