benchmark_patients.json not found

[northwestwitch]

Hi! I'm trying to set up a mme server for my institution and this reference-server looks like a good starting point! While following the instructions I get stuck at the command mme-server quickstart

where I get this error message:

INFO:mme_server.cli:Downloading file from: https://raw.githubusercontent.com/ga4gh/mme-apis/hotfix/v1.0b/testing/benchmark_patients.json Traceback (most recent call last): File "/Users/chiararasi/miniconda3/envs/py36/bin/mme-server", line 11, in load_entry_point('mme-server', 'console_scripts', 'mme-server')() File "/Users/chiararasi/Documents/work/GITs/reference-server/mme_server/cli.py", line 221, in main function(*kwargs) File "/Users/chiararasi/Documents/work/GITs/reference-server/mme_server/cli.py", line 53, in quickstart index_file('patients', data_filename, data_url) File "/Users/chiararasi/Documents/work/GITs/reference-server/mme_server/cli.py", line 57, in index_file fetch_resource(filename, url) File "/Users/chiararasi/Documents/work/GITs/reference-server/mme_server/cli.py", line 76, in fetch_resource urlretrieve(url, filename) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 248, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 223, in urlopen return opener.open(url, data, timeout) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 532, in open response = meth(req, response) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 642, in http_response 'http', request, response, code, msg, hdrs) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 570, in error return self._call_chain(args) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(*args) File "/Users/chiararasi/miniconda3/envs/py36/lib/python3.6/urllib/request.py", line 650, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found

Could it be that benchmark_patients.json was removed or renamed?

Thanks in advance! Chiara

[northwestwitch]

If you modify the cli to download the patient data from "https://raw.githubusercontent.com/ga4gh/mme-apis/master/testing/benchmark_patients.json" it works!

[northwestwitch]

Another update: if you use the above benchmark_patients.json file, one of the tests fail. Specifically there is an assertion error in test_fuzzy_search occurring with the code: self.assertEqual(hits[0]['_id'], 'P0001059')

Full error message: `` Traceback (most recent call last): File "/Users/chiararasi/Documents/work/GITs/reference-server/mme_server/tests/test_app.py", line 133, in test_fuzzy_search self.assertEqual(hits[0]['_id'], 'P0001059') AssertionError: 'P0001058' != 'P0001059'

• P0001058 ? ^
• P0001059 ? ^ ``

[Relequestual]

This may be due to not using a specific version of HPO for the tests. Unfortunatly, I don't know if this reference server is maintained or not. Will wait to hear back from @buske

[buske]

Hi @northwestwitch, thank you so much for the feedback and sorry for this issues you've run into. Yes, it looks like this source file has moved, but the one you're using might be a slightly different version. I'll take a look and update the tests and file url accordingly. Thanks for pointing this out!

[northwestwitch]

You're welcome! :)

[buske]

Fixed by #11