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ReinV / SCOPE

Search and Chemical Ontology Plotting Environment
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Connection to EuropePMC fails continuously #31

Closed magnuspalmblad closed 3 years ago

magnuspalmblad commented 3 years ago

Right now (2021-09-09, 15:30 CEST), it seems impossible to establish a connection to EuropePMC (after the initial return). Does this work for you right now?

This is what I get:

(base) C:\Users\Magnus Palmblad\Downloads\SCOPE-master>cat queries/input_queries.txt
NMR, (Metabolomics OR metabonomics) AND (METHODS:"Nuclear Magnetic Resonance" OR METHODS:NMR OR METHODS:"NMR spectrometry" OR METHODS:"nuclear magnetic resonance spectrometry" OR METHODS:"NMR spectroscopy" OR METHODS:"nuclear magnetic resonance (NMR) spectroscopy")
LCMS, (Metabolomics OR metabonomics) AND (METHODS:"LC/MS" OR METHODS:"LC-MS" OR METHODS:"LC MS" OR METHODS:"liquid chromatography mass spectrometry" OR METHODS:"liquid chromatography/mass spectrometry" OR METHODS:"LCMS")
(base) C:\Users\Magnus Palmblad\Downloads\SCOPE-master>python search_query.py -i queries/input_queries.txt
searching with: (Metabolomics OR metabonomics) AND (METHODS:"Nuclear Magnetic Resonance" OR METHODS:NMR OR METHODS:"NMR spectrometry" OR METHODS:"nuclear magnetic resonance spectrometry" OR METHODS:"NMR spectroscopy" OR METHODS:"nuclear magnetic resonance (NMR) spectroscopy")
searching publications...
total hits: 5172
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
magnuspalmblad commented 3 years ago

It seems the problem is on the server side:

(base) C:\Users\Magnus Palmblad\Downloads\SCOPE-master>cat queries/input_queries.txt
NMR, (Metabolomics OR metabonomics) AND (METHODS:"Nuclear Magnetic Resonance" OR METHODS:NMR OR METHODS:"NMR spectrometry" OR METHODS:"nuclear magnetic resonance spectrometry" OR METHODS:"NMR spectroscopy" OR METHODS:"nuclear magnetic resonance (NMR) spectroscopy")
LCMS, (Metabolomics OR metabonomics) AND (METHODS:"LC/MS" OR METHODS:"LC-MS" OR METHODS:"LC MS" OR METHODS:"liquid chromatography mass spectrometry" OR METHODS:"liquid chromatography/mass spectrometry" OR METHODS:"LCMS")
(base) C:\Users\Magnus Palmblad\Downloads\SCOPE-master>python search_query.py -i queries/input_queries.txt
searching with: (Metabolomics OR metabonomics) AND (METHODS:"Nuclear Magnetic Resonance" OR METHODS:NMR OR METHODS:"NMR spectrometry" OR METHODS:"nuclear magnetic resonance spectrometry" OR METHODS:"NMR spectroscopy" OR METHODS:"nuclear magnetic resonance (NMR) spectroscopy")
searching publications...
total hits: 5172
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
1/6 pages retrieved
connection failed
connection failed
connection failed
connection failed
2/6 pages retrieved
connection failed
connection failed
connection failed
connection failed
3/6 pages retrieved
4/6 pages retrieved
connection failed
connection failed
connection failed
connection failed
connection failed
connection failed
ReinV commented 3 years ago

When I ran the script with the query examples this morning I did not have any problems. So I think indeed it's on the server side. It's frustrating sometimes, but apart from waiting I'm not sure if there is much we can do on the script side so to say?

ReinV commented 3 years ago

I'm running the script now and got no "connection failed" statements.

searching with: (Metabolomics OR metabonomics) AND (METHODS:"Nuclear Magnetic Resonance" OR METHODS:NMR OR METHODS:"NMR spectrometry" OR METHODS:"nuclear magnetic resonance spectrometry" OR METHODS:"NMR spectroscopy" OR METHODS:"nuclear magnetic resonance (NMR) spectroscopy") searching publications... total hits: 5172 1/6 pages retrieved 2/6 pages retrieved 3/6 pages retrieved 4/6 pages retrieved 5/6 pages retrieved 6/6 pages retrieved NMR query results are written to file

magnuspalmblad commented 3 years ago

Yes, it seems to work better now, from here too.