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View Code? Open in Web Editor NEWSource code for Journal club bot at https://twitter.com/JC_pathogenomic
License: GNU General Public License v3.0
Source code for Journal club bot at https://twitter.com/JC_pathogenomic
License: GNU General Public License v3.0
Papers are retrieved from pubmed. Currently based on Last name & initials. This is problematic for generic names, e.g. Smith A. Need to add more specific search parameters via Topic or maybe affiliation.
All API calls throw exceptions when unsuccessful. Currently exceptions are thrown and halts all threads. This is not good.
No real comments in source. need to update
>>> handle = Entrez.esearch(db="pubmed", term="Alikhan NF", field="author", retmode="xml", retmax=10)
>>> record = Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ubuntu/anaconda2/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 376, in read
record = handler.read(handle)
File "/home/ubuntu/anaconda2/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 205, in read
self.parser.ParseFile(handle)
File "/home/ubuntu/anaconda2/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 513, in externalEntityRefHandler
self.dtd_urls.append(url)
UnboundLocalError: local variable 'url' referenced before assignment
Might be the cause of the bot failing now? Not sure why the url
variable is listed as absent because handle.url
returns:
>>> handle.url
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?term=Alikhan+NF&retmax=10&retmode=xml&tool=biopython&db=pubmed&field=author&email=gibsongroupbot%40gmail.com'
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