The journalbot from happykhan

journalbot's People

Contributors

Watchers

journalbot's Issues

More specific Author searching

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.

Better Exception handling.,

All API calls throw exceptions when unsuccessful. Currently exceptions are thrown and halts all threads. This is not good.

Need Comments

No real comments in source. need to update

Entrez issue

>>> 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'

Recommend Projects