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pubmed2bibtex.py
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Thu, Jan 30, 16:22

pubmed2bibtex.py
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"""
Perform a query on PubMed, and transform it in BibTeX.
Usage: pubmed2bibtex.py <Query> <BibTeX file>
Example:
python pubmed2bibtex.py 'Gobry' gobry.bib
"""
import sys, logging
from twisted.internet import reactor
from Pyblio import Registry, Store, Adapter, init_logging
from Pyblio.External import PubMed
# Do you want some debug information?
#init_logging()
#log = logging.getLogger('pyblio')
#log.setLevel(logging.DEBUG)
query, output = sys.argv[1:]
# Create a database that is capable of storing Web of Science results.
Registry.load_default_settings()
s = Registry.getSchema('org.pybliographer/pubmed/0.1')
# Create a temporary in-memory database
fmt = Store.get('memory')
db = fmt.dbcreate(None, s)
# Initialize the connection to the database
remote = PubMed.PubMed(db)
# Perform a search. In return, we obtain the result set that will be
# filled in with the results, and a deferred that will fire once the
# query is over.
d, rs = remote.search(query, maxhits=20)
def success(total):
print "pubmed: successfully fetched %d/%d records" % (len(db.entries), total)
reactor.stop()
# We filled db with pubmed data. To save it as BibTeX, we get an
# adapter from PubMed to BibTeX
bibtex = Adapter.adapt_schema(db, 'org.pybliographer/bibtex/0.1')
# Now we have a "virtual" bibtex database, that we can actually
# save as a BibTeX file
from Pyblio.Parsers.Semantic.BibTeX import Writer
w = Writer()
w.write(open(output, 'w'), bibtex.entries, bibtex)
return
def failure(failure):
print "pubmed: sorry, the query failed"
print failure
reactor.stop()
# We register the actions to perform upon success and failure
d.addCallback(success).addErrback(failure)
# Showtime! This will exit when reactor.stop() is invoked above.
reactor.run()

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