def setUp(self):
pubmed.connect('MYTOOl', '*****@*****.**')
self.term = "science[journal] AND breast cancer AND 2008[pdat]"
self.results_list = [
'19008416', '18927361', '18787170', '18487186', '18239126',
'18239125'
]
def setUp(self):
pubmed.connect('MYTOOl', '*****@*****.**')
self.ids = [
'19008416', '18927361', '18787170', '18487186', '18239126',
'18239125'
]
def test_connection(self):
pubmed.connect('MYTOOl', '*****@*****.**')
assert pubmed.settings.tool == 'MYTOOl'
assert pubmed.settings.email == '*****@*****.**'
#!/usr/bin/env python
'''
This script performs a PubMed search and returns a list of article IDs.
'''
from litter_getter import pubmed
pubmed.connect("PUBMED", '*****@*****.**')
#search_term = """science[journal] AND sorghum AND 2018[pdat]"""
search_term = """science[journal] AND breast cancer AND 2008[pdat]"""
search = pubmed.PubMedSearch(term=search_term)
search.get_ids_count()
print("ID count: {0}".format(search.id_count))
id_list = search.get_ids()
print("IDs: {0}".format(id_list))
def ready(self):
from . import signals # noqa
from litter_getter import pubmed
pubmed.connect(settings.PUBMED_TOOL, settings.PUBMED_EMAIL)
from litter_getter import pubmed
# import xml.dom.minidom
import xml.etree.ElementTree as ET
# register with user account
pubmed.connect('4310661ddba8abf80e4be5c7c0850ae71d09')
def getMetaData(papersToFind):
ids = []
for paper in papersToFind:
ids.append(paper.s.pubmed_id)
fetch = pubmed.PubMedFetch(id_list=ids)
refs = fetch.get_content()
for num, id in enumerate(refs):
papersToFind[num].s.abstract = refs[num]['abstract']
papersToFind[num].s.paper_authors = ', '.join(refs[num]['authors'])
papersToFind[num].s.title = refs[num]['title']
papersToFind[
num].s.source_url = "https://www.ncbi.nlm.nih.gov/pubmed/" + papersToFind[
num].s.pubmed_id
papersToFind[num].s.doi = refs[num]['doi']
papersToFind[num].s.abstract = refs[num]['abstract']
root = ET.fromstring(refs[num]["xml"])
if root[0].find('Article'):
if root[0].find('Article').find('Journal'):
papersToFind[num].s.journal = root[0].find('Article').find(
def ready(self):
from . import signals # noqa
from litter_getter import pubmed
if settings.PUBMED_API_KEY:
pubmed.connect(settings.PUBMED_API_KEY)