def import_stuff(file_list):
for filename in file_list:
article_doc = pq(filename=filename)
try:
article_tag = article_doc('article')
article_type = article_tag.attr('article-type')
if article_type != DESIRED_ARTICLE_TYPE:
logging.debug("Skipping article of type %s" % article_type)
continue
(pmid, pmc) = pubmed_ids(article_doc)
logging.info("Processing article %d / %d" % (pmc, pmid))
save_article_to_neo4j(article_doc)
except Exception as e:
# When in doubt, wrap it all in a massive try/except for bonus insanity!
logging.error(e)
def import_stuff(file_list):
for filename in file_list:
article_doc = pq(filename=filename)
try:
article_tag = article_doc('article')
article_type = article_tag.attr('article-type')
if article_type != DESIRED_ARTICLE_TYPE:
logging.debug("Skipping article of type %s" % article_type)
continue
(pmid, pmc) = pubmed_ids(article_doc)
logging.info("Processing article %d / %d" % (pmc, pmid))
save_article_to_neo4j(article_doc)
except Exception as e:
# When in doubt, wrap it all in a massive try/except for bonus insanity!
logging.error(e)
def save_article_to_neo4j(article_doc):
# Which key? PMC
(pmid, pmc) = pubmed_ids(article_doc)
pmc_str = str(pmc)
pmid_str = str(pmid)
try:
node = one_index_to_rule_them_all.get('pmc', pmc_str)[0]
except IndexError:
node = gdb.node()
node['pmc'] = pmc
node['pmid'] = pmid
node['title'] = article_doc('article-title').text()
one_index_to_rule_them_all.add('pmc', pmc_str, node)
one_index_to_rule_them_all.add('pmid', pmid_str, node)
def save_article_to_neo4j(article_doc):
# Which key? PMC
(pmid, pmc) = pubmed_ids(article_doc)
pmc_str = str(pmc)
pmid_str = str(pmid)
try:
node = one_index_to_rule_them_all.get('pmc', pmc_str)[0]
except IndexError:
node = gdb.node()
node['pmc'] = pmc
node['pmid'] = pmid
node['title'] = article_doc('article-title').text()
one_index_to_rule_them_all.add('pmc', pmc_str, node)
one_index_to_rule_them_all.add('pmid', pmid_str, node)
