def pubmed_ids_to_d(pmids):
print "fetching articles..."
articles = pubmedpy.batch_fetch(pmids)
print "ok."
articles = [article for article in articles if len(article) >= 3]
pmids_d = {}
none_to_str = lambda x: x if x is not None else ""
for article in articles:
title_text = article.get("TI")
ab_text = article.get("AB")
authors = none_to_str(article.get("AU"))
journal = none_to_str(article.get("JT"))
keywords = none_to_str(article.get("MH"))
pmid = int(article["PMID"])
pmids_d[pmid] = {
"title": title_text,
"abstract": ab_text,
"journal": journal,
"keywords": keywords,
"pmid": pmid,
"authors": authors,
}
return pmids_d
def pubmed_ids_to_db(pmids, db_path):
print "fetching articles..."
articles = pubmedpy.batch_fetch(pmids)
print "ok."
pmids_to_abs = {}
none_to_str = lambda x: x if x is not None else ""
for article in articles:
title_text = article.get("TI")
ab_text = article.get("AB")
authors = none_to_str(article.get("AU"))
journal = none_to_str(article.get("JT"))
keywords = none_to_str(article.get("MH"))
pmid = int(article["PMID"])
pmids_to_abs[pmid] = {"title":title_text, "abstract":ab_text, "journal":journal,\
"keywords":keywords, "pmid":pmid, "authors":authors}
d_to_sql(pmids_to_abs, db_path, "chris")
def pubmed_ids_to_db(pmids, db_path):
print "fetching articles..."
articles = pubmedpy.batch_fetch(pmids)
print "ok."
pmids_to_abs = {}
none_to_str = lambda x: x if x is not None else ""
for article in articles:
title_text = article.get("TI")
ab_text = article.get("AB")
authors = none_to_str(article.get("AU"))
journal = none_to_str(article.get("JT"))
keywords = none_to_str(article.get("MH"))
pmid = int(article["PMID"])
pmids_to_abs[pmid] = {"title":title_text, "abstract":ab_text, "journal":journal,\
"keywords":keywords, "pmid":pmid, "authors":authors}
d_to_sql(pmids_to_abs, db_path, "chris")
def pubmed_ids_to_d(pmids):
print "fetching articles..."
articles = pubmedpy.batch_fetch(pmids)
print "ok."
articles = [article for article in articles if len(article) >= 3]
pmids_d = {}
none_to_str = lambda x: x if x is not None else ""
for article in articles:
title_text = article.get("TI")
ab_text = article.get("AB")
authors = none_to_str(article.get("AU"))
journal = none_to_str(article.get("JT"))
keywords = none_to_str(article.get("MH"))
pmid = int(article["PMID"])
pmids_d[pmid] = {"title":title_text, "abstract":ab_text, "journal":journal,\
"keywords":keywords, "pmid":pmid, "authors":authors}
return pmids_d
