diff options
| -rw-r--r-- | scripts/pub_med.py | 19 |
1 files changed, 13 insertions, 6 deletions
diff --git a/scripts/pub_med.py b/scripts/pub_med.py index f3e8861..4b5a19b 100644 --- a/scripts/pub_med.py +++ b/scripts/pub_med.py @@ -4,8 +4,12 @@ feature can be extended to others e.g pmc """ +# pylint: disable=C0301 + import functools import json +import requests + from Bio import Entrez @@ -21,13 +25,14 @@ def fetch_pub_details(id_list, db_name, retmode="xml", email="alexanderkabua@gma """ Entrez.email = email if db_name.lower() == "pubmed": - handle = Entrez.efetch(db=db_name, retmode="xml", + handle = Entrez.efetch(db=db_name, retmode=retmode, id=",".join(id_list)) results = Entrez.read(handle) handle.close() return extract_pub_metadata(results) + return [] def extract_pub_metadata(papers): """ @@ -70,7 +75,7 @@ def fetch_pubmed_id(query, db_name, max_search_count, ret_mode="xml", email="ale Entrez.email = email handle = Entrez.esearch(db=db_name, sort="relevance", - retmax=max_search_count, ret_mode="xml", term=query) + retmax=max_search_count, ret_mode=ret_mode, term=query) results = Entrez.read(handle) handle.close() if results.get("IdList"): @@ -79,6 +84,8 @@ def fetch_pubmed_id(query, db_name, max_search_count, ret_mode="xml", email="ale "id_list": results.get("IdList") } + return None + def fetch_all_queries(input_file, max_search_count=1, db_name="pubmed"): """ @@ -96,7 +103,7 @@ def fetch_all_queries(input_file, max_search_count=1, db_name="pubmed"): pub_data = [] doc_ids = {} - with open(input_file, "r") as file_handler: + with open(input_file, "r", encoding="utf-8") as file_handler: search_dict = json.load(file_handler) for (filename, file_obj) in search_dict.items(): @@ -129,7 +136,7 @@ def dump_all_to_file(response, doc_ids, output_file): data[doc_id] = [pub_meta] # - with open(output_file, "w+") as file_handler: + with open(output_file, "w+", encoding="utf-8") as file_handler: json.dump(data, file_handler, indent=4) @@ -175,6 +182,6 @@ def search_pubmed_lossy(pubmed_id, db_name): if __name__ == '__main__': - (pub_data, doc_ids) = fetch_all_queries( + (pub_metadata, doc_ids_metadata) = fetch_all_queries( input_file="parsed_all_files.json", max_search_count=1) - dump_all_to_file(pub_data, doc_ids, "output_file.json") + dump_all_to_file(pub_metadata, doc_ids_metadata, "output_file.json") |