New script eu_search_results_json.py

Author: Nathan Watson

encode_utils/scripts/eu_search_results_json.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+###
+# © 2018 The Board of Trustees of the Leland Stanford Junior University
+# Nathaniel Watson
+# nathankw@stanford.edu
+###
+
+"""
+Provided a search URL that is specific to the ENCODE Portal, saves the search results as JSON
+in the specified output file. The search results are stored as a list of JSON objects.
+
+|
+"""
+
+import argparse
+import json
+import os
+import sys
+
+import encode_utils.connection as euc
+from encode_utils.parent_argparser import dcc_login_parser
+
+# Check that Python3 is being used
+v = sys.version_info
+if v < (3, 3):
+    raise Exception("Requires Python 3.3 or greater.")
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description = __doc__,
+        parents=[dcc_login_parser],
+        formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-l", "--limit", type=int, help="The number of search results to get back. Leave blank if you want all.") 
+    parser.add_argument("-u", "--url", required=True, help="The ENCODE Portal URL that you use for searching. Wrap this in quotes to make sure its all treated as one argument.")
+    parser.add_argument("-o", "--outfile", required=True, help="The JSON output file containing the search results.")
+    return parser
+
+def main():
+    parser = get_parser()
+    args = parser.parse_args()
+    dcc_mode = args.dcc_mode
+    limit = args.limit
+    outfile = args.outfile
+    url = args.url
+
+    if dcc_mode:
+        conn = euc.Connection(dcc_mode)
+    else:
+        # Default dcc_mode taken from environment variable DCC_MODE.
+        conn = euc.Connection()
+
+    fout = open(outfile, "w")
+    results = conn.search(limit=limit, url=url) #returns a list of search results
+    fout.write(json.dumps(results))
+    fout.close()
+
+
+if __name__ == "__main__":
+    main()