created taxonomy retriever

providers.yaml

@@ -28,7 +28,11 @@
   resources:
       html: ["http://www.uniprot.org/taxonomy/%i"]
       xml: ["http://www.uniprot.org/taxonomy/%i.rdf"]
+      xml_ncbi: ["https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=%i"]
   check_existence: "http://www.uniprot.org/taxonomy/%i"
+  retriever:
+      type: 'external'
+      location: 'scripts/retrieve_taxonomy.py'
 - name: SequenceOntology
   prefixes: ["SO", "so"]
   resources:

scripts/retrieve_taxonomy.py

+#!/usr/bin/env python3
+
+import env
+import dbxref.config
+import dbxref.resolver
+import requests
+import xml.etree.ElementTree as ET
+import logging
+import json
+import argparse
+
+logger = logging.getLogger(__name__)
+ns = {'TaxaSet': 'https://eutils.ncbi.nlm.nih.gov/'}
+
+def main():
+	parser = argparse.ArgumentParser(description='Retrieve taxonomy xml documents for dbxrefs and convert them into json')
+	parser.add_argument('--basic', '-b', action='store_true', help='Include dbxref and ......................')
+	parser.add_argument('dbxrefs', nargs=argparse.REMAINDER)
+	args = parser.parse_args()
+	resolved = dbxref.resolver.resolve(args.dbxrefs, check_existence=False)
+	documents = []
+	for entry in resolved:
+		xml_url = entry['locations']['xml_ncbi'][0]
+		logger.debug('URL: %s', xml_url)
+		r = requests.get(xml_url)
+		logger.debug('Content: %s', r.text)
+		root = ET.fromstring(r.text)
+
+		output = {'id': entry['dbxref']}
+		error = root.find('ERROR')
+		if error is not None:
+			output['message'] = error.text.strip()
+		else:
+			for child in root.findall('Taxon'):
+				output['name'] = child.find('ScientificName').text.strip()
+				lineage = child.find('Lineage')
+				if lineage.text is not None:
+					output['lineage'] = lineage.text.strip()
+				else:
+					output['lineage'] = 'No lineage found'
+		if 'name' not in output and 'message' not in output:
+			output['message'] = 'No entries found! Possibly invalid ID provided'
+		documents.append(output)
+	print (json.dumps(documents))
+
+main()