Refactor string handling into main method, away from resolve and retrieve

dbxref/main.py

@@ -2,6 +2,7 @@
 import argparse
 import os
 import logging
+from dbxref import resolver
 
 def main():
     parser = argparse.ArgumentParser(description='Lookup locations of database cross references and retrieve them as json')
@@ -38,13 +39,12 @@ def info(args, config):
     print ('info')
 
 def resolve(args, config):
-    from dbxref import resolver
     import json
-    print(json.dumps(resolver.resolve(args.dbxrefs, check_existence=args.no_check)))
+    print(json.dumps(resolver.resolve(resolver.convert_to_dbxrefs(args.dbxrefs), check_existence=args.no_check)))
 
 def retrieve(args, config):
     from dbxref import retriever
-    retriever.retrieve(args.dbxrefs)
+    retriever.retrieve(resolver.convert_to_dbxrefs(args.dbxrefs))
 
 if __name__ == "__main__":
     main()

dbxref/resolver.py

@@ -18,13 +18,12 @@ STATUS_CHECK_NOT_SUPPORTED='check of status not supported'
 STATUS_CHECK_TIMEOUT='status check timed out'
 STATUS_UNSUPPORTED_DB='database unsupported'
 
-def resolve(strings, check_existence=True):
+def resolve(dbxrefs, check_existence=True):
     results = []
-    for s in strings:
+    for dbxref in dbxrefs:
         status = STATUS_NOT_CHECKED
         if check_existence:
-           status = check_dbxref_exists(s)
-        dbxref = convert_string_to_dbxref(s)
+           status = check_dbxref_exists(dbxref)
         if dbxref['db'] in providers:
             provider = providers[dbxref['db']]
             locations = {}
@@ -38,8 +37,11 @@ def resolve(strings, check_existence=True):
             results.append({'dbxref': dbxref['db'] + ':' + dbxref['id'], 'status': STATUS_UNSUPPORTED_DB})
     return results
 
-def check_dbxref_exists(string):
-    dbxref = convert_string_to_dbxref(string)
+def convert_to_dbxrefs(strings):
+  '''convert a list of strings to dbxref maps with db and id attribute'''
+  return list(map(convert_string_to_dbxref, strings))
+
+def check_dbxref_exists(dbxref):
     if dbxref['db'] in providers:
         provider = providers[dbxref['db']]
         urls = []

dbxref/retriever.py

@@ -2,14 +2,12 @@ import logging
 logger = logging.getLogger(__name__)
 
 from dbxref.config import load_providers
-from dbxref.resolver import convert_string_to_dbxref
 from itertools import groupby
 import json
 
 providers = load_providers()
 
-def retrieve(strings, location=''):
-    dbxrefs = list(map(convert_string_to_dbxref, strings))
+def retrieve(dbxrefs, location=''):
     sorted(dbxrefs, key=lambda x: x['db'])
     results = []
     for key, dbxrefs in groupby(dbxrefs, lambda x: x['db']):

tests/test_resolver.py

@@ -18,7 +18,7 @@ class TestDbxrefResolve(unittest.TestCase):
 
 
     def test_resolve_enzyme(self):
-        self.assertNotEqual(resolver.resolve(["EC:1.1.1.1"]), [])
+        self.assertNotEqual(resolver.resolve(resolver.convert_to_dbxrefs(["EC:1.1.1.1"])), [])
 
     def test_check_dbxref_exists(self):
         import logging
@@ -67,7 +67,7 @@ class TestDbxrefResolve(unittest.TestCase):
 
         for d in data:
             with self.subTest(d=d):
-                self.assertEqual(resolver.check_dbxref_exists(d[0]), d[1] )
+                self.assertEqual(resolver.check_dbxref_exists(resolver.convert_string_to_dbxref(d[0])), d[1] )
 
     def test_check_urls(self):
         import json