build: rate limiting tests to NCBI Entrez

tests/ref/test_ref_utils.py

@@ -3,11 +3,15 @@
 import Bio.Entrez
 import ftplib
 import os
+import random
 import shutil
+import string
 import tempfile
+import time
 import unittest
 
-Bio.Entrez.email = '[email protected]'
+email_suffix = ''.join(random.choice(string.ascii_letters + string.digits) for i in range(8))
+Bio.Entrez.email = 'biosimulators.daemon-{}@gmail.com'.format(email_suffix)
 
 
 class RefUtilsTestCase(unittest.TestCase):
@@ -19,7 +23,10 @@ def tearDown(self):
 
     def test_search_entrez_records(self):
         self.assertEqual(utils.search_entrez_records('pmc', '23184105[pmid]')['IdList'], ['5813803'])
+        time.sleep(1)
+
         self.assertEqual(utils.search_entrez_records('pmc', 'abc[pmid]')['Count'], '0')
+        time.sleep(1)
 
         with self.assertRaisesRegex(TypeError, 'must be a non-empty string'):
             utils.search_entrez_records('pmc', None)
@@ -30,6 +37,7 @@ def test_search_entrez_records(self):
 
     def test_get_entrez_record(self):
         self.assertEqual(utils.get_entrez_record('pmc', '5813803')['Id'], '5813803')
+        time.sleep(1)
 
         with self.assertRaisesRegex(ValueError, 'is not a valid id'):
             utils.get_entrez_record('pubmed', 'abc')
@@ -39,38 +47,54 @@ def test_get_entrez_record(self):
 
     def test_get_pubmed_central_id(self):
         self.assertEqual(utils.get_pubmed_central_id('23184105'), 'PMC5813803')
+        time.sleep(1)
+
         self.assertEqual(utils.get_pubmed_central_id('1234'), None)
+        time.sleep(1)
+
         self.assertEqual(utils.get_pubmed_central_id(1234), None)
+        time.sleep(1)
+
         self.assertEqual(utils.get_pubmed_central_id('abc'), None)
+        time.sleep(1)
+
         self.assertEqual(utils.get_pubmed_central_id(None), None)
+        time.sleep(1)
 
     def test_get_reference_from_pubmed(self):
         ref = utils.get_reference_from_pubmed('1234')
         self.assertEqual(ref.journal, 'Drug metabolism and disposition: the biological fate of chemicals')
         self.assertEqual(ref.year, '1975')
+        time.sleep(1)
 
         ref = utils.get_reference_from_pubmed('23184105')
         self.assertEqual(ref.year, '2012')
         self.assertEqual(ref.pubmed_central_id, 'PMC5813803')
         self.assertEqual(ref.doi, '10.1542/peds.2012-2758')
+        time.sleep(1)
 
         ref = utils.get_reference_from_pubmed(pubmed_id=None, doi='10.1542/peds.2012-2758')
         self.assertEqual(ref.year, '2012')
         self.assertEqual(ref.pubmed_id, '23184105')
         self.assertEqual(ref.pubmed_central_id, 'PMC5813803')
         self.assertEqual(ref.doi, '10.1542/peds.2012-2758')
+        time.sleep(1)
 
         ref = utils.get_reference_from_pubmed(pubmed_id=None, doi='10.1103/PhysRevLett.127.104301x')
         self.assertEqual(ref, None)
+        time.sleep(1)
 
         ref = utils.get_reference_from_pubmed(None, None)
         self.assertEqual(ref, None)
+        time.sleep(1)
 
         with self.assertRaisesRegex(ValueError, 'not a valid id'):
             utils.get_reference_from_pubmed(pubmed_id='abc')
+        time.sleep(1)
 
         with self.assertRaises(ValueError):
             utils.get_reference_from_pubmed('000')
+        time.sleep(1)
 
     def test_get_reference_from_crossref(self):
         ref = utils.get_reference_from_crossref('10.1542/peds.2012-2758')
@@ -109,6 +133,7 @@ def test_get_reference(self):
         self.assertEqual(ref.pubmed_id, '23184105')
         self.assertEqual(ref.pubmed_central_id, 'PMC5813803')
         self.assertEqual(ref.doi, '10.1542/peds.2012-2758')
+        time.sleep(1)
 
         ref = utils.get_reference(doi='10.1542/peds.2012-2758')
         self.assertIn(ref.authors, authors)
@@ -117,9 +142,11 @@ def test_get_reference(self):
         self.assertEqual(ref.pubmed_id, '23184105')
         self.assertEqual(ref.pubmed_central_id, 'PMC5813803')
         self.assertEqual(ref.doi, '10.1542/peds.2012-2758')
+        time.sleep(1)
 
         ref = utils.get_reference(pubmed_id='1234')
         self.assertEqual(ref.doi, None)
+        time.sleep(1)
 
         with self.assertRaises(ValueError):
             utils.get_reference()