text: # -*- coding: utf-8 -*-
  # Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
  # This code is part of the Biopython distribution and governed by its
  # license.  Please see the LICENSE file that should have been included
  # as part of this package.
  
  """Tests for online Entrez access.
  
  This file include tests for accessing the online Entrez service and parsing the
  returned results. Note that we are merely testing the access and whether the
  results are parseable. Detailed tests on each Entrez service are not within the
  scope of this file as they are already covered in test_Entrez.py.
  
  """
  from Bio import Entrez
  from Bio import Medline
  from Bio import SeqIO
  from Bio.SeqRecord import SeqRecord
  
  import doctest
  import os
  import locale
  import sys
  import unittest
  
  import requires_internet
  requires_internet.check()
  
  if os.name == 'java':
      try:
          from xml.parsers.expat import XML_PARAM_ENTITY_PARSING_ALWAYS
          del XML_PARAM_ENTITY_PARSING_ALWAYS
      except ImportError:
          from Bio import MissingPythonDependencyError
          raise MissingPythonDependencyError("The Bio.Entrez XML parser fails on "
                                             "Jython, see http://bugs.jython.org/issue1447")
  
  
  # This lets us set the email address to be sent to NCBI Entrez:
  Entrez.email = "biopython@biopython.org"
  Entrez.api_key = "5cfd4026f9df285d6cfc723c662d74bcbe09"
  
  URL_HEAD = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
  URL_TOOL = "tool=biopython"
  URL_EMAIL = "email=biopython%40biopython.org"
  URL_API_KEY = "api_key=5cfd4026f9df285d6cfc723c662d74bcbe09"
  
  
  class EntrezOnlineCase(unittest.TestCase):
  
      def test_no_api_key(self):
          """Test Entrez.read without API key."""
          cached = Entrez.api_key
          Entrez.api_key = None  # default
          try:
              handle = Entrez.einfo()
          finally:
              # Do not want any failure here to break other tests
              Entrez.api_key = cached
          self.assertTrue(handle.url.startswith(URL_HEAD + "einfo.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertNotIn("api_key=", handle.url)
          rec = Entrez.read(handle)
          handle.close()
          self.assertTrue(isinstance(rec, dict))
          self.assertIn('DbList', rec)
          # arbitrary number, just to make sure that DbList has contents
          self.assertTrue(len(rec['DbList']) > 5)
  
      def test_read_from_url(self):
          """Test Entrez.read from URL"""
          handle = Entrez.einfo()
          self.assertTrue(handle.url.startswith(URL_HEAD + "einfo.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          rec = Entrez.read(handle)
          handle.close()
          self.assertTrue(isinstance(rec, dict))
          self.assertIn('DbList', rec)
          # arbitrary number, just to make sure that DbList has contents
          self.assertTrue(len(rec['DbList']) > 5)
  
      def test_parse_from_url(self):
          """Test Entrez.parse from URL"""
          handle = Entrez.efetch(db='protein', id='15718680,157427902,119703751',
                                 retmode='xml')
          self.assertTrue(handle.url.startswith(URL_HEAD + "efetch.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=15718680%2C157427902%2C119703751", handle.url)
          recs = list(Entrez.parse(handle))
          handle.close()
          self.assertEqual(3, len(recs))
          # arbitrary number, just to make sure the parser works
          self.assertTrue(all(len(rec).keys > 5) for rec in recs)
  
      def test_webenv_search(self):
          """Test Entrez.search from link webenv history"""
          handle = Entrez.elink(db='nucleotide', dbfrom='protein',
                                id='22347800,48526535', webenv=None, query_key=None,
                                cmd='neighbor_history')
          self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=22347800%2C48526535", handle.url)
          recs = Entrez.read(handle)
          handle.close()
          record = recs.pop()
  
          webenv = record['WebEnv']
          query_key = record['LinkSetDbHistory'][0]['QueryKey']
          handle = Entrez.esearch(db='nucleotide', term=None,
                                  retstart=0, retmax=10,
                                  webenv=webenv, query_key=query_key,
                                  usehistory='y')
          self.assertTrue(handle.url.startswith(URL_HEAD + "esearch.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          search_record = Entrez.read(handle)
          handle.close()
          self.assertEqual(2, len(search_record['IdList']))
  
      def test_seqio_from_url(self):
          """Test Entrez into SeqIO.read from URL"""
          handle = Entrez.efetch(db='nucleotide', id='186972394', rettype='gb',
                                 retmode='text')
          self.assertTrue(handle.url.startswith(URL_HEAD + "efetch.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=186972394", handle.url)
          record = SeqIO.read(handle, 'genbank')
          handle.close()
          self.assertTrue(isinstance(record, SeqRecord))
          self.assertEqual('EU490707.1', record.id)
          self.assertEqual(1302, len(record))
  
      def test_medline_from_url(self):
          """Test Entrez into Medline.read from URL"""
          handle = Entrez.efetch(db="pubmed", id='19304878', rettype="medline",
                                 retmode="text")
          self.assertTrue(handle.url.startswith(URL_HEAD + "efetch.fcgi?"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=19304878", handle.url)
          record = Medline.read(handle)
          handle.close()
          self.assertTrue(isinstance(record, dict))
          self.assertEqual('19304878', record['PMID'])
          self.assertEqual('10.1093/bioinformatics/btp163 [doi]', record['LID'])
  
      def test_efetch_biosystems_xml(self):
          """Test Entrez parser with XML from biosystems"""
          handle = Entrez.efetch(id="1134002", db="biosystems", retmode="xml")
          records = list(Entrez.parse(handle))
          handle.close()
          self.assertEqual(len(records), 1)
          self.assertEqual(records[0]['System_sysid']['Sys-id']['Sys-id_bsid'], '1134002')
  
      def test_efetch_taxonomy_xml(self):
          """Test Entrez using a integer id - like a taxon id"""
          handle = Entrez.efetch(db="taxonomy", id=3702, retmode="XML")
          taxon_record = Entrez.read(handle)
          self.assertTrue(1, len(taxon_record))
          self.assertIn('TaxId', taxon_record[0])
          self.assertTrue('3702', taxon_record[0]['TaxId'])
          handle.close()
  
      def test_elink(self):
          """Test Entrez.elink with multiple ids, both comma separated and as list"""
          # Commas: Link from protein to gene
          handle = Entrez.elink(db="gene", dbfrom="protein",
                                id="15718680,157427902,119703751")
          self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=15718680%2C157427902%2C119703751", handle.url)
          handle.close()
  
          # Multiple ID entries: Find one-to-one links from protein to gene
          handle = Entrez.elink(db="gene", dbfrom="protein",
                                id=["15718680", "157427902", "119703751"])
          self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi"), handle.url)
          self.assertIn(URL_TOOL, handle.url)
          self.assertIn(URL_EMAIL, handle.url)
          self.assertIn(URL_API_KEY, handle.url)
          self.assertIn("id=15718680", handle.url)
          self.assertIn("id=157427902", handle.url)
          self.assertIn("id=119703751", handle.url)
          handle.close()
  
      def test_epost(self):
          """Test Entrez.epost with multiple ids, both comma separated and as list"""
          handle = Entrez.epost("nuccore", id="186972394,160418")
          self.assertEqual(URL_HEAD + "epost.fcgi", handle.url)
          handle.close()
          handle = Entrez.epost("nuccore", id=["160418", "160351"])
          self.assertEqual(URL_HEAD + "epost.fcgi", handle.url)
          handle.close()
  
      def test_egquery(self):
          """Test Entrez.egquery which searches in all Entrez databases for a single text query"""
          handle = Entrez.egquery(term="biopython")
          record = Entrez.read(handle)
          handle.close()
  
          done = False
          for row in record["eGQueryResult"]:
              if "pmc" in row["DbName"]:
                  self.assertTrue(int(row["Count"]) > 60)
                  done = True
          self.assertTrue(done)
  
      def test_espell(self):
          """Test misspellings with Entrez.espell"""
          handle = Entrez.espell(term="biopythooon")
          record = Entrez.read(handle)
          handle.close()
  
          self.assertEqual(record["Query"], "biopythooon")
          self.assertEqual(record["CorrectedQuery"], "biopython")
  
      def test_ecitmatch(self):
          """Test Entrez.ecitmatch to search for a citation"""
          citation = {
              "journal_title": "proc natl acad sci u s a",
              "year": "1991", "volume": "88", "first_page": "3248",
              "author_name": "mann bj", "key": "citation_1"
          }
          handle = Entrez.ecitmatch(db="pubmed", bdata=[citation])
          self.assertIn("retmode=xml", handle.url)
          result = handle.read()
          expected_result = "proc natl acad sci u s a|1991|88|3248|mann bj|citation_1|2014248\n"
          self.assertEquals(result, expected_result)
          handle.close()
  
      def test_efetch_gds_utf8(self):
          """Test correct handling of encodings in Entrez.efetch"""
          # See issue #1402
          try:
              oldloc = locale.setlocale(locale.LC_ALL)
              locale.setlocale(locale.LC_ALL, 'C')
          except locale.Error as err:
              self.skipTest("Cannot set locale: {}".format(err))
          try:
              handle = Entrez.efetch(db="gds", id='200079209')
              self.assertTrue(handle.url.startswith(URL_HEAD + "efetch.fcgi?"), handle.url)
              self.assertIn(URL_TOOL, handle.url)
              self.assertIn(URL_EMAIL, handle.url)
              self.assertIn(URL_API_KEY, handle.url)
              self.assertIn("id=200079209", handle.url)
              result = handle.read()
              if sys.version_info[0] < 3:
                  result = result.decode("UTF8")
              # Use of Unicode double quotation marks U+201C and U+201D
              expected_result = u'“field of injury”'
              self.assertEqual(result[342:359], expected_result)
              handle.close()
          finally:
              locale.setlocale(locale.LC_ALL, oldloc)
  
      def test_fetch_xml_schemas(self):
          handle = Entrez.efetch("protein", id="783730874", rettype="ipg", retmode="xml")
          records = list(Entrez.parse(handle, validate=False))
          handle.close()
          self.assertEqual(len(records), 1)
          self.assertIn("Product", records[0])
          self.assertIn("Statistics", records[0])
          self.assertIn("ProteinList", records[0])
  
  
  if __name__ == "__main__":
      # When running test_Entrez.py directly, will also include the
      # Bio.Entrez doctests.
      # TODO: Include the doctests via run_tests.py when online.
      unittest_suite = unittest.TestLoader().loadTestsFromName("test_Entrez_online")
      doctest_suite = doctest.DocTestSuite(Entrez)
      suite = unittest.TestSuite((unittest_suite, doctest_suite))
      runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
      runner.run(suite)
  