Esempio n. 1
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    def test_construct_cgi_epost2(self):
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
        variables = {'db': 'nuccore', 'id': ["160418", "160351"]}
        post = True

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
Esempio n. 2
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    def test_construct_cgi_epost2(self):
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
        variables = {'db': 'nuccore', 'id': ["160418", "160351"]}
        post = True

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
Esempio n. 3
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    def test_construct_cgi_epost1(self):
        cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi"
        variables = {"db": "nuccore", "id": "186972394,160418"}
        post = True

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
Esempio n. 4
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 def test_construct_cgi_einfo(self):
     """Test constructed url for request to Entrez."""
     cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"
     params = Entrez._construct_params(params=None)
     options = Entrez._encode_options(ecitmatch=False, params=params)
     result_url = Entrez._construct_cgi(cgi, post=False, options=options)
     self.assertTrue(result_url.startswith(URL_HEAD + "einfo.fcgi?"), result_url)
     self.assertIn(URL_TOOL, result_url)
     self.assertIn(URL_EMAIL, result_url)
Esempio n. 5
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 def test_construct_cgi_einfo(self):
     """Test constructed url for request to Entrez."""
     cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
     params = Entrez._construct_params(params=None)
     options = Entrez._encode_options(ecitmatch=False, params=params)
     result_url = Entrez._construct_cgi(cgi, post=False, options=options)
     self.assertTrue(result_url.startswith(URL_HEAD + "einfo.fcgi?"),
                     result_url)
     self.assertIn(URL_TOOL, result_url)
     self.assertIn(URL_EMAIL, result_url)
Esempio n. 6
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    def test_construct_cgi_elink1(self):
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
        variables = {'cmd': 'neighbor_history', 'db': 'nucleotide',
                     'dbfrom': 'protein', 'id': '22347800,48526535',
                     'query_key': None, 'webenv': None}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi?"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertIn("id=22347800%2C48526535", result_url)
Esempio n. 7
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    def test_construct_cgi_ecitmatch(self):
        citation = {
            "journal_title": "proc natl acad sci u s a",
            "year": "1991", "volume": "88", "first_page": "3248",
            "author_name": "mann bj", "key": "citation_1"
        }
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi'
        variables = Entrez._update_ecitmatch_variables({'db': 'pubmed',
                                                        'bdata': [citation]})
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=True, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertIn("retmode=xml", result_url)
Esempio n. 8
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    def test_construct_cgi_efetch(self):
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
        variables = {'db': 'protein', 'id': '15718680,157427902,119703751',
                     'retmode': 'xml'}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "efetch.fcgi?"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
                        result_url)
Esempio n. 9
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    def test_construct_cgi_elink2(self):
        """Commas: Link from protein to gene."""
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
        variables = {'db': 'gene', 'dbfrom': 'protein',
                     'id': '15718680,157427902,119703751'}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
                        result_url)
Esempio n. 10
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    def test_construct_cgi_elink1(self):
        cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
        variables = {"cmd": "neighbor_history", "db": "nucleotide",
                     "dbfrom": "protein", "id": "22347800,48526535",
                     "query_key": None, "webenv": None}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi?"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertIn("id=22347800%2C48526535", result_url)
        self.assertIn(URL_API_KEY, result_url)
Esempio n. 11
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    def test_construct_cgi_efetch(self):
        cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
        variables = {"db": "protein", "id": "15718680,157427902,119703751",
                     "retmode": "xml"}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "efetch.fcgi?"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
                        result_url)
        self.assertIn(URL_API_KEY, result_url)
Esempio n. 12
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    def test_construct_cgi_elink3(self):
        """Multiple ID entries: Find one-to-one links from protein to gene."""
        cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
        variables = {'db': 'gene', 'dbfrom': 'protein',
                     'id': ["15718680", "157427902", "119703751"]}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertIn("id=15718680", result_url)
        self.assertIn("id=157427902", result_url)
        self.assertIn("id=119703751", result_url)
Esempio n. 13
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    def test_construct_cgi_elink2(self):
        """Commas: Link from protein to gene."""
        cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
        variables = {"db": "gene", "dbfrom": "protein",
                     "id": "15718680,157427902,119703751"}
        post = False

        params = Entrez._construct_params(variables)
        options = Entrez._encode_options(ecitmatch=False, params=params)
        result_url = Entrez._construct_cgi(cgi, post=post, options=options)
        self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
                        result_url)
        self.assertIn(URL_TOOL, result_url)
        self.assertIn(URL_EMAIL, result_url)
        self.assertIn("id=15718680%2C157427902%2C119703751", result_url,
                      result_url)
        self.assertIn(URL_API_KEY, result_url)