1 from __future__ import absolute_import, print_function
5 from pprint import pprint
6 from unittest import TestCase, TestSuite, defaultTestLoader, skip
8 from htsworkflow.submission.encoded import (ENCODED,
13 class TestEncoded(TestCase):
14 def test_prepare_url(self):
15 encode = ENCODED('www.encodeproject.org')
18 ('/experiments', 'https://www.encodeproject.org/experiments'),
19 ('/experiments/ENCLB045ZZZ',
20 'https://www.encodeproject.org/experiments/ENCLB045ZZZ'),
21 ('https://www.encodeproject.org/experiments/ENCLB045ZZZ',
22 'https://www.encodeproject.org/experiments/ENCLB045ZZZ'),
24 for url, result in tests:
25 self.assertEqual(encode.prepare_url(url), result)
27 def test_validate(self):
30 schema_file = os.path.join(os.path.dirname(__file__), 'library.json')
31 schema = json.loads(open(schema_file, 'r').read())
33 obj = {u'@id': u'/libraries/ENCLB045ZZZ/',
34 u'@type': [u'Library', u'Item'],
35 u'accession': u'ENCLB045ZZZ',
37 u'alternate_accessions': [],
38 u'award': u'/awards/U54HG006998/',
39 u'biosample': u'/biosamples/ENCBS089RNA/',
40 u'date_created': u'2014-01-14T19:44:51.061770+00:00',
42 u'extraction_method': u'Ambion mirVana',
43 u'fragmentation_method': u'chemical (Nextera tagmentation)',
44 u'lab': u'/labs/barbara-wold/',
45 u'library_size_selection_method': u'SPRI beads',
46 u'lysis_method': u'Ambion mirVana',
47 u'nucleic_acid_term_id': u'SO:0000871',
48 u'nucleic_acid_term_name': u'polyadenylated mRNA',
49 u'schema_version': u'2',
50 u'size_range': u'>200',
51 u'status': u'released',
52 u'strand_specificity': False,
53 u'submitted_by': u'/users/0e3dde9b-aaf9-42dd-87f7-975a85072ed2/',
55 u'uuid': u'42c46028-708f-4347-a3df-2c82dfb021c4'}
56 encode = ENCODED('www.encodeproject.org')
57 encode.schemas[u'library'] = schema
59 self.assertTrue('@id' in obj)
61 def test_create_context(self):
62 linked_id = {'@type': '@id'}
63 library = { '@id': '/libraries/1234', '@type': ['Library', 'Item'] }
65 encode = ENCODED('www.encodeproject.org')
66 url = encode.prepare_url(library['@id'])
67 context = encode.create_jsonld_context(library, url)
68 self.assertEqual(context['@vocab'], 'https://www.encodeproject.org/profiles/Library.json#')
69 self.assertEqual(context['award'], linked_id )
70 self._verify_context(context, 'Library')
71 # namespaces not added yet.
72 self.assertRaises(AssertionError, self._verify_namespaces, context)
73 encode.add_jsonld_namespaces(context)
74 self._verify_namespaces(context)
76 def test_add_context(self):
77 """Checking to make sure nested @base and @vocab urls are set correctly
80 "nucleic_acid_term_name": "RNA",
81 "accession": "ENCLB044ZZZ",
82 "@id": "/libraries/ENCLB044ZZZ/",
83 "schema_version": "1",
88 "lysis_method": "Ambion mirVana",
89 "nucleic_acid_term_id": "SO:0000356",
91 "biosample_term_name": "GM12878",
92 "description": "B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus",
93 "accession": "ENCBS090RNA",
94 "date_created": "2013-10-29T21:15:29.144260+00:00",
95 "@id": "/biosamples/ENCBS090RNA/",
97 "brenton-graveley:GM12878-2",
98 "thomas-gingeras:191WC"
100 "organism": "/organisms/human/",
108 encode = ENCODED('www.encodeproject.org')
109 bio_base = encode.prepare_url(obj['biosample']['@id'])
111 url = encode.prepare_url('/libraries/ENCLB044ZZZ/?format=json&embed=False')
112 obj_type = encode.get_object_type(obj)
113 schema_url = encode.get_schema_url(obj_type)
114 encode.add_jsonld_context(obj, url)
116 self.assertEqual(obj['biosample']['@context']['@base'], bio_base)
117 self.assertEqual(obj['@context']['@vocab'], schema_url)
118 self._verify_context(obj['@context'], 'Library')
119 self._verify_namespaces(obj['@context'])
120 self._verify_context(obj['biosample']['@context'], 'Biosample')
121 self.assertEqual(obj['@context']['rdf'], 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
122 self.assertEqual(obj['@context']['OBO'], 'http://purl.obolibrary.org/obo/')
125 def test_convert_search_to_jsonld(self):
126 example = {'count': {'biosamples': 2},
127 'portal_title': 'ENCODE',
129 'notification': 'Success',
131 '@id': '/search/?searchTerm=wold',
135 u'@id': u'/biosamples/ENCBS125ENC/',
136 u'@type': [u'Biosample', u'Item'],
137 u'accession': u'ENCBS125ENC',
138 u'award.rfa': u'ENCODE2-Mouse',
139 u'biosample_term_name': u'myocyte',
140 u'biosample_type': u'in vitro differentiated cells',
141 u'characterizations.length': [],
142 u'constructs.length': [],
143 u'lab.title': u'Barbara Wold, Caltech',
144 u'life_stage': u'unknown',
145 u'organism.name': u'mouse',
146 u'source.title': u'Barbara Wold',
147 u'status': u'CURRENT',
148 u'treatments.length': []},
149 {u'@id': u'/biosamples/ENCBS126ENC/',
150 u'@type': [u'Biosample', u'Item'],
151 u'accession': u'ENCBS126ENC',
152 u'award.rfa': u'ENCODE2-Mouse',
153 u'biosample_term_name': u'myocyte',
154 u'biosample_type': u'in vitro differentiated cells',
155 u'characterizations.length': [],
156 u'constructs.length': [],
157 u'lab.title': u'Barbara Wold, Caltech',
158 u'life_stage': u'unknown',
159 u'organism.name': u'mouse',
160 u'source.title': u'Barbara Wold',
161 u'status': u'CURRENT',
162 u'treatments.length': []},
165 encode = ENCODED('www.encodeproject.org')
166 result = encode.convert_search_to_jsonld(example)
167 for obj in result['@graph']:
168 self.assertNotIn('award.rfa', obj)
170 def _verify_context(self, context, obj_type):
171 for context_key in [None, obj_type]:
172 for k in ENCODED_CONTEXT[context_key]:
173 self.assertIn(k, context)
174 self.assertEqual(ENCODED_CONTEXT[context_key][k], context[k])
176 def _verify_namespaces(self, context):
177 for k in ENCODED_NAMESPACES:
178 self.assertIn(k, context)
179 self.assertEqual(ENCODED_NAMESPACES[k], context[k])
184 defaultTestLoader.loadTestsFromTestCase(TestEncoded))
187 if __name__ == "__main__":
188 from unittest import main
189 main(defaultTest='suite')