htsworkflow/submission/test/test_encoded.py

   1 import json
   2 import os
   3 from pprint import pprint
   4 from unittest2 import TestCase, TestSuite, defaultTestLoader, skip
   5
   6 from htsworkflow.submission.encoded import ENCODED
   7
   8 class TestEncoded(TestCase):
   9     def test_prepare_url(self):
  10         encode = ENCODED('test.encodedcc.edu')
  11
  12         tests = [
  13             ('/experiments', 'http://test.encodedcc.edu/experiments'),
  14             ('/experiments/ENCLB045ZZZ',
  15              'http://test.encodedcc.edu/experiments/ENCLB045ZZZ'),
  16             ('http://submit.encodedcc.edu/experiments/ENCLB045ZZZ',
  17              'http://submit.encodedcc.edu/experiments/ENCLB045ZZZ'),
  18         ]
  19         for url, result in tests:
  20             self.assertEqual(encode.prepare_url(url), result)
  21
  22     def test_validate(self):
  23         """Test validation
  24         """
  25         schema_file = os.path.join(os.path.dirname(__file__), 'library.json')
  26         schema = json.loads(open(schema_file, 'r').read())
  27
  28         obj = {u'@id': u'/libraries/ENCLB045ZZZ/',
  29                u'@type': [u'library', u'item'],
  30                u'accession': u'ENCLB045ZZZ',
  31                u'aliases': [],
  32                u'alternate_accessions': [],
  33                u'award': u'/awards/U54HG006998/',
  34                u'biosample': u'/biosamples/ENCBS089RNA/',
  35                u'date_created': u'2014-01-14T19:44:51.061770+00:00',
  36                u'depleted_in_term_id': [],
  37                u'depleted_in_term_name': [],
  38                u'documents': [],
  39                u'extraction_method': u'Ambion mirVana',
  40                u'fragmentation_method': u'Illumina/Nextera tagmentation',
  41                u'lab': u'/labs/barbara-wold/',
  42                u'library_size_selection_method': u'SPRI beads',
  43                u'lysis_method': u'Ambion mirVana',
  44                u'nucleic_acid_term_id': u'SO:0000871',
  45                u'nucleic_acid_term_name': u'polyadenylated mRNA',
  46                u'paired_ended': False,
  47                u'schema_version': u'2',
  48                u'size_range': u'>200',
  49                u'status': u'CURRENT',
  50                u'strand_specificity': False,
  51                u'submitted_by': u'/users/0e3dde9b-aaf9-42dd-87f7-975a85072ed2/',
  52                u'treatments': [],
  53                u'uuid': u'42c46028-708f-4347-a3df-2c82dfb021c4'}
  54         encode = ENCODED('submit.encodedcc.org')
  55         encode.schemas[u'library'] = schema
  56         encode.validate(obj)
  57         self.assertTrue('@id' in obj)
  58
  59     def test_add_context(self):
  60         """Checking to make sure nested @base and @vocab urls are set correctly
  61         """
  62         obj = {
  63             "nucleic_acid_term_name": "RNA",
  64             "accession": "ENCLB044ZZZ",
  65             "@id": "/libraries/ENCLB044ZZZ/",
  66             "schema_version": "1",
  67             "@type": [
  68                 "library",
  69                 "item"
  70             ],
  71             "lysis_method": "Ambion mirVana",
  72             "nucleic_acid_term_id": "SO:0000356",
  73             "biosample": {
  74                 "biosample_term_name": "GM12878",
  75                 "description": "B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus",
  76                 "accession": "ENCBS090RNA",
  77                 "date_created": "2013-10-29T21:15:29.144260+00:00",
  78                 "@id": "/biosamples/ENCBS090RNA/",
  79                 "aliases": [
  80                 "brenton-graveley:GM12878-2",
  81                 "thomas-gingeras:191WC"
  82                 ],
  83                 "organism": "/organisms/human/",
  84                 "@type": [
  85                 "biosample",
  86                 "item"
  87                 ]
  88             },
  89         }
  90
  91         encode = ENCODED('test.encodedcc.org')
  92         bio_base = encode.prepare_url(obj['biosample']['@id'])
  93
  94         url = encode.prepare_url('/libraries/ENCLB044ZZZ/?format=json&embed=False')
  95         schema_url = encode.get_schema_url(obj)
  96         encode.add_jsonld_context(obj, encode.context, url)
  97
  98         self.assertEqual(obj['biosample']['@context']['@base'], bio_base)
  99         self.assertEqual(obj['@context']['@vocab'], schema_url)
 100
 101
 102 def suite():
 103     suite = TestSuite()
 104     suite.addTests(
 105         defaultTestLoader.loadTestsFromTestCase(TestEncoded))
 106     return suite
 107
 108 if __name__ == "__main__":
 109     from unittest2 import main
 110     main(defaultTest='suite')