class TestOntology(TestCase):
def setUp(self):
self.ontology = Ontology(999999999)
def testConvertToID(self):
self.assertEqual(convert_to_id('ENA', 'ontology'), 999999999)
def testConvertFromID(self):
self.assertEqual(convert_from_id(999999999, 'ontology'), 'ENA')
def testShortNameProperty(self):
self.assertEqual(self.ontology.shortname, 'ENA')
def testTerms(self):
obs = self.ontology.terms
self.assertEqual(obs, [
'Whole Genome Sequencing',
'Metagenomics',
'Transcriptome Analysis',
'Resequencing',
'Epigenetics',
'Synthetic Genomics',
'Forensic or Paleo-genomics',
'Gene Regulation Study',
'Cancer Genomics',
'Population Genomics',
'RNASeq',
'Exome Sequencing',
'Pooled Clone Sequencing',
'Other'])
def test_user_defined_terms(self):
obs = self.ontology.user_defined_terms
self.assertEqual(obs, [])
def test_term_type(self):
obs = self.ontology.term_type('RNASeq')
self.assertEqual('ontology', obs)
obs = self.ontology.term_type('Sasquatch')
self.assertEqual('not_ontology', obs)
self.ontology.add_user_defined_term('Test Term')
obs = self.ontology.term_type('Test Term')
self.assertEqual('user_defined', obs)
def test_add_user_defined_term(self):
self.assertFalse('Test Term' in self.ontology.user_defined_terms)
pre = len(self.ontology.user_defined_terms)
self.ontology.add_user_defined_term('Test Term')
post = len(self.ontology.user_defined_terms)
self.assertTrue('Test Term' in self.ontology.user_defined_terms)
self.assertEqual(post-pre, 1)
def testContains(self):
self.assertTrue('Metagenomics' in self.ontology)
self.assertFalse('NotATerm' in self.ontology)
class TestOntology(TestCase):
def setUp(self):
self.ontology = Ontology(999999999)
def testConvertToID(self):
self.assertEqual(convert_to_id('ENA', 'ontology'), 999999999)
def testConvertFromID(self):
self.assertEqual(convert_from_id(999999999, 'ontology'), 'ENA')
def testShortNameProperty(self):
self.assertEqual(self.ontology.shortname, 'ENA')
def testTerms(self):
obs = self.ontology.terms
self.assertEqual(obs, [
'Whole Genome Sequencing', 'Metagenomics',
'Transcriptome Analysis', 'Resequencing', 'Epigenetics',
'Synthetic Genomics', 'Forensic or Paleo-genomics',
'Gene Regulation Study', 'Cancer Genomics', 'Population Genomics',
'RNASeq', 'Exome Sequencing', 'Pooled Clone Sequencing', 'Other'
])
def test_user_defined_terms(self):
obs = self.ontology.user_defined_terms
self.assertEqual(obs, [])
def test_term_type(self):
obs = self.ontology.term_type('RNASeq')
self.assertEqual('ontology', obs)
obs = self.ontology.term_type('Sasquatch')
self.assertEqual('not_ontology', obs)
self.ontology.add_user_defined_term('Test Term')
obs = self.ontology.term_type('Test Term')
self.assertEqual('user_defined', obs)
def test_add_user_defined_term(self):
self.assertFalse('Test Term' in self.ontology.user_defined_terms)
pre = len(self.ontology.user_defined_terms)
self.ontology.add_user_defined_term('Test Term')
post = len(self.ontology.user_defined_terms)
self.assertTrue('Test Term' in self.ontology.user_defined_terms)
self.assertEqual(post - pre, 1)
def testContains(self):
self.assertTrue('Metagenomics' in self.ontology)
self.assertFalse('NotATerm' in self.ontology)
def __init__(self, preprocessed_data_id, study_title, study_abstract,
investigation_type, empty_value='no_data',
new_investigation_type=None, pmids=None, **kwargs):
self.preprocessed_data_id = preprocessed_data_id
self.study_title = study_title
self.study_abstract = study_abstract
self.investigation_type = investigation_type
self.empty_value = empty_value
self.new_investigation_type = new_investigation_type
self.sequence_files = []
self.study_xml_fp = None
self.sample_xml_fp = None
self.experiment_xml_fp = None
self.run_xml_fp = None
self.submission_xml_fp = None
self.pmids = pmids if pmids is not None else []
self.ebi_dir = self._get_ebi_dir()
if self.investigation_type == 'Other' and \
self.new_investigation_type is None:
raise ValueError("If the investigation_type is 'Other' you have "
" to specify a value for new_investigation_type.")
ontology = Ontology(convert_to_id('ENA', 'ontology'))
if ontology.term_type(self.investigation_type) == 'not_ontology':
raise ValueError("The investigation type must be part of ENA's "
"ontology, '%s' is not valid" %
self.investigation_type)
# dicts that map investigation_type to library attributes
lib_strategies = {'metagenome': 'POOLCLONE',
'mimarks-survey': 'AMPLICON'}
lib_selections = {'mimarks-survey': 'PCR'}
lib_sources = {}
# if the investigation_type is 'Other' we should use the value in
# the new_investigation_type attribute to retrieve this information
if self.investigation_type == 'Other':
key = self.new_investigation_type
else:
key = self.investigation_type
self.library_strategy = lib_strategies.get(key, "OTHER")
self.library_source = lib_sources.get(key, "METAGENOMIC")
self.library_selection = lib_selections.get(key, "unspecified")
# This allows addition of other arbitrary study metadata
self.additional_metadata = self._stringify_kwargs(kwargs)
# This will hold the submission's samples, keyed by the sample name
self.samples = {}
def __init__(self,
preprocessed_data_id,
study_title,
study_abstract,
investigation_type,
empty_value='no_data',
new_investigation_type=None,
pmids=None,
**kwargs):
self.preprocessed_data_id = preprocessed_data_id
self.study_title = study_title
self.study_abstract = study_abstract
self.investigation_type = investigation_type
self.empty_value = empty_value
self.new_investigation_type = new_investigation_type
self.sequence_files = []
self.study_xml_fp = None
self.sample_xml_fp = None
self.experiment_xml_fp = None
self.run_xml_fp = None
self.submission_xml_fp = None
self.pmids = pmids if pmids is not None else []
self.ebi_dir = self._get_ebi_dir()
if self.investigation_type == 'Other' and \
self.new_investigation_type is None:
raise ValueError("If the investigation_type is 'Other' you have "
" to specify a value for new_investigation_type.")
ontology = Ontology(convert_to_id('ENA', 'ontology'))
if ontology.term_type(self.investigation_type) == 'not_ontology':
raise ValueError("The investigation type must be part of ENA's "
"ontology, '%s' is not valid" %
self.investigation_type)
# dicts that map investigation_type to library attributes
lib_strategies = {
'metagenome': 'POOLCLONE',
'mimarks-survey': 'AMPLICON'
}
lib_selections = {'mimarks-survey': 'PCR'}
lib_sources = {}
# if the investigation_type is 'Other' we should use the value in
# the new_investigation_type attribute to retrieve this information
if self.investigation_type == 'Other':
key = self.new_investigation_type
else:
key = self.investigation_type
self.library_strategy = lib_strategies.get(key, "OTHER")
self.library_source = lib_sources.get(key, "METAGENOMIC")
self.library_selection = lib_selections.get(key, "unspecified")
# This allows addition of other arbitrary study metadata
self.additional_metadata = self._stringify_kwargs(kwargs)
# This will hold the submission's samples, keyed by the sample name
self.samples = {}
