class PubmedTests(unittest.TestCase):
EMAIL = '*****@*****.**'
def setUp(self):
self.pubmed = Pubmed(self.EMAIL,
progress_callback=progress_callback,
error_callback=error_callback)
def test_pubmed_object_creation(self):
self.assertRaises(ValueError, Pubmed, 'faulty_email')
def test_mesh_headings_to_class(self):
input_headings = [
'heading1 & heading2/heading3,heading4/*heading5',
'heading1/heading2/*heading3',
]
self.assertEqual(_mesh_headings_to_class(input_headings), 'heading1')
def test_date_to_iso(self):
# Correct inputs.
input_dates = [
'2015 Nov',
'2015',
'2015 Sep-Oct',
'2015 Fall',
]
correct_results = [
1446336000.0,
1420070400.0,
1441065600.0,
1441065600.0,
]
for date, result in zip(input_dates, correct_results):
self.assertEqual(_date_to_iso(date), result)
# Unexpected inputs.
unexpected_input = '2015 Unexpected'
self.assertWarns(
RuntimeWarning,
_date_to_iso,
unexpected_input,
)
self.assertEqual(type(_date_to_iso(unexpected_input)), type(np.nan))
def test_record_to_corpus(self):
mock_records = [
{
'FAU': ['Mock Author 1', 'Mock Author 2'],
'TI': 'Mock title',
'MH': ['heading1/heading2'],
'AB': 'Mock abstract',
'DP': '2015 Sep',
'PMID': 1,
},
]
correct_metas = np.array([[
'Mock Author 1 Mock Author 2', 'Mock title', 'heading1/heading2',
'Mock abstract', 'http://www.ncbi.nlm.nih.gov/pubmed/?term=1',
1441065600.0
]],
dtype=object)
correct_classes = np.array(['heading1'])
# Perform asserting.
meta_values, class_values = _records_to_corpus_entries(
mock_records, PUBMED_TEXT_FIELDS)
corpus = _corpus_from_records(mock_records, PUBMED_TEXT_FIELDS)
self.assertCountEqual(meta_values[0], correct_metas[0])
self.assertCountEqual(class_values, correct_classes)
self.assertIsNotNone(corpus)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
def test_pubmed_search_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
self.pubmed._search_for_records(terms=test_terms,
authors=authors,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end)
# The only certain check is to make sure we got all the parameters.
self.assertIsNotNone(self.pubmed.record_id_list)
self.assertIsNotNone(self.pubmed.search_record_count)
self.assertIsNotNone(self.pubmed.search_record_web_env)
self.assertIsNotNone(self.pubmed.search_record_query_key)
# Faulty input check.
self.assertRaises(ValueError,
self.pubmed._search_for_records,
terms=test_terms,
authors=None,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
def test_pubmed_retrieve_record_batch(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
offset = 0
num_requested_records = 5
# Attempt to retrieve without searching first.
self.assertRaises(ValueError, self.pubmed._retrieve_record_batch,
offset, num_requested_records)
# Must search for records first.
self.pubmed._search_for_records(test_terms, authors, pub_date_start,
pub_date_end)
# Retrieve the records.
data = self.pubmed._retrieve_record_batch(offset,
num_requested_records)
self.assertEqual(len(data), num_requested_records)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(test_terms, authors, pub_date_start,
pub_date_end)
# Retrieve the records and build a corpus.
corpus = self.pubmed._retrieve_records(num_records)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted(
[field_name for field_name, field_tag in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name for m in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_records_no_cache(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(test_terms, authors, pub_date_start,
pub_date_end)
# Retrieve the records and build a corpus.
corpus = self.pubmed._retrieve_records(num_records, use_cache=False)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted(
[field_name for field_name, field_tag in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name for m in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_download_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Retrieve the records and build a corpus.
corpus = self.pubmed.download_records(test_terms, authors,
pub_date_start, pub_date_end,
num_records)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted(
[field_name for field_name, field_tag in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name for m in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch_exception)
def test_entrez_search_exceptions(self):
# Search exception.
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
self.assertWarns(RuntimeWarning,
self.pubmed._search_for_records,
terms=test_terms,
authors=authors,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch_exception)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_record_batch_exception(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(test_terms, authors, pub_date_start,
pub_date_end)
self.assertWarns(RuntimeWarning,
self.pubmed._retrieve_records,
num_records,
use_cache=False)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost_exception)
def test_pubmed_epost_exception(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(test_terms, authors, pub_date_start,
pub_date_end)
self.assertWarns(RuntimeWarning,
self.pubmed._retrieve_records,
num_records,
use_cache=False)
class PubmedTests(unittest.TestCase):
EMAIL = '*****@*****.**'
def setUp(self):
self.pubmed = Pubmed(
self.EMAIL,
progress_callback=progress_callback,
error_callback=error_callback
)
def test_pubmed_object_creation(self):
self.assertRaises(
ValueError,
Pubmed,
'faulty_email'
)
def test_mesh_headings_to_class(self):
input_headings = [
'heading1 & heading2/heading3,heading4/*heading5',
'heading1/heading2/*heading3',
]
self.assertEqual(_mesh_headings_to_class(input_headings), 'heading1')
def test_date_to_iso(self):
# Correct inputs.
input_dates = [
'2015 Nov',
'2015',
'2015 Sep-Oct',
'2015 Fall',
]
correct_results = [
'2015-11-01',
'2015-01-01',
'2015-09-01',
'2015-09-01',
]
for date, result in zip(input_dates, correct_results):
self.assertEqual(_date_to_iso(date), result)
# Unexpected inputs.
unexpected_input = '2015 Unexpected'
self.assertWarns(
RuntimeWarning,
_date_to_iso,
unexpected_input,
)
self.assertEqual(type(_date_to_iso(unexpected_input)), type(np.nan))
def test_record_to_corpus(self):
mock_records = [
{
'FAU': ['Mock Author 1', 'Mock Author 2'],
'TI': 'Mock title',
'MH': ['heading1/heading2'],
'AB': 'Mock abstract',
'DP': '2015 Sep',
'PMID': 1,
},
]
correct_metas = np.array([
[
'Mock Author 1 Mock Author 2',
'Mock title',
'heading1/heading2',
'Mock abstract',
'http://www.ncbi.nlm.nih.gov/pubmed/?term=1',
1441065600.0
]
], dtype=object)
correct_classes = np.array([
'heading1'
])
# Perform asserting.
corpus = _corpus_from_records(mock_records, PUBMED_TEXT_FIELDS)
meta_values, class_values = _records_to_corpus_entries(
mock_records,
PUBMED_TEXT_FIELDS,
corpus.domain[PUBMED_FIELD_DATE]
)
self.assertCountEqual(meta_values[0], correct_metas[0])
self.assertCountEqual(class_values, correct_classes)
self.assertIsNotNone(corpus)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
def test_pubmed_search_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
self.pubmed._search_for_records(
terms=test_terms,
authors=authors,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end
)
# The only certain check is to make sure we got all the parameters.
self.assertIsNotNone(self.pubmed.record_id_list)
self.assertIsNotNone(self.pubmed.search_record_count)
self.assertIsNotNone(self.pubmed.search_record_web_env)
self.assertIsNotNone(self.pubmed.search_record_query_key)
# Faulty input check.
self.assertRaises(
ValueError,
self.pubmed._search_for_records,
terms=test_terms,
authors=None,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end
)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
def test_pubmed_retrieve_record_batch(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
offset = 0
num_requested_records = 5
# Attempt to retrieve without searching first.
self.assertRaises(
ValueError,
self.pubmed._retrieve_record_batch,
offset,
num_requested_records
)
# Must search for records first.
self.pubmed._search_for_records(
test_terms,
authors,
pub_date_start,
pub_date_end
)
# Retrieve the records.
data = self.pubmed._retrieve_record_batch(
offset,
num_requested_records
)
self.assertEqual(len(data), num_requested_records)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(
test_terms,
authors,
pub_date_start,
pub_date_end
)
# Retrieve the records and build a corpus.
corpus = self.pubmed._retrieve_records(num_records)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted([field_name
for field_name, field_tag
in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name
for m
in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_records_no_cache(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(
test_terms,
authors,
pub_date_start,
pub_date_end
)
# Retrieve the records and build a corpus.
corpus = self.pubmed._retrieve_records(
num_records,
use_cache=False
)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted([field_name
for field_name, field_tag
in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name
for m
in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_download_records(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Retrieve the records and build a corpus.
corpus = self.pubmed.download_records(
test_terms,
authors,
pub_date_start,
pub_date_end,
num_records
)
self.assertEqual(len(corpus), num_records)
meta_fields = sorted([field_name
for field_name, field_tag
in PUBMED_TEXT_FIELDS])
test_meta_fields = sorted([m.name
for m
in corpus.domain.metas])
self.assertEqual(meta_fields, test_meta_fields)
@patch('Bio.Entrez.esearch', mock_entrez.esearch_exception)
def test_entrez_search_exceptions(self):
# Search exception.
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
self.assertWarns(
RuntimeWarning,
self.pubmed._search_for_records,
terms=test_terms,
authors=authors,
pub_date_start=pub_date_start,
pub_date_end=pub_date_end
)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch_exception)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost)
def test_pubmed_retrieve_record_batch_exception(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(
test_terms,
authors,
pub_date_start,
pub_date_end
)
self.assertWarns(
RuntimeWarning,
self.pubmed._retrieve_records,
num_records,
use_cache=False
)
@patch('Bio.Entrez.esearch', mock_entrez.esearch)
@patch('Bio.Entrez.read', mock_entrez.read)
@patch('Bio.Entrez.efetch', mock_entrez.efetch)
@patch('Bio.Medline.parse', mock_entrez.parse)
@patch('Bio.Entrez.epost', mock_entrez.epost_exception)
def test_pubmed_epost_exception(self):
test_terms = ['orchid']
authors = []
pub_date_start = '2011/07/07'
pub_date_end = '2014/07/07'
num_records = 5
# Must search for records first.
self.pubmed._search_for_records(
test_terms,
authors,
pub_date_start,
pub_date_end
)
self.assertWarns(
RuntimeWarning,
self.pubmed._retrieve_records,
num_records,
use_cache=False
)
