def test_configurable_cachedir(self):
""" Test that `cachedir` keyword argument is fully supported in modes:
cachedir == 'default' <-- assumed working since other tests use this.
cachedir is None
cachedir is 'some/path'
cachedir is '~/path'
"""
cachedir = TEST_CACHEDIR
# start with cachedir==None; test that no cachedir is created.
fetch = MedGenFetcher(cachedir=None)
assert not os.path.exists(cachedir)
fetch = MedGenFetcher(cachedir=cachedir)
assert os.path.exists(cachedir)
os.unlink(fetch._cache_path)
os.rmdir(cachedir)
fetch = MedGenFetcher(cachedir='~/testcachedir')
assert os.path.exists(os.path.expanduser('~/testcachedir'))
os.unlink(fetch._cache_path)
os.rmdir(os.path.expanduser('~/testcachedir'))
class TestMedGenFetcher(unittest.TestCase):
def setUp(self):
self.fetch = MedGenFetcher()
def tearDown(self):
pass
def test_fetch_concepts_for_known_gene(self):
hugo = 'ACVRL1'
result = self.fetch.uids_by_term(hugo + '[gene]')
assert result is not None
assert result[0] == '324960'
def test_fetch_concepts_for_incorrect_term(self):
term = 'AVCRL'
result = self.fetch.uids_by_term(term + '[gene]')
assert result == []
def test_configurable_cachedir(self):
""" Test that `cachedir` keyword argument is fully supported in modes:
cachedir == 'default' <-- assumed working since other tests use this.
cachedir is None
cachedir is 'some/path'
cachedir is '~/path'
"""
cachedir = TEST_CACHEDIR
# start with cachedir==None; test that no cachedir is created.
fetch = MedGenFetcher(cachedir=None)
assert not os.path.exists(cachedir)
fetch = MedGenFetcher(cachedir=cachedir)
assert os.path.exists(cachedir)
os.unlink(fetch._cache_path)
os.rmdir(cachedir)
fetch = MedGenFetcher(cachedir='~/testcachedir')
assert os.path.exists(os.path.expanduser('~/testcachedir'))
os.unlink(fetch._cache_path)
os.rmdir(os.path.expanduser('~/testcachedir'))
import unittest, os
from metapub import MedGenFetcher
hugos = ['ACVRL1', 'FOXP3', 'ATM']
TEST_CACHEDIR = 'tests/testcachedir'
fetch = MedGenFetcher()
class TestMedGenFetcher(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_fetch_concepts_for_known_gene(self):
hugo = 'ACVRL1'
result = fetch.uids_by_term(hugo + '[gene]')
assert result is not None
assert result[0] == '324960'
def test_fetch_concepts_for_incorrect_term(self):
term = 'AVCRL'
result = fetch.uids_by_term(term + '[gene]')
assert result == []
def test_attributes_on_medgen_concept(self):
concept = fetch.concept_by_uid(324960)
from __future__ import absolute_import, print_function, unicode_literals
import sys
from metapub import MedGenFetcher
# example of CUID: C0000039
try:
cui = sys.argv[1]
except IndexError:
print('Supply a ConceptID (CUI) to this script as its argument.')
sys.exit()
####
import logging
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("eutils").setLevel(logging.WARNING)
####
fetch = MedGenFetcher()
uid = fetch.uid_for_cui(cui)
print(uid)
from __future__ import absolute_import, print_function, unicode_literals
import sys
from metapub import MedGenFetcher
from metapub import PubMedFetcher
try:
cui = sys.argv[1]
except IndexError:
print("Supply CUI (Concept ID) as argument to this script.")
sys.exit()
pmfetch = PubMedFetcher()
fetch = MedGenFetcher()
concept = fetch.concept_by_cui(cui)
print("#### CUI: %s" % cui)
print("# %s" % concept.title)
print("#")
print("#")
pmids = fetch.pubmeds_for_cui(cui)
for pmid in pmids:
print("#### %s" % pmid)
pma = pmfetch.article_by_pmid(pmid)
print(pma.year, pma.title, pma.journal)
print("")
def setUp(self):
self.fetch = MedGenFetcher()
HAS_GENES_ONLY = False
try:
term = sys.argv[1]
except IndexError:
print('Supply a Hugo gene name to this script as its argument.')
sys.exit()
####
import logging
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("eutils").setLevel(logging.INFO)
####
fetch = MedGenFetcher()
uids = fetch.uids_by_term(term)
print('Found %i Medgen concepts for term "%s"' % (len(uids), term))
# TODO: Term Hierarchy Children (only 1 tier below), Term Hierarchy Parents (only 1 tier above)
headers = ['CUI', 'Title', 'Semantic Type', 'MedGenUID',
'OMIM ID', 'Modes of Inheritance', 'Assoc Genes', 'PMIDS' ]
table = []
def _join_or_NA(some_list, select=None, joiner=','):
'returns a joined string or NA if empty'
if some_list and select:
return joiner.join(item[select] for item in some_list)
elif some_list:
try:
term = sys.argv[1]
except IndexError:
print(
'Supply a disease/syndrome/condition name in quotation marks as the argument to this script.'
)
sys.exit()
####
import logging
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("eutils").setLevel(logging.INFO)
####
fetch = MedGenFetcher()
uids = fetch.uids_by_term(term)
print(uids)
headers = [
'CUI',
'Title',
'Semantic Type',
'MedGenUID',
'OMIM ID',
'Modes of Inheritance',
'Assoc Genes',
]
table = []
from tabulate import tabulate
from metapub import MedGenFetcher
try:
input_gene = sys.argv[1]
except IndexError:
print('Supply a Hugo gene name to this script as its argument.')
sys.exit()
####
import logging
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("eutils").setLevel(logging.INFO)
####
fetch = MedGenFetcher()
uids = fetch.uids_by_term(input_gene + '[gene]')
print(uids)
# TODO: Term Hierarchy Children (only 1 tier below), Term Hierarchy Parents (only 1 tier above)
headers = [
'CUI',
'Hugo',
'Title',
'Semantic Type',
'MedGenUID',
'OMIM ID',
'Modes of Inheritance',
'Assoc Genes',
]