def get_pubmed_data(self, max=None, pmids=None):
if pmids:
query_pmids = pmids
else:
all_pmids = datasources.ochsner.get_all_pmids()
if not max:
max = len(all_pmids)
query_pmids = all_pmids[0:max]
pubmed_request = """pubmed.pubmed_id,
ochsner.found_geo_data_submission,
ochsner.found_arrayexpress_data_submission,
ochsner.found_smd_data_submission,
ochsner.found_any_data_submission,
ochsner.list_data_ids,
pubmed.is_humans,
pubmed.is_animals,
pubmed.is_mice,
pubmed.is_fungi,
pubmed.is_bacteria,
pubmed.is_plants,
pubmed.is_viruses,
pubmed.is_cultured_cells,
pubmed.is_cancer,
pubmed.date_published,
pubmed.authors,
pubmed.journal,
pubmed.number_times_cited_in_pmc,
isi.impact_factor
"""
data = dataset.collect_data(query_pmids, pubmed_request)
csv_data = dataset.csv_format(data)
if False:
FILENAME = "../../results/aim2b_part2_pubmed.txt"
writer = open(FILENAME, "w")
for row in csv_data:
writer.write("\t".join([str(col) for col in row]))
writer.write("\r\n")
writer.close()
assert_equals(len(csv_data), 1 + len(query_pmids))
return (csv_data)
def get_pubmed_data(self, max=None, pmids=None):
if pmids:
query_pmids = pmids
else:
all_pmids = datasources.ochsner.get_all_pmids()
if not max:
max = len(all_pmids)
query_pmids = all_pmids[0:max]
pubmed_request = """pubmed.pubmed_id,
ochsner.found_geo_data_submission,
ochsner.found_arrayexpress_data_submission,
ochsner.found_smd_data_submission,
ochsner.found_any_data_submission,
ochsner.list_data_ids,
pubmed.is_humans,
pubmed.is_animals,
pubmed.is_mice,
pubmed.is_fungi,
pubmed.is_bacteria,
pubmed.is_plants,
pubmed.is_viruses,
pubmed.is_cultured_cells,
pubmed.is_cancer,
pubmed.date_published,
pubmed.authors,
pubmed.journal,
pubmed.number_times_cited_in_pmc,
isi.impact_factor
"""
data = dataset.collect_data(query_pmids, pubmed_request)
csv_data = dataset.csv_format(data)
if False:
FILENAME = "../../results/aim2b_part2_pubmed.txt"
writer = open(FILENAME, "w")
for row in csv_data:
writer.write("\t".join([str(col) for col in row]))
writer.write("\r\n")
writer.close()
assert_equals(len(csv_data), 1+len(query_pmids))
return(csv_data)
def test_collect_data(self):
response = dataset.collect_data(gold_pmids, test_data_request)
assert_equals(response, test_data_collect_response)
def test_get_back_pmid(self):
response = dataset.collect_data(gold_pmids, "pubmed.pubmed_id")
assert_equals(response, [['pmid'] + gold_pmids])
def test_collect_data(self):
response = dataset.collect_data(gold_pmids, test_data_request)
assert_equals(response, test_data_collect_response)
def test_get_back_pmid(self):
response = dataset.collect_data(gold_pmids, "pubmed.pubmed_id")
assert_equals(response, [['pmid'] + gold_pmids])
def test_collect_data(self):
# gold_pmids = datasources.portal_pmids.get_all_pmids()
response = dataset.collect_data(gold_pmids, test_data_request)
assert_equals(response, test_data_response)
