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report on info (pubs only) at the organ level
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# encoding: utf-8 | ||
# | ||
# | ||
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import pymysql, argparse, getpass, sys, csv | ||
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def _get_names(connection, bmid): | ||
# Get hgnc name | ||
cursor = connection.cursor() | ||
cursor.execute('SELECT name FROM biomarker_names WHERE biomarker_id = %s and isHgnc = 1', (bmid,)) | ||
if cursor.rowcount > 0: | ||
hgnc_name = cursor.fetchone()[0] | ||
else: | ||
hgnc_name = '«unknown»' | ||
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# Get default name | ||
cursor = connection.cursor() | ||
cursor.execute('SELECT name FROM biomarker_names WHERE biomarker_id = %s and isPrimary = 1', (bmid,)) | ||
if cursor.rowcount > 0: | ||
default_name = cursor.fetchone()[0] | ||
else: | ||
default_name = '«unknown»' | ||
return hgnc_name, default_name | ||
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def generate_publications_report(connection): | ||
with open('organ-pubs.csv', 'w', newline='', encoding='utf-8') as csvfile: | ||
writer = csv.writer(csvfile) | ||
writer.writerow(['BM ID', 'HGNC name', 'Default name', 'Organ', 'PubMed ID', 'Pub title']) | ||
cursor = connection.cursor() | ||
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cursor.execute(''' | ||
SELECT organ_data_publications.publication_id, organ_data_publications.organ_data_id | ||
FROM organ_data_publications | ||
''') | ||
for publication_id, organ_data_id in cursor.fetchall(): | ||
cursor2 = connection.cursor() | ||
cursor2.execute(''' | ||
SELECT | ||
organ_data.biomarker_id, | ||
organs.name, | ||
publications.pubmed_id, | ||
publications.title | ||
FROM | ||
organs, publications, organ_data | ||
WHERE | ||
publications.id = %s AND | ||
organ_data.id = %s AND | ||
organ_data.organ_id = organs.id | ||
''', (publication_id, organ_data_id)) | ||
for bmid, organ_name, pubmed, pub_title in cursor2.fetchall(): | ||
hgnc_name, default_name = _get_names(connection, bmid) | ||
writer.writerow([bmid, hgnc_name, default_name, organ_name, pubmed, pub_title]) | ||
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def generate_reports(connection): | ||
generate_publications_report(connection) | ||
# No need for this one, there's only 1 | ||
# generate_resources_report(connection) | ||
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def main(): | ||
parser = argparse.ArgumentParser(description="Show organ-specifics'") | ||
parser.add_argument('-H', '--host', default='localhost', help='MySQL host; default %(default)s') | ||
parser.add_argument('-D', '--database', default='cbmdb', help='MySQL database, default %(default)s') | ||
parser.add_argument('-u', '--user', default='cbmdb', help='MySQL user; default %(default)s') | ||
parser.add_argument('-p', '--password', help='MySQL password; will be prompted if not given') | ||
args = parser.parse_args() | ||
user = args.user | ||
password = args.password if args.password else getpass.getpass(u'Password for MySQL user "{}": '.format(user)) | ||
connection = pymysql.connect(host=args.host, user=user, password=password, database=args.database) | ||
generate_reports(connection) | ||
sys.exit(0) | ||
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if __name__ == '__main__': | ||
main() |