report on info (pubs only) at the organ level

setup.cfg

@@ -50,3 +50,4 @@ console_scripts =
     zombie              = edrn.bmdb.maureen_zombie_report:main
     kristen             = edrn.bmdb.kristen_report:main
     rdfcompare          = edrn.bmdb.compare:main
+    organ-specifics     = edrn.bmdb.organ_specifics:main

src/edrn/bmdb/organ_specifics.py

@@ -0,0 +1,78 @@
+# encoding: utf-8
+#
+# 
+
+import pymysql, argparse, getpass, sys, csv
+
+
+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»'
+
+    # 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
+
+
+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()
+
+        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])
+
+
+def generate_reports(connection):
+    generate_publications_report(connection)
+    # No need for this one, there's only 1
+    # generate_resources_report(connection)
+
+
+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)
+
+
+if __name__ == '__main__':
+    main()