Mercurial > repos > greg > ensure_synced
comparison ensure_synced.py @ 6:68ca17b451f2 draft
Uploaded
author | greg |
---|---|
date | Fri, 17 Dec 2021 17:46:31 +0000 |
parents | 81232205b179 |
children | 59edc91d0bea |
comparison
equal
deleted
inserted
replaced
5:a7be280fa304 | 6:68ca17b451f2 |
---|---|
33 args.update(url.query) | 33 args.update(url.query) |
34 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.' | 34 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.' |
35 self.conn = psycopg2.connect(**args) | 35 self.conn = psycopg2.connect(**args) |
36 | 36 |
37 def get_affy_ids_from_db(self): | 37 def get_affy_ids_from_db(self): |
38 cmd = "SELECT affy_id FROM sample WHERE genotype_id NOT IN (SELECT id FROM genotype WHERE coral_mlg_clonal_id = 'failed') ORDER BY affy_id;" | 38 cmd = "SELECT coral_mlg_rep_sample_id, coral_mlg_clonal_id FROM genotype WHERE coral_mlg_rep_sample_id IS NOT NULL AND coral_mlg_rep_sample_id != '' AND coral_mlg_clonal_id != 'failed' ORDER BY coral_mlg_rep_sample_id;” |
39 cur = self.conn.cursor() | 39 cur = self.conn.cursor() |
40 cur.execute(cmd) | 40 cur.execute(cmd) |
41 rows = cur.fetchall() | 41 rows = cur.fetchall() |
42 for row in rows: | 42 for row in rows: |
43 self.affy_ids_from_db.append(row[0]) | 43 self.affy_ids_from_db.append(row[0]) |