Mercurial > repos > greg > ensure_synced

comparison ensure_synced.py @ 7:59edc91d0bea draft

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author greg
date Fri, 17 Dec 2021 17:55:08 +0000
parents 68ca17b451f2
children aaa6ae7c64de
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6:68ca17b451f2 7:59edc91d0bea
3 3
4 import argparse 4 import argparse
5 import sys 5 import sys
6 6
7 import psycopg2 7 import psycopg2
8 8 from sqlalchemy import create_engine
9 from sqlalchemy import MetaData 9 from sqlalchemy import MetaData
10 from sqlalchemy import create_engine
11 from sqlalchemy.engine.url import make_url 10 from sqlalchemy.engine.url import make_url
12 11
13 metadata = MetaData() 12 metadata = MetaData()
14 13
15 SKIP_VALS = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT'] 14 SKIP_VALS = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
33 args.update(url.query) 32 args.update(url.query)
34 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.' 33 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
35 self.conn = psycopg2.connect(**args) 34 self.conn = psycopg2.connect(**args)
36 35
37 def get_affy_ids_from_db(self): 36 def get_affy_ids_from_db(self):
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;” 37 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() 38 cur = self.conn.cursor()
40 cur.execute(cmd) 39 cur.execute(cmd)
41 rows = cur.fetchall() 40 rows = cur.fetchall()
42 for row in rows: 41 for row in rows:
43 self.affy_ids_from_db.append(row[0]) 42 self.affy_ids_from_db.append(row[0])