comparison ensure_synced.py @ 6:68ca17b451f2 draft

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5:a7be280fa304

        args.update(url.query)
        assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
        self.conn = psycopg2.connect(**args)

    def get_affy_ids_from_db(self):
        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;"
        cur = self.conn.cursor()
        cur.execute(cmd)
        rows = cur.fetchall()
        for row in rows:
            self.affy_ids_from_db.append(row[0])

6:68ca17b451f2

        args.update(url.query)
        assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
        self.conn = psycopg2.connect(**args)

    def get_affy_ids_from_db(self):
        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;”
        cur = self.conn.cursor()
        cur.execute(cmd)
        rows = cur.fetchall()
        for row in rows:
            self.affy_ids_from_db.append(row[0])