Mercurial > repos > devteam > cummerbund
comparison cummeRbund_options.py @ 2:ac2ebc60ef5d draft
Uploaded corrected dynamic options
author | devteam |
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date | Mon, 16 Mar 2015 15:43:02 -0400 |
parents | f3012521ea79 |
children | c3b54a4b7741 |
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1:f3012521ea79 | 2:ac2ebc60ef5d |
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1 from galaxy import eggs | 1 import sqlite3 |
2 eggs.require( 'SQLAlchemy' ) | |
3 eggs.require( 'pysqlite>=2' ) | |
4 from sqlalchemy import * | |
5 from sqlalchemy.sql import and_ | |
6 from sqlalchemy.orm import sessionmaker | |
7 from sqlalchemy.orm import scoped_session | |
8 | 2 |
9 def get_genes( database_path ): | 3 def get_genes( database_path ): |
10 dburi = 'sqlite:///%s' % database_path | 4 conn = sqlite3.connect( database_path ) |
11 engine = create_engine( dburi ) | 5 gene_ids = conn.execute( 'SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name' ) |
12 meta = MetaData( bind=engine ) | |
13 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) ) | |
14 gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' ) | |
15 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ] | 6 return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ] |
16 | 7 |
17 def get_samples( database_path ): | 8 def get_samples( database_path ): |
18 dburi = 'sqlite:///%s' % database_path | 9 conn = sqlite3.connect( database_path ) |
19 engine = create_engine( dburi ) | 10 samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' ) |
20 meta = MetaData( bind=engine ) | |
21 db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) ) | |
22 samples = db_session.execute( 'select sample_name from samples order by sample_name' ) | |
23 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ] | 11 return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ] |