<gh_stars>1-10
import MySQLdb
import os
from splicegraph import *


spliceCalcs={'HUMAN_SPLICE_03':
             TableGroup(db='HUMAN_SPLICE_03',suffix='JUN03',clusters='cluster_JUN03',
                        exons='exon_formJUN03',splices='splice_verification_JUN03',
                        genomic='genomic_cluster_JUN03',mrna='mrna_seqJUN03',
                        protein='protein_seqJUN03'),
             'HUMAN_SPLICE':
             TableGroup(db='HUMAN_SPLICE',suffix='jan02',clusters='cluster_jan02',
                        exons='HUMAN_ISOFORMS.exon_form_4',splices='splice_verification_jan02',
                        genomic='genomic_cluster_jan02',mrna='HUMAN_ISOFORMS.mrna_seq_4',
                        protein='HUMAN_ISOFORMS.protein_seq_4'),
             'MOUSE_SPLICE':
             TableGroup(db='MOUSE_SPLICE',suffix='jan02',clusters='cluster_jan02',
                        exons='MOUSE_ISOFORMS.exon_form_2',splices='splice_verification_jan02',
                        genomic='genomic_cluster_jan02',mrna='MOUSE_ISOFORMS.mrna_seq_2',
                        protein='MOUSE_ISOFORMS.protein_seq_2'),
             'MOUSE_SPLICE_03':
             TableGroup(db='MOUSE_SPLICE_03',suffix='JUN03',clusters='cluster_JUN03',
                        exons='exon_formJUN03',splices='splice_verification_JUN03',
                        genomic='genomic_cluster_JUN03',mrna='mrna_seqJUN03',
                        protein='protein_seqJUN03')
             }


def getUserCursor(db):
    'get a cursor as the current user'
    db=MySQLdb.connect(db=db,read_default_file=os.environ['HOME']+'/.my.cnf',compress=True)
    return db.cursor()

             
def getSpliceGraphFromDB(dbgroup,loadAll=False):
    """load data from MySQL using the designated database table group.
    If loadAll true, then load the entire splice graph into memory."""
    cursor=getUserCursor(dbgroup.db)
    import sys
    print >>sys.stderr,'Reading database schema...'
    idDict={}
    tables=describeDBTables(dbgroup.db,cursor,idDict)
    if hasattr(dbgroup,'suffix'):
        tables=suffixSubset(tables,dbgroup.suffix) # SET OF TABLES ENDING IN JUN03
        idDict=indexIDs(tables) # CREATE AN INDEX OF THEIR PRIMARY KEYS
    for t in dbgroup.values():
        if t is not None and '.' in t and t not in tables: # THIS TABLE COMES FROM ANOTHER DATABASE...
            tables[t]=SQLTable(t,cursor) # SO GET IT FROM OTHER DATABASE

    # LOAD DATA & BUILD THE SPLICE GRAPH
    return loadSpliceGraph(tables,dbgroup.clusters,dbgroup.exons,dbgroup.splices,
                           dbgroup.genomic,dbgroup.mrna,dbgroup.protein,loadAll)


def localCopy(localFile,cpCommand):
    'if not already present on local file location, run cpCommand'
    if not os.access(localFile,os.R_OK):
        cmd=cpCommand % localFile
        print 'copying data:',cmd
        exit_code=os.system(cmd)
        if exit_code!=0:
            raise OSError((exit_code,'command failed: %s' % cmd))
    return localFile
