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Fix lib/galaxy/datatypes/proteomics.py

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This commit is contained in:
Jim Johnson
2015-07-05 05:28:06 -05:00
parent ab4dc39a67
commit bc36230af3
1 changed files with 9 additions and 6 deletions
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lib/galaxy/datatypes/proteomics.py
+9 -6
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@@ -9,7 +9,10 @@ from galaxy.datatypes import data
from galaxy.datatypes.data import Text
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.binary import SQlite
from galaxy.datatypes.tabular import Tabular
from galaxy.util import sqlite
log = logging.getLogger(__name__)
@@ -399,16 +402,17 @@ class Sf3(Binary):
"""Class describing a Scaffold SF3 files"""
file_ext = "sf3"
class MzSQLite( SQlite ):
class MzSQlite( SQlite ):
"""Class describing a Proteomics Sqlite database """
file_ext = "mz.sqlite"
def set_meta( self, dataset, overwrite = True, **kwd ):
super( MzSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd )
def set_meta( self, dataset, overwrite=True, **kwd ):
super( MzSQlite, self ).set_meta( dataset, overwrite=overwrite, **kwd )
def sniff( self, filename ):
if super( MzSQLite, self ).sniff( filename ):
mz_table_names = [ "DBSequence", "Modification", "Peaks", "Peptide", "PeptideEvidence", "Score", "SearchDatabase", "Source", "SpectraData", "Spectrum", "SpectrumIdentification]
if super( MzSQlite, self ).sniff( filename ):
mz_table_names = ["DBSequence", "Modification", "Peaks", "Peptide", "PeptideEvidence", "Score", "SearchDatabase", "Source", "SpectraData", "Spectrum", "SpectrumIdentification"]
try:
conn = sqlite.connect( filename )
c = conn.cursor()
@@ -422,4 +426,3 @@ class MzSQLite( SQlite ):
except Exception, e:
log.warn( '%s, sniff Exception: %s', self, e )
return False