Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite

This is a SQLite schema for representing Peptide Spectral Matches from mzid and mzML datatypes.

lib/galaxy/datatypes/proteomics.py

@@ -398,3 +398,28 @@ class XHunterAslFormat(Binary):
 class Sf3(Binary):
     """Class describing a Scaffold SF3 files"""
     file_ext = "sf3"
+
+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 sniff( self, filename ):
+        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()
+                tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+                result = c.execute( tables_query ).fetchall()
+                result = map( lambda x: x[0], result )
+                for table_name in mz_table_names:
+                    if table_name not in result:
+                        return False
+                return True
+            except Exception, e:
+                log.warn( '%s, sniff Exception: %s', self, e )
+        return False
+