Merge pull request #359 from chrisfilo/enh/mysql

Added MySQL interface.

Author: satra

CHANGES

@@ -1,7 +1,7 @@
 Since last release
 ==================
 
-* ENH: New interfaces: nipy.Similarity, WatershedBEM
+* ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM
 
 * FIX: Afni outputs should inherit from TraitedSpec
 

nipype/interfaces/io.py

@@ -1113,6 +1113,7 @@ def capture_provenance():
 def push_provenance():
     pass
 
+    
 class SQLiteSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
     database_file = File(exists=True, mandatory = True)
     table_name = traits.Str(mandatory=True)
@@ -1158,3 +1159,61 @@ def _list_outputs(self):
         conn.commit()
         c.close()
         return None
+
+
+class MySQLSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
+    host = traits.Str('localhost', mandatory=True,
+                      requires=['username', 'password'],
+                      xor=['config'], usedefault=True)
+    config = File(mandatory=True, xor=['host'], desc="MySQL Options File (same format as my.cnf)")
+    database_name = traits.Str(mandatory=True, desc='Otherwise known as the schema name')
+    table_name = traits.Str(mandatory=True)
+    username = traits.Str()
+    password = traits.Str()
+
+
+class MySQLSink(IOBase):
+    """ Very simple frontend for storing values into MySQL database.
+
+        Examples
+        --------
+
+        >>> sql = MySQLSink(input_names=['subject_id', 'some_measurement'])
+        >>> sql.inputs.database_name = 'my_database'
+        >>> sql.inputs.table_name = 'experiment_results'
+        >>> sql.inputs.username = 'root'
+        >>> sql.inputs.password = 'secret'
+        >>> sql.inputs.subject_id = 's1'
+        >>> sql.inputs.some_measurement = 11.4
+        >>> sql.run() # doctest: +SKIP
+
+    """
+    input_spec = MySQLSinkInputSpec
+
+    def __init__(self, input_names, **inputs):
+
+        super(MySQLSink, self).__init__(**inputs)
+
+        self._input_names = filename_to_list(input_names)
+        add_traits(self.inputs, [name for name in self._input_names])
+
+    def _list_outputs(self):
+        """Execute this module.
+        """
+        import MySQLdb
+        if isdefined(self.inputs.config):
+            conn = MySQLdb.connect(db=self.inputs.database_name, 
+                                   read_default_file=self.inputs.config)
+        else:
+            conn = MySQLdb.connect(host=self.inputs.host,
+                                   user=self.inputs.username,
+                                   passwd=self.inputs.password,
+                                   db=self.inputs.database_name)
+        c = conn.cursor()
+        c.execute("REPLACE INTO %s (" % self.inputs.table_name +
+                  ",".join(self._input_names) + ") VALUES (" +
+                  ",".join(["%s"] * len(self._input_names)) + ")",
+                  [getattr(self.inputs, name) for name in self._input_names])
+        conn.commit()
+        c.close()
+        return None