fixes

system/dataset.py

@@ -57,8 +57,8 @@ class Dataset:
         else:
             raise ValueError, "Array input must be of ArrayType"
                         
-    def __str__(self):
-        return self._name + ":\n" + "Dim names: " +  self._dims.__str__()
+    #def __str__(self):
+    #    return self._name + ":\n" + "Dim names: " +  self._dims.__str__()
 
     def __iter__(self):
         """Returns an iterator over dimensions of dataset."""
@@ -181,7 +181,7 @@ class Dataset:
         if idents==None:
             index = array_sort(self._map[dim].values())
         else:
-            index = [self._map[dim][key] for key in idents]
+            index = [self._map[dim][key] for key in idents if self._map[dim].has_key(key)]
         return asarray(index)        
         
 class CategoryDataset(Dataset):
@@ -236,7 +236,7 @@ class GraphDataset(Dataset):
         
     def asnetworkx(self,nx_type='graph'):
         dim = self.get_dim_name()[0]
-        ids = self.get_identifiers(dim)
+        ids = self.get_identifiers(dim,sorted=True)
         adj_mat = self.asarray()
         G = self._graph_from_adj_matrix(adj_mat,labels=ids)
         self.has_graph = True
@@ -271,11 +271,6 @@ class GraphDataset(Dataset):
         return G
 
 Dataset._all_dims=set()
-
-class Selection:
-    """Handles selected identifiers along each dimension of a dataset"""
-    def __init__(self):
-        self.current_selection={}
         
 class ReverseDict(dict):
     """
@@ -300,7 +295,7 @@ def to_file(filepath,dataset,name=None):
     """
     if not name:
         name = dataset._name
-    data = shelve.open(filepath,protocol=2)
+    data = shelve.open(filepath,flag='c',protocol=2)
     if data: #we have an append 
         names = data.keys()
         if name in names:
@@ -311,7 +306,7 @@ def to_file(filepath,dataset,name=None):
 
 def from_file(filepath):
     """Read dataset from file """
-    data = shelve.open(filepath)
+    data = shelve.open(filepath,flag='r')
     out_data = []
     for name in data.keys():
         sub_data = data[name]
@@ -324,3 +319,7 @@ def from_file(filepath):
             
     return out_data
     
+class Selection:
+    """Handles selected identifiers along each dimension of a dataset"""
+    def __init__(self):
+        self.current_selection={}