fix bugs in import data

py/dt.py

@@ -1595,7 +1595,7 @@ def idco_code_to_idca_dummy(self, oldvarname, newvarname, complib='zlib', comple
 
 
 	@staticmethod
-	def CSV_idco(filename, caseid=None, choice=None, weight=None, savename=None, alts={}, csv_args=(), csv_kwargs={}, complib='zlib', complevel=1, **kwargs):
+	def CSV_idco(filename, caseid=None, choice=None, weight=None, savename=None, alts={}, csv_args=(), csv_kwargs={}, complib='zlib', complevel=1, overwrite=0, **kwargs):
 		'''Creates a new larch DT based on an :ref:`idco` CSV data file.
 
 		The input data file should be an :ref:`idco` data file, with the first line containing the column headings.
@@ -1646,22 +1646,31 @@ def CSV_idco(filename, caseid=None, choice=None, weight=None, savename=None, alt
 
 
 		self = DT(filename=savename, complevel=complevel, complib=complib, **kwargs)
-		self.import_idco(filename, *csv_args, caseid_column=None, **csv_kwargs)
+		self.import_idco(filename, *csv_args, caseid_column=None, overwrite=overwrite, **csv_kwargs)
 
 		h5filters = _tb.Filters(complevel=complevel, complib=complib)
 
 
 		altscodes_seq = sorted(alts)
-
+
+		if overwrite>0 and 'altids' in self.alts._v_node._v_children:
+			self.h5f.remove_node(self.alts._v_node, 'altids', recursive=True)
 		h5altids = self.h5f.create_carray(self.alts._v_node, 'altids', _tb.Int64Atom(), shape=(len(alts),), filters=h5filters, title='elemental alternative code numbers')
+
 		h5altids[:] = numpy.asarray(altscodes_seq)
 
+		if overwrite>0 and 'names' in self.alts._v_node._v_children:
+			self.h5f.remove_node(self.alts._v_node, 'names', recursive=True)
 		h5altnames = self.h5f.create_vlarray(self.alts._v_node, 'names', _tb.VLUnicodeAtom(), filters=h5filters, title='elemental alternative names')
 		for an in altscodes_seq:
 			h5altnames.append( str(alts[an][0]) )
+
 		# Weight
 		if weight:
+			if overwrite>0 and '_weight_' in self.idco._v_node._v_children:
+				self.h5f.remove_node(self.idco._v_node, '_weight_', recursive=True)
 			self.h5f.create_soft_link(self.idco._v_node, '_weight_', target='/larch/idco/'+weight)
+
 		# Choice
 		try:
 			self.choice_idco = {a:aa[2] for a,aa in alts.items()}
@@ -2063,7 +2072,7 @@ def import_dbf(cls, dbffile, omxfile, shape, o, d, cols, smallest_zone_number=1)
 		return omx
 
 
-	def import_idco(self, filepath_or_buffer, caseid_column=None, *args, **kwargs):
+	def import_idco(self, filepath_or_buffer, caseid_column=None, overwrite=0, *args, **kwargs):
 		"""Import an existing CSV or similar file in idco format into this HDF5 file.
 		
 		This function relies on :func:`pandas.read_csv` to read and parse the input data.
@@ -2081,6 +2090,10 @@ def import_idco(self, filepath_or_buffer, caseid_column=None, *args, **kwargs):
 			If given, this is the column of the input data file to use as caseids.  It must be 
 			given if the caseids do not already exist in the HDF5 file.  If it is given and
 			the caseids do already exist, a `LarchError` is raised.
+		overwrite : int
+			If positive, existing data with same name will be overwritten.  If zero (the default)
+			existing data with same name will be not overwritten and tables.exceptions.NodeError
+			will be raised.  If negative, existing data will not be overwritten but no errors will be raised.
 		
 		Raises
 		------
@@ -2142,12 +2155,9 @@ def convert_datetime_time_to_epoch_seconds(tm):
 						col_array = df[col].astype('S{}'.format(maxlen)).values
 						tb_atom = _tb.Atom.from_dtype(col_array.dtype)
 				col = make_valid_identifier(col)
-#				if not col.isidentifier():
-#					log.warn("  column %s is not a valid python identifier, converting to _%s",col,col)
-#					col = "_"+col
-#				if keyword.iskeyword(col):
-#					log.warn("  column %s is a python keyword, converting to _%s",col,col)
-#					col = "_"+col
+				if overwrite and col in self.idco._v_node._v_children:
+					# delete the old data
+					self.h5f.remove_node(self.idco._v_node, col, recursive=True)
 				h5var = self.h5f.create_carray(self.idco._v_node, col, tb_atom, shape=col_array.shape)
 				h5var[:] = col_array
 				if original_source:

py/omx.py

@@ -104,7 +104,7 @@ def crop(self, shape0, shape1=None, *, complevel=1, complib='zlib'):
 				self.add_lookup(i, self.lookup._v_children[i][:shape0], overwrite=True, complevel=complevel, complib=complib, ignore_shape=True)
 			elif self.lookup[i].shape[1] == start1:
 				self.add_lookup(i, self.lookup._v_children[i][:shape1], overwrite=True, complevel=complevel, complib=complib, ignore_shape=True)
-
+		self.shape = (shape0, shape1)
 
 
 	def add_blank_lookup(self, name, atom=None, shape=None, complevel=1, complib='zlib', **kwargs):