--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py	Tue Aug 23 14:54:04 2016 -0400
@@ -0,0 +1,86 @@
+import os
+import sys
+import tempfile
+
+from icqsol.shapes.icqShapeManager import ShapeManager
+from icqsol.bem.icqLaplaceSolver import LaplaceSolver
+
+PLY = 'ply'
+POLYDATA = 'POLYDATA'
+VTK = 'vtk'
+
+
+def asbool(val):
+    return str(val).lower() in ['yes', 'true']
+
+
+def get_format_and_type(galaxy_ext):
+    # Define the output file format and type.
+    format = None
+    datatype = None
+    if galaxy_ext in ['vtkascii', 'vtkbinary']:
+        format = VTK
+    elif galaxy_ext in ['plyascii', 'plybinary']:
+        format = PLY
+    if galaxy_ext in ['vtkascii', 'plyascii']:
+        datatype = 'ascii'
+    elif galaxy_ext in ['vtkbinary', 'plybinary']:
+        datatype = 'binary'
+    return format, datatype
+
+
+def get_input_file_path(tmp_dir, input_file, format):
+    """
+    iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
+    writing files, so the Galaxy dataset naming convention of
+    setting all file extensions as .dat must be handled.
+    """
+    file_path = get_temporary_file_path(tmp_dir, format)
+    # Remove the file so we can create a symlink.
+    os.remove(file_path)
+    os.symlink(input_file, file_path)
+    return file_path
+
+
+def get_laplace_solver(shape_data, max_edge_length=float('inf')):
+    return LaplaceSolver(shape_data, max_edge_length=max_edge_length)
+
+
+def get_shape_manager(format=None, dataset_type=None):
+    # Instantiate a ShapeManager.
+    return ShapeManager(file_format=format, vtk_dataset_type=dataset_type)
+
+
+def get_temp_dir(prefix='tmp-vtk-', dir=None):
+    """
+    Return a temporary directory.
+    """
+    return tempfile.mkdtemp(prefix=prefix, dir=dir)
+
+
+def get_tempfilename(dir=None, suffix=None):
+    """
+    Return a temporary file name.
+    """
+    if suffix is None:
+        s = None
+    elif suffix.startswith('.'):
+        s = suffix
+    else:
+        s = '.%s' % suffix
+    fd, name = tempfile.mkstemp(suffix=s, dir=dir)
+    os.close(fd)
+    return name
+
+
+def get_temporary_file_path(tmp_dir, file_extension):
+    """
+    Return the path to a temporary file with a valid VTK format
+    file extension.
+    """
+    return get_tempfilename(tmp_dir, file_extension)
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()