Mercurial > repos > greg > icqsol_add_surface_field_from_expression

comparison icqsol_utils.py @ 0:d59a9d960f67 draft

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author greg
date Sat, 14 Nov 2015 14:14:45 -0500
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children a3a2663a687f
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-1:000000000000 0:d59a9d960f67
1 import os
2 import sys
3 import tempfile
4
5 POLYDATA='POLYDATA'
6
7 def asbool( val ):
8 return str( val ).lower() in [ 'yes', 'true' ]
9
10 def get_format_and_type( galaxy_ext ):
11 # Define the output file format and type.
12 format = None
13 datatype = None
14 if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]:
15 format = 'vtk'
16 elif galaxy_ext in [ 'plyascii', 'plybinary' ]:
17 format = 'ply'
18 if galaxy_ext in [ 'vtkascii', 'plyascii' ]:
19 datatype = 'ascii'
20 elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]:
21 datatype = 'binary'
22 return format, datatype
23
24 def get_input_file_path( tmp_dir, input_file, format ):
25 """
26 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
27 writing files, so the Galaxy dataset naming convention of
28 setting all file extensions as .dat must be handled.
29 """
30 file_path = get_temporary_file_path( tmp_dir, format )
31 # Remove the file so we can create a symlink.
32 os.remove( file_path )
33 os.symlink( input_file, file_path )
34 return file_path
35
36 def get_temp_dir( prefix='tmp-vtk-', dir=None ):
37 """
38 Return a temporary directory.
39 """
40 return tempfile.mkdtemp( prefix=prefix, dir=dir )
41
42 def get_tempfilename( dir=None, suffix=None ):
43 """
44 Return a temporary file name.
45 """
46 fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
47 os.close( fd )
48 return name
49
50 def get_temporary_file_path( tmp_dir, file_extension ):
51 """
52 Return the path to a temporary file with a valid VTK format
53 file extension.
54 """
55 return get_tempfilename( tmp_dir, file_extension )
56
57 def stop_err( msg ):
58 sys.stderr.write( "%s\n" % msg )
59 sys.exit()