Mercurial > repos > greg > icqsol_scale_shape

comparison icqsol_utils.py @ 0:c8b87f2bb2e8 draft

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Uploaded
author greg
date Sat, 05 Dec 2015 10:36:31 -0500
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children d7c8a1ad787d
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-1:000000000000 0:c8b87f2bb2e8
1 import os
2 import sys
3 import tempfile
4
5 PLY = 'ply'
6 POLYDATA = 'POLYDATA'
7 VTK = 'vtk'
8
9
10 def asbool(val):
11 return str(val).lower() in ['yes', 'true']
12
13
14 def get_format_and_type(galaxy_ext):
15 # Define the output file format and type.
16 format = None
17 datatype = None
18 if galaxy_ext in ['vtkascii', 'vtkbinary']:
19 format = VTK
20 elif galaxy_ext in ['plyascii', 'plybinary']:
21 format = PLY
22 if galaxy_ext in ['vtkascii', 'plyascii']:
23 datatype = 'ascii'
24 elif galaxy_ext in ['vtkbinary', 'plybinary']:
25 datatype = 'binary'
26 return format, datatype
27
28
29 def get_input_file_path(tmp_dir, input_file, format):
30 """
31 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
32 writing files, so the Galaxy dataset naming convention of
33 setting all file extensions as .dat must be handled.
34 """
35 file_path = get_temporary_file_path(tmp_dir, format)
36 # Remove the file so we can create a symlink.
37 os.remove(file_path)
38 os.symlink(input_file, file_path)
39 return file_path
40
41
42 def get_temp_dir(prefix='tmp-vtk-', dir=None):
43 """
44 Return a temporary directory.
45 """
46 return tempfile.mkdtemp(prefix=prefix, dir=dir)
47
48
49 def get_tempfilename(dir=None, suffix=None):
50 """
51 Return a temporary file name.
52 """
53 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
54 os.close(fd)
55 return name
56
57
58 def get_temporary_file_path(tmp_dir, file_extension):
59 """
60 Return the path to a temporary file with a valid VTK format
61 file extension.
62 """
63 return get_tempfilename(tmp_dir, file_extension)
64
65
66 def stop_err(msg):
67 sys.stderr.write("%s\n" % msg)
68 sys.exit()