Mercurial > repos > greg > icqsol_add_surface_field_from_expression

comparison icqsol_utils.py @ 5:a3a2663a687f draft

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Uploaded
author greg
date Fri, 04 Dec 2015 09:20:18 -0500
parents d59a9d960f67
children 0d67a350bb1d
comparison
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4:efd3754c5d41 5:a3a2663a687f
1 import os 1 import os
2 import sys 2 import sys
3 import tempfile 3 import tempfile
4 4
5 POLYDATA='POLYDATA' 5 POLYDATA = 'POLYDATA'
6 6
7 def asbool( val ):
8 return str( val ).lower() in [ 'yes', 'true' ]
9 7
10 def get_format_and_type( galaxy_ext ): 8 def asbool(val):
9 return str(val).lower() in ['yes', 'true']
10
11
12 def get_format_and_type(galaxy_ext):
11 # Define the output file format and type. 13 # Define the output file format and type.
12 format = None 14 format = None
13 datatype = None 15 datatype = None
14 if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]: 16 if galaxy_ext in ['vtkascii', 'vtkbinary']:
15 format = 'vtk' 17 format = 'vtk'
16 elif galaxy_ext in [ 'plyascii', 'plybinary' ]: 18 elif galaxy_ext in ['plyascii', 'plybinary']:
17 format = 'ply' 19 format = 'ply'
18 if galaxy_ext in [ 'vtkascii', 'plyascii' ]: 20 if galaxy_ext in ['vtkascii', 'plyascii']:
19 datatype = 'ascii' 21 datatype = 'ascii'
20 elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]: 22 elif galaxy_ext in ['vtkbinary', 'plybinary']:
21 datatype = 'binary' 23 datatype = 'binary'
22 return format, datatype 24 return format, datatype
23 25
24 def get_input_file_path( tmp_dir, input_file, format ): 26
27 def get_input_file_path(tmp_dir, input_file, format):
25 """ 28 """
26 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and 29 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
27 writing files, so the Galaxy dataset naming convention of 30 writing files, so the Galaxy dataset naming convention of
28 setting all file extensions as .dat must be handled. 31 setting all file extensions as .dat must be handled.
29 """ 32 """
30 file_path = get_temporary_file_path( tmp_dir, format ) 33 file_path = get_temporary_file_path(tmp_dir, format)
31 # Remove the file so we can create a symlink. 34 # Remove the file so we can create a symlink.
32 os.remove( file_path ) 35 os.remove(file_path)
33 os.symlink( input_file, file_path ) 36 os.symlink(input_file, file_path)
34 return file_path 37 return file_path
35 38
36 def get_temp_dir( prefix='tmp-vtk-', dir=None ): 39
40 def get_temp_dir(prefix='tmp-vtk-', dir=None):
37 """ 41 """
38 Return a temporary directory. 42 Return a temporary directory.
39 """ 43 """
40 return tempfile.mkdtemp( prefix=prefix, dir=dir ) 44 return tempfile.mkdtemp(prefix=prefix, dir=dir)
41 45
42 def get_tempfilename( dir=None, suffix=None ): 46
47 def get_tempfilename(dir=None, suffix=None):
43 """ 48 """
44 Return a temporary file name. 49 Return a temporary file name.
45 """ 50 """
46 fd, name = tempfile.mkstemp( suffix=suffix, dir=dir ) 51 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
47 os.close( fd ) 52 os.close(fd)
48 return name 53 return name
49 54
50 def get_temporary_file_path( tmp_dir, file_extension ): 55
56 def get_temporary_file_path(tmp_dir, file_extension):
51 """ 57 """
52 Return the path to a temporary file with a valid VTK format 58 Return the path to a temporary file with a valid VTK format
53 file extension. 59 file extension.
54 """ 60 """
55 return get_tempfilename( tmp_dir, file_extension ) 61 return get_tempfilename(tmp_dir, file_extension)
56 62
57 def stop_err( msg ): 63
58 sys.stderr.write( "%s\n" % msg ) 64 def stop_err(msg):
65 sys.stderr.write("%s\n" % msg)
59 sys.exit() 66 sys.exit()