Mercurial > repos > greg > icqsol_refine_shape
view icqsol_utils.py @ 0:a38daf377d55 draft
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author | greg |
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date | Sat, 14 Nov 2015 14:02:47 -0500 |
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children | 5107ac19d47a |
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import os import sys import tempfile POLYDATA='POLYDATA' 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_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. """ fd, name = tempfile.mkstemp( suffix=suffix, 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()