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