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