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