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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 from icqsol.shapes.icqShapeManager import ShapeManager
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6 from icqsol.bem.icqLaplaceSolver import LaplaceSolver
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7
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8 PLY = 'ply'
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9 POLYDATA = 'POLYDATA'
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10 VTK = 'vtk'
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11
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12
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13 def asbool(val):
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14 return str(val).lower() in ['yes', 'true']
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15
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16
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17 def get_format_and_type(galaxy_ext):
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18 # Define the output file format and type.
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19 format = None
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20 datatype = None
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21 if galaxy_ext in ['vtkascii', 'vtkbinary']:
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22 format = VTK
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23 elif galaxy_ext in ['plyascii', 'plybinary']:
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24 format = PLY
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25 if galaxy_ext in ['vtkascii', 'plyascii']:
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26 datatype = 'ascii'
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27 elif galaxy_ext in ['vtkbinary', 'plybinary']:
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28 datatype = 'binary'
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29 return format, datatype
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30
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31
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32 def get_input_file_path(tmp_dir, input_file, format):
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33 """
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34 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
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35 writing files, so the Galaxy dataset naming convention of
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36 setting all file extensions as .dat must be handled.
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37 """
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38 file_path = get_temporary_file_path(tmp_dir, format)
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39 # Remove the file so we can create a symlink.
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40 os.remove(file_path)
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41 os.symlink(input_file, file_path)
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42 return file_path
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43
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44
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45 def get_laplace_solver(shape_data, max_edge_length=float('inf')):
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46 return LaplaceSolver(shape_data, max_edge_length=max_edge_length)
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47
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48
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49 def get_shape_manager(format=None, dataset_type=None):
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50 # Instantiate a ShapeManager.
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51 return ShapeManager(file_format=format, vtk_dataset_type=dataset_type)
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52
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53
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54 def get_temp_dir(prefix='tmp-vtk-', dir=None):
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55 """
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56 Return a temporary directory.
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57 """
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58 return tempfile.mkdtemp(prefix=prefix, dir=dir)
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59
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60
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61 def get_tempfilename(dir=None, suffix=None):
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62 """
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63 Return a temporary file name.
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64 """
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65 if suffix is None:
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66 s = None
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67 elif suffix.startswith('.'):
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68 s = suffix
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69 else:
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70 s = '.%s' % suffix
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71 fd, name = tempfile.mkstemp(suffix=s, dir=dir)
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72 os.close(fd)
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73 return name
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74
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75
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76 def get_temporary_file_path(tmp_dir, file_extension):
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77 """
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78 Return the path to a temporary file with a valid VTK format
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79 file extension.
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80 """
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81 return get_tempfilename(tmp_dir, file_extension)
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82
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83
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84 def stop_err(msg):
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85 sys.stderr.write("%s\n" % msg)
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86 sys.exit()
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