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1 import os
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2 import shutil
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3 import sys
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4 import tempfile
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5
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6 BUFF_SIZE = 1048576
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7
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8
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9 def cleanup_before_exit(tmp_dir):
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10 """
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11 Remove temporary files and directories prior to tool exit.
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12 """
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13 if tmp_dir and os.path.exists(tmp_dir):
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14 shutil.rmtree(tmp_dir)
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15
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16
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17 def get_base_cmd_bunwarpj(jvm_memory):
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18 if jvm_memory in [None, 'None']:
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19 jvm_memory_str = ''
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20 else:
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21 jvm_memory_str = '-Xmx%s' % jvm_memory
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22 # The following bunwarpj_base_cmd string will look something like this:
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23 # "java %s -cp $JAR_DIR/ij-1.49k.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.1.jar \
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24 # bunwarpj.bUnwarpJ_" % (jvm_memory_str)
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25 # See the bunwarpj.sh script for the fiji 20151222
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26 # bioconda recipe in github.
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27 bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str
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28 return bunwarpj_base_cmd
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29
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30
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31 def get_base_command_imagej2(memory_size=None, macro=None, jython_script=None):
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32 imagej2_executable = get_imagej2_executable()
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33 if imagej2_executable is None:
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34 return None
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35 cmd = '%s --ij2 --headless --debug' % imagej2_executable
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36 if memory_size is not None:
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37 memory_size_cmd = ' -DXms=%s -DXmx=%s' % (memory_size, memory_size)
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38 cmd += memory_size_cmd
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39 if macro is not None:
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40 cmd += ' --macro %s' % os.path.abspath(macro)
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41 if jython_script is not None:
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42 cmd += ' --jython %s' % os.path.abspath(jython_script)
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43 return cmd
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44
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45
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46 def get_file_extension(image_format):
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47 """
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48 Return a valid bioformats file extension based on the received
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49 value of image_format(e.g., "gif" is returned as ".gif".
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50 """
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51 return '.%s' % image_format
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52
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53
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54 def get_file_name_without_extension(file_path):
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55 """
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56 Eliminate the .ext from the received file name, assuming that
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57 the file name consists of only a single '.'.
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58 """
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59 if os.path.exists(file_path):
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60 path, name = os.path.split(file_path)
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61 name_items = name.split('.')
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62 return name_items[0]
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63 return None
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64
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65
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66 def get_imagej2_executable():
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67 """
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68 Fiji names the ImageJ executable different names for different
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69 architectures, but our bioconda recipe allows us to do this.
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70 """
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71 return 'ImageJ'
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72
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73
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74 def get_input_image_path(tmp_dir, input_file, image_format):
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75 """
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76 Bioformats uses file extensions (e.g., .job, .gif, etc)
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77 when reading and writing image files, so the Galaxy dataset
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78 naming convention of setting all file extensions as .dat
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79 must be handled.
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80 """
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81 image_path = get_temporary_image_path(tmp_dir, image_format)
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82 # Remove the file so we can create a symlink.
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83 os.remove(image_path)
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84 os.symlink(input_file, image_path)
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85 return image_path
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86
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87
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88 def get_platform_info_dict():
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89 '''Return a dict with information about the current platform.'''
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90 platform_dict = {}
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91 sysname, nodename, release, version, machine = os.uname()
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92 platform_dict['os'] = sysname.lower()
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93 platform_dict['architecture'] = machine.lower()
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94 return platform_dict
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95
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96
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97 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
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98 tmp_stderr.close()
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99 """
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100 Return a stderr string of reasonable size.
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101 """
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102 # Get stderr, allowing for case where it's very large.
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103 tmp_stderr = open(tmp_err, 'rb')
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104 stderr_str = ''
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105 buffsize = BUFF_SIZE
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106 try:
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107 while True:
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108 stderr_str += tmp_stderr.read(buffsize)
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109 if not stderr_str or len(stderr_str) % buffsize != 0:
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110 break
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111 except OverflowError:
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112 pass
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113 tmp_stderr.close()
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114 if include_stdout:
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115 tmp_stdout = open(tmp_out, 'rb')
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116 stdout_str = ''
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117 buffsize = BUFF_SIZE
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118 try:
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119 while True:
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120 stdout_str += tmp_stdout.read(buffsize)
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121 if not stdout_str or len(stdout_str) % buffsize != 0:
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122 break
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123 except OverflowError:
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124 pass
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125 tmp_stdout.close()
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126 if include_stdout:
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127 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
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128 return stderr_str
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129
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130
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131 def get_temp_dir(prefix='tmp-imagej-', dir=None):
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132 """
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133 Return a temporary directory.
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134 """
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135 return tempfile.mkdtemp(prefix=prefix, dir=dir)
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136
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137
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138 def get_tempfilename(dir=None, suffix=None):
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139 """
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140 Return a temporary file name.
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141 """
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142 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
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143 os.close(fd)
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144 return name
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145
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146
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147 def get_temporary_image_path(tmp_dir, image_format):
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148 """
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149 Return the path to a temporary file with a valid image format
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150 file extension that can be used with bioformats.
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151 """
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152 file_extension = get_file_extension(image_format)
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153 return get_tempfilename(tmp_dir, file_extension)
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154
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155
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156 def handle_none_type(val, val_type='float'):
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157 if val is None:
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158 return ' None'
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159 else:
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160 if val_type == 'float':
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161 return ' %.3f' % val
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162 elif val_type == 'int':
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163 return ' %d' % val
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164 return ' %s' % val
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165
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166
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167 def stop_err(msg):
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168 sys.stderr.write(msg)
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169 sys.exit(1)
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