Mercurial > repos > galaxyp > msconvert
comparison msconvert_wrapper.py @ 8:d2c61663e33c draft
Uploaded
author | galaxyp |
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date | Fri, 26 Sep 2014 14:44:54 -0400 |
parents | 37e5502441cc |
children | dd4ba10d0c45 |
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7:37e5502441cc | 8:d2c61663e33c |
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43 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) | 43 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) |
44 returncode = proc.wait() | 44 returncode = proc.wait() |
45 if returncode != 0: | 45 if returncode != 0: |
46 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) | 46 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) |
47 finally: | 47 finally: |
48 print open(tmp_stderr_name, "r").read() | 48 print(( open(tmp_stderr_name, "r").read() )) |
49 print open(tmp_stdout_name, "r").read() | 49 print(( open(tmp_stdout_name, "r").read() )) |
50 | 50 |
51 | 51 |
52 def delete_file(path): | 52 def delete_file(path): |
53 if os.path.exists(path): | 53 if os.path.exists(path): |
54 try: | 54 try: |
165 _add_filter(filters_file, filter) | 165 _add_filter(filters_file, filter) |
166 _add_filter_line_from_file(filters_file, options, file_num=file_num) | 166 _add_filter_line_from_file(filters_file, options, file_num=file_num) |
167 | 167 |
168 filters_file.close() | 168 filters_file.close() |
169 if debug: | 169 if debug: |
170 print open(filters_file_path, "r").read() | 170 print(( open(filters_file_path, "r").read() )) |
171 return filters_file_path | 171 return filters_file_path |
172 | 172 |
173 | 173 |
174 def _build_base_cmd(options): | 174 def _build_base_cmd(options): |
175 to_extension = options.toextension | 175 to_extension = options.toextension |
193 def _run(base_cmd, output_dir='output', inputs=[], debug=False): | 193 def _run(base_cmd, output_dir='output', inputs=[], debug=False): |
194 inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs]) | 194 inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs]) |
195 os.mkdir(output_dir) | 195 os.mkdir(output_dir) |
196 cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str) | 196 cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str) |
197 if debug: | 197 if debug: |
198 print cmd | 198 print(cmd) |
199 execute(cmd) | 199 execute(cmd) |
200 output_files = os.listdir(output_dir) | 200 output_files = os.listdir(output_dir) |
201 assert len(output_files) == 1 | 201 assert len(output_files) == 1 |
202 output_file = output_files[0] | 202 output_file = output_files[0] |
203 return os.path.join(output_dir, output_file) | 203 return os.path.join(output_dir, output_file) |
232 input_files = [] | 232 input_files = [] |
233 for i, input in enumerate(options.inputs): | 233 for i, input in enumerate(options.inputs): |
234 input_base = None | 234 input_base = None |
235 if len(options.input_names) > i: | 235 if len(options.input_names) > i: |
236 input_base = options.input_names[i] | 236 input_base = options.input_names[i] |
237 input_base = input_base.replace("'", "").replace("\"", "") | |
238 print("1- input_base: %s" % input_base) | |
237 if not input_base: | 239 if not input_base: |
238 input_base = 'input%s' % i | 240 input_base = 'input%s' % i |
241 print("2- input_base: %s" % input_base) | |
239 if not input_base.lower().endswith(options.fromextension.lower()): | 242 if not input_base.lower().endswith(options.fromextension.lower()): |
240 input_file = '%s.%s' % (input_base, options.fromextension) | 243 input_file = '%s.%s' % (input_base, options.fromextension) |
244 print("3- input_base: %s" % input_base) | |
245 print("3- input_file: %s" % input_file) | |
241 else: | 246 else: |
242 input_file = input_base | 247 input_file = input_base |
248 print("4- input_base: %s" % input_base) | |
249 print("4- input_file: %s" % input_file) | |
243 input_file = input_file | 250 input_file = input_file |
244 copy_to_working_directory(input, input_file) | 251 copy_to_working_directory(input, input_file) |
245 input_files.append(input_file) | 252 input_files.append(input_file) |
246 | 253 |
247 cmd = _build_base_cmd(options) | 254 cmd = _build_base_cmd(options) |