Mercurial > repos > pieterlukasse > nist_wrapper

comparison nist_wrapper.py @ 16:c21e96bb68c8

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added clean-up after execution
author pieter.lukasse@wur.nl
date Fri, 23 Jan 2015 14:57:55 +0100
parents 92cf554fca03
children 82368bd06e1d
comparison
equal deleted inserted replaced
15:76d6d8a5fa29 16:c21e96bb68c8
83 o.write(line) 83 o.write(line)
84 o.close() 84 o.close()
85 85
86 return new_nist_home 86 return new_nist_home
87 87
88 def _clean_up_NIST(new_nist_home):
89 '''
90 remove folder
91 '''
92 utils.remove_dir(new_nist_home)
93
88 def _run_NIST(new_nist_home, output_file, is_wine, log_file, job_size): 94 def _run_NIST(new_nist_home, output_file, is_wine, log_file, job_size):
89 ''' 95 '''
90 - run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2 96 - run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2
91 - monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1" 97 - monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1"
92 - when ready: 98 - when ready:
96 > finish 102 > finish
97 ''' 103 '''
98 # to avoid conflicts in the orphan process killing (see end of this method), we will 104 # to avoid conflicts in the orphan process killing (see end of this method), we will
99 # only run NIST again after previous nistms.exe process has been killed: 105 # only run NIST again after previous nistms.exe process has been killed:
100 # TODO : solution is currently only for wine (in the windows context the solution is not there yet, but parallel calls are not expected as in windows we only run tests one by one for now) 106 # TODO : solution is currently only for wine (in the windows context the solution is not there yet, but parallel calls are not expected as in windows we only run tests one by one for now)
101 # if is_wine:
102 # while True:
103 # # check if process exists. If not, break loop and continue
104 # pid = utils.get_process_pid("nistms.exe")
105 # if pid == -1:
106 # break
107 # time.sleep(2)
108 107
109 108
110 # remove old file, if it is there: 109 # remove old file, if it is there:
111 file_to_monitor = new_nist_home+"/MSSEARCH/SRCREADY.TXT" 110 file_to_monitor = new_nist_home+"/MSSEARCH/SRCREADY.TXT"
112 if os.path.exists(file_to_monitor): 111 if os.path.exists(file_to_monitor):
152 #stays open...and orphan..killing it: 151 #stays open...and orphan..killing it:
153 152
154 if is_wine: 153 if is_wine:
155 # pid = utils.get_process_pid("nistms.exe") 154 # pid = utils.get_process_pid("nistms.exe")
156 # os.kill(pid, 9) 155 # os.kill(pid, 9)
157 os.killpg(pro.pid, 9) 156 os.killpg(pro.pid, 9)
158 else: 157 else:
159 # windows case: 158 # windows case:
160 proc_name = "nistms.exe" 159 proc_name = "nistms.exe"
161 os.system("taskkill /f /im " + proc_name) 160 os.system("taskkill /f /im " + proc_name)
162 161
316 # run NIST search command: 315 # run NIST search command:
317 spectra_dict = utils.get_spectra_file_as_dict(spectrum_file) 316 spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
318 job_size = len(spectra_dict) 317 job_size = len(spectra_dict)
319 _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file, job_size) 318 _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file, job_size)
320 319
320 # clean-up NIST environment:
321 _clean_up_NIST(new_nist_home)
322
321 # write output tabular: 323 # write output tabular:
322 hits_dict = utils.get_nist_out_as_dict(nist_output_file) 324 hits_dict = utils.get_nist_out_as_dict(nist_output_file)
323 utils.save_dict_as_tsv(hits_dict, final_output_file) 325 utils.save_dict_as_tsv(hits_dict, final_output_file)
324 326
325 # create report: 327 # create report: