comparison nist_wrapper.py @ 9:8c20185752da

better logging

8:35e4707e0ac3

    new_nist_home = nist_home_dir+uuid_value
    utils.copy_dir(nist_home_dir, new_nist_home)
    
    utils.copy_file(spectrum_file, new_nist_home+"/spectrum_file.msp")
    
    log_file.write("configuring NIST input...")
    # remove old file:
    os.remove(new_nist_home+"/MSSEARCH/AUTOIMP.MSD")
    with open(new_nist_home + "/MSSEARCH/AUTOIMP.MSD", "a") as text_file:
        if is_wine:
            text_file.write("C:\\NIST" + uuid_value + "\\MSSEARCH\\temp.msd")

        replacement_text = "C:\\NIST" + uuid_value
    
    # remove old file
    os.remove(new_nist_home+"/MSSEARCH/nistms.INI")
    # make new one
    log_file.write("configuring NIST ini...")
    o = open(new_nist_home+"/MSSEARCH/nistms.INI","a") #open for append
    # TODO : this loop/replace below is a bit limited to specific variables...either test different NIST versions or make more generic (harder in case of wine, or we need extra "home in .INI file"  parameter):
    for line in open(nist_ini_file):
        if "Library Directory=" in line:
            line = "Library Directory="+ new_nist_home + "\\MSSEARCH\\\n"

    
    exec_path = new_nist_home + "/MSSEARCH/nistms$.exe" 
    
    pro = ""
    if is_wine:
        log_file.write("calling wine with " + exec_path)
        print "calling wine with " + exec_path
        cmd = ["wine "+ exec_path + " /INSTRUMENT /PAR=2"]
        # The os.setsid() is passed in the argument preexec_fn so
        # it's run after the fork() and before  exec() to run the shell.
        pro = subprocess.Popen(cmd, stdout=subprocess.PIPE, 

        subprocess.call(cmd)
     
    
    timeSleeping = 0
    # monitor process by checking state file:
    log_file.write("monitoring SRCREADY.TXT...")
    while True and timeSleeping < 20:
        # check if SRCREADY.TXT is there already:
        if os.path.exists(file_to_monitor):
            break
        time.sleep(2)

        
    # kill process:
    #p.terminate() - not needed, nistm$ will terminate...nistms.exe is the one that 
    #stays open...and orphan..killing it:
    
    log_file.write("killing wine process...")
    if is_wine:
#         pid = utils.get_process_pid("nistms.exe")
#         os.kill(pid, 9)
        os.killpg(pro.pid, 9)    
    else:

    is_wine = False
    if "wine" in nist_home_dir:
        is_wine = True
    
    uuid_value = str(uuid.uuid4()) 
    log_file = open(output_log_file,'w')

    # prepare NIST environment for running:
    new_nist_home = _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, log_file)
    
    # run NIST search command:
    _run_NIST(new_nist_home, nist_output_file, is_wine, log_file)

    # write output tabular:
    hits_dict = utils.get_nist_out_as_dict(nist_output_file) 
    utils.save_dict_as_tsv(hits_dict, final_output_file)
    

    if len(sys.argv) > 6:
        spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
        _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict)


    log_file.close()
    #_save_data(enriched_data, headers, output_result)
    
    seconds_end = int(round(time.time()))
    print "Took " + str(seconds_end - seconds_start) + " seconds"
                      

9:8c20185752da

    new_nist_home = nist_home_dir+uuid_value
    utils.copy_dir(nist_home_dir, new_nist_home)
    
    utils.copy_file(spectrum_file, new_nist_home+"/spectrum_file.msp")
    
    utils.log_message(log_file, "configuring NIST input...")
    # remove old file:
    os.remove(new_nist_home+"/MSSEARCH/AUTOIMP.MSD")
    with open(new_nist_home + "/MSSEARCH/AUTOIMP.MSD", "a") as text_file:
        if is_wine:
            text_file.write("C:\\NIST" + uuid_value + "\\MSSEARCH\\temp.msd")

        replacement_text = "C:\\NIST" + uuid_value
    
    # remove old file
    os.remove(new_nist_home+"/MSSEARCH/nistms.INI")
    # make new one
    utils.log_message(log_file, "configuring NIST ini...")
    o = open(new_nist_home+"/MSSEARCH/nistms.INI","a") #open for append
    # TODO : this loop/replace below is a bit limited to specific variables...either test different NIST versions or make more generic (harder in case of wine, or we need extra "home in .INI file"  parameter):
    for line in open(nist_ini_file):
        if "Library Directory=" in line:
            line = "Library Directory="+ new_nist_home + "\\MSSEARCH\\\n"

    
    exec_path = new_nist_home + "/MSSEARCH/nistms$.exe" 
    
    pro = ""
    if is_wine:
        utils.log_message(log_file, "calling wine with " + exec_path)
        print "calling wine with " + exec_path
        cmd = ["wine "+ exec_path + " /INSTRUMENT /PAR=2"]
        # The os.setsid() is passed in the argument preexec_fn so
        # it's run after the fork() and before  exec() to run the shell.
        pro = subprocess.Popen(cmd, stdout=subprocess.PIPE, 

        subprocess.call(cmd)
     
    
    timeSleeping = 0
    # monitor process by checking state file:
    utils.log_message(log_file, "monitoring SRCREADY.TXT...")
    while True and timeSleeping < 20:
        # check if SRCREADY.TXT is there already:
        if os.path.exists(file_to_monitor):
            break
        time.sleep(2)

        
    # kill process:
    #p.terminate() - not needed, nistm$ will terminate...nistms.exe is the one that 
    #stays open...and orphan..killing it:
    
    utils.log_message(log_file, "killing wine process...")
    if is_wine:
#         pid = utils.get_process_pid("nistms.exe")
#         os.kill(pid, 9)
        os.killpg(pro.pid, 9)    
    else:

    is_wine = False
    if "wine" in nist_home_dir:
        is_wine = True
    
    uuid_value = str(uuid.uuid4()) 
    
    # prepare NIST environment for running:
    new_nist_home = _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, output_log_file)
    
    # run NIST search command:
    _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file)

    # write output tabular:
    hits_dict = utils.get_nist_out_as_dict(nist_output_file) 
    utils.save_dict_as_tsv(hits_dict, final_output_file)
    

    if len(sys.argv) > 6:
        spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
        _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict)


    #_save_data(enriched_data, headers, output_result)
    
    seconds_end = int(round(time.time()))
    print "Took " + str(seconds_end - seconds_start) + " seconds"