--- a/nist_wrapper.py	Thu Jan 22 21:52:00 2015 +0100
+++ b/nist_wrapper.py	Thu Jan 22 22:06:00 2015 +0100
@@ -22,7 +22,7 @@
 
 
 
-def _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine):
+def _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, log_file):
     '''
      executes the following steps:
      - copy  nist_home_dir folder to  nist_home_dir+_uuid
@@ -48,6 +48,7 @@
     
     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:
@@ -70,6 +71,7 @@
     # 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):
@@ -83,7 +85,7 @@
     
     return new_nist_home
 
-def _run_NIST(new_nist_home, output_file, is_wine):
+def _run_NIST(new_nist_home, output_file, is_wine, log_file):
     '''
       - run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2
       - monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1"
@@ -114,6 +116,7 @@
     
     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
@@ -130,6 +133,7 @@
     
     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):
@@ -141,6 +145,7 @@
     #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)
@@ -287,21 +292,23 @@
     spectrum_file = sys.argv[3]
     nist_output_file = sys.argv[4]
     final_output_file = sys.argv[5]
+    output_log_file = sys.argv[6]
     # html report pars:
     output_html_report = None
     output_html_report_files_path = None
-    if len(sys.argv) > 6:
-        output_html_report = sys.argv[6]
-        output_html_report_files_path = sys.argv[7]
+    if len(sys.argv) > 7:
+        output_html_report = sys.argv[7]
+        output_html_report_files_path = sys.argv[8]
     
     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)
+    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)
@@ -316,6 +323,7 @@
         _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()))