# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1421961263 -3600
# Node ID 8c20185752dae0b4f1f7fd091ef0b2b244b64aa1
# Parent  35e4707e0ac367fc3fdf4a26c8532b869784b706
better logging

diff -r 35e4707e0ac3 -r 8c20185752da nist_wrapper.py
--- a/nist_wrapper.py	Thu Jan 22 22:07:40 2015 +0100
+++ b/nist_wrapper.py	Thu Jan 22 22:14:23 2015 +0100
@@ -48,7 +48,7 @@
     
     utils.copy_file(spectrum_file, new_nist_home+"/spectrum_file.msp")
     
-    log_file.write("configuring NIST input...")
+    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:
@@ -71,7 +71,7 @@
     # remove old file
     os.remove(new_nist_home+"/MSSEARCH/nistms.INI")
     # make new one
-    log_file.write("configuring NIST ini...")
+    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):
@@ -116,7 +116,7 @@
     
     pro = ""
     if is_wine:
-        log_file.write("calling wine with " + exec_path)
+        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
@@ -133,7 +133,7 @@
     
     timeSleeping = 0
     # monitor process by checking state file:
-    log_file.write("monitoring SRCREADY.TXT...")
+    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):
@@ -145,7 +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...")
+    utils.log_message(log_file, "killing wine process...")
     if is_wine:
 #         pid = utils.get_process_pid("nistms.exe")
 #         os.kill(pid, 9)
@@ -305,13 +305,12 @@
         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)
+    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, log_file)
+    _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) 
@@ -323,7 +322,6 @@
         _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()))
diff -r 35e4707e0ac3 -r 8c20185752da utils.py
--- a/utils.py	Thu Jan 22 22:07:40 2015 +0100
+++ b/utils.py	Thu Jan 22 22:14:23 2015 +0100
@@ -11,7 +11,10 @@
 def copy_dir(src, dst):
     shutil.copytree(src, dst)
 
-    
+def log_message(log_file, log_message):
+    with open(log_file, "a") as text_file:
+        text_file.write(log_message + "\n")
+        
 def copy_file(src, dst):  
     shutil.copy(src, dst)