Kill wget if it takes too long

2 files changed, 27 insertions, 1 deletions

diff --git a/Code/download_and_map.py b/Code/download_and_map.py
index bc1c190..ebc742d 100644
--- a/Code/download_and_map.py
+++ b/Code/download_and_map.py
@@ -15,7 +15,7 @@
 # Last reviewed 31 July 2018
 # Last revised 10 Feb 2021
 
-import os, sys, glob, json
+import os, signal, sys, glob, json
 import fnmatch
 import time
 import re
@@ -349,6 +349,17 @@ def read_run_ids_from_file(fname):
     return list(set(lst))
 
 
+def kill_process(process_name):
+    try:
+        for line in os.popen('ps ax | grep ' + process_name + ' | grep -v grep'):
+            fields = line.split()
+            if fields[4] == process_name:
+                pid = fields[0]
+                os.kill(int(pid), signal.SIGKILL)
+        return True
+    except Exception as e:
+        print(f'{e}')
+        return False
 
 
 ## main
@@ -370,6 +381,7 @@ if not last_session_finished(DOWNLOADED_SRA_ID_LOG_FILE): # last session not fin
     write_network_log_file(s, UPDATE_NETWORK_LOG_FILE)
     if age_of_file_in_hours(DOWNLOADED_SRA_ID_LOG_FILE) > 24: # add DONE to the log file anyway
         append_done(DOWNLOADED_SRA_ID_LOG_FILE)
+    kill_process('wget')
     sys.exit()
 
 rna_data_info_dict = read_ena_data_info_json(RNA_SEQ_INFO_FILE) # rna_data_info_dict contains only RNA-seq IDs.
diff --git a/Code/killprocess.py b/Code/killprocess.py
new file mode 100644
index 0000000..d2237aa
--- /dev/null
+++ b/Code/killprocess.py
@@ -0,0 +1,14 @@
+import os, signal
+def kill_process(process_name):
+    try:
+        for line in os.popen('ps ax | grep ' + process_name + ' | grep -v grep'):
+            fields = line.split()
+            if fields[4] == process_name:
+                pid = fields[0]
+                os.kill(int(pid), signal.SIGKILL)
+        return True
+    except Exception as e:
+        print(f'{e}')
+        return False
+
+kill_process('sleep')