Add safeguard for parsing top command

CHANGELOG.rst

@@ -3,6 +3,12 @@
 Change Log
 ==========
 
+5.4.2
+=====
+
+* Safeguard against unexpected output from top command
+
+
 5.4.1
 =====
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "5.4.1"
+version = "5.4.2"
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

tibanna/top.py

@@ -1,4 +1,7 @@
 import datetime
+from . import create_logger
+
+logger = create_logger(__name__)
 
 
 class Top(object):
@@ -100,7 +103,11 @@ def parse_contents(self, contents):
             if is_in_table:
                 if timestamp not in self.processes:
                     self.processes[timestamp] = []
-                process = Process(line)
+                try:
+                    process = Process(line)
+                except:
+                    logger.info(f"Could not process line from top command: {line}")
+                    continue
                 if not self.should_skip_process(process):
                     self.processes[timestamp].append(Process(line))