From 3a5a8be75825db9700fa99b14b0396637e5e5cbe Mon Sep 17 00:00:00 2001
From: Alexander Veit <53857412+alexander-veit@users.noreply.github.com>
Date: Tue, 6 Aug 2024 11:03:39 -0400
Subject: [PATCH] Add safeguard for parsing top command (#409)

---
 CHANGELOG.rst  | 6 ++++++
 pyproject.toml | 2 +-
 tibanna/top.py | 9 ++++++++-
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 2dcbf23c..73b5526f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -3,6 +3,12 @@
 Change Log
 ==========
 
+5.4.2
+=====
+
+* Safeguard against unexpected output from top command
+
+
 5.4.1
 =====
 
diff --git a/pyproject.toml b/pyproject.toml
index 3b529388..55d6e95c 100644
--- a/pyproject.toml
+++ b/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 <support@4dnucleome.org>"]
 license = "MIT"
diff --git a/tibanna/top.py b/tibanna/top.py
index efb5aaca..2a90a42c 100644
--- a/tibanna/top.py
+++ b/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))