[med-svn] [Git][med-team/toil][master] 2 commits: Add patch to handle errors when testing on ec2.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
69c58c29 by Michael R. Crusoe at 2023-02-06T19:21:52+01:00
Add patch to handle errors when testing on ec2.

- - - - -
00b14cbc by Michael R. Crusoe at 2023-02-06T19:24:07+01:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/ec2_error.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+toil (5.9.2-2) unstable; urgency=medium
+
+  * Add patch to handle errors when testing on ec2.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 06 Feb 2023 19:24:07 +0100
+
 toil (5.9.2-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/ec2_error.patch
=====================================
@@ -0,0 +1,28 @@
+commit 9524076964fa3ccb63dc54f83a9dd9d51984eb5c
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Date:   Mon Feb 6 19:00:08 2023 +0100
+Forwarded: https://github.com/DataBiosphere/toil/pull/4371
+
+    AWS: better handle errors getting EC2 identity.
+
+diff --git a/src/toil/lib/aws/__init__.py b/src/toil/lib/aws/__init__.py
+index 03c45848..3b1d493d 100644
+--- a/src/toil/lib/aws/__init__.py
++++ b/src/toil/lib/aws/__init__.py
+@@ -31,6 +31,7 @@ from typing import (Any,
+                     Union)
+ from urllib.error import URLError
+ from urllib.request import urlopen
++from http.client import HTTPException
+ 
+ logger = logging.getLogger(__name__)
+ 
+@@ -164,7 +165,7 @@ def running_on_ec2() -> bool:
+     try:
+         urlopen('http://169.254.169.254/latest/dynamic/instance-identity/document', timeout=1)
+         return True
+-    except (URLError, socket.timeout):
++    except (URLError, socket.timeout, HTTPException):
+         return False
+ 
+ def running_on_ecs() -> bool:


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+ec2_error.patch
 exit_code_exception
 setting_version.patch
 no_galaxy_lib



View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/b0793ed220db2263a9e947229b479da46083443a...00b14cbcb22eea0330beed336b567b08aac09a56

-- 
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/b0793ed220db2263a9e947229b479da46083443a...00b14cbcb22eea0330beed336b567b08aac09a56
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