From 657b1552380f8838cea05eefc36038e66fabd518 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 6 Jul 2020 16:25:21 +0200
Subject: [PATCH] actually `set -e` for non-legacy tools

before strict mode was only used if the command block
was absent
---
 lib/galaxy/tool_util/parser/xml.py            | 12 ++++++----
 test/functional/tools/samples_tool_conf.xml   |  1 +
 .../functional/tools/strict_shell_profile.xml | 23 +++++++++++++++++++
 3 files changed, 31 insertions(+), 5 deletions(-)
 create mode 100644 test/functional/tools/strict_shell_profile.xml

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 0a4b9613f74..39ba1a977be 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -488,12 +488,14 @@ class XmlToolSource(ToolSource):
 
     def parse_strict_shell(self):
         command_el = self._command_el
-        if command_el is not None:
-            return string_as_bool(command_el.get("strict", "False"))
-        elif self.legacy_defaults:
-            return False
+        if self.legacy_defaults:
+            default = "False"
         else:
-            return True
+            default = "True"
+        if command_el is not None:
+            return string_as_bool(command_el.get("strict", default))
+        else:
+            return string_as_bool(default)
 
     def parse_help(self):
         help_elem = self.root.find('help')
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 4db887d296f..7945698d06b 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -57,6 +57,7 @@
   <tool file="metadata_column_names.xml" />
   <tool file="strict_shell.xml" />
   <tool file="strict_shell_default_off.xml" />
+  <tool file="strict_shell_profile.xml" />
   <tool file="detect_errors.xml" />
   <tool file="detect_errors_aggressive.xml" />
   <tool file="qc_stdout.xml" />
diff --git a/test/functional/tools/strict_shell_profile.xml b/test/functional/tools/strict_shell_profile.xml
new file mode 100644
index 00000000000..f397200e8c4
--- /dev/null
+++ b/test/functional/tools/strict_shell_profile.xml
@@ -0,0 +1,23 @@
+<tool id="strict_shell_profile" name="strict_shell_profile" version="1.0.0" profile="16.04">
+    <command detect_errors="exit_code">
+        echo "Hello" > $out_file1
+        ; sh -c "exit $exit_code"
+        ; sh -c "exit 0"
+    </command>
+    <inputs>
+        <param name="exit_code" type="integer" value="0" label="exit code"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" />
+    </outputs>
+    <tests>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="exit_code" value="0" />
+        </test>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="exit_code" value="1" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>