From 62fcf2d43ff2c21f9236f4aff304d8998c4be1c3 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 12 Apr 2019 20:37:57 +0200
Subject: [PATCH 1/3] test asserts: check if asserts work as expected

---
 test/functional/tools/job_properties.xml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/test/functional/tools/job_properties.xml b/test/functional/tools/job_properties.xml
index 1bad9a7f4e2..74cb66737c1 100644
--- a/test/functional/tools/job_properties.xml
+++ b/test/functional/tools/job_properties.xml
@@ -32,11 +32,14 @@
         </collection>
     </outputs>
     <tests>
+        <!-- test for assert_command, -stdout, and stderr -->
         <test expect_exit_code="0">
             <param name="thebool" value="true" />
             <output name="out_file1" file="simple_line.txt" />
             <assert_command>
                 <has_text text="really" />
+                <not_has_text text="REALLY" />
+                <has_text_matching text="r.a.ly" />
             </assert_command>
             <assert_stdout>
                 <has_line line="The bool is true" />
@@ -45,6 +48,23 @@
                 <has_line line="The bool is really true" />
             </assert_stderr>
         </test>
+        <!-- same test with negated assert conditions -> should fail (using not_has_text instead of the nonexistent not_has_line) -->
+        <test expect_exit_code="0">
+            <param name="thebool" value="true" />
+            <output name="out_file1" file="simple_line.txt" />
+            <assert_command>
+                <not_has_text text="really" />
+                <has_text text="REALLY" />
+                <has_text_matching text="R.A.LY" />
+            </assert_command>
+<!--            <assert_stdout>-->
+<!--                <not_has_text text="The bool is true" />-->
+<!--            </assert_stdout>-->
+<!--            <assert_stderr>-->
+<!--                <not_has_text text="The bool is really true" />-->
+<!--            </assert_stderr>-->
+        </test>
+        <!-- test for expected exit code -->
         <test expect_exit_code="2">
             <param name="thebool" value="false" />
             <output name="out_file1" file="simple_line_alternative.txt" />
@@ -58,6 +78,7 @@
                 <has_line line="The bool is very not true" />
             </assert_stderr>
         </test>
+        <!-- ??? -->
         <test expect_exit_code="127" expect_failure="true">
             <param name="thebool" value="true" />
             <param name="failbool" value="true" />

From 4437021938fa640b6baae01a636c386f4d599f29 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 30 Jul 2019 13:28:41 +0200
Subject: [PATCH 2/3] Fix ignored assert_command tests

These were swalled becasue the `raw_test_dict` already
lists them under `command_line`, not `command`.
(https://github.com/galaxyproject/galaxy/blob/418f1220c8f6b21bcf3b4ddcf9d19f29bdb2c373/lib/galaxy/tools/test.py#L49)
---
 lib/galaxy/tool_util/verify/interactor.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 54d1442577d..b64a4d28e02 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1064,7 +1064,7 @@ class ToolTestDescription(object):
         self.exception = processed_test_dict.get("exception", None)
 
         self.output_collections = map(TestCollectionOutputDef.from_dict, processed_test_dict.get("output_collections", []))
-        self.command_line = processed_test_dict.get("command", None)
+        self.command_line = processed_test_dict.get("command_line", None)
         self.stdout = processed_test_dict.get("stdout", None)
         self.stderr = processed_test_dict.get("stderr", None)
         self.expect_exit_code = processed_test_dict.get("expect_exit_code", None)

From 32aeb78a6dbf9075067c1f37f9fc23856dda34d7 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 31 Jul 2019 09:53:36 +0200
Subject: [PATCH 3/3] Revert "test asserts: check if asserts work as expected"

This reverts commit 53cb2c1c484dc6dcd59614faf84996a06b652bfc.
---
 test/functional/tools/job_properties.xml | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/test/functional/tools/job_properties.xml b/test/functional/tools/job_properties.xml
index 74cb66737c1..1bad9a7f4e2 100644
--- a/test/functional/tools/job_properties.xml
+++ b/test/functional/tools/job_properties.xml
@@ -32,14 +32,11 @@
         </collection>
     </outputs>
     <tests>
-        <!-- test for assert_command, -stdout, and stderr -->
         <test expect_exit_code="0">
             <param name="thebool" value="true" />
             <output name="out_file1" file="simple_line.txt" />
             <assert_command>
                 <has_text text="really" />
-                <not_has_text text="REALLY" />
-                <has_text_matching text="r.a.ly" />
             </assert_command>
             <assert_stdout>
                 <has_line line="The bool is true" />
@@ -48,23 +45,6 @@
                 <has_line line="The bool is really true" />
             </assert_stderr>
         </test>
-        <!-- same test with negated assert conditions -> should fail (using not_has_text instead of the nonexistent not_has_line) -->
-        <test expect_exit_code="0">
-            <param name="thebool" value="true" />
-            <output name="out_file1" file="simple_line.txt" />
-            <assert_command>
-                <not_has_text text="really" />
-                <has_text text="REALLY" />
-                <has_text_matching text="R.A.LY" />
-            </assert_command>
-<!--            <assert_stdout>-->
-<!--                <not_has_text text="The bool is true" />-->
-<!--            </assert_stdout>-->
-<!--            <assert_stderr>-->
-<!--                <not_has_text text="The bool is really true" />-->
-<!--            </assert_stderr>-->
-        </test>
-        <!-- test for expected exit code -->
         <test expect_exit_code="2">
             <param name="thebool" value="false" />
             <output name="out_file1" file="simple_line_alternative.txt" />
@@ -78,7 +58,6 @@
                 <has_line line="The bool is very not true" />
             </assert_stderr>
         </test>
-        <!-- ??? -->
         <test expect_exit_code="127" expect_failure="true">
             <param name="thebool" value="true" />
             <param name="failbool" value="true" />