From 61fb3319292dfb2dd596441ab66f6ddb47def111 Mon Sep 17 00:00:00 2001
From: "michael.dsilva" <michael.dsilva@aarnet.edu.au>
Date: Mon, 23 Sep 2024 16:54:55 +1000
Subject: [PATCH 1/6] move error to stderr + try a test for it

---
 tools/aarnetfilesender/filesender.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index 368b47f2..e985aae7 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -10,7 +10,7 @@
 #set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()
 
 #if $apiuser == "" or $apikey == "":
-    echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" &&
+    echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" >&2 &&
     exit 1;
 #end if
 
@@ -41,6 +41,9 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
     <tests>
         <test expect_exit_code="1" expect_failure="true">
             <param name="data" value="summary_statistics.txt"/>
+            <assert_stderr>
+                <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" />
+            </assert_stderr>
         </test>
     </tests>
     <help>

From 1176d7c3efce10e27a7c89589164c20df680b58c Mon Sep 17 00:00:00 2001
From: "michael.dsilva" <michael.dsilva@aarnet.edu.au>
Date: Tue, 24 Sep 2024 14:10:04 +1000
Subject: [PATCH 2/6] FileSender: @TomHarrop suggested a test using hidden
 input types to get around userpref values being missing

---
 tools/aarnetfilesender/filesender.xml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index e985aae7..bd316c87 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -6,6 +6,11 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+#if $test != "":
+    filesender -h 2>&1 &&
+    exit 0;
+#end if
+
 #set $apiuser = $__user__.extra_preferences.get('aarnet_filesender_account|username', "").strip()
 #set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()
 
@@ -34,6 +39,7 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
     <inputs>
         <param name="data" type="data" format="txt,data" multiple="true" optional="false" label="Datasets to be sent:" />
         <param name="to" type="text" optional="true" label="Email address of recipent:"><sanitizer sanitize="False"/></param>
+        <param name="test" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="output" format="txt" hidden="false"/>
@@ -45,6 +51,13 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
                 <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" />
             </assert_stderr>
         </test>
+        <test>
+            <param name="data" value="summary_statistics.txt"/>
+            <param name="test" value="true"/>
+            <assert_contents>
+                <has_text text="usage:"/>
+            </assert_contents>
+        </test>
     </tests>
     <help>
 **What it does**

From d2454d35fc012b78fa8797a4b89680bcc83b4dda Mon Sep 17 00:00:00 2001
From: "michael.dsilva" <michael.dsilva@aarnet.edu.au>
Date: Tue, 24 Sep 2024 14:33:20 +1000
Subject: [PATCH 3/6] missing output

---
 tools/aarnetfilesender/filesender.xml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index bd316c87..40e67bac 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -54,9 +54,11 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
         <test>
             <param name="data" value="summary_statistics.txt"/>
             <param name="test" value="true"/>
-            <assert_contents>
-                <has_text text="usage:"/>
-            </assert_contents>
+            <output name="output" value="output.txt" format="txt">
+                <assert_contents>
+                    <has_text text="usage:"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From e3d423d9de2c8b86d0c9657f406a6043bb8841a5 Mon Sep 17 00:00:00 2001
From: "michael.dsilva" <michael.dsilva@aarnet.edu.au>
Date: Tue, 24 Sep 2024 14:44:26 +1000
Subject: [PATCH 4/6] more test fixes

---
 tools/aarnetfilesender/filesender.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index 40e67bac..986a48b3 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -7,7 +7,7 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
 #if $test != "":
-    filesender -h 2>&1 &&
+    filesender -h >$output 2>&1 &&
     exit 0;
 #end if
 
@@ -54,7 +54,7 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
         <test>
             <param name="data" value="summary_statistics.txt"/>
             <param name="test" value="true"/>
-            <output name="output" value="output.txt" format="txt">
+            <output name="output">
                 <assert_contents>
                     <has_text text="usage:"/>
                 </assert_contents>

From 3bbea6d1fd454af0da9a6a34786ae91fcfb24827 Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Tue, 24 Sep 2024 16:27:11 +1000
Subject: [PATCH 5/6] assert_stdout

---
 tools/aarnetfilesender/filesender.xml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index 986a48b3..f55dbdd2 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -3,11 +3,11 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 #if $test != "":
-    filesender -h >$output 2>&1 &&
+    filesender -h  &&
     exit 0;
 #end if
 
@@ -37,8 +37,10 @@ mkdir filestosend &&
 filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f "galaxy-no-reply@usegalaxy.org.au" -r '$to' filestosend >$output 2>&1
     ]]></command>
     <inputs>
-        <param name="data" type="data" format="txt,data" multiple="true" optional="false" label="Datasets to be sent:" />
-        <param name="to" type="text" optional="true" label="Email address of recipent:"><sanitizer sanitize="False"/></param>
+        <param name="data" type="data" format="txt,data" multiple="true" optional="false" label="Datasets to be sent:"/>
+        <param name="to" type="text" optional="true" label="Email address of recipent:">
+            <sanitizer sanitize="False"/>
+        </param>
         <param name="test" type="hidden" value=""/>
     </inputs>
     <outputs>
@@ -48,17 +50,15 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res
         <test expect_exit_code="1" expect_failure="true">
             <param name="data" value="summary_statistics.txt"/>
             <assert_stderr>
-                <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" />
+                <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section"/>
             </assert_stderr>
         </test>
         <test>
             <param name="data" value="summary_statistics.txt"/>
             <param name="test" value="true"/>
-            <output name="output">
-                <assert_contents>
-                    <has_text text="usage:"/>
-                </assert_contents>
-            </output>
+            <assert_stdout>
+                <has_text text="File Sender CLI client"/>
+            </assert_stdout>
         </test>
     </tests>
     <help>

From 174fadad867b72112476ed2991f1dab921714110 Mon Sep 17 00:00:00 2001
From: "michael.dsilva" <michael.dsilva@aarnet.edu.au>
Date: Wed, 25 Sep 2024 08:56:11 +1000
Subject: [PATCH 6/6] dont like two spaces

---
 tools/aarnetfilesender/filesender.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml
index f55dbdd2..2b8c8c2d 100644
--- a/tools/aarnetfilesender/filesender.xml
+++ b/tools/aarnetfilesender/filesender.xml
@@ -7,7 +7,7 @@
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 #if $test != "":
-    filesender -h  &&
+    filesender -h &&
     exit 0;
 #end if