From 583fb1dc237d80ebbc5418e1b7a8d3ecdd00603a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 27 Mar 2024 17:51:43 +0100
Subject: [PATCH 1/4] add text for not matching pattern

---
 tools/text_processing/text_processing/grep.xml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/tools/text_processing/text_processing/grep.xml b/tools/text_processing/text_processing/grep.xml
index ad7ef265e7..99a7c35081 100644
--- a/tools/text_processing/text_processing/grep.xml
+++ b/tools/text_processing/text_processing/grep.xml
@@ -125,6 +125,21 @@
             <param name="color" value="NOCOLOR" />
             <output name="output" file="egrep_results1.txt" />
         </test>
+        <test><!-- tests regex;matching nothing -->
+            <param name="infile" value="egrep1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-G" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="not existent pattern" />
+            <param name="lines_before" value="0" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="NOCOLOR" />
+            <output name="output">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[

From 6edfda9b8604bbf21ce35e627583c9450c679ed7 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 27 Mar 2024 23:19:41 +0100
Subject: [PATCH 2/4] grep accept exit code 1 as success

and use `--no-group-separator`
---
 .../text_processing/text_processing/grep.xml  | 34 ++++++++++++++-----
 1 file changed, 26 insertions(+), 8 deletions(-)

diff --git a/tools/text_processing/text_processing/grep.xml b/tools/text_processing/text_processing/grep.xml
index 99a7c35081..a12f61f254 100644
--- a/tools/text_processing/text_processing/grep.xml
+++ b/tools/text_processing/text_processing/grep.xml
@@ -8,6 +8,9 @@
         <requirement type="package" version="3.11">grep</requirement>
         <requirement type="package" version="4.8">sed</requirement><!-- for ansi2html.sh -->
     </requirements>
+    <stdio>
+        <exit_code range="2:" level="fatal" description="grep failed" />
+    </stdio>
     <version_command>grep --version | head -n 1</version_command>
     <command>
 <![CDATA[
@@ -23,14 +26,15 @@
                 -- '${url_paste}'
                 '${infile}' | '$__tool_directory__/ansi2html.sh' > '${output}'
         #else:
-            grep
+                grep
                 $regex_type
                 -A $lines_after
                 -B $lines_before
+                --no-group-separator
                 $invert
                 $case_sensitive
                  -- '${url_paste}'
-                '${infile}' | grep -v "^--$" > '${output}'
+                '${infile}' > '${output}'
         #end if
 ]]>
     </command>
@@ -78,8 +82,8 @@
         </data>
     </outputs>
     <tests>
+        <!-- grep a FASTA file for sequences with specific motif -->
         <test>
-            <!-- grep a FASTA file for sequences with specific motif -->
             <param name="infile" value="grep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
             <param name="regex_type" value="-P" />
@@ -90,9 +94,9 @@
             <param name="color" value="NOCOLOR" />
             <output name="output" file="grep_results1.txt" />
         </test>
-        <test>
-            <!-- grep a FASTA file for sequences with specific motif -
+        <!-- grep a FASTA file for sequences with specific motif -
              show highlighed output -->
+        <test>
             <param name="infile" value="grep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
             <param name="regex_type" value="-P" />
@@ -103,7 +107,8 @@
             <param name="color" value="COLOR" />
             <output name="output" file="grep_results2.html" />
         </test>
-        <test><!-- tests egrep -->
+        <!-- tests egrep -->
+        <test>
             <param name="infile" value="egrep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
             <param name="regex_type" value="-E" />
@@ -114,7 +119,8 @@
             <param name="color" value="NOCOLOR" />
             <output name="output" file="egrep_results1.txt" />
         </test>
-        <test><!-- tests basic regex; + must be backslashed to match -->
+        <!-- tests basic regex; + must be backslashed to match -->
+        <test>
             <param name="infile" value="egrep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
             <param name="regex_type" value="-G" />
@@ -125,7 +131,8 @@
             <param name="color" value="NOCOLOR" />
             <output name="output" file="egrep_results1.txt" />
         </test>
-        <test><!-- tests regex;matching nothing -->
+        <!-- tests regex;matching nothing -->
+        <test>
             <param name="infile" value="egrep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
             <param name="regex_type" value="-G" />
@@ -140,6 +147,17 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- tests invalid regex; i.e. that we still get exit code 2 -->
+        <test expect_failure="true" expect_exit_code="2">
+            <param name="infile" value="egrep1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-G" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="\(" />
+            <param name="lines_before" value="0" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="NOCOLOR" />
+        </test>
     </tests>
     <help>
 <![CDATA[

From 288f8bef36ccf645454d44bb45a677d46d424c13 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 27 Mar 2024 23:24:19 +0100
Subject: [PATCH 3/4] bump

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

diff --git a/tools/text_processing/text_processing/macros.xml b/tools/text_processing/text_processing/macros.xml
index e841880757..3771bf8598 100644
--- a/tools/text_processing/text_processing/macros.xml
+++ b/tools/text_processing/text_processing/macros.xml
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">9.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.1</token>
     <xml name="stdio">
         <stdio>

From b985ba7bea101c1bf59b2639aba4fcc44eff6772 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 27 Mar 2024 23:25:32 +0100
Subject: [PATCH 4/4] indentation

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

diff --git a/tools/text_processing/text_processing/grep.xml b/tools/text_processing/text_processing/grep.xml
index a12f61f254..f7d531884d 100644
--- a/tools/text_processing/text_processing/grep.xml
+++ b/tools/text_processing/text_processing/grep.xml
@@ -26,7 +26,7 @@
                 -- '${url_paste}'
                 '${infile}' | '$__tool_directory__/ansi2html.sh' > '${output}'
         #else:
-                grep
+            grep
                 $regex_type
                 -A $lines_after
                 -B $lines_before