From f33369f89747ed27d2f7e95de6b533fd39c63302 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Tue, 10 Dec 2024 15:05:50 -0600
Subject: [PATCH 1/3] tiffcomment: fix `-version`, `-no-upgrade`, `-debug`,
 `-trace`

---
 .../src/loci/formats/tools/TiffComment.java    | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
index 45d5aadcc6f..a22a5a48659 100644
--- a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
+++ b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
@@ -40,6 +40,7 @@
 
 import loci.common.Constants;
 import loci.common.DataTools;
+import loci.common.DebugTools;
 import loci.common.RandomAccessInputStream;
 import loci.common.RandomAccessOutputStream;
 import loci.formats.FormatException;
@@ -73,8 +74,6 @@ public static void main(String[] args) throws FormatException, IOException {
       return;
     }
 
-    CommandLineTools.runUpgradeCheck(args);
-
     // parse flags
     boolean edit = false;
     String newComment = null;
@@ -106,9 +105,22 @@ else if (newComment.equals("-")) {
           }
         }
       }
-      else System.out.println("Warning: unknown flag: " + args[i]);
+      else if (args[i].equals(CommandLineTools.VERSION)) {
+        CommandLineTools.printVersion();
+      }
+      else if (args[i].equals("-debug")) {
+        DebugTools.setRootLevel("DEBUG");
+      }
+      else if (args[i].equals("-trace")) {
+        DebugTools.setRootLevel("TRACE");
+      }
+      else if (!args[i].equals(CommandLineTools.NO_UPGRADE_CHECK)) {
+        System.out.println("Warning: unknown flag: " + args[i]);
+      }
     }
 
+    CommandLineTools.runUpgradeCheck(args);
+
     // process files
     for (String file : files) {
       if (edit) {

From 47661c26993043accc42730a12a5464c9ab827e7 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Thu, 12 Dec 2024 09:22:07 -0600
Subject: [PATCH 2/3] Document additional tiffcomment options

---
 .../src/loci/formats/tools/TiffComment.java               | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
index a22a5a48659..1760de361c8 100644
--- a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
+++ b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
@@ -56,7 +56,7 @@ public static void main(String[] args) throws FormatException, IOException {
     if (args.length == 0) {
       System.out.println("Usage:");
       System.out.println(
-        "tiffcomment [-set comment] [-edit] file1 [file2 ...]");
+        "tiffcomment [-version] [-debug] [-trace] [-no-upgrade] [-set comment] [-edit] file1 [file2 ...]");
       System.out.println();
 
       System.out.println("This tool requires an ImageDescription tag to be " +
@@ -71,6 +71,12 @@ public static void main(String[] args) throws FormatException, IOException {
       System.out.println("  * '-', to enter the comment using stdin.  " +
         "Entering a blank line will");
       System.out.println("    terminate reading from stdin.");
+      System.out.println();
+      System.out.println("Additional options:");
+      System.out.println("    -version: print the library version");
+      System.out.println(" -no-upgrade: do not perform the upgrade check");
+      System.out.println("      -debug: enable DEBUG-level logging");
+      System.out.println("      -trace: enable TRACE-level logging");
       return;
     }
 

From b8d3ae1835477f63fb42ed7ef23318afaf5fcafb Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Thu, 12 Dec 2024 11:18:59 -0600
Subject: [PATCH 3/3] Exit after printing version

---
 .../bio-formats-tools/src/loci/formats/tools/TiffComment.java  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
index 1760de361c8..506dac3ba1d 100644
--- a/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
+++ b/components/bio-formats-tools/src/loci/formats/tools/TiffComment.java
@@ -73,7 +73,7 @@ public static void main(String[] args) throws FormatException, IOException {
       System.out.println("    terminate reading from stdin.");
       System.out.println();
       System.out.println("Additional options:");
-      System.out.println("    -version: print the library version");
+      System.out.println("    -version: print the library version and exit");
       System.out.println(" -no-upgrade: do not perform the upgrade check");
       System.out.println("      -debug: enable DEBUG-level logging");
       System.out.println("      -trace: enable TRACE-level logging");
@@ -113,6 +113,7 @@ else if (newComment.equals("-")) {
       }
       else if (args[i].equals(CommandLineTools.VERSION)) {
         CommandLineTools.printVersion();
+        return;
       }
       else if (args[i].equals("-debug")) {
         DebugTools.setRootLevel("DEBUG");