From 0cad068bf447b7a44c3710d2ef0d7902bf8a8db1 Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Tue, 31 May 2022 11:08:04 -0400
Subject: [PATCH 1/5] Fix regression in launcher script
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Symlinks called “*” will not be created when there are no shared plugins or
  luts
- Broken symlinks into shared directories will be removed
- Symlink changes will be printed to the terminal
---
 imagej-1.53r-unix-script.patch | 36 ++++++++++++++++++++++------------
 imagej.spec                    |  9 ++++++++-
 2 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/imagej-1.53r-unix-script.patch b/imagej-1.53r-unix-script.patch
index edf6cb0..1d4b75e 100644
--- a/imagej-1.53r-unix-script.patch
+++ b/imagej-1.53r-unix-script.patch
@@ -1,6 +1,6 @@
 diff -Naur old/imagej.sh new/imagej.sh
---- old/imagej.sh	2022-05-30 08:40:52.860341530 -0400
-+++ new/imagej.sh	2022-05-30 09:23:56.439575119 -0400
+--- old/imagej.sh	2022-05-31 09:41:01.115425825 -0400
++++ new/imagej.sh	2022-05-31 11:03:48.189864410 -0400
 @@ -9,6 +9,9 @@
  # Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $
  # $Revision: 51 $
@@ -48,7 +48,7 @@ diff -Naur old/imagej.sh new/imagej.sh
  # LOG FILE
  #ij_log="${ij_tmp}/log.txt"
  # default behaviour when an ImageJ window is already open
-@@ -84,44 +81,45 @@
+@@ -84,44 +81,57 @@
  declare -i max_mem
  declare -i free_mem
  
@@ -110,13 +110,25 @@ diff -Naur old/imagej.sh new/imagej.sh
 +# Make symbolic links from shared plugins, macros and luts 
 +for x in plugins macros luts
 +do
-+	for p in "${ij_data_path}/${x}"/*
-+	do
-+		if [[ ! -e "${ij_user_path}/${x}/$(basename "${p}")" ]]
-+		then
-+			ln -s "${p}" "${ij_user_path}/${x}/"
-+		fi
-+	done
++	# Add new symlinks
++	find "${ij_data_path}/${x}" -mindepth 1 -maxdepth 1 |
++		while read -r p
++		do
++			if [[ ! -e "${ij_user_path}/${x}/$(basename "${p}")" ]]
++			then
++				ln -vs "${p}" "${ij_user_path}/${x}/"
++			fi
++		done
++	# Clean up broken symlinks into the shared directory
++	find "${ij_user_path}/${x}" -mindepth 1 -maxdepth 1 -type l -printf '%p %l\n' |
++		while read -r p l
++		do
++			if [[ ! -e "${p}" ]] && \
++				[[ "$(dirname "${l}")" = "${ij_data_path}/${x}" ]]
++			then
++				rm -vf "${p}"
++			fi
++		done
 +done
 +
 +# enable plugins to be compiled with imageJ
@@ -125,7 +137,7 @@ diff -Naur old/imagej.sh new/imagej.sh
  # End Site specific variables ---------------------------------------------------------
  
  # other variables 
-@@ -320,7 +318,7 @@
+@@ -320,7 +330,7 @@
  
  # Resolving ij.jar path.  If ij.jar is a symbolic link to ij_<version>.jar
  # this allows updating ij.jar without crashing running sessions
@@ -134,7 +146,7 @@ diff -Naur old/imagej.sh new/imagej.sh
                                           
  for mod_jar in ${ij_path}/lib/*jar  ; do
      modules="${modules:-}${modules+:}$mod_jar"
-@@ -470,9 +468,9 @@
+@@ -470,9 +480,9 @@
  fi
  
  if (( $verbosity > 0 )) ; then
diff --git a/imagej.spec b/imagej.spec
index a6641cf..7c6906c 100644
--- a/imagej.spec
+++ b/imagej.spec
@@ -1,6 +1,6 @@
 Name:           imagej
 Version:        1.53r
-Release:        1%{?dist}
+Release:        2%{?dist}
 Summary:        Image Processing and Analysis in Java
 
 License:        Public Domain
@@ -110,6 +110,13 @@ desktop-file-install --vendor=''                     \
 
 
 %changelog
+* Tue May 31 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53r-2
+- Fix regression in launcher script
+- Symlinks called “*” will not be created when there are no shared plugins or
+  luts
+- Broken symlinks into shared directories will be removed
+- Symlink changes will be printed to the terminal
+
 * Mon May 30 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53r-1
 - Adjust versioning scheme
 - Update to 1.53r (close RHBZ#1609549)

From ac2ebd3da7b7590d92f943ff71a48aa596ad9dbd Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Tue, 31 May 2022 12:43:59 -0400
Subject: [PATCH 2/5] Make sure the upstream VERSION is set correctly

- Use the initial numeric <pkgrel> field of the Release as the BUILD
---
 imagej.spec | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/imagej.spec b/imagej.spec
index 7c6906c..7019457 100644
--- a/imagej.spec
+++ b/imagej.spec
@@ -1,6 +1,6 @@
 Name:           imagej
 Version:        1.53r
-Release:        2%{?dist}
+Release:        3%{?dist}
 Summary:        Image Processing and Analysis in Java
 
 License:        Public Domain
@@ -63,6 +63,14 @@ sed -r -i \
     -e 's#@PKGDATADIR@#%{_datadir}/imagej#' \
     imagej.sh
 
+# Make sure the upstream version number is set correctly, and use the initial
+# numeric <pkgrel> field of the Release as the BUILD.
+%global pkgrel %(echo '%{release}' | sed -r 's/[^[:digit:]].*$//')
+sed -r -i \
+    -e 's/(public static final String VERSION = )"[^"]+";/\1"%{version}";/' \
+    -e 's/(public static final String BUILD = )"[^"]+";/\1"%{pkgrel}";/' \
+    source/ij/ImageJ.java
+
 
 %build
 cd source
@@ -110,6 +118,10 @@ desktop-file-install --vendor=''                     \
 
 
 %changelog
+* Tue May 31 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53r-3
+- Make sure the upstream VERSION is set correctly
+- Use the initial numeric <pkgrel> field of the Release as the BUILD
+
 * Tue May 31 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53r-2
 - Fix regression in launcher script
 - Symlinks called “*” will not be created when there are no shared plugins or

From afaba7e36177b732f1d7e3fb57c227cea127fae5 Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Thu, 29 Dec 2022 09:43:30 -0500
Subject: [PATCH 3/5] Update to 1.53v (close RHBZ#2121261)

---
 .gitignore  |   2 +-
 imagej.png  | Bin 0 -> 13012 bytes
 imagej.spec |  11 +++++++----
 sources     |   3 +--
 4 files changed, 9 insertions(+), 7 deletions(-)
 create mode 100644 imagej.png

diff --git a/.gitignore b/.gitignore
index 4723b59..13662c1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,6 @@ macros.zip
 /ij148e-src.zip
 /imagej-1.48-patch0.patch
 /imagej-1.48-patch1.patch
-/imagej.png
 /ij150h-src.zip
 /ij153r-src.zip
+/ij153v-src.zip
diff --git a/imagej.png b/imagej.png
new file mode 100644
index 0000000000000000000000000000000000000000..e98d80779736d2b9b06e1d32b85de0e413ee28e0
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z-U)vzop1&3HUA(5cti<?T#JDgYW*D#*Odk^YF0J6;)ds^4nMXbH&sCct$tIIT)>pC
z4K(6{u9N%4;Xl>_JWtT@nab#!QM+i?Dfuw~Q9kAc2tU9F^Wcw(ndAijmIGD)D<&i`
zA3|^tcm~q(*E%QK0Q{;vxbuK=zP}-_v{7F@0-5Sc0JtXqll}ddZP>W}qVvyLdX?N5
zTAeqtD~*}KrPAbhV`8+d4~=S4NUjn9^u*58#e@*QFf>fQe~pBKHAt23EEp|^0EkKR
z_Bb#HPSs}=UyKVp?>MGl5~f56z+)gtk{t*_z)FGi<>PMaJh*h+;~0Vuu@EEvTXy9&
zU)0}1b$1&0Qc`4D2}dHaj`p^WbW>AjIHX5X4XJcQ$CBoTWQv%S^lU5YRdUT%%}{k+
z^WqJS2sS<MSV{Ifx^hIv;{lWT*=f;w=EN;4M$n(2&-rzX3q&&tk}iqVjN?fLeH}-Z
z#2_O@2$rPs2@_8@qOZb*$ev%qqUZ)!BnT}eLoFe^@80h|{7-x=y>P2}md?^k=>Gwl
W!bY+z)8N1W0000<MNUMnLSTZF#2+C5

literal 0
HcmV?d00001

diff --git a/imagej.spec b/imagej.spec
index 7019457..3784b20 100644
--- a/imagej.spec
+++ b/imagej.spec
@@ -1,11 +1,11 @@
 Name:           imagej
-Version:        1.53r
-Release:        3%{?dist}
+Version:        1.53v
+Release:        1%{?dist}
 Summary:        Image Processing and Analysis in Java
 
 License:        Public Domain
-URL:            https://rsbweb.nih.gov/ij/index.html
-Source0:        https://rsbweb.nih.gov/ij/download/src/ij%(echo '%{version}' | tr -d .)-src.zip
+URL:            https://imagej.net/ij/index.html
+Source0:        https://imagej.net/ij/download/src/ij%(echo '%{version}' | tr -d .)-src.zip
 Source1:        imagej.desktop
 Source2:        https://rsbweb.nih.gov/ij/macros/macros.zip
 Source3:        https://rsb.info.nih.gov/ij/download/linux/unix-script.txt
@@ -118,6 +118,9 @@ desktop-file-install --vendor=''                     \
 
 
 %changelog
+* Thu Dec 29 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53v-1
+- Update to 1.53v (close RHBZ#2121261)
+
 * Tue May 31 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53r-3
 - Make sure the upstream VERSION is set correctly
 - Use the initial numeric <pkgrel> field of the Release as the BUILD
diff --git a/sources b/sources
index 88c24ec..fa3a086 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,2 @@
-SHA512 (ij153r-src.zip) = 2f062754dcf37716a22f12e9af3969ee6ef7ccd26d85cf6df760225e44876ff787884016c5d9367fe390c48a688de89678d24bede4dcea702a3bc4adb28c31a5
-SHA512 (imagej.png) = 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
+SHA512 (ij153v-src.zip) = 7436b3d1cc2461569f0091023d11b9b9b972a1ed05db30ff46568a3e61a0c049e4e43998d6e6567cdcfb6feb43d033dd695148d9e8ac7be301cb24dd6d8d7739
 SHA512 (macros.zip) = 383dd4131c3bc9f810c297f2846105592bcf34a09cbaa590c5ffb8a71217bb6eba7b0cbab4ab259feb740ac87e05d439e19cfb17fc67c9150f60a1711657bfd3

From a06cc2e696e16dfece6cead96554a8f174367e5b Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Fri, 10 Mar 2023 14:38:27 -0500
Subject: [PATCH 4/5] Convert License to SPDX

---
 imagej.spec | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/imagej.spec b/imagej.spec
index 3784b20..e7b10c2 100644
--- a/imagej.spec
+++ b/imagej.spec
@@ -3,7 +3,16 @@ Version:        1.53v
 Release:        1%{?dist}
 Summary:        Image Processing and Analysis in Java
 
-License:        Public Domain
+# From https://imagej.nih.gov/ij/disclaimer.html:
+#   ImageJ was developed at the National Institutes of Health by an employee of
+#   the Federal Government in the course of his official duties. Pursuant to
+#   Title 17, Section 105 of the United States Code, this software is not
+#   subject to copyright protection and is in the public domain. ImageJ is an
+#   experimental system. NIH assumes no responsibility whatsoever for its use
+#   by other parties, and makes no guarantees, expressed or implied, about its
+#   quality, reliability, or any other characteristic.
+# https://gitlab.com/fedora/legal/fedora-license-data/-/commit/b216f9bcb1c3195b4ddb14674d95e299f669903a
+License:        LicenseRef-Fedora-Public-Domain
 URL:            https://imagej.net/ij/index.html
 Source0:        https://imagej.net/ij/download/src/ij%(echo '%{version}' | tr -d .)-src.zip
 Source1:        imagej.desktop

From a499d1818d4f698e9e2c3d6c869354b458451a36 Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Fri, 10 Mar 2023 12:44:43 -0500
Subject: [PATCH 5/5] Update to 1.54c (close RHBZ#2175999)

---
 .gitignore  | 1 +
 imagej.spec | 5 ++++-
 sources     | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 13662c1..26aacb8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ macros.zip
 /ij150h-src.zip
 /ij153r-src.zip
 /ij153v-src.zip
+/ij154c-src.zip
diff --git a/imagej.spec b/imagej.spec
index e7b10c2..b2e64f1 100644
--- a/imagej.spec
+++ b/imagej.spec
@@ -1,5 +1,5 @@
 Name:           imagej
-Version:        1.53v
+Version:        1.54c
 Release:        1%{?dist}
 Summary:        Image Processing and Analysis in Java
 
@@ -127,6 +127,9 @@ desktop-file-install --vendor=''                     \
 
 
 %changelog
+* Fri Mar 10 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 1.54c-1
+- Update to 1.54c (close RHBZ#2175999)
+
 * Thu Dec 29 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 1.53v-1
 - Update to 1.53v (close RHBZ#2121261)
 
diff --git a/sources b/sources
index fa3a086..7968760 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-SHA512 (ij153v-src.zip) = 7436b3d1cc2461569f0091023d11b9b9b972a1ed05db30ff46568a3e61a0c049e4e43998d6e6567cdcfb6feb43d033dd695148d9e8ac7be301cb24dd6d8d7739
+SHA512 (ij154c-src.zip) = 392f134b05aef266e735e2936bddda9b92c952a935a679f279adb7691581cca41c5537ec8f3ce7a0698af639c2b1a23ad0568a2b75c50148fb2cf32bf9427d56
 SHA512 (macros.zip) = 383dd4131c3bc9f810c297f2846105592bcf34a09cbaa590c5ffb8a71217bb6eba7b0cbab4ab259feb740ac87e05d439e19cfb17fc67c9150f60a1711657bfd3