science/orthanc: Update to 1.12.9 and unbreak

Fix service start based on:
    https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=227
Improve RC script to allow user flags
Fix mismatched db paths
Release notes:
    https://orthanc.uclouvain.be/hg/orthanc/file/Orthanc-1.12.9/NEWS

PR:             290458 275624 275623 275622
Approved by:    portmgr (blanket, unbreak)

science/orthanc/Makefile

@@ -1,6 +1,5 @@
 PORTNAME=	orthanc
-DISTVERSION=	1.12.6
-PORTREVISION=	4
+DISTVERSION=	1.12.9
 CATEGORIES=	science
 MASTER_SITES=	https://orthanc.uclouvain.be/downloads/sources/orthanc/
 DISTNAME=	Orthanc-${PORTVERSION}
@@ -12,24 +11,19 @@ WWW=		https://www.orthanc-server.com/
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-BUILD_DEPENDS=	protoc:devel/protobuf
-
+BUILD_DEPENDS=	protoc:devel/protobuf \
+		googletest>0:devel/googletest
 LIB_DEPENDS=	libboost_atomic.so:devel/boost-libs \
 		libcivetweb.so:www/civetweb \
 		libcurl.so:ftp/curl \
 		libdcmtkcharls.so:graphics/dcmtk \
-		libgtest.so:devel/googletest \
-		libicuuc.so:devel/icu \
 		libjsoncpp.so:devel/jsoncpp \
 		libpng16.so:graphics/png \
 		libprotobuf.so:devel/protobuf \
 		libpugixml.so:textproc/pugixml \
-		libtiff.so:graphics/tiff \
 		libuuid.so:misc/libuuid
 
 USES=		cmake gnome iconv jpeg lua python:build sqlite ssl
-USE_GNOME=	libxml2
-USE_LDCONFIG=	yes
 
 USE_RC_SUBR=	orthanc
 

science/orthanc/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1739138261
-SHA256 (Orthanc-1.12.6.tar.gz) = aa5b6d6309965ed360625b5572e79068e6c501b603163e330629f2f0a56a0fe9
-SIZE (Orthanc-1.12.6.tar.gz) = 2089779
+TIMESTAMP = 1761178767
+SHA256 (Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2
+SIZE (Orthanc-1.12.9.tar.gz) = 2165182

science/orthanc/files/orthanc.in

@@ -23,13 +23,13 @@ desc="Lightweight DICOM server for healthcare and medical research"
 load_rc_config $name
 
 : ${orthanc_enable:=NO}
-: ${orthanc_flags="%%ETCDIR%%/orthanc.json"}
+: ${orthanc_config="%%ETCDIR%%/orthanc.json"}
 
 start_precmd=orthanc_prestart
 pidfile=/var/run/orthanc.pid
 procname=%%PREFIX%%/sbin/Orthanc
 command=/usr/sbin/daemon
-command_args=" -f -p ${pidfile} -u orthanc ${procname} ${orthanc_flags}"
+command_args=" --output-file /var/log/orthanc --sighup --child-pidfile ${pidfile} --user orthanc ${procname} ${orthanc_flags} ${orthanc_config}"
 
 orthanc_prestart()
 {

science/orthanc/files/patch-OrthancFramework_Sources_Images_JpegWriter.cpp

@@ -1,11 +0,0 @@
---- OrthancFramework/Sources/Images/JpegWriter.cpp.orig	2024-12-17 16:33:40 UTC
-+++ OrthancFramework/Sources/Images/JpegWriter.cpp
-@@ -187,7 +187,7 @@ namespace Orthanc
-      **/
-     unsigned long size;
- #else
--    size_t size;
-+    unsigned long size;
- #endif
- 
-     if (setjmp(jerr.GetJumpBuffer())) 

science/orthanc/files/patch-OrthancServer_Resources_Configuration.json

@@ -5,13 +5,13 @@
    // raw DICOM instances). Backslashes must be either escaped by
    // doubling them, or replaced by forward slashes "/".
 -  "StorageDirectory" : "OrthancStorage",
-+  "StorageDirectory" : "/var/db/orthanc/db-v5",
++  "StorageDirectory" : "/var/db/orthanc/db/db-v5",
  
    // Path to the directory that holds the SQLite index (if unset, the
    // value of StorageDirectory is used). This index could be stored on
    // a RAM-drive or a SSD device for performance reasons.
 -  "IndexDirectory" : "OrthancStorage",
-+  "IndexDirectory" : "/var/db/orthanc/db-v5",
++  "IndexDirectory" : "/var/db/orthanc/db/db-v5",
  
    // Path to the directory where Orthanc stores its large temporary
    // files. The content of this folder can be safely deleted once

science/orthanc/files/patch-OrthancServer_Sources_Database_PrepareDatabase.sql

@@ -0,0 +1,13 @@
+--- OrthancServer/Sources/Database/PrepareDatabase.sql.orig	2025-08-11 16:02:50 UTC
++++ OrthancServer/Sources/Database/PrepareDatabase.sql
+@@ -160,4 +160,9 @@ -- The "1" corresponds to the "GlobalProperty_Database
+ 
+ -- Set the version of the database schema
+ -- The "1" corresponds to the "GlobalProperty_DatabaseSchemaVersion" enumeration
+-INSERT INTO GlobalProperties VALUES (1, "6");
++-- Upstream code has (1, "6"), which causes startup to fail on FreeBSD
++-- E1023 08:43:05.328003             MAIN Connection.cpp:169] SQLite execute error: no such column: "6" - should this be a string literal in single-quotes? (1)
++-- Apparently due to sqlite 3.41+ being stricter about string literals
++-- Debian packages currently uses 3.34
++-- https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=227
++INSERT INTO GlobalProperties VALUES (1, 6);