science/orthanc: Revive port

Orthanc is a Lightweight DICOM server for healthcare and medical
research.

PR:		242546
Approved by:	lwhsu (mentor)

7 files changed, 230 insertions, 0 deletions

diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile
new file mode 100644
index 000000000000..9e7f31c21893
--- /dev/null
+++ b/science/orthanc/Makefile
@@ -0,0 +1,57 @@
+# Created by: maintainer.freebsd@xpoundit.com
+
+PORTNAME=	orthanc
+DISTVERSION=	1.9.3
+CATEGORIES=	science
+MASTER_SITES=	https://www.orthanc-server.com/downloads/get.php?path=/orthanc/
+DISTNAME=	Orthanc-${PORTVERSION}
+
+MAINTAINER=	maintainer.freebsd@xpoundit.com
+COMMENT=	Lightweight DICOM server for healthcare and medical research
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+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 \
+		libpugixml.so:textproc/pugixml \
+		libtiff.so:graphics/tiff \
+		libuuid.so:misc/e2fsprogs-libuuid
+
+USES=		cmake gnome iconv jpeg lua python:build sqlite ssl
+USE_GNOME=	libxml2
+USE_LDCONFIG=	yes
+
+WRKSRC=		${WRKDIR}/Orthanc-${PORTVERSION}
+
+CMAKE_SOURCE_PATH=	${WRKSRC}/OrthancServer
+CMAKE_OFF=	BUILD_CONNECTIVITY_CHECKS UNIT_TESTS_WITH_HTTP_CONNEXIONS
+CMAKE_ON=	USE_SYSTEM_BOOST USE_SYSTEM_CIVETWEB USE_SYSTEM_DCMTK \
+		USE_SYSTEM_GOOGLE_TEST USE_SYSTEM_JSONCPP USE_SYSTEM_LIBICONV \
+		USE_SYSTEM_LIBJPEG USE_SYSTEM_LIBPNG USE_SYSTEM_LUA \
+		USE_SYSTEM_OPENSSL USE_SYSTEM_PUGIXML USE_SYSTEM_SQLITE \
+		USE_SYSTEM_UUID USE_SYSTEM_ZLIB
+CFLAGS+=	-DNDEBUG
+CXXFLAGS+=	-DNDEBUG
+
+USE_RC_SUBR=	orthanc
+
+USERS=		orthanc
+GROUPS=		orthanc
+
+PLIST_SUB+=	PORTVERSION=${PORTVERSION}
+
+post-install:
+	${MKDIR} ${STAGEDIR}/var/db/orthanc/db/db-v5
+	${MKDIR} ${STAGEDIR}${DATADIR}/plugins
+	${MKDIR} ${STAGEDIR}${ETCDIR}
+	${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' ${CMAKE_SOURCE_PATH}/Resources/Configuration.json
+	${CP} ${CMAKE_SOURCE_PATH}/Resources/Configuration.json ${STAGEDIR}${ETCDIR}/orthanc.json.sample
+
+.include <bsd.port.mk>
diff --git a/science/orthanc/distinfo b/science/orthanc/distinfo
new file mode 100644
index 000000000000..ed25e78020f7
--- /dev/null
+++ b/science/orthanc/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1620899601
+SHA256 (Orthanc-1.9.3.tar.gz) = 41cc35a3d15ecb0d7b834e8e28a740cc4ffa1f333c019a764228d60e96608960
+SIZE (Orthanc-1.9.3.tar.gz) = 1818313
diff --git a/science/orthanc/files/orthanc.in b/science/orthanc/files/orthanc.in
new file mode 100644
index 000000000000..85d6af45d8a1
--- /dev/null
+++ b/science/orthanc/files/orthanc.in
@@ -0,0 +1,40 @@
+#!/bin/sh
+
+# $FreeBSD$
+#
+# PROVIDE: orthanc
+# REQUIRE: LOGIN
+# KEYWORD: shutdown
+#
+# Add these lines to /etc/rc.conf.local or /etc/rc.conf
+# to enable this service:
+#
+# orthanc_enable (bool):	Set to NO by default.
+#				Set it to YES to enable Orthanc.
+# orthanc_flags (str):		Set to %%ETCDIR%%/orthanc.json
+#				by default.
+
+. /etc/rc.subr
+
+name=orthanc
+rcvar=orthanc_enable
+desc="Lightweight DICOM server for healthcare and medical research"
+
+load_rc_config $name
+
+: ${orthanc_enable:=NO}
+: ${orthanc_flags="%%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}"
+
+orthanc_prestart()
+{
+	# Have to empty rc_flags so they don't get passed to daemon(8)
+	rc_flags=""
+}
+
+run_rc_command "$1"
diff --git a/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake
new file mode 100644
index 000000000000..b1cd8bd06165
--- /dev/null
+++ b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake
@@ -0,0 +1,64 @@
+--- OrthancFramework/Resources/CMake/CivetwebConfiguration.cmake.orig	2021-05-12 13:54:35 UTC
++++ OrthancFramework/Resources/CMake/CivetwebConfiguration.cmake
+@@ -98,32 +98,38 @@ else()
+ 
+   cmake_reset_check_state()
+   set(CMAKE_REQUIRED_LIBRARIES dl pthread)
+-  CHECK_LIBRARY_EXISTS(civetweb mg_start "" HAVE_CIVETWEB_LIB)
+-  if (NOT HAVE_CIVETWEB_LIB)
+-    message(FATAL_ERROR "Please install the libcivetweb-dev package")
+-  endif()
+ 
+-  link_libraries(civetweb)
++  find_library(CIVETWEB_LIB NAMES civetweb PATHS
++    /usr/lib
++    /usr/local/lib
++  )
+ 
+-  # Check whether the system distribution of civetweb contains the
+-  # patch "../Patches/civetweb-1.13.patch" that allows to disable
+-  # keep-alive on selected HTTP connections. This is useful to speed
+-  # up multipart transfers, as encountered in DICOMweb.
+-  CHECK_LIBRARY_EXISTS(civetweb mg_disable_keep_alive "" CIVETWEB_HAS_DISABLE_KEEP_ALIVE_1)  # From "../Patches/civetweb-1.13.patch"
+-  CHECK_LIBRARY_EXISTS(civetweb mg_disable_connection_keep_alive "" CIVETWEB_HAS_DISABLE_KEEP_ALIVE_2)  # From civetweb >= 1.14
+-  if (CIVETWEB_HAS_DISABLE_KEEP_ALIVE_1 OR
+-      CIVETWEB_HAS_DISABLE_KEEP_ALIVE_2)
+-    add_definitions(
+-      -DCIVETWEB_HAS_DISABLE_KEEP_ALIVE=1
+-      -DCIVETWEB_HAS_WEBDAV_WRITING=1
+-      )
+-    message("Performance: Your system-wide distribution of civetweb is configured for best performance")
++  if (CIVETWEB_LIB)
++    CHECK_LIBRARY_EXISTS(${CIVETWEB_LIB} mg_start "" HAVE_CIVETWEB_LIB)
++    if (NOT HAVE_CIVETWEB_LIB)
++      message(FATAL_ERROR "Unable to use mg_start from civetweb library")
++    endif()
++
++    CHECK_LIBRARY_EXISTS(${CIVETWEB_LIB} mg_disable_keep_alive "" CIVETWEB_HAS_DISABLE_KEEP_ALIVE)
++    if (CIVETWEB_HAS_DISABLE_KEEP_ALIVE)
++      add_definitions(
++        -DCIVETWEB_HAS_DISABLE_KEEP_ALIVE=1
++        -DCIVETWEB_HAS_WEBDAV_WRITING=1
++        )
++      message("Performance: Your system-wide distribution of civetweb is configured for best performance")
++    else()
++      message(WARNING "Performance: Your system-wide distribution of civetweb does not feature the mg_disable_keep_alive() function, and WebDAV will only be available for read-only access")
++      add_definitions(
++        -DCIVETWEB_HAS_DISABLE_KEEP_ALIVE=0
++        -DCIVETWEB_HAS_WEBDAV_WRITING=0
++        )
++    endif()
++
++    get_filename_component(CIVETWEB_LIB_PATH ${CIVETWEB_LIB} DIRECTORY)
++    link_directories(${CIVETWEB_LIB_PATH})
++    link_libraries(civetweb)
+   else()
+-    message(WARNING "Performance: Your system-wide distribution of civetweb does not feature the mg_disable_keep_alive() function, and WebDAV will only be available for read-only access")
+-    add_definitions(
+-      -DCIVETWEB_HAS_DISABLE_KEEP_ALIVE=0
+-      -DCIVETWEB_HAS_WEBDAV_WRITING=0
+-      )
++    message(FATAL_ERROR "Unable to find the civetweb library")
+   endif()
+ 
+   unset(CMAKE_REQUIRED_LIBRARIES)  # This reset must be after "CHECK_LIBRARY_EXISTS"
diff --git a/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json
new file mode 100644
index 000000000000..91f978822db2
--- /dev/null
+++ b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json
@@ -0,0 +1,25 @@
+--- OrthancServer/Resources/Configuration.json.orig	2021-01-29 09:36:16 UTC
++++ OrthancServer/Resources/Configuration.json
+@@ -10,12 +10,12 @@
+   // Path to the directory that holds the heavyweight files (i.e. the
+   // raw DICOM instances). Backslashes must be either escaped by
+   // doubling them, or replaced by forward slashes "/".
+-  "StorageDirectory" : "OrthancStorage",
++  "StorageDirectory" : "/var/db/orthanc/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",
+ 
+   // Path to the directory where Orthanc stores its large temporary
+   // files. The content of this folder can be safely deleted once
+@@ -53,6 +53,7 @@
+   // find shared libraries. Backslashes must be either escaped by
+   // doubling them, or replaced by forward slashes "/".
+   "Plugins" : [
++    "%%PREFIX%%/share/orthanc/plugins/"
+   ],
+ 
+   // Maximum number of processing jobs that are simultaneously running
diff --git a/science/orthanc/pkg-descr b/science/orthanc/pkg-descr
new file mode 100644
index 000000000000..9ab8479c6127
--- /dev/null
+++ b/science/orthanc/pkg-descr
@@ -0,0 +1,23 @@
+Orthanc aims at providing a simple, yet powerful standalone DICOM server. It
+is designed to improve the DICOM flows in hospitals and to support research
+about the automated analysis of medical images. Orthanc lets its users focus
+on the content of the DICOM files, hiding the complexity of the DICOM format
+and of the DICOM protocol.
+
+Orthanc can turn any computer running Windows, Linux, FreeBSD or OS X into a
+DICOM store (in other words, a mini-PACS system). Its architecture is
+lightweight and standalone, meaning that no complex database administration
+is required, nor the installation of third-party dependencies.
+
+What makes Orthanc unique is the fact that it provides a RESTful API. Thanks
+to this major feature, it is possible to drive Orthanc from any computer
+language. The DICOM tags of the stored medical images can be downloaded in
+the JSON file format. Furthermore, standard PNG images can be generated
+on-the-fly from the DICOM instances by Orthanc.
+
+Orthanc also features a plugin mechanism to add new modules that extends the
+core capabilities of its REST API. A Web viewer, a PostgreSQL database
+back-end, a MySQL database back-end, and a reference implementation of
+DICOMweb are currently freely available as plugins.
+
+WWW: https://www.orthanc-server.com/
diff --git a/science/orthanc/pkg-plist b/science/orthanc/pkg-plist
new file mode 100644
index 000000000000..3c86361bc527
--- /dev/null
+++ b/science/orthanc/pkg-plist
@@ -0,0 +1,18 @@
+@owner orthanc
+@group orthanc
+@mode 700
+@dir %%DATADIR%%/plugins
+@dir /var/db/orthanc/db/db-v5
+@dir /var/db/orthanc/db
+@dir /var/db/orthanc
+@mode 600
+@sample %%ETCDIR%%/orthanc.json.sample
+@mode
+bin/OrthancRecoverCompressedFile
+include/orthanc/OrthancCDatabasePlugin.h
+include/orthanc/OrthancCPlugin.h
+sbin/Orthanc
+%%DATADIR%%/plugins/libModalityWorklists.so
+%%DATADIR%%/plugins/libModalityWorklists.so.%%PORTVERSION%%
+%%DATADIR%%/plugins/libServeFolders.so
+%%DATADIR%%/plugins/libServeFolders.so.%%PORTVERSION%%