diff options
Diffstat (limited to 'science')
-rw-r--r-- | science/Makefile | 4 | ||||
-rw-r--r-- | science/orthanc-dicomweb/Makefile | 43 | ||||
-rw-r--r-- | science/orthanc-dicomweb/distinfo | 3 | ||||
-rw-r--r-- | science/orthanc-dicomweb/pkg-descr | 4 | ||||
-rw-r--r-- | science/orthanc-postgresql/Makefile | 39 | ||||
-rw-r--r-- | science/orthanc-postgresql/distinfo | 2 | ||||
-rw-r--r-- | science/orthanc-postgresql/pkg-descr | 4 | ||||
-rw-r--r-- | science/orthanc-webviewer/Makefile | 55 | ||||
-rw-r--r-- | science/orthanc-webviewer/distinfo | 13 | ||||
-rw-r--r-- | science/orthanc-webviewer/pkg-descr | 7 | ||||
-rw-r--r-- | science/orthanc/Makefile | 92 | ||||
-rw-r--r-- | science/orthanc/distinfo | 5 | ||||
-rw-r--r-- | science/orthanc/files/orthanc.in | 40 | ||||
-rw-r--r-- | science/orthanc/files/patch-Resources_Configuration.json | 25 | ||||
-rw-r--r-- | science/orthanc/pkg-descr | 20 | ||||
-rw-r--r-- | science/orthanc/pkg-plist | 19 |
16 files changed, 0 insertions, 375 deletions
diff --git a/science/Makefile b/science/Makefile index a595fa444119..775b586db71e 100644 --- a/science/Makefile +++ b/science/Makefile @@ -122,10 +122,6 @@ SUBDIR += nifticlib SUBDIR += openbabel SUBDIR += openkim - SUBDIR += orthanc - SUBDIR += orthanc-dicomweb - SUBDIR += orthanc-postgresql - SUBDIR += orthanc-webviewer SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile deleted file mode 100644 index 20ba8d4ef54f..000000000000 --- a/science/orthanc-dicomweb/Makefile +++ /dev/null @@ -1,43 +0,0 @@ -# Created by: mp39590@gmail.com -# $FreeBSD$ - -PORTNAME= orthanc-dicomweb -PORTVERSION= 0.4 -PORTREVISION= 4 -CATEGORIES= science net -MASTER_SITES= http://orthanc-server.com/downloads/get.php?path=/plugin-dicom-web/ -DISTNAME= OrthancDicomWeb-${PORTVERSION} -DIST_SUBDIR= orthanc - -MAINTAINER= mp39590@gmail.com -COMMENT= WADO and DICOMweb support for Orthanc - -LICENSE= AGPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING - -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc -LIB_DEPENDS= libgdcmCommon.so:devel/gdcm \ - libboost_filesystem.so:devel/boost-libs \ - libboost_thread.so:devel/boost-libs \ - libboost_system.so:devel/boost-libs \ - libboost_date_time.so:devel/boost-libs \ - libboost_regex.so:devel/boost-libs \ - libboost_locale.so:devel/boost-libs \ - libjsoncpp.so:devel/jsoncpp \ - libuuid.so:misc/e2fsprogs-libuuid \ - libpugixml.so:textproc/pugixml \ - libgtest.so:devel/googletest - -USES= cmake:outsource localbase python:build -WRKSRC= ${WRKDIR}/OrthancDicomWeb-${PORTVERSION} - -PLIST_FILES= share/orthanc/plugins/libOrthancDicomWeb.so \ - share/orthanc/plugins/libOrthancDicomWeb.so.${PORTVERSION} - -post-patch: - @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/Orthanc/Resources/CMake/*.cmake - -do-test: - @cd ${BUILD_WRKSRC} && ./UnitTests - -.include <bsd.port.mk> diff --git a/science/orthanc-dicomweb/distinfo b/science/orthanc-dicomweb/distinfo deleted file mode 100644 index cba434945410..000000000000 --- a/science/orthanc-dicomweb/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1503168795 -SHA256 (orthanc/OrthancDicomWeb-0.4.tar.gz) = 84963f45e496fcd028fdbc3219bca250fb8b95e07a886dda8942111df77ffd26 -SIZE (orthanc/OrthancDicomWeb-0.4.tar.gz) = 156133 diff --git a/science/orthanc-dicomweb/pkg-descr b/science/orthanc-dicomweb/pkg-descr deleted file mode 100644 index 3d1936f55270..000000000000 --- a/science/orthanc-dicomweb/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -This plugin extends the RESTful API of Orthanc with WADO and DICOMweb -support. - -WWW: http://www.orthanc-server.com/ diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile deleted file mode 100644 index aebddf46b3d8..000000000000 --- a/science/orthanc-postgresql/Makefile +++ /dev/null @@ -1,39 +0,0 @@ -# Created by: mp39590@gmail.com -# $FreeBSD$ - -PORTNAME= orthanc-portgresql -PORTVERSION= 2.0 -PORTREVISION= 8 -CATEGORIES= science graphics -MASTER_SITES= http://orthanc-server.com/downloads/get.php?path=/plugin-postgresql/ -DISTNAME= OrthancPostgreSQL-${PORTVERSION} -DIST_SUBDIR= orthanc - -MAINTAINER= mp39590@gmail.com -COMMENT= PostgreSQL plugin for Orthanc - -LICENSE= AGPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING - -BUILD_DEPENDS= orthanc>=0.9.4:science/orthanc -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libjsoncpp.so:devel/jsoncpp - -## UnitTests require running PostgreSQL server, so it's pointless to build/run them -CMAKE_ARGS= -DBUILD_UNIT_TESTS=OFF - -CXXFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib - -USES= cmake:outsource pgsql python:build -WRKSRC= ${WRKDIR}/OrthancPostgreSQL-${PORTVERSION} - -PLIST_FILES= share/orthanc/plugins/libOrthancPostgreSQLIndex.so \ - share/orthanc/plugins/libOrthancPostgreSQLIndex.so.${PORTVERSION} \ - share/orthanc/plugins/libOrthancPostgreSQLStorage.so \ - share/orthanc/plugins/libOrthancPostgreSQLStorage.so.${PORTVERSION} - -post-extract: - @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/Resources/CMake/*.cmake - -.include <bsd.port.mk> diff --git a/science/orthanc-postgresql/distinfo b/science/orthanc-postgresql/distinfo deleted file mode 100644 index 2cf39b4682ec..000000000000 --- a/science/orthanc-postgresql/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (orthanc/OrthancPostgreSQL-2.0.tar.gz) = d9ef74b016ac89e8e298ab6e5e98a9b4831c198377e254c231309c12f52c378d -SIZE (orthanc/OrthancPostgreSQL-2.0.tar.gz) = 99020 diff --git a/science/orthanc-postgresql/pkg-descr b/science/orthanc-postgresql/pkg-descr deleted file mode 100644 index 78b856494f60..000000000000 --- a/science/orthanc-postgresql/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -The plugin replaces the default SQLite engine of Orthanc with a -PostgreSQL back-end. - -WWW: http://www.orthanc-server.com/ diff --git a/science/orthanc-webviewer/Makefile b/science/orthanc-webviewer/Makefile deleted file mode 100644 index 3013d6ac5c3e..000000000000 --- a/science/orthanc-webviewer/Makefile +++ /dev/null @@ -1,55 +0,0 @@ -# Created by: mp39590@gmail.com -# $FreeBSD$ - -PORTNAME= orthanc-webviewer -PORTVERSION= 2.3 -PORTREVISION= 4 -CATEGORIES= science graphics -MASTER_SITES= http://orthanc-server.com/downloads/get.php?path=/plugin-webviewer/:main \ - http://www.orthanc-server.com/downloads/third-party/WebViewer/:thirdparty -DISTFILES= OrthancWebViewer-${PORTVERSION}.tar.gz:main \ - jsPanel-2.3.3-fixed.zip:thirdparty \ - cornerstone-0.11.0.zip:thirdparty \ - jquery-ui-1.11.3.zip:thirdparty \ - pako-0.2.5.zip:thirdparty \ - js-url-1.8.6.zip:thirdparty -DIST_SUBDIR= orthanc - -MAINTAINER= mp39590@gmail.com -COMMENT= Web viewer plugin for Orthanc - -LICENSE= AGPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING - -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc \ - gtest-config:devel/googletest -LIB_DEPENDS= libgdcmCommon.so:devel/gdcm \ - libboost_system.so:devel/boost-libs \ - libboost_thread.so:devel/boost-libs \ - libboost_filesystem.so:devel/boost-libs \ - libjsoncpp.so:devel/jsoncpp \ - libsqlite3.so:databases/sqlite3 \ - libuuid.so:misc/e2fsprogs-libuuid \ - libgtest.so:devel/googletest - -USES= cmake:outsource localbase python:build -WRKSRC= ${WRKDIR}/OrthancWebViewer-${PORTVERSION} - -PLIST_FILES= share/orthanc/plugins/libOrthancWebViewer.so \ - share/orthanc/plugins/libOrthancWebViewer.so.${PORTVERSION} - -post-extract: - ${MKDIR} ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/jsPanel-2.3.3-fixed.zip ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/cornerstone-0.11.0.zip ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/jquery-ui-1.11.3.zip ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/pako-0.2.5.zip ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/js-url-1.8.6.zip ${WRKSRC}/ThirdPartyDownloads - -post-patch: - @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/Orthanc/Resources/CMake/*.cmake - -post-build: - @cd ${BUILD_WRKSRC} && ./UnitTests - -.include <bsd.port.mk> diff --git a/science/orthanc-webviewer/distinfo b/science/orthanc-webviewer/distinfo deleted file mode 100644 index ae8548d8c7ba..000000000000 --- a/science/orthanc-webviewer/distinfo +++ /dev/null @@ -1,13 +0,0 @@ -TIMESTAMP = 1503851520 -SHA256 (orthanc/OrthancWebViewer-2.3.tar.gz) = e9f8b89fb2a63373cccd55267680a953ec49073872dbb8747bc662b4d7955c5e -SIZE (orthanc/OrthancWebViewer-2.3.tar.gz) = 162475 -SHA256 (orthanc/jsPanel-2.3.3-fixed.zip) = 958a15c7009efbb865da62b5850a3a39661c62696e38b151c7f988f4ac445595 -SIZE (orthanc/jsPanel-2.3.3-fixed.zip) = 826542 -SHA256 (orthanc/cornerstone-0.11.0.zip) = 1bada9f1f2981968f72daa352e712abea5cac3e0417fe59176f70a23261f1da9 -SIZE (orthanc/cornerstone-0.11.0.zip) = 935277 -SHA256 (orthanc/jquery-ui-1.11.3.zip) = 045b52f293bf4f77c6689569064327495edd9e6434839b78a56299c555130282 -SIZE (orthanc/jquery-ui-1.11.3.zip) = 400437 -SHA256 (orthanc/pako-0.2.5.zip) = e493010e1b1af5c149631994365ed31e15722eed2d17cc1d95bd9af151f2005f -SIZE (orthanc/pako-0.2.5.zip) = 704378 -SHA256 (orthanc/js-url-1.8.6.zip) = ef2c7f50921ba64ac434eacf025669f1e6f39b5584100ffa8194a3edc08d43d3 -SIZE (orthanc/js-url-1.8.6.zip) = 54717 diff --git a/science/orthanc-webviewer/pkg-descr b/science/orthanc-webviewer/pkg-descr deleted file mode 100644 index c69229a71fea..000000000000 --- a/science/orthanc-webviewer/pkg-descr +++ /dev/null @@ -1,7 +0,0 @@ -Web viewer plugin allows easy serial view of medical images stored in -Orthanc server in a browser, using HTML5 technology. -Demo: http://youtu.be/ub5IxlVqoOE - -The plugin can't be used for diagnostic purposes. - -WWW: http://www.orthanc-server.com/ diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile deleted file mode 100644 index b70da3fb08f1..000000000000 --- a/science/orthanc/Makefile +++ /dev/null @@ -1,92 +0,0 @@ -# Created by: mp39590@gmail.com -# $FreeBSD$ - -PORTNAME= orthanc -PORTVERSION= 1.3.0 -PORTREVISION= 4 -CATEGORIES= science graphics net www -MASTER_SITES= http://orthanc-server.com/downloads/get.php?path=/orthanc/:main \ - http://www.montefiore.ulg.ac.be/~jodogne/Orthanc/ThirdPartyDownloads/:mongoose -DISTFILES= Orthanc-${PORTVERSION}.tar.gz:main \ - mongoose-3.8.tgz:mongoose -DIST_SUBDIR= ${PORTNAME} - -MAINTAINER= mp39590@gmail.com -COMMENT= RESTful DICOM server for healthcare and medical research - -# GPLv3 license, with the OpenSSL exception. -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING - -BROKEN= fails to build with boost 1.66, see bug 224177 -BROKEN_powerpc64= fails to configure: CMake: Looking for C++ include pugixml.hpp - not found -DEPRECATED= Broken for more than 3 months -EXPIRATION_DATE= 2018-06-06 - -LIB_DEPENDS= libcurl.so:ftp/curl \ - libjsoncpp.so:devel/jsoncpp \ - libuuid.so:misc/e2fsprogs-libuuid \ - libboost_filesystem.so:devel/boost-libs \ - libboost_thread.so:devel/boost-libs \ - libboost_system.so:devel/boost-libs \ - libboost_date_time.so:devel/boost-libs \ - libboost_regex.so:devel/boost-libs \ - libboost_locale.so:devel/boost-libs \ - libdcmdsig.so:devel/dcmtk \ - libcharls.so:devel/dcmtk \ - libdcmjpls.so:devel/dcmtk \ - libsqlite3.so:databases/sqlite3 \ - libpng.so:graphics/png \ - libgtest.so:devel/googletest \ - libpugixml.so:textproc/pugixml - -CMAKE_ARGS= -DDCMTK_LIBRARIES="dcmdsig;charls;dcmjpls" \ - -DDCMTK_DIR="${LOCALBASE}" \ - -DDCMTK_DICTIONARY_DIR="${LOCALBASE}/share/dcmtk" \ - -DUSE_SYSTEM_MONGOOSE=OFF \ - -DUNIT_TESTS_WITH_HTTP_CONNEXIONS=OFF - -USES= cmake:outsource dos2unix jpeg lua:51 python:build ssl -CFLAGS+= -I${LOCALBASE}/include -DOS2UNIX_FILES= CMakeLists.txt -USE_LDCONFIG= yes -USE_RC_SUBR= orthanc -WRKSRC= ${WRKDIR}/Orthanc-${PORTVERSION} -USERS= orthanc -GROUPS= orthanc -PLIST_SUB+= PORTVERSION=${PORTVERSION} - -# This is mongoose sources, downloaded from Orthanc author homepage. Orthanc -# requires mongoose webserver, but after version 3.8, mongoose developers has -# changed the license from MIT to GPLv2 only. This action made illegal to -# combine new mongoose versions with GPLv3 only Orthanc. -# We download sources manually and pass USE_SYSTEM_MONGOOSE=OFF to Orthanc -# cmake variables to tell that mongoose is not presented on the host OS and -# should be build together with the software instead. -# https://www.mail-archive.com/mongoose-users@googlegroups.com/msg00625.html -post-patch: - ${MKDIR} ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/mongoose-3.8.tgz ${WRKSRC}/ThirdPartyDownloads - # Orthanc hardcodes /usr/local paths for libs and includes. - @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/Resources/CMake/*.cmake - -# There is no way to disable building of test units without a patch, on other -# hand it brings only one build dependency (devel/googletest) and running it was -# helpful in early bug detection in Debian. -# Some tests require connections to be made to the outside world, this is -# definitely unsupported behaviour and therefor those tests are disabled with -# cmake variable above (-DUNIT_TESTS_WITH_HTTP_CONNEXIONS=OFF). -# -# Tests run is temporary disabled: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=215393 -#post-build: -# @cd ${BUILD_WRKSRC} && ./UnitTests - -post-install: - ${MKDIR} ${STAGEDIR}/var/db/orthanc/db/db-v5 - ${MKDIR} ${STAGEDIR}${DATADIR}/plugins - ${MKDIR} ${STAGEDIR}${ETCDIR} - ${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' ${WRKSRC}/Resources/Configuration.json - ${CP} ${WRKSRC}/Resources/Configuration.json ${STAGEDIR}${ETCDIR}/orthanc.json.sample - ${STRIP_CMD} ${STAGEDIR}${DATADIR}/plugins/libServeFolders.so.${PORTVERSION} - -.include <bsd.port.mk> diff --git a/science/orthanc/distinfo b/science/orthanc/distinfo deleted file mode 100644 index 14471b8ebf02..000000000000 --- a/science/orthanc/distinfo +++ /dev/null @@ -1,5 +0,0 @@ -TIMESTAMP = 1508149082 -SHA256 (orthanc/Orthanc-1.3.0.tar.gz) = a68b3c3fda8ea5cd065d356b314737634d8088d6ab2380c9ccfa433cc8fe61de -SIZE (orthanc/Orthanc-1.3.0.tar.gz) = 1231636 -SHA256 (orthanc/mongoose-3.8.tgz) = 6afc2c377614a01a24b78560a62d1316b29372afe08eae3715b56c877be71c6e -SIZE (orthanc/mongoose-3.8.tgz) = 1577314 diff --git a/science/orthanc/files/orthanc.in b/science/orthanc/files/orthanc.in deleted file mode 100644 index 3dcf4cd38fe0..000000000000 --- a/science/orthanc/files/orthanc.in +++ /dev/null @@ -1,40 +0,0 @@ -#!/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="RESTful 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-Resources_Configuration.json b/science/orthanc/files/patch-Resources_Configuration.json deleted file mode 100644 index e5db076ecf62..000000000000 --- a/science/orthanc/files/patch-Resources_Configuration.json +++ /dev/null @@ -1,25 +0,0 @@ ---- Resources/Configuration.json.orig 2017-07-19 11:10:48 UTC -+++ 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", - - // Enable the transparent compression of the DICOM instances - "StorageCompression" : false, -@@ -41,6 +41,7 @@ - // find shared libraries. Backslashes must be either escaped by - // doubling them, or replaced by forward slashes "/". - "Plugins" : [ -+ "%%PREFIX%%/share/orthanc/plugins/" - ], - - diff --git a/science/orthanc/pkg-descr b/science/orthanc/pkg-descr deleted file mode 100644 index 1438133bfceb..000000000000 --- a/science/orthanc/pkg-descr +++ /dev/null @@ -1,20 +0,0 @@ -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 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 lets its users focus on the content of the DICOM files, hiding -the complexity of the DICOM format and of the DICOM protocol. - -WWW: http://www.orthanc-server.com/ diff --git a/science/orthanc/pkg-plist b/science/orthanc/pkg-plist deleted file mode 100644 index ddcea532f3b0..000000000000 --- a/science/orthanc/pkg-plist +++ /dev/null @@ -1,19 +0,0 @@ -@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 -include/orthanc/OrthancCDatabasePlugin.h -include/orthanc/OrthancCPlugin.h -include/orthanc/OrthancCppDatabasePlugin.h -%%DATADIR%%/plugins/libServeFolders.so -%%DATADIR%%/plugins/libServeFolders.so.%%PORTVERSION%% -%%DATADIR%%/plugins/libModalityWorklists.so -%%DATADIR%%/plugins/libModalityWorklists.so.%%PORTVERSION%% -bin/OrthancRecoverCompressedFile -sbin/Orthanc |