mirror of
https://codeberg.org/guix/guix.git
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9efddd7dae
Fixes guix/guix#1386 * gnu/packages/medical.scm (orthanc-mysql): [phases] {fix-mysql-include-path}: Swap to SEARCH-INPUT-DIRECTORY, see guix/guix#1385. Change-Id: I879001041733c03bd1e5dd8659c0e3c67fc8b6ee
433 lines
17 KiB
Scheme
433 lines
17 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2017 Quiliro <quiliro@fsfla.org>
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;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
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;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages medical)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system pyproject)
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#:use-module (guix build-system python)
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#:use-module (guix build-system qt)
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#:use-module (guix download)
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#:use-module (guix gexp)
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#:use-module (guix git-download)
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#:use-module (guix hg-download)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bash) ; wrap-program
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages databases)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages image)
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#:use-module (gnu packages image-processing)
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#:use-module (gnu packages kde-frameworks) ; kirigami
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#:use-module (gnu packages linux)
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#:use-module (gnu packages lua)
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-crypto)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages qt)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages sqlite)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages web)
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#:use-module (gnu packages xml))
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(define-public mygnuhealth
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(package
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(name "mygnuhealth")
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(version "2.2.1")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "MyGNUHealth" version))
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(sha256
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(base32
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"1jcrriccqzb4jx7zayhiqmpvi3cvfy3bbf9zr3m83878f94yww8j"))))
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(build-system python-build-system)
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(arguments
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(list
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#:imported-modules `(,@%python-build-system-modules
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,@%qt-build-system-modules)
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#:modules `(((guix build qt-build-system) #:prefix qt:)
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(guix build python-build-system)
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(guix build utils))
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#:phases #~(modify-phases %standard-phases
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(add-after 'install 'qt-wrap
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(assoc-ref qt:%standard-phases 'qt-wrap))
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(add-before 'check 'env-setup
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(lambda _
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(mkdir-p "/tmp/mygh/")
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(setenv "HOME" "/tmp"))))))
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(native-inputs (list python-pyside-2))
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(inputs (list bash-minimal
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kirigami-5
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python
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python-bcrypt
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python-matplotlib
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python-requests
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python-tinydb
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qtbase-5
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qtdeclarative-5
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qtgraphicaleffects
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qtquickcontrols-5
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qtquickcontrols2-5
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qtsvg-5))
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(home-page "https://www.gnuhealth.org")
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(synopsis "The GNU Health Personal Health Record")
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(description
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"This package provides GNUHealth Personal Health Record
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application for desktop and mobile devices that integrates with the GNU
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Health Federation.")
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(license license:gpl3+)))
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(define-public openmolar-1
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(package
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(name "openmolar")
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(version "1.1.6-g81838c85")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://static.openmolar.com/om1/releases/openmolar-" version
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".tar.gz"))
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(sha256
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(base32 "09vrfqn511vswnj2q9m7srlwdgz066qvqpmja6sg1yl1ibh3cbpr"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'patch-/usr
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* '("setup.py"
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"src/openmolar/settings/localsettings.py")
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(("/usr") #$output))))
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(add-after 'unpack 'set-acceptable-version
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(lambda _
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(substitute* "src/openmolar/settings/version.py"
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((#$version) "1.1.6")))))))
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(native-inputs
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(list python-setuptools python-wheel))
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(inputs (list python-pyqtwebengine
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python-pyqt+qscintilla
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python-mysqlclient
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qscintilla))
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(propagated-inputs (list qtwebengine-5))
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(home-page "https://openmolar.com/om1")
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(synopsis "Dental practice management software")
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(description
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"Openmolar is a dental practice management suite. Its
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functionality includes appointments, patient records, treatment planning,
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billing etc. It is a full featured, reliable and thoroughly tested
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application and has been translated into many languages.")
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(license license:gpl3+)))
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(define-public orthanc
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(package
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(name "orthanc")
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(version "1.12.7")
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(source
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(origin
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(method hg-fetch)
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(uri (hg-reference (url "https://orthanc.uclouvain.be/hg/orthanc")
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(changeset "a30cc2fa7250")))
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(file-name (hg-file-name name version))
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(sha256
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(base32 "1n8v0dh17g9ihny8cpq63qd6ai5l95i5h3sz9vwzfnd7q3qh0rb9"))))
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(build-system cmake-build-system)
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(arguments
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(list
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#:configure-flags
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#~(list (string-append "-DDCMTK_DICTIONARY_DIR="
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#$(this-package-input "dcmtk") "/share/dcmtk-"
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#$(package-version (this-package-input "dcmtk")))
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;; Building Connectivity Checks plugin requires the network.
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"-DBUILD_CONNECTIVITY_CHECKS=OFF"
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;; Disable 4 tests that require the network.
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"-DUNIT_TESTS_WITH_HTTP_CONNEXIONS=OFF")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'chdir
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(lambda _
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;; The OrthancServer/ subdirectory contains the root
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;; CMakeLists.txt file.
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(chdir "OrthancServer")))
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(add-after 'unpack 'remove-localtime-requirement
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(lambda _
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;; /etc/localtime is not present in the build container;
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;; don't let that stop the build.
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(substitute* "OrthancFramework/Sources/Toolbox.cpp"
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(("if \\(!SystemToolbox::IsExistingFile\\(LOCALTIME\\)\\)")
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"if (false)"))))
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;; There is no test target; simply run the binary.
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "./UnitTests")))))))
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(native-inputs (list doxygen
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glibc-utf8-locales ;for one test
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googletest
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python))
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(inputs (list boost
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civetweb
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curl
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dcmtk
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jsoncpp
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libjpeg-turbo
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libpng
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lua
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openssl
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protobuf
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pugixml
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`(,util-linux "lib") ;for uuid.h
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sqlite
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unzip))
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(home-page "https://orthanc-server.com")
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(synopsis
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"Standalone @acronym{DICOM, Digital Imaging and Communications in
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Medicine} server")
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(description
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"Orthanc is a standalone @acronym{DICOM, Digital Imaging and
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Communications in Medicine} server with a RESTful API and plugin
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mechanism for extending its functionality.")
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(license license:gpl3+)))
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(define-public orthanc-postgresql
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;; No tags provided.
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(let ((changeset "ddc98844d931")
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(revision "0"))
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(package
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(name "orthanc-postgresql")
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(version (git-version "7.2" revision changeset))
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(source
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(origin
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(method hg-fetch)
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(uri (hg-reference
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(url "https://orthanc.uclouvain.be/hg/orthanc-databases")
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(changeset changeset)))
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(file-name (hg-file-name name version))
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(sha256
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(base32 "1zv2lrj0f3fahmdyiwyj70ayv5ysa3cj33i58fbk7hy2zclrkjzf"))))
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(build-system cmake-build-system)
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(arguments
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(list
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#:configure-flags
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#~(list
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;; Don't try to download the Orthanc source code.
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"-DORTHANC_FRAMEWORK_SOURCE=path"
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(string-append "-DORTHANC_FRAMEWORK_ROOT="
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#$(package-source (this-package-input "orthanc"))
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"/OrthancFramework/Sources"))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'chdir
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(lambda _
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;; The PostgreSQL/ subdirectory contains the root
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;; CMakeLists.txt file.
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(chdir "PostgreSQL")))
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;; There is no test target; simply run the binary.
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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;; The tests rely on a PostgreSQL test server
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;; being available.
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(let ((pgdata "/tmp/pgdata")
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(host "/tmp")
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(port "5432")
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;; This username is hard-coded in tests.
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(username "postgres")
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(password "")
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(database "orthanctest"))
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(invoke "initdb" pgdata)
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(invoke "pg_ctl" "-D" pgdata
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"-o" (string-append "-k " host)
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"start")
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(invoke "createdb" "-h" host database)
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(invoke "createuser" "-h" host username)
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;; The tests include managing Large Objects.
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(invoke "psql" "-h" host "-d" database "-c"
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(string-append "ALTER ROLE " username
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" WITH SUPERUSER;"))
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(invoke "./UnitTests" host port username password
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database))))))))
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(native-inputs
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(list googletest
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python))
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(inputs
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(list boost
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jsoncpp
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openssl
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orthanc
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postgresql
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protobuf
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unzip
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(list util-linux "lib") ; <uuid.h>
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zlib))
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(home-page "https://orthanc-server.com")
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(synopsis "PostgreSQL plugins for Orthanc")
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(description
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"This package provides plugins to use PostgreSQL as the database
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backend of an Orthanc @acronym{DICOM, Digital Imaging and Communications in
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Medicine} server instead of SQLite.")
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(license license:agpl3+))))
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(define-public orthanc-mysql
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;; No tags provided.
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(let ((changeset "a6300ccf6683")
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(revision "0"))
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(package
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(name "orthanc-mysql")
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(version (git-version "5.2" revision changeset))
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(source
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(origin
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(method hg-fetch)
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(uri (hg-reference
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(url "https://orthanc.uclouvain.be/hg/orthanc-databases")
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(changeset changeset)))
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(file-name (hg-file-name name version))
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(sha256
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(base32 "0hi3bawj117lk7lrxpa6h7vq4hx9jwqb3m5pwn3726hnf4kmp4jc"))))
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(build-system cmake-build-system)
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(arguments
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(list
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#:configure-flags
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#~(list
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;; Don't try to download the Orthanc source code.
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"-DORTHANC_FRAMEWORK_SOURCE=path"
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(string-append "-DORTHANC_FRAMEWORK_ROOT="
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#$(package-source (this-package-input "orthanc"))
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"/OrthancFramework/Sources"))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'chdir
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(lambda _
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;; The MySQL/ subdirectory contains the root CMakeLists.txt
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;; file.
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(chdir "MySQL")))
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(add-after 'unpack 'fix-mysql-include-path
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(lambda* (#:key inputs #:allow-other-keys)
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;; Help it find mysql.h, either from mysql in this package or
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;; from mariadb:dev in orthanc-mariadb.
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(substitute* "Resources/CMake/MariaDBConfiguration.cmake"
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(("/usr/include/mysql")
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(search-input-directory inputs "include/mysql")))))
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;; There is no test target; simply run the binary.
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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;; The tests rely on a MySQL or MariaDB test server
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;; being available.
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(let ((datadir "/tmp/mysql")
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(socket "/tmp/mysql/mysqld.sock")
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(username "root")
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(password "")
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(database "orthanctest"))
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(invoke "mysqld" "--initialize-insecure"
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(string-append "--datadir=" datadir))
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(spawn "mysqld"
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(list
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"mysqld"
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;; Respect '--datadir'.
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"--no-defaults"
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(string-append "--datadir=" datadir)
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(string-append "--socket=" socket)
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;; For one test.
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"--max_allowed_packet=32m"))
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(sleep 1)
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(invoke "mysql"
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(string-append "--socket=" socket)
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"-u" username
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"-e" "CREATE DATABASE orthanctest;")
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(invoke "./UnitTests" socket username password
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database))))))))
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(native-inputs
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(list googletest
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python))
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(inputs
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(list boost
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curl
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jsoncpp
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mysql
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openssl
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orthanc
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protobuf
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unzip
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(list util-linux "lib") ; <uuid.h>
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zlib))
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(home-page "https://orthanc-server.com")
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(synopsis "MySQL plugins for Orthanc")
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(description
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"This package provides plugins to use MySQL or MariaDB as the database
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backend of an Orthanc @acronym{DICOM, Digital Imaging and Communications in
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Medicine} server instead of SQLite.")
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(license license:agpl3+))))
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;; Provide this variant without MySQL to save MariaDB users ~340 MiB
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;; of disk space.
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(define-public orthanc-mariadb
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(package/inherit orthanc-mysql
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(name "orthanc-mariadb")
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(arguments
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(substitute-keyword-arguments (package-arguments orthanc-mysql)
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((#:phases phases)
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#~(modify-phases #$phases
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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;; The tests rely on a MySQL or MariaDB test server
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;; being available.
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(let ((datadir "/tmp/mysql")
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(socket "/tmp/mysql/mysqld.sock")
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(username "root")
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(password "")
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(database "orthanctest"))
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(invoke "mariadb-install-db"
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(string-append "--datadir=" datadir)
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"--auth-root-authentication-method=normal")
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(spawn "mysqld"
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(list
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"mysqld"
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;; Respect '--datadir'.
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"--no-defaults"
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(string-append "--datadir=" datadir)
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(string-append "--socket=" socket)
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;; For one test.
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"--max-allowed-packet=32m"))
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(sleep 1)
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(invoke "mysql"
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(string-append "--socket=" socket)
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"-u" username
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"-e" "CREATE DATABASE orthanctest;")
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(invoke "./UnitTests" socket username password
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database)))))))))
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(native-inputs (modify-inputs (package-native-inputs orthanc-mysql)
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(prepend mariadb))) ;for tests
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(inputs (modify-inputs (package-inputs orthanc-mysql)
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(delete "mysql")
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(prepend `(,mariadb "dev")
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`(,mariadb "lib"))))
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(synopsis "MariaDB plugins for Orthanc")))
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