sagitter pushed to openms (master). "Set environment variables in desktop files"

Fri May 15 17:08:58 UTC 2015

From c3432ce973b19d36ca9cbd733537c6143c3e4122 Mon Sep 17 00:00:00 2001
From: sagitter <sagitter at fedoraproject.org>
Date: Fri, 15 May 2015 19:08:45 +0200
Subject: Set environment variables in desktop files

diff --git a/openms-revert_TOPP_PeakPickerWavelet_test.patch b/openms-revert_TOPP_PeakPickerWavelet_test.patch
new file mode 100644
index 0000000..30e540e
--- /dev/null
+++ b/openms-revert_TOPP_PeakPickerWavelet_test.patch
@@ -0,0 +1,14 @@
+--- src/tests/topp/CMakeLists.orig.txt	2015-04-09 17:57:04.000000000 +0200
++++ src/tests/topp/CMakeLists.txt	2015-05-13 10:48:06.645814337 +0200
+@@ -983,8 +983,8 @@
+ # 3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah string, they will be ignore.
+ # Note that this string occurs twice in the file.
+ #
+-add_test("TOPP_PeakPickerWavelet_3_out1" ${DIFF} -in1 PeakPickerWavelet_3.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_2Dopt_output.mzML -whitelist "3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah")
+-set_tests_properties("TOPP_PeakPickerWavelet_3_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_3")
++#add_test("TOPP_PeakPickerWavelet_3_out1" ${DIFF} -in1 PeakPickerWavelet_3.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_2Dopt_output.mzML -whitelist "3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah")
++#set_tests_properties("TOPP_PeakPickerWavelet_3_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_3")
+ add_test("TOPP_PeakPickerWavelet_4" ${TOPP_BIN_PATH}/PeakPickerWavelet  -test -ini ${DATA_DIR_TOPP}/PeakPickerWavelet_parameters.ini -in ${DATA_DIR_TOPP}/PeakPickerWavelet_input.mzML -out PeakPickerWavelet_4.tmp -threads 2)
+ add_test("TOPP_PeakPickerWavelet_4_out1" ${DIFF} -in1 PeakPickerWavelet_4.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_output.mzML)
+ set_tests_properties("TOPP_PeakPickerWavelet_4_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_4")
+
diff --git a/openms.spec b/openms.spec
index 4235454..237faa9 100644
--- a/openms.spec
+++ b/openms.spec
@@ -8,7 +8,7 @@
 Name:      openms
 Summary:   LC/MS data management and analyses
 Version:   2.0.0
-Release:   10%{?dist}
+Release:   11%{?dist}
 License:   BSD
 URL:       http://open-ms.sourceforge.net/
 Source0:   https://github.com/OpenMS/OpenMS/archive/Release2.0.0.tar.gz#/OpenMS-Release%{version}.tar.gz
@@ -16,10 +16,8 @@ Source0:   https://github.com/OpenMS/OpenMS/archive/Release2.0.0.tar.gz#/OpenMS-
 ##TOPPView, TOPPAS, INIFileEditor .desktop and icon files
 Source1:   TOPPView.xpm
 Source2:   TOPPAS.xpm
-Source3:   toppview.desktop
-Source4:   toppas.desktop
-Source5:   INIFileEditor.xpm
-Source6:   inifileeditor.desktop
+Source3:   INIFileEditor.xpm
+Source4:   inifileeditor.desktop
 
 BuildRequires: qt-devel >= 4.7, qt-x11, qtwebkit-devel
 BuildRequires: cmake >= 2.8 
@@ -52,6 +50,9 @@ Patch2: %{name}-remove_testflag.patch
 ##Fix mzML unittests
 Patch3: %{name}-fix-python_tests.patch
 
+##https://github.com/hroest/OpenMS/commit/6164699056398c043fc1bf0592ff0e9ba9a69cee
+Patch4: %{name}-revert_TOPP_PeakPickerWavelet_test.patch
+
 %description
 OpenMS is an open-source C++ library for LC/MS data management and analyses.
 It offers an infrastructure for the rapid development 
@@ -158,6 +159,12 @@ find . -type f -name "*.png" -exec convert {} -strip {} \;
 
 %patch2 -p0
 
+%if 0%{?fedora} < 22
+%ifarch %{arm}
+%patch4 -p0
+%endif
+%endif
+
 %build
 
 export LDFLAGS="%{__global_ldflags} -Wl,--as-needed"
@@ -225,13 +232,23 @@ popd
 mkdir -p %{buildroot}%{_datadir}/icons/TOPP/pixmaps
 install -pm 644 %{SOURCE1} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
 install -pm 644 %{SOURCE2} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
-install -pm 644 %{SOURCE5} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
+install -pm 644 %{SOURCE3} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
 
 ##Install toppas/toppview/inifileeditor .desktop files
 mkdir -p %{buildroot}%{_datadir}/applications
-desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE3}
-desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE4}
-desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE6}
+desktop-file-install \
+ --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPAS %U" \
+ --set-icon=%{_datadir}/icons/TOPP/pixmaps/TOPPAS.xpm \
+ --dir=%{buildroot}%{_datadir}/applications share/OpenMS/DESKTOP/toppas.desktop
+
+desktop-file-install \
+ --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPView %U" \
+ --set-icon=%{_datadir}/icons/TOPP/pixmaps/TOPPView.xpm \
+ --dir=%{buildroot}%{_datadir}/applications share/OpenMS/DESKTOP/toppview.desktop
+
+desktop-file-install \
+ --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS INIFileEditor %U" \
+ --dir=%{buildroot}%{_datadir}/applications %{SOURCE4}
 
 ##Install Tutorials executable
 mkdir -p %{buildroot}%{_bindir}
@@ -458,6 +475,10 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %endif
 
 %changelog
+* Fri May 15 2015 Antonio Trande <sagitter at fedoraproject.org> 2.0.0-11
+- Fix PeakPickerWavelet test
+- Set environment variables in desktop files
+
 * Fri May 08 2015 Antonio Trande <sagitter at fedoraproject.org> 2.0.0-10
 - Excluded TOPP_XTandemAdapter_ test
 
diff --git a/toppas.desktop b/toppas.desktop
deleted file mode 100644
index 24d4f0c..0000000
--- a/toppas.desktop
+++ /dev/null
@@ -1,9 +0,0 @@
-[Desktop Entry]
-Name=TOPPAS
-Categories=Science;Biology;Chemistry;
-Comment=An workflow engine for mass spectrometry data analysis
-Exec=env OPENMS_DATA_PATH=/usr/share/OpenMS TOPPAS %U
-Icon=/usr/share/icons/TOPP/pixmaps/TOPPAS.xpm
-Terminal=false
-Type=Application
-StartupNotify=true
diff --git a/toppview.desktop b/toppview.desktop
deleted file mode 100644
index eba972b..0000000
--- a/toppview.desktop
+++ /dev/null
@@ -1,9 +0,0 @@
-[Desktop Entry]
-Name=TOPPView
-Categories=Science;Biology;Chemistry;
-Comment=Viewer for mass spectrometry data
-Exec=env OPENMS_DATA_PATH=/usr/share/OpenMS TOPPView %U
-Icon=/usr/share/icons/TOPP/pixmaps/TOPPView.xpm
-Terminal=false
-Type=Application
-StartupNotify=true
-- 
cgit v0.10.2


	http://pkgs.fedoraproject.org/cgit/openms.git/commit/?h=master&id=c3432ce973b19d36ca9cbd733537c6143c3e4122
