* [gentoo-commits] proj/sci:master commit in: sci-biology/OBO-Edit/, profiles/
@ 2021-01-19 10:47 Andrew Ammerlaan
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From: Andrew Ammerlaan @ 2021-01-19 10:47 UTC (permalink / raw
To: gentoo-commits
commit: cdd700699de2b2f26d6265fc317f7003d89a2b68
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 10:46:45 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 10:47:03 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cdd70069
sci-biology/OBO-Edit: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild | 53 ----------------------
...O-Edit-2.1.1.6.ebuild => OBO-Edit-2.3.1.ebuild} | 41 +++++++----------
3 files changed, 16 insertions(+), 79 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 6afd1ca5c..297270976 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -89,4 +89,3 @@ sci-biology/mreps
sci-biology/mRNAmarkup
sci-biology/mrsfast
sci-biology/MuSeqBox
-sci-biology/OBO-Edit
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
deleted file mode 100644
index 1724e13c3..000000000
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator java-pkg-2
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
-HOMEPAGE="http://www.oboedit.org/" # no https, invalid certificate
-SRC_URI="
- https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/${MY_PV}_unix_install4j.sh/download -> OBO-Edit_unix_install4j-${PV}.sh
- https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/ReleaseNotes-${PV}.txt"
-
-LICENSE="OBO-Edit" # Artistic-like
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-arch/rpm2targz"
-RDEPEND="virtual/jre"
-
-S="${WORKDIR}"
-
-src_install(){
- dodir /opt/OBO-Edit2/.install4j
-
- sed \
- -e "s#\"\${D}\"#"${D}"#g" \
- "${FILESDIR}"/response.varfile \
- > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
-
- sed \
- -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" \
- -i "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh || die "failed to set userHome value"
-
- sh "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh \
- -q -overwrite \
- --varfile="${D}"/opt/OBO-Edit2/.install4j/response.varfile \
- --destination="${D}"/opt/OBO-Edit2 \
- -dir "${D}"/opt/OBO-Edit2 \
- || die "Failed to run the self-extracting ${DISTDIR}/OBO-Edit_unix_install4j-"${PV}".sh file"
- find . -name firstrun -delete || die
-
- esvn_clean
-
- insinto /opt/
- doins -r OBO-Edit2
- chmod 755 "${ED}"/opt/OBO-Edit2/* || die
-
- dodoc "${DISTDIR}"/ReleaseNotes-2.1.0.txt
-}
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
similarity index 60%
rename from sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
rename to sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
index e4d3b9304..29550a0fc 100644
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
+++ b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
@@ -1,25 +1,19 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-inherit eutils toolchain-funcs versionator java-pkg-2
+inherit toolchain-funcs java-pkg-2
-# MY_PV=$(replace_all_version_separators '-')
-MY_PV="oboedit_2_1_1-b6"
-MY_VER="2.1.1-b6"
-MY_PV=$(replace_all_version_separators '-')
+MY_PV="${PV//./_}"
DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
HOMEPAGE="http://www.oboedit.org/" # no https, invalid certificate
-SRC_URI="
- https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_VER}/${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh
- https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_PV}/ReleaseNotes-${MY_VER}.txt -> ${PN}_ReleaseNotes-${PV}.txt"
+SRC_URI="https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/oboedit_${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh"
LICENSE="OBO-Edit" # Artistic-like
SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
DEPEND="app-arch/rpm2targz"
RDEPEND="virtual/jre"
@@ -35,14 +29,16 @@ pkg_setup() {
}
src_prepare(){
+ default
dodir /opt/OBO-Edit2/.install4j /usr/bin
+ cp "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh "${WORKDIR}" || die
# /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile
sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \
- sed -e "s#\"\${TMPDIR}\"#"${TMPDIR}"#g" | \
+ sed -e "s#\"\${HOME}\"#"${HOME}"#g" | \
sed -e "s@sys.symlinkDir=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \
> "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
- cp -r "${D}"/opt/OBO-Edit2/.install4j "${TMPDIR}" || die
+ cp -r "${D}"/opt/OBO-Edit2/.install4j "${HOME}" || die
# for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it
# found via JAVA_HOME or similar variables
@@ -50,11 +46,11 @@ src_prepare(){
# trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work
sed \
- -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir="${TMPDIR}" -Dsys.symlinkDir="${D}"usr/bin -Djava.util.prefs.systemRoot="${TMPDIR}"@" \
- -i "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh \
+ -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${HOME}" -Dinstall4j.jvmDir="${HOME}" -Dsys.symlinkDir="${D}"usr/bin -Djava.util.prefs.systemRoot="${HOME}"@" \
+ -i "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh \
|| die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found"
- chmod u+rx "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh || die
+ chmod u+rx "${WORKDIR}/${PN}"_unix_install4j-"${PV}".sh || die
}
src_install(){
@@ -64,19 +60,14 @@ src_install(){
# chmod a-w "${TMPDIR}"/.install4j/response.varfile
INSTALL4J_KEEP_TEMP="yes" \
- HOME="${TMPDIR}" \
- sh "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \
- --varfile="${TMPDIR}"/.install4j/response.varfile \
+ sh "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \
+ --varfile="${HOME}"/.install4j/response.varfile \
--destination="${D}"/opt/OBO-Edit2 \
-dir "${D}"/opt/OBO-Edit2 \
- || die "Failed to run the self-extracting ${DISTDIR}/${PN}_unix_install4j-${PV}.sh file"
+ || die "Failed to run the self-extracting ${WORKDIR}/${PN}_unix_install4j-${PV}.sh file"
find . -name firstrun -delete || die
- esvn_clean
-
- dodoc "${DISTDIR}"/"${PN}"_ReleaseNotes-"${PV}".txt
-
echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die
doenvd 99OBO-Edit
}
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