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Commit 18bd848f authored by Piotr Gawron's avatar Piotr Gawron
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idebian release including support for both tomcat7 and tomcat8 

tomcat7 is not supported in new debian stretch relase
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CHANGELOG
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minerva (11.0.0) stable; urgency=medium minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the userlogin
* Bug fix: sbgn import
* Bug fix: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
minerva (10.0.5) stable; urgency=medium minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs * Bug fix: interacting drugs can be found for RNAs
......
debian/create-debian-pkg.sh
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...@@ -49,6 +49,8 @@ gzip $SRC_DIR/minerva.txt ...@@ -49,6 +49,8 @@ gzip $SRC_DIR/minerva.txt
#copy configuration of logrotate #copy configuration of logrotate
cp debian/logrotate/* $SRC_DIR/ cp debian/logrotate/* $SRC_DIR/
cp debian/scripts/common.sh $SRC_DIR/
#copy changelog file #copy changelog file
cp CHANGELOG $ROOT_DIR/debian/template/changelog cp CHANGELOG $ROOT_DIR/debian/template/changelog
...@@ -150,22 +152,17 @@ find -name '*.ex' ! -name 'minerva*' -type f -exec rm -f {} + ...@@ -150,22 +152,17 @@ find -name '*.ex' ! -name 'minerva*' -type f -exec rm -f {} +
#our pre/post inst/rm scripts use __CURRENT_VERSION__ as a version of currently #our pre/post inst/rm scripts use __CURRENT_VERSION__ as a version of currently
#installed package #installed package
sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/preinst
sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/postinst
sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/prerm
sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/postrm
sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/preinst
sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/postinst
sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/prerm
sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/postrm
sed -i "s/__CURRENT_VERSION__/$current_version/g" common.sh
sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh
#__DB_SCRIPT_DIR__ in our scripts points to place where db schema files are placed #__DB_SCRIPT_DIR__ in our scripts points to place where db schema files are placed
#in the filesystem where package is installed #in the filesystem where package is installed
sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postinst sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh
sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postrm
sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/prerm sed -i -e "1r common.sh" debian/postinst
sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/preinst sed -i -e "1r common.sh" debian/postrm
sed -i -e "1r common.sh" debian/preinst
sed -i -e "1r common.sh" debian/prerm
#put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not #put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
#escaped #escaped
......
debian/scripts/common.sh 0 → 100644
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#file with common script functions for postrm/prerm/postinst/preinst
log(){
echo "$@" >>__LOG_FILE__
}
LOG_FILE="__LOG_FILE__"
DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
#new (current) version of the package
CURRENT_VERSION="__CURRENT_VERSION__"
#if we update package then this will be the old version of the package
OLD_VERSION=$2
if [ "$OLD_VERSION" = "$CURRENT_VERSION" ]
then
OLD_VERSION="";
fi
TOMCAT_PACKAGE="";
TOMCAT7_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat7|grep "install ok installed")
TOMCAT8_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat8|grep "install ok installed")
if [ "$TOMCAT7_OK" != "" ];
then
TOMCAT_PACKAGE='tomcat7'
fi
if [ "$TOMCAT8_OK" != "" ];
then
TOMCAT_PACKAGE='tomcat8'
fi
debian/template/control
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− 1
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...@@ -13,4 +13,4 @@ Description: Standalone web application for visualization, exploration and ...@@ -13,4 +13,4 @@ Description: Standalone web application for visualization, exploration and
Tomcat server later to change the address. Tomcat server later to change the address.
Section: science Section: science
Homepage: http://r3lab.uni.lu/web/minerva-website/ Homepage: http://r3lab.uni.lu/web/minerva-website/
Depends: ${misc:Depends}, tomcat7, oracle-java8-set-default, postgresql (>=9.3) Depends: ${misc:Depends}, tomcat7 | tomcat8, oracle-java8-set-default, postgresql (>=9.3)
debian/template/install
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minerva.war /var/lib/tomcat7/webapps minerva.war /usr/share/minerva/
debian/template/postinst
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− 24
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...@@ -13,28 +13,11 @@ ...@@ -13,28 +13,11 @@
# <conflicting-package> <version> # <conflicting-package> <version>
# for details, see http://www.debian.org/doc/debian-policy/ or # for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package # the debian-policy package
log(){
echo "$@" >>__LOG_FILE__
}
log "Running postinst" $1 $2; log "Running postinst" $1 $2;
# we execute it here because if some packages are missing then dpkg will return non-zero exit code # we execute it here because if some packages are missing then dpkg will return non-zero exit code
set -e set -e
#new (current) version of the package
CURRENT_VERSION="__CURRENT_VERSION__"
#if we update package then this will be the old version of the package
OLD_VERSION=$2
DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
if [ "$OLD_VERSION" = "$CURRENT_VERSION" ]
then
OLD_VERSION="";
fi
case "$1" in case "$1" in
configure) configure)
invoke-rc.d postgresql start invoke-rc.d postgresql start
...@@ -42,9 +25,9 @@ case "$1" in ...@@ -42,9 +25,9 @@ case "$1" in
#if we install #if we install
if [ "$OLD_VERSION" = "" ] if [ "$OLD_VERSION" = "" ]
then then
su - postgres -c "createuser -d -r -s map_viewer" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "createuser -d -r -s map_viewer" >>$LOG_FILE 2>>$LOG_FILE
su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql" >>$LOG_FILE 2>>$LOG_FILE
su - postgres -c "createdb -O map_viewer map_viewer" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "createdb -O map_viewer map_viewer" >>$LOG_FILE 2>>$LOG_FILE
hba_conf=`su - postgres -c "psql -t -P format=unaligned -c 'show hba_file';"`; hba_conf=`su - postgres -c "psql -t -P format=unaligned -c 'show hba_file';"`;
cp $hba_conf $hba_conf".bac" cp $hba_conf $hba_conf".bac"
...@@ -53,13 +36,13 @@ case "$1" in ...@@ -53,13 +36,13 @@ case "$1" in
invoke-rc.d postgresql restart invoke-rc.d postgresql restart
#install base version of the framework #install base version of the framework
su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0.sql" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0.sql" >>$LOG_FILE 2>>$LOG_FILE
#install patch to current version #install patch to current version
su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0_to_$CURRENT_VERSION\".sql\"" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0_to_$CURRENT_VERSION\".sql\"" >>$LOG_FILE 2>>$LOG_FILE
else else
#if we update the package #if we update the package
su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_$OLD_VERSION\"_to_\"$CURRENT_VERSION\".sql\"" >>__LOG_FILE__ 2>>__LOG_FILE__ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_$OLD_VERSION\"_to_\"$CURRENT_VERSION\".sql\"" >>$LOG_FILE 2>>$LOG_FILE
fi fi
#print a disclaimer #print a disclaimer
...@@ -78,7 +61,8 @@ case "$1" in ...@@ -78,7 +61,8 @@ case "$1" in
#we have to restart tomcat, because application was started on the old database and it might crash during deplyment #we have to restart tomcat, because application was started on the old database and it might crash during deplyment
#for instance in the new war file there was init script that uses some new database features, but they are not #for instance in the new war file there was init script that uses some new database features, but they are not
#availble when new war is deployed from debian package, so tomcat will catch SQL exception and stop deployment #availble when new war is deployed from debian package, so tomcat will catch SQL exception and stop deployment
invoke-rc.d tomcat7 restart ln -s /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d $TOMCAT_PACKAGE restart
;; ;;
*) *)
echo "postinst called with unknown argument \`$1'" >&2 echo "postinst called with unknown argument \`$1'" >&2
......
debian/template/postrm
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...@@ -7,9 +7,6 @@ ...@@ -7,9 +7,6 @@
# * <old-postrm> `upgrade' <new-version> # * <old-postrm> `upgrade' <new-version>
# for details, see http://www.debian.org/doc/debian-policy/ or # for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package # the debian-policy package
log(){
echo "$@" >>__LOG_FILE__
}
log "Running postrm" $1 $2; log "Running postrm" $1 $2;
...@@ -27,13 +24,15 @@ set -e ...@@ -27,13 +24,15 @@ set -e
case "$1" in case "$1" in
upgrade) upgrade)
rm -rf /var/lib/tomcat7/webapps/minerva rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
invoke-rc.d tomcat7 start || true rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d postgresql start || true # invoke-rc.d $TOMCAT_PACKAGE start || true
# invoke-rc.d postgresql start || true
;; ;;
remove) remove)
rm -rf /var/lib/tomcat7/webapps/minerva rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
invoke-rc.d tomcat7 start || true rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ] if [ "" = "$POSTGRES_OK" ]
then then
log "No postgresql package found."; log "No postgresql package found.";
...@@ -44,7 +43,7 @@ case "$1" in ...@@ -44,7 +43,7 @@ case "$1" in
fi fi
;; ;;
abort-install) abort-install)
invoke-rc.d tomcat7 start || true invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ]; if [ "" = "$POSTGRES_OK" ];
then then
......
debian/template/preinst
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...@@ -9,11 +9,6 @@ ...@@ -9,11 +9,6 @@
# for details, see http://www.debian.org/doc/debian-policy/ or # for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package # the debian-policy package
log(){
echo "$@" >>__LOG_FILE__
}
log "Running preinst" $1 $2; log "Running preinst" $1 $2;
# we execute it here because if some packages are missing then dpkg will return non-zero exit code # we execute it here because if some packages are missing then dpkg will return non-zero exit code
...@@ -29,11 +24,11 @@ ln -s $path $DEFAULT_JAVA_SYMLINK ...@@ -29,11 +24,11 @@ ln -s $path $DEFAULT_JAVA_SYMLINK
case "$1" in case "$1" in
install|upgrade) install|upgrade)
invoke-rc.d tomcat7 stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true invoke-rc.d postgresql stop || true
;; ;;
abort-upgrade) abort-upgrade)
invoke-rc.d tomcat7 stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true invoke-rc.d postgresql stop || true
;; ;;
*) *)
......
debian/template/prerm
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...@@ -8,14 +8,9 @@ set -e ...@@ -8,14 +8,9 @@ set -e
# * <new-preinst> `upgrade' <old-version> # * <new-preinst> `upgrade' <old-version>
# for details, see http://www.debian.org/doc/debian-policy/ or # for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package # the debian-policy package
log(){
echo "$@" >>__LOG_FILE__
}
log "Running preinst" $1 $2; log "Running preinst" $1 $2;
DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
# we execute it here because if some packages are missing then dpkg will return non-zero exit code # we execute it here because if some packages are missing then dpkg will return non-zero exit code
set -e set -e
...@@ -30,11 +25,11 @@ su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz ...@@ -30,11 +25,11 @@ su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz
case "$1" in case "$1" in
upgrade) upgrade)
invoke-rc.d tomcat7 stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true invoke-rc.d postgresql stop || true
;; ;;
remove) remove)
invoke-rc.d tomcat7 stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true invoke-rc.d postgresql stop || true
;; ;;
*) *)
......
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