diff --git a/CHANGELOG b/CHANGELOG index c2676d95aba4ed7e0ebf37528b679ace16e4272e..5ddd8c6f4e09fcd6ca9040e2e1f8b6b705d83b68 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,5 +1,21 @@ 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 * Bug fix: interacting drugs can be found for RNAs diff --git a/debian/create-debian-pkg.sh b/debian/create-debian-pkg.sh index f390d7a4080cc8f5a1a37433c3bbfd97d6f5a930..1a6936e6fc9fa7c2cd17bd88b313eb2a8acc7a19 100755 --- a/debian/create-debian-pkg.sh +++ b/debian/create-debian-pkg.sh @@ -49,6 +49,8 @@ gzip $SRC_DIR/minerva.txt #copy configuration of logrotate cp debian/logrotate/* $SRC_DIR/ +cp debian/scripts/common.sh $SRC_DIR/ + #copy changelog file cp CHANGELOG $ROOT_DIR/debian/template/changelog @@ -150,22 +152,17 @@ find -name '*.ex' ! -name 'minerva*' -type f -exec rm -f {} + #our pre/post inst/rm scripts use __CURRENT_VERSION__ as a version of currently #installed package -sed -i "s/__CURRENT_VERSION__/$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__/$LOG_FILE/g" common.sh #__DB_SCRIPT_DIR__ in our scripts points to place where db schema files are placed #in the filesystem where package is installed -sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postinst -sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postrm -sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/prerm -sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/preinst +sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh + +sed -i -e "1r common.sh" debian/postinst +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 $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not #escaped diff --git a/debian/scripts/common.sh b/debian/scripts/common.sh new file mode 100644 index 0000000000000000000000000000000000000000..951364c4390b4471b53074878ab0a731f1abd9fe --- /dev/null +++ b/debian/scripts/common.sh @@ -0,0 +1,29 @@ +#file with common script functions for postrm/prerm/postinst/preinst +log(){ + echo "$@" >>__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 diff --git a/debian/template/control b/debian/template/control index 25913b4c153d4c4f53324c1e96d205742ce30b35..dcb5946ab20574544cfcc59508f78714bc39af25 100644 --- a/debian/template/control +++ b/debian/template/control @@ -13,4 +13,4 @@ Description: Standalone web application for visualization, exploration and Tomcat server later to change the address. Section: science Homepage: http://r3lab.uni.lu/web/minerva-website/ -Depends: ${misc:Depends}, tomcat7, oracle-java8-set-default, postgresql (>=9.3) +Depends: ${misc:Depends}, tomcat7 | tomcat8, oracle-java8-set-default, postgresql (>=9.3) diff --git a/debian/template/install b/debian/template/install index 493361aaa4fa86ab02bede0f7ff7a1f42c031491..7e81d5fb433700abf97710e8570f13708aa0b5ef 100644 --- a/debian/template/install +++ b/debian/template/install @@ -1 +1 @@ -minerva.war /var/lib/tomcat7/webapps +minerva.war /usr/share/minerva/ diff --git a/debian/template/postinst b/debian/template/postinst index a1b144da74bc63a39bcf6be638790e68c0688b04..cc4aef4bd91f2c189a8e6c14a4886400db69af53 100644 --- a/debian/template/postinst +++ b/debian/template/postinst @@ -13,28 +13,11 @@ # <conflicting-package> <version> # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package -log(){ - echo "$@" >>__LOG_FILE__ -} log "Running postinst" $1 $2; # we execute it here because if some packages are missing then dpkg will return non-zero exit code 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 configure) invoke-rc.d postgresql start @@ -42,9 +25,9 @@ case "$1" in #if we install if [ "$OLD_VERSION" = "" ] then - 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 "createdb -O map_viewer 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 "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';"`; cp $hba_conf $hba_conf".bac" @@ -53,13 +36,13 @@ case "$1" in invoke-rc.d postgresql restart #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 - 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 #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 #print a disclaimer @@ -78,7 +61,8 @@ case "$1" in #we have to restart tomcat, because application was started on the old database and it might crash during deplyment #for instance in the new war file there was init script that uses some new database features, but they are not #availble when new war is deployed from debian package, so tomcat will catch SQL exception and stop deployment - invoke-rc.d tomcat7 restart + ln -s /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war + invoke-rc.d $TOMCAT_PACKAGE restart ;; *) echo "postinst called with unknown argument \`$1'" >&2 diff --git a/debian/template/postrm b/debian/template/postrm index 1bbb913d1ea531617049d130f6a4fd0d442be495..89144fb629ef34fd3761bc2c749f6cebfcfd4840 100644 --- a/debian/template/postrm +++ b/debian/template/postrm @@ -7,9 +7,6 @@ # * <old-postrm> `upgrade' <new-version> # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package -log(){ - echo "$@" >>__LOG_FILE__ -} log "Running postrm" $1 $2; @@ -27,13 +24,15 @@ set -e case "$1" in upgrade) - rm -rf /var/lib/tomcat7/webapps/minerva - invoke-rc.d tomcat7 start || true - invoke-rc.d postgresql start || true + rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva + rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war +# invoke-rc.d $TOMCAT_PACKAGE start || true +# invoke-rc.d postgresql start || true ;; remove) - rm -rf /var/lib/tomcat7/webapps/minerva - invoke-rc.d tomcat7 start || true + rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva + rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war + invoke-rc.d $TOMCAT_PACKAGE start || true if [ "" = "$POSTGRES_OK" ] then log "No postgresql package found."; @@ -44,7 +43,7 @@ case "$1" in fi ;; abort-install) - invoke-rc.d tomcat7 start || true + invoke-rc.d $TOMCAT_PACKAGE start || true if [ "" = "$POSTGRES_OK" ]; then diff --git a/debian/template/preinst b/debian/template/preinst index 1abc655eb13bdd0e7687c11f932d13629824dd1d..c6ad957eb6803a810a043143bf5845e16a3017ef 100644 --- a/debian/template/preinst +++ b/debian/template/preinst @@ -9,11 +9,6 @@ # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package - -log(){ - echo "$@" >>__LOG_FILE__ -} - log "Running preinst" $1 $2; # 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 case "$1" in install|upgrade) - invoke-rc.d tomcat7 stop || true + invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d postgresql stop || true ;; abort-upgrade) - invoke-rc.d tomcat7 stop || true + invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d postgresql stop || true ;; *) diff --git a/debian/template/prerm b/debian/template/prerm index d6c80c445fb07e3c6621618992daf9ed789f71b0..c43b60f8fa2c3f996db03de69cc8b7e261d9220e 100644 --- a/debian/template/prerm +++ b/debian/template/prerm @@ -8,14 +8,9 @@ set -e # * <new-preinst> `upgrade' <old-version> # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package -log(){ - echo "$@" >>__LOG_FILE__ -} log "Running preinst" $1 $2; -DB_SCRIPT_DIR="__DB_SCRIPT_DIR__" - # we execute it here because if some packages are missing then dpkg will return non-zero exit code set -e @@ -30,11 +25,11 @@ su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz case "$1" in upgrade) - invoke-rc.d tomcat7 stop || true + invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d postgresql stop || true ;; remove) - invoke-rc.d tomcat7 stop || true + invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d postgresql stop || true ;; *) diff --git a/persist/src/db/11/fix_db_20170616.sql b/persist/src/db/11.0.0/fix_db_20170616.sql similarity index 100% rename from persist/src/db/11/fix_db_20170616.sql rename to persist/src/db/11.0.0/fix_db_20170616.sql diff --git a/persist/src/db/11/fix_db_20170627.sql b/persist/src/db/11.0.0/fix_db_20170627.sql similarity index 100% rename from persist/src/db/11/fix_db_20170627.sql rename to persist/src/db/11.0.0/fix_db_20170627.sql diff --git a/persist/src/db/11/fix_db_20170628.sql b/persist/src/db/11.0.0/fix_db_20170628.sql similarity index 100% rename from persist/src/db/11/fix_db_20170628.sql rename to persist/src/db/11.0.0/fix_db_20170628.sql diff --git a/persist/src/db/11/fix_db_20170629.sql b/persist/src/db/11.0.0/fix_db_20170629.sql similarity index 100% rename from persist/src/db/11/fix_db_20170629.sql rename to persist/src/db/11.0.0/fix_db_20170629.sql diff --git a/persist/src/db/11/fix_db_20170705.sql b/persist/src/db/11.0.0/fix_db_20170705.sql similarity index 100% rename from persist/src/db/11/fix_db_20170705.sql rename to persist/src/db/11.0.0/fix_db_20170705.sql diff --git a/persist/src/db/11/fix_db_20170714.sql b/persist/src/db/11.0.0/fix_db_20170714.sql similarity index 100% rename from persist/src/db/11/fix_db_20170714.sql rename to persist/src/db/11.0.0/fix_db_20170714.sql diff --git a/persist/src/db/11/fix_db_20170725.sql b/persist/src/db/11.0.0/fix_db_20170725.sql similarity index 100% rename from persist/src/db/11/fix_db_20170725.sql rename to persist/src/db/11.0.0/fix_db_20170725.sql diff --git a/persist/src/db/11/fix_db_20170731.sql b/persist/src/db/11.0.0/fix_db_20170731.sql similarity index 100% rename from persist/src/db/11/fix_db_20170731.sql rename to persist/src/db/11.0.0/fix_db_20170731.sql