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Commit 8a7783ea authored by Piotr Gawron's avatar Piotr Gawron
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debian scripts use either default db properties (from... 

debian scripts use either default db properties (from persist/main/src/resource/db.properties file) or user defined db properties (/etc/minerva/db.properties)
parent 012cefe5
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1 merge request!284Resolve "database configuration should be outside war file"
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debian/create-debian-pkg.sh
+ 17
− 0
View file @ 8a7783ea
...@@ -70,6 +70,14 @@ then ...@@ -70,6 +70,14 @@ then
exit 1; exit 1;
fi fi
#default connection params (if /etc/minerva/db.properties is not defined)
DB_HOST=`cat persist/src/main/resources/db.properties |grep "uri" |cut -f3 -d"/" |cut -f1 -d":"`
DB_PORT=`cat persist/src/main/resources/db.properties |grep "uri" |cut -f3 -d"/" |cut -f2 -d":"`
DB_DATABASE_NAME=`cat persist/src/main/resources/db.properties |grep "uri" |cut -f4 -d"/"`
DB_USERNAME=`cat persist/src/main/resources/db.properties |grep "username" |cut -f2 -d"="`
DB_PASSWORD=`cat persist/src/main/resources/db.properties |grep "password" |cut -f2 -d"="`
#------------------------------------------ #------------------------------------------
# Now we have all db schema diff files. Let's start preparing # Now we have all db schema diff files. Let's start preparing
# debian package # debian package
...@@ -107,11 +115,20 @@ sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh ...@@ -107,11 +115,20 @@ sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh
#in the filesystem where package is installed #in the filesystem where package is installed
sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh
sed -i "s/__DB_HOST__/$DB_HOST/g" common.sh
sed -i "s/__DB_PORT__/$DB_PORT/g" common.sh
sed -i "s/__DB_DATABASE_NAME__/$DB_DATABASE_NAME/g" common.sh
sed -i "s/__DB_USERNAME__/$DB_USERNAME/g" common.sh
sed -i "s/__DB_PASSWORD__/$DB_PASSWORD/g" common.sh
sed -i -e "1r common.sh" debian/postinst sed -i -e "1r common.sh" debian/postinst
sed -i -e "1r common.sh" debian/postrm sed -i -e "1r common.sh" debian/postrm
sed -i -e "1r common.sh" debian/preinst sed -i -e "1r common.sh" debian/preinst
sed -i -e "1r common.sh" debian/prerm 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 $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
#escaped #escaped
echo db_0.sql /usr/share\/minerva/schema >> debian/install echo db_0.sql /usr/share\/minerva/schema >> debian/install
......
debian/scripts/common.sh
+ 71
− 0
View file @ 8a7783ea
...@@ -27,3 +27,74 @@ if [ "$TOMCAT8_OK" != "" ]; ...@@ -27,3 +27,74 @@ if [ "$TOMCAT8_OK" != "" ];
then then
TOMCAT_PACKAGE='tomcat8' TOMCAT_PACKAGE='tomcat8'
fi fi
POSTGRES_OK=$(dpkg-query -W --showformat='${Status}\n' postgresql|grep "install ok installed")
DB_HOST="__DB_HOST__"
DB_PORT="__DB_PORT__"
DB_DATABASE_NAME="__DB_DATABASE_NAME__"
DB_USERNAME="__DB_USERNAME__"
DB_PASSWORD="__DB_PASSWORD__"
if [ -f /etc/minerva/db.properties ]; then
DB_PROPERTIES_FILE="/etc/minerva/db.properties"
log "$DB_PROPERTIES_FILE file found"
DB_HOST=`cat $DB_PROPERTIES_FILE |grep "uri" |cut -f3 -d"/" |cut -f1 -d":"`
DB_PORT=`cat $DB_PROPERTIES_FILE |grep "uri" |cut -f3 -d"/" |cut -f2 -d":"`
DB_DATABASE_NAME=`cat $DB_PROPERTIES_FILE |grep "uri" |cut -f4 -d"/"`
DB_USERNAME=`cat $DB_PROPERTIES_FILE |grep "username" |cut -f2 -d"="`
DB_PASSWORD=`cat $DB_PROPERTIES_FILE |grep "password" |cut -f2 -d"="`
fi
#if we connect to something that is not in localhost then we need to provide login and password
#because we won't have access to it as postgres user
if [ "$DB_HOST" != "localhost" ] && [ "$DB_HOST" != "127.0.0.1" ]
then
log "DB is located on the remote server: $DB_HOST"
IS_REMOTE_DB=true
else
log "DB is at localhost: $DB_HOST"
IS_REMOTE_DB=false
fi
exec_sql(){
log "Execute SQL : '$1'"
echo "$1" |PGPASSWORD=$DB_PASSWORD psql -h $DB_HOST -p $DB_PORT -U $DB_USERNAME $DB_DATABASE_NAME >>$LOG_FILE 2>>$LOG_FILE
}
exec_sql_file(){
log "Execute SQL file: $1"
PGPASSWORD=$DB_PASSWORD psql -h $DB_HOST -p $DB_PORT -U $DB_USERNAME $DB_DATABASE_NAME -f $1 >>$LOG_FILE 2>>$LOG_FILE
}
create_db(){
if [ $IS_REMOTE_DB = false ]
then
su - postgres -c "createuser -d -r -s -p $DB_PORT $DB_USERNAME" >>$LOG_FILE 2>>$LOG_FILE
log "User created"
su - postgres -c "echo \"ALTER USER $DB_USERNAME WITH PASSWORD '$DB_PASSWORD';\"| psql -p $DB_PORT " >>$LOG_FILE 2>>$LOG_FILE
log "User credentials updated"
su - postgres -c "createdb -p $DB_PORT -O $DB_USERNAME $DB_DATABASE_NAME" >>$LOG_FILE 2>>$LOG_FILE
log "Db created"
hba_conf=`su - postgres -c "psql -t -P format=unaligned -c 'show hba_file';"`;
cp $hba_conf $hba_conf".bac"
cat $hba_conf".bac" |grep -v "all[ \t]*peer" >$hba_conf
printf "local all all md5\n" >>$hba_conf
invoke-rc.d postgresql restart
else
log "HOST is remote, assuming db and user are already there"
fi
}
stop_postgres() {
if [ $IS_REMOTE_DB = false ]
then
invoke-rc.d postgresql stop || true
fi
}
start_postgres() {
if [ $IS_REMOTE_DB = false ]
then
invoke-rc.d postgresql restart
fi
}
debian/template/postinst
+ 5
− 13
View file @ 8a7783ea
...@@ -21,29 +21,21 @@ set -e ...@@ -21,29 +21,21 @@ set -e
case "$1" in case "$1" in
configure) configure)
invoke-rc.d postgresql start start_postgres
#if we install #if we install
if [ "$OLD_VERSION" = "" ] if [ "$OLD_VERSION" = "" ]
then then
su - postgres -c "createuser -d -r -s map_viewer" >>$LOG_FILE 2>>$LOG_FILE create_db
su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql" >>$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"
cat $hba_conf".bac" |grep -v "all[ \t]*peer" >$hba_conf
printf "local all all md5\n" >>$hba_conf
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>>$LOG_FILE exec_sql_file "$DB_SCRIPT_DIR/db_0.sql"
#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 exec_sql_file "$DB_SCRIPT_DIR/db_0_to_${CURRENT_VERSION}.sql"
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>>$LOG_FILE exec_sql_file "$DB_SCRIPT_DIR/db_${OLD_VERSION}_to_${CURRENT_VERSION}.sql"
fi fi
#print a disclaimer #print a disclaimer
......
debian/template/postrm
+ 23
− 25
View file @ 8a7783ea
...@@ -10,15 +10,6 @@ ...@@ -10,15 +10,6 @@
log "Running postrm" $1 $2; log "Running postrm" $1 $2;
log "Checking postgresql...";
POSTGRES_OK=$(dpkg-query -W --showformat='${Status}\n' postgresql|grep "install ok installed")
if [ "" = "$POSTGRES_OK" ]
then
log "postgresql not found";
else
log "postgresql found";
fi
# 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
...@@ -26,34 +17,41 @@ case "$1" in ...@@ -26,34 +17,41 @@ case "$1" in
upgrade) upgrade)
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
# invoke-rc.d $TOMCAT_PACKAGE start || true
# invoke-rc.d postgresql start || true
;; ;;
remove) remove)
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d $TOMCAT_PACKAGE start || true invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ] if [ $IS_REMOTE_DB = true ]
then then
log "No postgresql package found."; exec_sql "drop owned by $DB_USERNAME;"
else else
invoke-rc.d postgresql start if [ "" = "$POSTGRES_OK" ]
su - postgres -c "dropdb map_viewer" then
su - postgres -c "dropuser map_viewer" log "No postgresql package found.";
else
start_postgres
su - postgres -c "dropdb -p $DB_PORT $DB_DATABASE_NAME"
su - postgres -c "dropuser -p $DB_PORT $DB_USERNAME"
fi
fi fi
;; ;;
abort-install) abort-install)
invoke-rc.d $TOMCAT_PACKAGE start || true invoke-rc.d $TOMCAT_PACKAGE start || true
if [ $IS_REMOTE_DB = true ]
if [ "" = "$POSTGRES_OK" ];
then then
log "No postgresql package found."; exec_sql "drop owned by $DB_USER"
else else
invoke-rc.d postgresql restart if [ "" = "$POSTGRES_OK" ];
su - postgres -c "dropdb map_viewer" then
su - postgres -c "dropuser map_viewer" log "No postgresql package found.";
else
start_postgres
su - postgres -c "dropdb -p $DB_PORT $DB_DATABASE_NAME"
su - postgres -c "dropuser -p $DB_PORT $DB_USERNAME"
fi
fi fi
;; ;;
*) *)
echo "postrm called with unknown argument \`$1'" >&2 echo "postrm called with unknown argument \`$1'" >&2
exit 1 exit 1
......
debian/template/preinst
+ 4
− 4
View file @ 8a7783ea
...@@ -24,12 +24,12 @@ ln -s $path $DEFAULT_JAVA_SYMLINK ...@@ -24,12 +24,12 @@ ln -s $path $DEFAULT_JAVA_SYMLINK
case "$1" in case "$1" in
install|upgrade) install|upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true stop_postgres
;; ;;
abort-upgrade) abort-upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true stop_postgres
;; ;;
*) *)
echo "preinst called with unknown argument \`$1'" >&2 echo "preinst called with unknown argument \`$1'" >&2
......
debian/template/prerm
+ 7
− 7
View file @ 8a7783ea
...@@ -17,20 +17,20 @@ set -e ...@@ -17,20 +17,20 @@ set -e
log Running prerm $1 $2; log Running prerm $1 $2;
invoke-rc.d postgresql start || true invoke-rc.d postgresql start || true
TIMESTAMP=$(date +"%F") TIMESTAMP=$(date +"%F_%H%M%S")
DUMP_FILE=$DB_SCRIPT_DIR/dump_$TIMESTAMP DUMP_FILE=$DB_SCRIPT_DIR/dump_$TIMESTAMP
log "dump map_viewer database to file $DUMP_FILE" log "dump $DB_DATABASE_NAME database to file $DUMP_FILE"
su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz PGPASSWORD=$DB_PASSWORD pg_dump -h $DB_HOST -p $DB_PORT -U $DB_USERNAME $DB_DATABASE_NAME | gzip > "$DUMP_FILE".gz
case "$1" in case "$1" in
upgrade) upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true stop_postgres
;; ;;
remove) remove)
invoke-rc.d $TOMCAT_PACKAGE stop || true invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true stop_postgres
;; ;;
*) *)
echo "prerm called with unknown argument \`$1'" >&2 echo "prerm called with unknown argument \`$1'" >&2
......
frontend-js/package-lock.json
+ 27
− 27
View file @ 8a7783ea
...@@ -45,38 +45,30 @@ ...@@ -45,38 +45,30 @@
"litemol": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412" "litemol": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412"
}, },
"dependencies": { "dependencies": {
"ProtVista": {
"version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"dev": true,
"requires": {
"d3": "3.5.17",
"file-saver": "1.3.3",
"jquery": "2.2.4",
"jszip": "3.1.4",
"underscore": "1.8.3"
},
"dependencies": {
"jquery": {
"version": "2.2.4",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
"integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
"dev": true
}
}
},
"jquery": { "jquery": {
"version": "3.3.1", "version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz", "resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==", "integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true "dev": true
}, }
"litemol": { }
"version": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412", },
"dev": true, "ProtVista": {
"requires": { "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"@types/react": "15.6.15", "dev": true,
"@types/react-dom": "15.5.7" "requires": {
} "d3": "3.5.17",
"file-saver": "1.3.3",
"jquery": "2.2.4",
"jszip": "3.1.4",
"underscore": "1.8.3"
},
"dependencies": {
"jquery": {
"version": "2.2.4",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
"integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
"dev": true
} }
} }
}, },
...@@ -2058,6 +2050,14 @@ ...@@ -2058,6 +2050,14 @@
"immediate": "3.0.6" "immediate": "3.0.6"
} }
}, },
"litemol": {
"version": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412",
"dev": true,
"requires": {
"@types/react": "15.6.15",
"@types/react-dom": "15.5.7"
}
},
"lodash": { "lodash": {
"version": "4.17.4", "version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz", "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",
......
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