Skip to content
Snippets Groups Projects
Commit e1648b98 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

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 343dda7d
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
debian/create-debian-pkg.sh
+ 17
− 0
View file @ e1648b98
......@@ -70,6 +70,14 @@ then
exit 1;
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
# debian package
......@@ -107,11 +115,20 @@ sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh
#in the filesystem where package is installed
sed -i "s/__DB_SCRIPT_DIR__/$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/postrm
sed -i -e "1r common.sh" debian/preinst
sed -i -e "1r common.sh" debian/prerm
#put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
#escaped
echo db_0.sql /usr/share\/minerva/schema >> debian/install
......
debian/scripts/common.sh
+ 71
− 0
View file @ e1648b98
......@@ -27,3 +27,74 @@ if [ "$TOMCAT8_OK" != "" ];
then
TOMCAT_PACKAGE='tomcat8'
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 @ e1648b98
......@@ -21,29 +21,21 @@ set -e
case "$1" in
configure)
invoke-rc.d postgresql start
start_postgres
#if we install
if [ "$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
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
create_db
#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
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
#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
#print a disclaimer
......
debian/template/postrm
+ 23
− 25
View file @ e1648b98
......@@ -10,15 +10,6 @@
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
set -e
......@@ -26,34 +17,41 @@ case "$1" in
upgrade)
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
# invoke-rc.d $TOMCAT_PACKAGE start || true
# invoke-rc.d postgresql start || true
;;
remove)
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ]
if [ $IS_REMOTE_DB = true ]
then
log "No postgresql package found.";
exec_sql "drop owned by $DB_USERNAME;"
else
invoke-rc.d postgresql start
su - postgres -c "dropdb map_viewer"
su - postgres -c "dropuser map_viewer"
if [ "" = "$POSTGRES_OK" ]
then
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
;;
abort-install)
;;
abort-install)
invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ];
if [ $IS_REMOTE_DB = true ]
then
log "No postgresql package found.";
exec_sql "drop owned by $DB_USER"
else
invoke-rc.d postgresql restart
su - postgres -c "dropdb map_viewer"
su - postgres -c "dropuser map_viewer"
if [ "" = "$POSTGRES_OK" ];
then
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
;;
;;
*)
echo "postrm called with unknown argument \`$1'" >&2
exit 1
......
debian/template/preinst
+ 4
− 4
View file @ e1648b98
......@@ -24,12 +24,12 @@ ln -s $path $DEFAULT_JAVA_SYMLINK
case "$1" in
install|upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
invoke-rc.d $TOMCAT_PACKAGE stop || true
stop_postgres
;;
abort-upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
invoke-rc.d $TOMCAT_PACKAGE stop || true
stop_postgres
;;
*)
echo "preinst called with unknown argument \`$1'" >&2
......
debian/template/prerm
+ 7
− 7
View file @ e1648b98
......@@ -17,20 +17,20 @@ set -e
log Running prerm $1 $2;
invoke-rc.d postgresql start || true
TIMESTAMP=$(date +"%F")
TIMESTAMP=$(date +"%F_%H%M%S")
DUMP_FILE=$DB_SCRIPT_DIR/dump_$TIMESTAMP
log "dump map_viewer database to file $DUMP_FILE"
su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz
log "dump $DB_DATABASE_NAME database to file $DUMP_FILE"
PGPASSWORD=$DB_PASSWORD pg_dump -h $DB_HOST -p $DB_PORT -U $DB_USERNAME $DB_DATABASE_NAME | gzip > "$DUMP_FILE".gz
case "$1" in
upgrade)
invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
invoke-rc.d $TOMCAT_PACKAGE stop || true
stop_postgres
;;
remove)
invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
invoke-rc.d $TOMCAT_PACKAGE stop || true
stop_postgres
;;
*)
echo "prerm called with unknown argument \`$1'" >&2
......
frontend-js/package-lock.json
+ 18
− 20
View file @ e1648b98
......@@ -35,6 +35,24 @@
"through": "2.3.8"
}
},
"MolStar": {
"version": "git://github.com/davidhoksza/MolStar.git#702c7417cd3dffdb45554b54ce49e27bc881b109",
"dev": true,
"requires": {
"ProtVista": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"downloadjs": "1.4.7",
"jquery": "3.3.1",
"litemol": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412"
},
"dependencies": {
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
}
}
},
"ProtVista": {
"version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"dev": true,
......@@ -2365,26 +2383,6 @@
}
}
},
"molstar": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/molstar/-/molstar-1.0.0.tgz",
"integrity": "sha1-2e0KopdXq1iOLnbtYUOHiZVi8rA=",
"dev": true,
"requires": {
"ProtVista": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"downloadjs": "1.4.7",
"jquery": "3.3.1",
"litemol": "github:dsehnal/LiteMol#67556b0de0d2428f9494136758cbf8a662f66412"
},
"dependencies": {
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
}
}
},
"ms": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz",
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment