diff --git a/debian/create-debian-pkg.sh b/debian/create-debian-pkg.sh
index 654df170b9de5f453019e137908583eb9650cc6b..1da14fa3436067f4a90d5deb5eecfa90b07266ec 100755
--- a/debian/create-debian-pkg.sh
+++ b/debian/create-debian-pkg.sh
@@ -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 $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
#escaped
echo db_0.sql /usr/share\/minerva/schema >> debian/install
diff --git a/debian/scripts/common.sh b/debian/scripts/common.sh
index 246724cb9444cdf4d2c503fe804ab3d973ffa338..2b5d61837f794dd009b68265814570874af93999 100644
--- a/debian/scripts/common.sh
+++ b/debian/scripts/common.sh
@@ -27,3 +27,74 @@ if [ "$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
+}
diff --git a/debian/template/postinst b/debian/template/postinst
index 2f2c3863a88d87c25e0f49a67687296261a2a16e..35037021f7e211c44b71872a9db765295f72f101 100644
--- a/debian/template/postinst
+++ b/debian/template/postinst
@@ -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
diff --git a/debian/template/postrm b/debian/template/postrm
index 89144fb629ef34fd3761bc2c749f6cebfcfd4840..6c517b351c62b103aaf36e2479c2f6cec49f9db0 100644
--- a/debian/template/postrm
+++ b/debian/template/postrm
@@ -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
diff --git a/debian/template/preinst b/debian/template/preinst
index c6ad957eb6803a810a043143bf5845e16a3017ef..84d76df53b7b63fb52764416c0e076a72484ccf9 100644
--- a/debian/template/preinst
+++ b/debian/template/preinst
@@ -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
diff --git a/debian/template/prerm b/debian/template/prerm
index c43b60f8fa2c3f996db03de69cc8b7e261d9220e..b131100dbb7790d8628054bd04fae91e19575a03 100644
--- a/debian/template/prerm
+++ b/debian/template/prerm
@@ -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
diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index a97b88ebea0165231b24e0f79ae9e7d6a983e105..d84bc1074518cb44283e90e34d2b94f587814a5d 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -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",