OpenSpecimen is a highly Configurable Biospecimen Management System, which enables to track the Complete Lifecycle of your Biospecimen Inventory from Collection to Utilization.
user: admin
password: Login@123>br/>
OpenSpecimen is a highly Configurable Biospecimen Management System, which enables to track the Complete Lifecycle of your Biospecimen Inventory from Collection to Utilization.
To login use:
user:admin
password:Login@123
" } diff --git a/configs/openspecimen/scripts/adduser.jar b/configs/openspecimen/scripts/adduser.jar deleted file mode 100755 index 220a4ad..0000000 Binary files a/configs/openspecimen/scripts/adduser.jar and /dev/null differ diff --git a/configs/openspecimen/scripts/defaultvar.sh b/configs/openspecimen/scripts/defaultvar.sh deleted file mode 100755 index 6afc80a..0000000 --- a/configs/openspecimen/scripts/defaultvar.sh +++ /dev/null @@ -1,15 +0,0 @@ -USED_DATABASE_TYPE="${USED_DATABASE_TYPE:-mysql}" -DATABASE_HOST="${DATABASE_HOST:-openspecimen-db}" -DATABASE_PORT="${DATABASE_PORT:-3306}" -DATABASE_DRIVER="${DATABASE_DRIVER:-com.mysql.jdbc.Driver}" -MYSQL_DATABASE="${MYSQL_DATABASE:-openspecimen}" -MYSQL_USER="${MYSQL_USER:-openspecimen}" -MYSQL_PASSWORD="${MYSQL_PASSWORD:-openspecimen}" -TOMCAT_MANAGER_USER="${TOMCAT_MANAGER_USER:-admin}" -TOMCAT_MANAGER_PASSWORD="${TOMCAT_MANAGER_PASSWORD:-admin}" -INSTITUTE_NAME="${INSTITUTE_NAME:-BIBBOX Demo Biobank}" -EMAIL_ADDRESS="${EMAIL_ADDRESS:-admin@bibbox.org}" -FIRST_NAME="${FIRST_NAME:-Admin}" -LAST_NAME="${LAST_NAME:-Bibbox}" -LOGIN_NAME="${LOGIN_NAME:-bibboxadmin}" -ADDRESS="${ADDRESS:-}" \ No newline at end of file diff --git a/configs/openspecimen/scripts/entrypoint.sh b/configs/openspecimen/scripts/entrypoint.sh deleted file mode 100755 index aba2d9a..0000000 --- a/configs/openspecimen/scripts/entrypoint.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash -echo "Starting OpenSpecimen Application!" - -. defaultvar.sh - -sed -e "s/__DB_PW/$MYSQL_PASSWORD/g" -e "s/__DB_USER/$MYSQL_USER/g" /var/lib/tomcat9/conf/context.xml.template > /var/lib/tomcat9/conf/context.xml - -#chown -R tomcat:tomcat /var/lib/openspecimen/plugins -#chown -R tomcat:tomcat /var/lib/openspecimen/data -#chown -R tomcat:tomcat /var/lib/tomcat9/webapps/ROOT - -echo "Wait for DB server to be ready" -/opt/scripts/waitforit.sh "${DATABASE_HOST}:${DATABASE_PORT}" - -/usr/share/tomcat9/bin/catalina.sh start - -tail -f /var/lib/tomcat9/logs/catalina.out -f /var/lib/tomcat9/openspecimen/data/logs/os.log diff --git a/configs/openspecimen/scripts/waitforit.sh b/configs/openspecimen/scripts/waitforit.sh deleted file mode 100755 index aaab978..0000000 --- a/configs/openspecimen/scripts/waitforit.sh +++ /dev/null @@ -1,182 +0,0 @@ -#!/usr/bin/env bash -# Use this script to test if a given TCP host/port are available - -#The MIT License (MIT) -#Copyright (c) 2016 Giles Hall -# -#Permission is hereby granted, free of charge, to any person obtaining a copy of -#this software and associated documentation files (the "Software"), to deal in -#the Software without restriction, including without limitation the rights to -#use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies -#of the Software, and to permit persons to whom the Software is furnished to do -#so, subject to the following conditions: -# -#The above copyright notice and this permission notice shall be included in all -#copies or substantial portions of the Software. -# -#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -#IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -#FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -#AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -#LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -#OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -#SOFTWARE. -# -cmdname=$(basename $0) - -echoerr() { if [[ $QUIET -ne 1 ]]; then echo "$@" 1>&2; fi } - -usage() -{ - cat << USAGE >&2 -Usage: - $cmdname host:port [-s] [-t timeout] [-- command args] - -h HOST | --host=HOST Host or IP under test - -p PORT | --port=PORT TCP port under test - Alternatively, you specify the host and port as host:port - -s | --strict Only execute subcommand if the test succeeds - -q | --quiet Don't output any status messages - -t TIMEOUT | --timeout=TIMEOUT - Timeout in seconds, zero for no timeout - -- COMMAND ARGS Execute command with args after the test finishes -USAGE - exit 1 -} - -wait_for() -{ - if [[ $TIMEOUT -gt 0 ]]; then - echoerr "$cmdname: waiting $TIMEOUT seconds for $HOST:$PORT" - else - echoerr "$cmdname: waiting for $HOST:$PORT without a timeout" - fi - start_ts=$(date +%s) - while : - do - (echo > /dev/tcp/$HOST/$PORT) >/dev/null 2>&1 - result=$? - if [[ $result -eq 0 ]]; then - end_ts=$(date +%s) - echoerr "$cmdname: $HOST:$PORT is available after $((end_ts - start_ts)) seconds" - break - fi - sleep 1 - done - return $result -} - -wait_for_wrapper() -{ - # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692 - if [[ $QUIET -eq 1 ]]; then - timeout $TIMEOUT $0 --quiet --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & - else - timeout $TIMEOUT $0 --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & - fi - PID=$! - trap "kill -INT -$PID" INT - wait $PID - RESULT=$? - if [[ $RESULT -ne 0 ]]; then - echoerr "$cmdname: timeout occurred after waiting $TIMEOUT seconds for $HOST:$PORT" - fi - return $RESULT -} - -# process arguments -while [[ $# -gt 0 ]] -do - case "$1" in - *:* ) - hostport=(${1//:/ }) - HOST=${hostport[0]} - PORT=${hostport[1]} - shift 1 - ;; - --child) - CHILD=1 - shift 1 - ;; - -q | --quiet) - QUIET=1 - shift 1 - ;; - -s | --strict) - STRICT=1 - shift 1 - ;; - -h) - HOST="$2" - if [[ $HOST == "" ]]; then break; fi - shift 2 - ;; - --host=*) - HOST="${1#*=}" - shift 1 - ;; - -p) - PORT="$2" - if [[ $PORT == "" ]]; then break; fi - shift 2 - ;; - --port=*) - PORT="${1#*=}" - shift 1 - ;; - -t) - TIMEOUT="$2" - if [[ $TIMEOUT == "" ]]; then break; fi - shift 2 - ;; - --timeout=*) - TIMEOUT="${1#*=}" - shift 1 - ;; - --) - shift - CLI="$@" - break - ;; - --help) - usage - ;; - *) - echoerr "Unknown argument: $1" - usage - ;; - esac -done - -if [[ "$HOST" == "" || "$PORT" == "" ]]; then - echoerr "Error: you need to provide a host and port to test." - usage -fi - -TIMEOUT=${TIMEOUT:-1000} -STRICT=${STRICT:-0} -CHILD=${CHILD:-0} -QUIET=${QUIET:-0} - -if [[ $CHILD -gt 0 ]]; then - wait_for - RESULT=$? - exit $RESULT -else - if [[ $TIMEOUT -gt 0 ]]; then - wait_for_wrapper - RESULT=$? - else - wait_for - RESULT=$? - fi -fi - -if [[ $CLI != "" ]]; then - if [[ $RESULT -ne 0 && $STRICT -eq 1 ]]; then - echoerr "$cmdname: strict mode, refusing to execute subprocess" - exit $RESULT - fi - exec $CLI -else - exit $RESULT -fi diff --git a/docker-compose.yml b/docker-compose.yml index 3cf3f1c..646b8a7 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -24,7 +24,7 @@ services: - SYS_NICE local-openspecimen-web: - image: bibbox/openspecimen:9-0-RC2 + image: bibbox/openspecimen:v10.1.RC1 container_name: local-openspecimen-web user: tomcat restart: unless-stopped @@ -34,6 +34,7 @@ services: - local-openspecimen-db:openspecimen-db environment: - DATABASE_HOST=openspecimen-db + - DATABASE_PORT=3306 - MYSQL_ROOT_PASSWORD=openspecimen - MYSQL_DATABASE=openspecimen - MYSQL_USER=openspecimen @@ -41,9 +42,8 @@ services: depends_on: - local-openspecimen-db volumes: - - ./data/os-data:/var/lib/tomcat9/openspecimen/data - - ./data/os-plugins:/var/lib/tomcat9/openspecimen/plugins + - ./data/os-data:/var/lib/openspecimen/data + - ./data/os-plugins:/var/lib/openspecimen/plugins - ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT - - ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh ports: - "9000:8080" diff --git a/docker-compose.yml.template b/docker-compose.yml.template index 5d6ecab..85c4b46 100644 --- a/docker-compose.yml.template +++ b/docker-compose.yml.template @@ -22,7 +22,7 @@ services: - ./configs/openspecimen.cnf:/etc/mysql/conf.d/openspecimen.cnf:ro §§INSTANCE-openspecimen-web: - image: bibbox/openspecimen:9-0-RC2 + image: bibbox/openspecimen:v10.1.RC1 container_name: §§INSTANCE-openspecimen-web restart: unless-stopped user: tomcat @@ -32,6 +32,7 @@ services: - §§INSTANCE-openspecimen-db:openspecimen-db environment: - DATABASE_HOST=openspecimen-db + - DATABASE_PORT=3306 - MYSQL_ROOT_PASSWORD=thispasswordisneverusededoutsidethecontainer - MYSQL_DATABASE=openspecimen - MYSQL_USER=§§MYSQL_DATABASE_USER @@ -44,9 +45,8 @@ services: depends_on: - §§INSTANCE-openspecimen-db volumes: - - ./data/os-data:/var/lib/tomcat9/openspecimen/data - - ./data/os-plugins:/var/lib/tomcat9/openspecimen/plugins + - ./data/os-data:/var/lib/openspecimen/data + - ./data/os-plugins:/var/lib/openspecimen/plugins - ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT - - ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh ports: - "9000:8080"