From 9f08f7fb5987576cdfc386396f490889ff648127 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 22 Mar 2012 16:04:10 +0100 Subject: File deletions --- aa-local.yaml | 41 ----------------------- aa-server.yaml | 41 ----------------------- base-install.sh | 0 config.sh | 3 +- environment_update.sh | 77 ------------------------------------------- install | 14 +------- kernlab.sh | 71 ---------------------------------------- nginx.conf | 42 ------------------------ openbabel.sh | 1 + opentox-ruby.sh | 91 --------------------------------------------------- ot-tools-root.sh | 82 ---------------------------------------------- ot-tools-user.sh | 83 ---------------------------------------------- production.yaml | 26 --------------- redis.sh | 79 -------------------------------------------- ruby.sh | 78 ------------------------------------------- test-ob-rb.rb | 1 - 16 files changed, 3 insertions(+), 727 deletions(-) delete mode 100644 aa-local.yaml delete mode 100644 aa-server.yaml mode change 100644 => 100755 base-install.sh delete mode 100755 environment_update.sh delete mode 100755 kernlab.sh delete mode 100644 nginx.conf delete mode 100755 opentox-ruby.sh delete mode 100644 ot-tools-root.sh delete mode 100644 ot-tools-user.sh delete mode 100644 production.yaml delete mode 100755 redis.sh delete mode 100755 ruby.sh delete mode 100644 test-ob-rb.rb diff --git a/aa-local.yaml b/aa-local.yaml deleted file mode 100644 index 75cccd0..0000000 --- a/aa-local.yaml +++ /dev/null @@ -1,41 +0,0 @@ -# OpenSSO Authorization -# set ":server: " to disable A&A -:authorization: - :server: AA - :free_request: #request-method not controlled by A&A - - "GET" - - "POST" - - "HEAD" - - "DELETE" - - "PUT" - :authenticate_request: #only for authenticated user - - "" - :authorize_request: #only for authenticated and authorizeduser - - "" -# Exceptions: - :free_uris: #request-method for uri not controlled by A&A - ? - :GET - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/ - - "http://SERVERNAMENGINX_PORT/model" - - "http://SERVERNAMENGINX_PORT/dataset" - - "http://SERVERNAMENGINX_PORT/validation" - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/ - ? - :GET - - :POST - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/ - - !ruby/regexp /sign_(in|out)$/ - ? - :PUT - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/ - ? - :DELETE - : - "http://SERVERNAMENGINX_PORT/task/cleanup" - - :authorize_exceptions: #request-method for uri only authenticated, no authorization - ? - :POST - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/ - - "http://SERVERNAMENGINX_PORT/dataset" - - "http://SERVERNAMENGINX_PORT/model" - - "http://SERVERNAMENGINX_PORT/validation" - - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/ diff --git a/aa-server.yaml b/aa-server.yaml deleted file mode 100644 index 75cccd0..0000000 --- a/aa-server.yaml +++ /dev/null @@ -1,41 +0,0 @@ -# OpenSSO Authorization -# set ":server: " to disable A&A -:authorization: - :server: AA - :free_request: #request-method not controlled by A&A - - "GET" - - "POST" - - "HEAD" - - "DELETE" - - "PUT" - :authenticate_request: #only for authenticated user - - "" - :authorize_request: #only for authenticated and authorizeduser - - "" -# Exceptions: - :free_uris: #request-method for uri not controlled by A&A - ? - :GET - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/ - - "http://SERVERNAMENGINX_PORT/model" - - "http://SERVERNAMENGINX_PORT/dataset" - - "http://SERVERNAMENGINX_PORT/validation" - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/ - ? - :GET - - :POST - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/ - - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/ - - !ruby/regexp /sign_(in|out)$/ - ? - :PUT - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/ - ? - :DELETE - : - "http://SERVERNAMENGINX_PORT/task/cleanup" - - :authorize_exceptions: #request-method for uri only authenticated, no authorization - ? - :POST - : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/ - - "http://SERVERNAMENGINX_PORT/dataset" - - "http://SERVERNAMENGINX_PORT/model" - - "http://SERVERNAMENGINX_PORT/validation" - - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/ diff --git a/base-install.sh b/base-install.sh old mode 100644 new mode 100755 diff --git a/config.sh b/config.sh index 5bf084c..bd7f1ab 100755 --- a/config.sh +++ b/config.sh @@ -21,8 +21,7 @@ REDIS_NUM_VER="2.2.2" # 4) Server settings. NGINX_SERVERNAME="toxcreate3.in-silico.ch" WWW_DEST="$OT_PREFIX/www" -UNICORN_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080" -OHM_PORT="" # set to port (no colon) +OHM_PORT="6381" # set to port (no colon) # Done. diff --git a/environment_update.sh b/environment_update.sh deleted file mode 100755 index d0beae4..0000000 --- a/environment_update.sh +++ /dev/null @@ -1,77 +0,0 @@ -#!/bin/sh -# Update script for OpenTox-ruby and webservices -# Authors: Andreas Maunz, David Vorgrimmler -# This script updates a productiv version of IST Opentox Services. All data will be saved and recovered. -# Make sure your web services are down befor running this script. -# You may modify some variables e.g. HOME, OTPREFIX, BACKUP_DIR. -# opentox/install is needed and has to be configured - -HOME="/home/opentox" -. $HOME/.opentox-ui.sh - -OTPREFIX="$HOME/opentox" -BACKUP_DIR="$OTPREFIX/ot-server-backup" -mkdir $BACKUP_DIR >/dev/null 2>&1 -mkdir -p $BACKUP_DIR/tmp/dataset/public >/dev/null 2>&1 -mkdir -p $BACKUP_DIR/tmp/model/public >/dev/null 2>&1 -mkdir -p $BACKUP_DIR/tmp/validation >/dev/null 2>&1 -#mkdir -p $BACKUP_DIR/tmp/log >/dev/null 2>&1 - - -echo "Creating backup of www..." -TAR_NAME=$BACKUP_DIR/"www_`date +%y%m%d`.tar.gz" - -if [ -e $TAR_NAME ] || tar czvf $TAR_NAME "$OTPREFIX/opentox-ruby/www"; then - echo - echo "Will delete www in 10s! Press Ctrl+C to abort..." - sleep 10 - sudo rm -rf "$OTPREFIX/opentox-ruby/www" -fi - - -NGINX="`which nginx`" -RAKE="`which rake`" - -if ! [ -e "$RAKE" ]; then - echo "Rake not found." - exit 1 -fi -if ! [ -e "$NGINX" ]; then - echo "Nginx not found." - exit 1 -fi -if ! cd "$OTPREFIX/install"; then - echo "$OTPREFIX/install dir not found" -fi - - -OTINSTALL="$OTPREFIX/install/opentox-webservices.sh" -if ! [ -e "$OTINSTALL" ]; then - echo "$OTINSTALL not found." - exit 1 -fi -chmod +x $OTINSTALL -`$OTINSTALL` -echo "$OTINSTALL script end." - - -OTRUBYINSTALL="$OTPREFIX/install/opentox-ruby.sh" -if ! [ -e "$OTRUBYINSTALL" ]; then - echo "$OTRUBYINSTALL not found." - exit 1 -fi -chmod +x $OTRUBYINSTALL -`$OTRUBYINSTALL` -echo "$OTRUBYINSTALL script end." - - -echo "Extracting backup of www..." -cd / -DEST_DATASET=`echo "$OTPREFIX/opentox-ruby/www/opentox/dataset/public/*yaml" | sed 's/.\(.*\)/\1/'` -DEST_MODEL=`echo "$OTPREFIX/opentox-ruby/www/opentox/model/public/*yaml" | sed 's/.\(.*\)/\1/'` -DEST_REPORTS=`echo "$OTPREFIX/opentox-ruby/www/opentox/validation/reports" | sed 's/.\(.*\)/\1/'` -tar xzvf $TAR_NAME --wildcards $DEST_DATASET -tar xzvf $TAR_NAME --wildcards $DEST_MODEL -tar xzvf $TAR_NAME $DEST_REPORTS -cd - -echo "End of script." diff --git a/install b/install index a486660..c3cf9a4 100755 --- a/install +++ b/install @@ -45,22 +45,10 @@ echo "Cleaning up $HOME/tmp files." rm -rf $HOME/tmp/openbabel* $HOME/tmp/kernlab* $HOME/tmp/ruby* . "./base-install.sh" -. "./ruby.sh" . "./openbabel.sh" -. "./kernlab.sh" -. "./opentox-ruby.sh" - -if [ "$install" != "gem" ] -then - . "./nginx.sh" - . "./redis.sh" - . "./opentox-webservices.sh" -fi echo echo "Installation finished and system configured." echo "Destination: '$OT_PREFIX'" -echo "Nginx: '$NGINX_DEST'" -echo "Redis: '$REDIS_DEST'" -echo "IMPORTANT: Include the file '$OT_UI_CONF' in your shell or system startup to have the system automatically configured." +echo "IMPORTANT: Include '$OT_UI_CONF' in your shell or system startup to have the system automatically configured." echo diff --git a/kernlab.sh b/kernlab.sh deleted file mode 100755 index 511874b..0000000 --- a/kernlab.sh +++ /dev/null @@ -1,71 +0,0 @@ -#!/bin/sh -# -# Installs Kernlab. -# Author: Christoph Helma, Andreas Maunz. -# - -. "`pwd`/utils.sh" -DIR="`pwd`" - -if [ "$(id -u)" = "0" ]; then - echo "This script must be run as non-root." 1>&2 - exit 1 -fi - -# Utils -WGET="`which wget`" -if [ ! -e "$WGET" ]; then - echo "'wget' missing. Install 'wget' first. Aborting..." - exit 1 -fi - -R="`which R`" -if [ ! -e "$R" ]; then - echo "'R' missing. Install 'R' first. Aborting..." - exit 1 -fi - -# Pkg -LOG="$HOME/tmp/`basename $0`-log.txt" - -echo -echo "Kernlab ('$LOG')." - -R_DONE=false -mkdir "$KL_DEST" >/dev/null 2>&1 -if [ ! -d "$KL_DEST" ]; then - echo "Install directory '$KL_DEST' is not available! Aborting..." - exit 1 -else - if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail - R_DONE=true - else - mkdir "$KL_DEST" >/dev/null 2>&1 - fi -fi - - -if ! $R_DONE; then - cd $HOME/tmp - URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download" - - export R_LIBS="$KL_DEST" # To install non-global - cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install" -fi - - -if [ ! -f $KL_CONF ]; then - - echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF" - echo "if ! [ -d \"$KL_DEST\" ]; then echo \"\$0: '$KL_DEST' is not a directory!\"; fi" >> "$KL_CONF" - echo "R package destination has been stored in '$KL_CONF'." - - if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then - echo ". \"$KL_CONF\"" >> $OT_UI_CONF - fi - -fi - -cd "$DIR" - diff --git a/nginx.conf b/nginx.conf deleted file mode 100644 index 9f87adf..0000000 --- a/nginx.conf +++ /dev/null @@ -1,42 +0,0 @@ -worker_processes 10; - -events { - worker_connections 1024; -} - -http { - - server_names_hash_bucket_size 256; - - passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER; - passenger_ruby RUBY_DEST/bin/ruby; - passenger_default_user USER; - passenger_log_level 2; - passenger_spawn_method conservative; - #passenger_use_global_queue on; - - include NGINX_DEST/conf/mime.types; - default_type application/octet-stream; - - sendfile on; - keepalive_timeout 65; - - # webservices - server { - listen NGINX_PORT; - client_max_body_size 5000m; - server_name SERVERNAME; - location / { - root WWW_DEST; - passenger_enabled on; - } - passenger_base_uri /compound; - passenger_base_uri /dataset; - passenger_base_uri /algorithm; - passenger_base_uri /model; - passenger_base_uri /task; - passenger_base_uri /validation; - passenger_base_uri /toxcreate; - } - -} diff --git a/openbabel.sh b/openbabel.sh index 367fb28..b51ed17 100755 --- a/openbabel.sh +++ b/openbabel.sh @@ -74,3 +74,4 @@ if [ ! -f "$OB_CONF" ]; then fi +cd "$DIR" diff --git a/opentox-ruby.sh b/opentox-ruby.sh deleted file mode 100755 index 9705682..0000000 --- a/opentox-ruby.sh +++ /dev/null @@ -1,91 +0,0 @@ -#!/bin/sh -# -# Installs Opentox-ruby gem. -# Author: Christoph Helma, Andreas Maunz. -# - -. "`pwd`/utils.sh" -DIR="`pwd`" - -if [ "$(id -u)" = "0" ]; then - echo "This script must be run as non-root." 1>&2 - exit 1 -fi - -# Utils -GIT="`which git`" -if [ ! -e "$GIT" ]; then - echo "'git' missing. Install 'git' first. Aborting..." - exit 1 -fi - -GEM="`which gem`" -if [ ! -e "$GEM" ]; then - echo "'gem' missing. Install 'gem' first. Aborting..." - exit 1 -fi - -RAKE="`which rake`" -if [ ! -e "$RAKE" ]; then - echo "'rake' missing. Install 'rake' first. Aborting..." - exit 1 -fi - - -# Pkg -LOG="$HOME/tmp/`basename $0`-log.txt" - -echo -echo "Opentox-ruby ('$LOG'):" - -for mygem in opentox-ruby builder jeweler; do - if ! $GEM list | sed 's/\ .*//g' | grep -x "$mygem" >/dev/null 2>&1; then - cmd="$GEM install $mygem" && run_cmd "$cmd" "$mygem" - fi -done - - -servername="`hostname`" -serverdomain="`dnsdomainname`" -if [ -n "$serverdomain" ]; then - servername="$servername"."$serverdomain" -fi -escapedserver="`echo $servername | sed 's/\/\\\//'`" - -if [ "$OT_BRANCH" = "development" ]; then - logger=":logger: backtrace" -else - logger="" -fi - -if [ "$OT_INSTALL" = "server" ]; then - aa="https:\/\/opensso.in-silico.ch" -else - aa="" -fi - -mkdir -p "$HOME/.opentox/config" >>$LOG 2>&1 -mkdir -p "$HOME/.opentox/log" >>$LOG 2>&1 -mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1 - -$GIT checkout production.yaml >>$LOG 2>&1 -$GIT checkout aa-$OT_INSTALL.yaml >>$LOG 2>&1 - -cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1" -cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2" - -if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then - mkdir -p $WWW_DEST/opentox >>$LOG 2>&1 - cd $WWW_DEST/opentox >>$LOG 2>&1 - rm -rf opentox-ruby >>$LOG 2>&1 - $GIT clone git://github.com/opentox/opentox-ruby.git >>$LOG 2>&1 - cd opentox-ruby >>$LOG 2>&1 - $GIT checkout -b $OT_BRANCH origin/$OT_BRANCH >>$LOG 2>&1 - cmd="$RAKE install" && run_cmd "$cmd" "Install" - GEM_LIB=`$GEM which opentox-ruby | sed 's/\/opentox-ruby.rb//'` - rm -rf "$GEM_LIB~" >>$LOG 2>&1 - mv "$GEM_LIB" "$GEM_LIB~" >>$LOG 2>&1 - cmd="ln -sf $WWW_DEST/opentox/opentox-ruby/lib $GEM_LIB" && run_cmd "$cmd" "Linking back" -fi - -cd "$DIR" diff --git a/ot-tools-root.sh b/ot-tools-root.sh deleted file mode 100644 index 7e1233b..0000000 --- a/ot-tools-root.sh +++ /dev/null @@ -1,82 +0,0 @@ -# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'): -# USE ONLY IF YOUR NGINX PORT IS less or equal to 1024 (PRIVILEGED) - -# Load server config -otconfig() { - source $HOME/.opentox-ui.sh -} - -# Update the version -otupdate() { - START_DIR=`pwd` - otconfig - cd $HOME/opentox-ruby/www/opentox - for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ; done - cd $HOME/opentox-ruby/www/opentox/algorithm/libfminer - mv libbbrc/Makefile libbbrc/Makefile~ - mv liblast/Makefile liblast/Makefile~ - if ! git pull; then - echo "Error! Pull for Fminer failed." - return 1 - fi - mv libbbrc/Makefile~ libbbrc/Makefile - mv liblast/Makefile~ liblast/Makefile - make -C libbbrc/ clean - make -C libbbrc/ ruby - make -C liblast/ clean - make -C liblast/ ruby - cd - - cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils - if ! git pull; then - echo "Error! Pull for Last-Utils failed." - return 1 - fi - cd - - cd opentox-ruby - LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'` - if [ -h $LINK_DIR ]; then - rm -f $LINK_DIR - fi - rake install - if ! [ -h $LINK_DIR ]; then - echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..." - rm -rf "$LINK_DIR~" - mv "$LINK_DIR" "$LINK_DIR~" - ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}` - fi - echo "Please execute 'otstart' to restart." - cd "$START_DIR" -} - -# Start the server -otstart() { - otconfig - otkill - sudo bash -c "nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &" - sudo bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &" - sleep 2 - if ! pgrep -u root nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi - if ! pgrep -u root redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi -} - -# Display log -alias otless='less $HOME/.opentox/log/production.log' - -# Tail log -alias ottail='tail -f $HOME/.opentox/log/production.log' - -# Reload the server -otreload() { - otconfig - sudo bash -c "nginx -s reload" -} - -# Kill the server -otkill() { - otconfig - sudo killall -u root nginx >/dev/null 2>&1 - sudo bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1" - while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done - while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done - for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done -} diff --git a/ot-tools-user.sh b/ot-tools-user.sh deleted file mode 100644 index 57c6c00..0000000 --- a/ot-tools-user.sh +++ /dev/null @@ -1,83 +0,0 @@ -# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'): -# USE ONLY IF YOUR NGINX PORT IS >1024 (NOT PRIVILEGED) - -# Load server config -otconfig() { - source $HOME/.opentox-ui.sh -} - -# Update the version -otupdate() { - START_DIR=`pwd` - otconfig - cd $HOME/opentox-ruby/www/opentox - for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ; done - cd $HOME/opentox-ruby/www/opentox/algorithm/libfminer - mv libbbrc/Makefile libbbrc/Makefile~ - mv liblast/Makefile liblast/Makefile~ - if ! git pull; then - echo "Error! Pull for Fminer failed." - return 1 - fi - mv libbbrc/Makefile~ libbbrc/Makefile - mv liblast/Makefile~ liblast/Makefile - make -C libbbrc/ clean - make -C libbbrc/ ruby - make -C liblast/ clean - make -C liblast/ ruby - cd - - cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils - if ! git pull; then - echo "Error! Pull for Last-Utils failed." - return 1 - fi - cd - - cd opentox-ruby - LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'` - if [ -h $LINK_DIR ]; then - rm -f $LINK_DIR - fi - rake install - if ! [ -h $LINK_DIR ]; then - echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..." - rm -rf "$LINK_DIR~" - mv "$LINK_DIR" "$LINK_DIR~" - ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}` - fi - echo "Please execute 'otstart' to restart." - cd "$START_DIR" -} - -# Start the server -otstart() { - otconfig - otkill - bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &" - bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &" - sleep 2 - if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi - if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi -} - -# Display log -alias otless='less $HOME/.opentox/log/production.log' - -# Tail log -alias ottail='tail -f $HOME/.opentox/log/production.log' - -# Reload the server -otreload() { - otconfig - bash -c "nginx -s reload" -} - -# Kill the server -otkill() { - otconfig - killall nginx >/dev/null 2>&1 - bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1" - while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done - while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done - for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done -} - diff --git a/production.yaml b/production.yaml deleted file mode 100644 index e0f39d4..0000000 --- a/production.yaml +++ /dev/null @@ -1,26 +0,0 @@ -:base_dir: WWW_DEST - -:services: -# make sure to enter a full uri (including training slash) - opentox-compound: "http://SERVERNAMENGINX_PORT/compound/" - opentox-dataset: "http://SERVERNAMENGINX_PORT/dataset/" - opentox-algorithm: "http://SERVERNAMENGINX_PORT/algorithm/" - opentox-model: "http://SERVERNAMENGINX_PORT/model/" - opentox-task: "http://SERVERNAMENGINX_PORT/task/" - opentox-toxcreate: "http://SERVERNAMENGINX_PORT/toxcreate/" - opentox-validation: "http://SERVERNAMENGINX_PORT/validation/" - opentox-ontology: "http://apps.ideaconsult.net:8080/ontology" - -:json_hosts: - - "localhost" - - "SERVERNAME" - - "webservices.in-silico.ch" - - "opentox.informatik.uni-freiburg.de" - -:ohm_port: OHM_PORT - -# Uncomment for verbose logging -LOGGER -:logger: debug -:backtrace: true - diff --git a/redis.sh b/redis.sh deleted file mode 100755 index f07d119..0000000 --- a/redis.sh +++ /dev/null @@ -1,79 +0,0 @@ -#!/bin/sh -# -# Installs Redis. -# Author: Christoph Helma, Andreas Maunz. -# - -. "`pwd`/utils.sh" -DIR=`pwd` - -if [ "$(id -u)" = "0" ]; then - echo "This script must be run as non-root." 1>&2 - exit 1 -fi - -# Utils -WGET="`which wget`" -if [ ! -e "$WGET" ]; then - echo "'wget' missing. Install 'wget' first. Aborting..." - exit 1 -fi - -LOG="$HOME/tmp/`basename $0`-log.txt" - -echo -echo "Redis ('$LOG'):" - - -REDIS_DONE=false -mkdir "$REDIS_DEST" >/dev/null 2>&1 -if [ ! -d "$REDIS_DEST" ]; then - echo "Install directory '$REDIS_DEST' is not available! Aborting..." - exit 1 -else - if ! rmdir "$REDIS_DEST" >/dev/null 2>&1; then # if not empty this will fail - REDIS_DONE=true - fi -fi - -if ! $REDIS_DONE; then - echo "vm.overcommit_memory = 1" | sudo tee -a /etc/sysctl.conf >>$LOG 2>&1 - - cd $OT_PREFIX - URI="http://redis.googlecode.com/files/redis-$REDIS_VER.tar.gz" - if ! [ -d "redis-$REDIS_VER" ]; then - cmd="$WGET $URI" && run_cmd "$cmd" "Download" - cmd="tar zxf redis-$REDIS_VER.tar.gz" && run_cmd "$cmd" "Unpack" - fi - cd redis-$REDIS_VER >>$LOG 2>&1 - cmd="make" && run_cmd "$cmd" "Make" - - if ! grep "daemonize yes" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then - echo "daemonize yes" > $REDIS_SERVER_CONF 2>$LOG - fi - - if ! grep "dir `pwd`" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then - echo "dir `pwd`" >> $REDIS_SERVER_CONF 2>$LOG - fi - - if ! grep "save 900 1" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then - echo "save 900 1" >> $REDIS_SERVER_CONF 2>$LOG - fi - - if ! grep "port $OHM_PORT" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then - echo "port $OHM_PORT" >> $REDIS_SERVER_CONF 2>$LOG - fi -fi - -if [ ! -f $REDIS_CONF ]; then - echo "if ! echo \"\$PATH\" | grep \"$REDIS_DEST\">/dev/null 2>&1; then export PATH=$REDIS_DEST/src:\$PATH; fi" >> "$REDIS_CONF" - echo "export OHM_PORT=$OHM_PORT" >> "$REDIS_CONF" - echo "Redis configuration has been stored in '$REDIS_CONF'." - - if ! grep ". \"$REDIS_CONF\"" $OT_UI_CONF; then - echo ". \"$REDIS_CONF\"" >> $OT_UI_CONF - fi - -fi - -cd "$DIR" diff --git a/ruby.sh b/ruby.sh deleted file mode 100755 index b88cfe2..0000000 --- a/ruby.sh +++ /dev/null @@ -1,78 +0,0 @@ -#!/bin/sh -# -# Installs Ruby enterprise edition and passenger gem. -# A configuration file is created and included in your '$OT_UI_CONF'. -# Author: Christoph Helma, Andreas Maunz. -# - -. "`pwd`/utils.sh" -DIR="`pwd`" - -if [ "$(id -u)" = "0" ]; then - echo "This script must be run as non-root." 1>&2 - exit 1 -fi - -# Utils -WGET="`which wget`" -if [ ! -e "$WGET" ]; then - echo "'wget' missing. Install 'wget' first. Aborting..." - exit 1 -fi -RBENV="`which rbenv`" -if [ ! -e "$RBENV" ]; then - echo "'rbenv' missing. Install 'rbenv' first. Aborting..." - exit 1 -fi - -# Pkg -LOG="$HOME/tmp/`basename $0`-log.txt" - -echo -echo "Ruby ('$RUBY_DEST', '$LOG')." - - -mkdir "$RUBY_DEST" >/dev/null 2>&1 -if [ ! -d "$RUBY_DEST" ]; then - echo "Install directory '$RUBY_DEST' is not available! Aborting..." - exit 1 -else - if ! rmdir "$RUBY_DEST" >/dev/null 2>&1; then # if not empty this will fail - RUBY_DONE=true - fi -fi - -if [ ! $RUBY_DONE ]; then - cd $HOME/tmp - URI="http://ftp.ruby-lang.org/pub/ruby/1.9/$RUBY_VER.tar.gz" - if ! [ -d "$RUBY_VER" ]; then - cmd="$WGET $URI" && run_cmd "$cmd" "Download" - cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack" - fi - cmd="cd $RUBY_VER" && run_cmd "$cmd" "cd" - cmd="./configure --prefix=$RUBY_DEST" && run_cmd "$cmd" "Configure" - cmd="make" && run_cmd "$cmd" "Make" - cmd="make install" && run_cmd "$cmd" "Install" - cmd="cd -" && run_cmd "$cmd" "cd" -fi - -cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv Update" - - -#GEM="`which gem`" -#if [ ! -e "$GEM" ]; then -# echo "'gem' missing. Install 'gem' first. Aborting..." -# exit 1 -#fi -# -#export PATH="$RUBY_DEST/bin:$PATH" -#cmd="$GEM sources -a http://gemcutter.org" && run_cmd "$cmd" "Add Gemcutter" -#cmd="$GEM sources -a http://rubygems.org" && run_cmd "$cmd" "Add Rubygems" -#GEMCONF="gem: --no-ri --no-rdoc" -#if ! grep "$GEMCONF" $HOME/.gemrc >>$LOG 2>&1; then -# echo "$GEMCONF" | tee -a $HOME/.gemrc >>$LOG 2>&1 -#fi - - - -cd "$DIR" diff --git a/test-ob-rb.rb b/test-ob-rb.rb deleted file mode 100644 index 62fda1e..0000000 --- a/test-ob-rb.rb +++ /dev/null @@ -1 +0,0 @@ -require 'openbabel' -- cgit v1.2.3