Merge branch 'master' of github.com:helma/opentox-install

Conflicts:
	config
	opentox-ruby.sh

7 files changed, 96 insertions, 50 deletions

diff --git a/aa-local.yaml b/aa-local.yaml
new file mode 100644
index 0000000..593ba56
--- /dev/null
+++ b/aa-local.yaml
@@ -0,0 +1,38 @@
+# 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:\/\/ESCAPEDSERVERNAME\/algorithm/
+      - "http://SERVERNAME/model"
+      - "http://SERVERNAME/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/validation\/[a-z,A-Z,\/,_\-]*$/
+    ? - :GET
+      - :POST
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/toxcreate/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/compound/
+
+    ? - :PUT
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/task/
+
+  :authorize_exceptions: #request-method for uri only authenticated, no authorization
+    ? - :POST
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/algorithm/
+      - "http://SERVERNAME/dataset"
+      - "http://SERVERNAME/model"
+      - "http://SERVERNAME/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERNAME\/validation\/[a-z,A-Z,\/,_\-]*$/
+ 
diff --git a/aa-server.yaml b/aa-server.yaml
new file mode 100644
index 0000000..593ba56
--- /dev/null
+++ b/aa-server.yaml
@@ -0,0 +1,38 @@
+# 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:\/\/ESCAPEDSERVERNAME\/algorithm/
+      - "http://SERVERNAME/model"
+      - "http://SERVERNAME/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/validation\/[a-z,A-Z,\/,_\-]*$/
+    ? - :GET
+      - :POST
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/toxcreate/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/compound/
+
+    ? - :PUT
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/task/
+
+  :authorize_exceptions: #request-method for uri only authenticated, no authorization
+    ? - :POST
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNAME\/algorithm/
+      - "http://SERVERNAME/dataset"
+      - "http://SERVERNAME/model"
+      - "http://SERVERNAME/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERNAME\/validation\/[a-z,A-Z,\/,_\-]*$/
+ 
diff --git a/config b/config
index cada2e2..6b18a2a 100644
--- a/config
+++ b/config
@@ -5,14 +5,18 @@
 # Linux distribution (currently only debian)
 distribution=debian
 
+# Choose a root password for the MySQL database
+# Please insert the correct password if mysql-server is already installed
+mysql_root=opentox
+
 # Installation type
 # Options:
-# gem	Installs only the opentox-ruby gem (useful, if you want to use external services with the opentox-ruby DSL)
-# local   local installation
-# server  inter or intranet server
-type=local
+# gem	  installs only the opentox-ruby gem (useful, if you want to use external services with the opentox-ruby DSL)
+# local   local installation (authentication and authorisation disabled)
+# server  inter or intranet server (authentication and authorisation enabled)
+type=server
 
 # Git branch of services
 # Options: master test development
 # "master" is the current stable version
-branch=master
+branch=development
diff --git a/install b/install
index 47e6be3..9a89730 100755
--- a/install
+++ b/install
@@ -6,7 +6,7 @@
 . ./openbabel.sh
 . ./kernlab.sh
 . ./opentox-ruby.sh
-if [ $install = "all" ]
+if [ $install != "gem" ]
 then
     . ./nginx.sh
     . ./redis.sh
diff --git a/nginx.conf b/nginx.conf
index f2c9bed..ce00e37 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -11,7 +11,9 @@ http {
     passenger_root /opt/ruby-enterprise-1.8.7-2010.03/lib/ruby/gems/1.8/gems/PASSENGER;
     passenger_ruby /opt/ruby-enterprise-1.8.7-2010.03/bin/ruby;
     passenger_default_user opentox;
-    passenger_log_level 3;
+    passenger_log_level 2;
+    passenger_spawn_method conservative;
+    #passenger_use_global_queue on;
 
     include       mime.types;
     default_type  application/octet-stream;
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 67616c9..595ee36 100644
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -10,6 +10,7 @@ dir=`pwd`
 
 # create config file
 servername=`hostname`.`dnsdomainname`
+escapedservername=`echo $servername|sed 's/\/\\\//'`
 if [ $branch = "development" ]
 then
     logger=":logger: backtrace"
@@ -26,14 +27,16 @@ fi
 
 mkdir -p $HOME/.opentox/config
 mkdir -p $HOME/.opentox/log
-sed -e "s/SERVERNAME/$servername/;s/LOGGER/$logger/;s/AA/$aa/" production.yaml > $HOME/.opentox/config/production.yaml
+#sed -e "s/SERVERNAME/$servername/;s/LOGGER/$logger/;s/AA/$aa/" production.yaml > $HOME/.opentox/config/production.yaml
+sed -e "s/PASSWORD/$password/;s/SERVERNAME/$servername/;s/ESCAPEDSERVERNAME/$escapedservername/;s/LOGGER/$logger/;s/AA/$aa/" production.yaml > $HOME/.opentox/config/production.yaml
+sed -e "s/PASSWORD/$password/;s/SERVERNAME/$servername/;s/ESCAPEDSERVERNAME/$escapedservername/;s/LOGGER/$logger/;s/AA/$aa/" aa-$type.yaml >> $HOME/.opentox/config/production.yaml
 
 # checkout development version and link lib to opentox-ruby gem
 if [ $branch = "development" ]
 then
     mkdir -p /var/www/opentox
     cd /var/www/opentox
-    git clone http://github.com/mguetlein/opentox-ruby.git 
+    git clone http://github.com/helma/opentox-ruby.git 
     cd opentox-ruby
     git checkout -t origin/$branch
     gem_lib=`gem which opentox-ruby`
diff --git a/production.yaml b/production.yaml
index ce19743..f6d19cd 100644
--- a/production.yaml
+++ b/production.yaml
@@ -18,45 +18,6 @@
 
 # Uncomment for verbose logging
 LOGGER
-#:logger: debug
-#:backtrace: true
+:logger: debug
+:backtrace: true
 
-# 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:\/\/ot\-dev\.in\-silico\.ch\/algorithm/
-      - "http://in-silico.ch/dataset"
-      - "http://ot-dev.in-silico.ch/model"
-      - "http://ot-dev.in-silico.ch/validation"
-      - !ruby/regexp /http:\/\/ot\-dev\.in-silico\.ch\/validation\/[a-z,A-Z,\/,_\-]*$/
-    ? - :GET
-      - :POST
-    : - !ruby/regexp /http:\/\/ot\-dev\.in\-silico\.ch\/toxcreate/
-      - !ruby/regexp /http:\/\/ot\-dev\.in\-silico\.ch\/task/
-      - !ruby/regexp /http:\/\/ot\-dev\.in\-silico\.ch\/compound/
-
-    ? - :PUT
-    : - !ruby/regexp /http:\/\/ot\-dev\.in\-silico\.ch\/task/
-
-  :authorize_exceptions: #request-method for uri only authenticated, no authorization
-    ? - :POST
-    : - !ruby/regexp /http:\/\/ot\-dev\.in\-silico\.ch\/algorithm/
-      - "http://ot-dev.in-silico.ch/dataset"
-      - "http://ot-dev.in-silico.ch/model"
-      - "http://ot-dev.in-silico.ch/validation"
-      - !ruby/regexp /http\:\/\/ot-dev\.in\-silico\.ch\/validation\/[a-z,A-Z,\/,_\-]*$/
-