Merge branch 'master' of github.com:/opentox/opentox.github.com

2 files changed, 36 insertions, 15 deletions

diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md
index 02946bb..12d9860 100644
--- a/_posts/2012-08-09-install-opentox-development-environment.md
+++ b/_posts/2012-08-09-install-opentox-development-environment.md
@@ -38,16 +38,16 @@ Conceptual approach:
 
 # Installation
 
-Installation (`development` at the point of writing this = 08/2012) tested with Debian 6.0.5 and Ubuntu 11.04. Installer available at [github](https://github.com/opentox/install).
+Installation (`development` at the point of writing this = 08/2014) tested with Debian 7.6 (wheezy), kernel 3.2.0-4-amd64, GNOME 3.4.2. Installer available at [github](https://github.com/opentox/install).
 
 Check you can run "sudo" commands (e.g. `sudo ls`), which is required for base packages. Install git:
 
     # Install git
     sudo apt-get install git 
 
-Add your public key at `https://github.com`. Download, configure and execute the installer:
+Download, configure and execute the installer (You might add your public key at `https://github.com`):
 
-    git clone git@github.com:opentox/install.git $HOME/install
+    git clone "https://github.com/opentox/install.git" $HOME/install
     cd $HOME/install
     git checkout development
     # First check config.sh with your favorite editor
@@ -57,6 +57,10 @@ This will prepare the system for opentox web services, including dependencies.
 
 # Install OpenTox services
 
+You can run the following steps with a script:
+
+    bash $HOME/install/service_install.sh
+
 Load environment (general):
 
     . $HOME/.opentox/config/install/config.sh
@@ -70,7 +74,7 @@ Load environment (with BASH):
 Download and install opentox-client and opentox-server:
     
     for f in opentox-client opentox-server; do 
-      git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
+      git clone "https://github.com/opentox/$f.git" $OT_PREFIX/$f
       cd $OT_PREFIX/$f
       git checkout development 2>/dev/null
     done 
@@ -81,8 +85,8 @@ Download and install opentox-client and opentox-server:
 
 Download and install services and tests:
 
-    for f in algorithm compound dataset feature model task opentox-test; do
-      git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
+    for f in algorithm compound dataset feature model validation task opentox-test; do
+      git clone "https://github.com/opentox/$f.git" $OT_PREFIX/$f
       cd $OT_PREFIX/$f
       git checkout development 2>/dev/null
       if [ -f $OT_PREFIX/$f/bin/$f-install ]; then
@@ -104,9 +108,9 @@ Add ot-tools to your `.bashrc`:
     echo '. $HOME/.opentox/ot-tools.sh' >> ~/.bashrc
     # source .bashrc or restart shell
 
-All ot-tools (`otconfig`, `otstart`, `otcheck`, `otreload`, `otkill`) are available in your shell. General usage: 
+All ot-tools (`otconfig`, `ottail`, `otless`, `otstart`, `otkill`, `otupdate_repo`) are available in your shell. General usage: 
 
-    [otstart|otcheck|otreload|otkill] [all|algorithm|compound|dataset|feature|
+    [otstart|otkill|otupdate_repo] [all|algorithm|compound|dataset|feature|
     model|task|validation|4store]
 
 `otconfig` is the only command not taking an argument. It sets the environment variables for all services. 
@@ -143,13 +147,14 @@ NOTE: Only installed service URIs are set in the config files. Model and validat
 
     cd $OT_PREFIX/opentox-test
     otconfig
-    ruby opentox-client.rb
-    ruby test/dataset-large.rb
+    ruby opentox-client-short.rb
+    # Or a longer test script
+    ruby opentox-client-all.rb
 
 
 The tests take some time and finish with a short report:
 
-    Finished tests in 44.690815s, 0.9622 tests/s, 4.4528 assertions/s.
-    43 tests, 199 assertions, 1 failures, 0 errors, 0 skips
+    Finished tests in 375.726618s, 0.2741 runs/s, 14.1193 assertions/s.
+    103 tests, 5305 assertions, 0 failures, 1 errors, 0 skips
 
 To test one specific service, run its script (`ruby [service_name].rb`) in `$OT_PREFIX/opentox-test/test`.
diff --git a/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md b/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md
index 2a9fa0f..f5eee46 100644
--- a/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md
+++ b/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md
@@ -14,7 +14,7 @@ A&A How it works
 [Description](/Installation/2012/09/03/authorization--authentication-flow-and-configuration/) see paragraphs **A&A How it works** and **A&A Flow opentox-ruby gem** for Versions below 3.0.0 .
 
 
-Configuration-file example
+Configuration Example
 ----
 Example A&A configuration for the dataset service. Configuration-file is **/home/USERNAME/.opentox/config/dataset.rb**  
 
@@ -27,7 +27,7 @@ Example A&A configuration for the dataset service. Configuration-file is **/home
       :authorize_exceptions => { [:GET,:POST] => [$dataset[:uri], "#{$dataset[:uri]}/test/task_error", "#{$dataset[:uri]}/test/error_in_task"] }
     }
 
-Configuration options
+Configuration Options
 ----
 * `$dataset = { :uri => "https://myserver.org/dataset" }` sets the URI to the dataset service itself.
 * `$aa = { :uri => nil }` turns A&A off.
@@ -36,4 +36,20 @@ Configuration options
 * `:authenticate_request => []` request methods that needs only Authentification. Request must have a valid subjectid, but no policy.
 * `:authorize_request => [:GET, :POST, :DELETE, :PUT]` request methods with authorization controll
 * `:authorize_exceptions => { [:GET,:POST] => [$dataset[:uri], "#{$dataset[:uri]}/test/task_error", "#{$dataset[:uri]}/test/error_in_task"] }` authorization exceptions defined as a Hash of request-methods-array keys mapped to URI-array values. In this case you are allowed to GET and POST to the base service URI to get a list of datasets or to POST a new dataset.
-  `"#{$dataset[:uri]}/test/error_in_task"` defines a URI used in a test call. 
\ No newline at end of file
+  `"#{$dataset[:uri]}/test/error_in_task"` defines a URI used in a test call.
+
+
+Configuration for Validation Service
+----
+Example A&A configuration for the validation service. Configuration-file is **/home/USERNAME/.opentox/config/validation.rb**
+
+Mind the `/#{Regexp.quote($validation[:uri])}\/[a-z,A-Z,\/,_\-]*$/`  entry in authorize exceptions to let authenticated users the possibility to create crossvalidations, reports and other objects under `/validation/` directory.
+
+    $validation = { :uri => "https://myserver.org/validation" }
+    $aa = {
+      :uri => 'https://opensso.in-silico.ch',
+      :free_request => [:HEAD],
+      :authenticate_request => [],
+      :authorize_request => [:GET, :POST, :DELETE, :PUT],
+      :authorize_exceptions => {[:GET,:POST] => [$validation[:uri], /#{Regexp.quote($validation[:uri])}\/[a-z,A-Z,\/,_\-]*$/, $task[:uri]]}
+    }