From 6b49cf9bbef88b7dbdaf60c2aca67c0e9c6519ee Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 26 Aug 2014 14:14:53 +0200 Subject: Update 2012-08-09-install-opentox-development-environment.md Added validation to service install --- _posts/2012-08-09-install-opentox-development-environment.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md index 02946bb..27d8725 100644 --- a/_posts/2012-08-09-install-opentox-development-environment.md +++ b/_posts/2012-08-09-install-opentox-development-environment.md @@ -81,7 +81,7 @@ 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 + for f in algorithm compound dataset feature model validation task opentox-test; do git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f cd $OT_PREFIX/$f git checkout development 2>/dev/null -- cgit v1.2.3 From 06f8152b265073a906e33e7fdea71e14e761d8c2 Mon Sep 17 00:00:00 2001 From: dv Date: Tue, 26 Aug 2014 17:21:46 +0200 Subject: Updated opentox install article. Tested with Debian 7.6. --- ...8-09-install-opentox-development-environment.md | 27 +++++++++++++--------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md index 27d8725..a2da3d3 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. 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 @@ -82,7 +86,7 @@ Download and install opentox-client and opentox-server: Download and install services and tests: for f in algorithm compound dataset feature model validation task opentox-test; 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 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`. -- cgit v1.2.3 From 3e187c4be0a68bbd49f5f692e51fe13f40a64a68 Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 26 Aug 2014 17:26:01 +0200 Subject: Update 2012-08-09-install-opentox-development-environment.md --- _posts/2012-08-09-install-opentox-development-environment.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md index a2da3d3..12d9860 100644 --- a/_posts/2012-08-09-install-opentox-development-environment.md +++ b/_posts/2012-08-09-install-opentox-development-environment.md @@ -38,7 +38,7 @@ Conceptual approach: # Installation -Installation (`development` at the point of writing this = 08/2014) tested with Debian 7.6 (wheezy), kernel 3.2.0-4-amd64. 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: -- cgit v1.2.3 From 8cdb874bbed18571cd13476d013e46c4eaeb5972 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Wed, 5 Nov 2014 11:46:09 +0100 Subject: add validation service A&A description --- ...tication-configuration-opentox-serverclient--300.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) 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..a22c221 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 @@ -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 + `"#{$dataset[:uri]}/test/error_in_task"` defines a URI used in a test call. + + +Configuration-file example for Validation service +---- +Example A&A configuration for the validation service. Configuration-file is **/home/USERNAME/.opentox/config/validation.rb** + +Mind the `/#{Regexp.quote($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($validation[:uri])}\/[a-z,A-Z,\/,_\-]*$/, $task[:uri]]} + } -- cgit v1.2.3 From 772a2c2c814b641498600b8405453fba186c8938 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Wed, 5 Nov 2014 11:47:39 +0100 Subject: add validation service A&A description --- ...ation--authentication-configuration-opentox-serverclient--300.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md b/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md index a22c221..f5eee46 100644 --- a/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md +++ b/_posts/2013-05-03-authorization--authentication-configuration-opentox-serverclient--300.md @@ -14,7 +14,7 @@ A&A How it works [Description](/Installation/2012/09/03/authorization--authentication-flow-and-configuration/) see paragraphs **A&A How it works** and **A&A Flow opentox-ruby gem** for Versions below 3.0.0 . -Configuration-file example +Configuration Example ---- Example A&A configuration for the dataset service. Configuration-file is **/home/USERNAME/.opentox/config/dataset.rb** @@ -27,7 +27,7 @@ Example A&A configuration for the dataset service. Configuration-file is **/home :authorize_exceptions => { [:GET,:POST] => [$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. @@ -39,7 +39,7 @@ Configuration options `"#{$dataset[:uri]}/test/error_in_task"` defines a URI used in a test call. -Configuration-file example for Validation service +Configuration for Validation Service ---- Example A&A configuration for the validation service. Configuration-file is **/home/USERNAME/.opentox/config/validation.rb** -- cgit v1.2.3