= Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem

Authors::     Robert Haines
Contact::     mailto:rhaines@manchester.ac.uk
URL::         http://www.taverna.org.uk/
Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
Copyright::   (c) 2010-2012 The University of Manchester, UK


== Synopsis

This is a Ruby library to interface with the Taverna 2 Server REST API.

== Installation

Ensure that gem itself is up to date:
  [sudo] gem update --system

Then simply install as you would any other gem:
  [sudo] gem install t2-server

In case of problems with the above the gem is available for download here:
https://rubygems.org/gems/t2-server

You can also download the source code from here:
https://github.com/myGrid/t2-server-gem

== Compatibility with Taverna Server versions

From version 0.9.0 this library is compatible with Taverna Server 2.3 onwards.
It is not compatible with any earlier version of Taverna Server due to breaking
changes in its REST interface. We strongly encourage all users to upgrade to
the current version of Taverna Server, but if that is not possible right now
then please continue to use version 0.6.1 of this library for the time being.

This version of the library should be compatible with any Ruby code that you
may have already written against earlier versions but you may see some warnings
about API deprecations. These are clearly marked [DEPRECATION] and will appear
on your console output. Anything marked as deprecated will be removed in
version 1.0.0 so you are advised to update your code at your earliest
convenience.

== Compatibility with Ruby versions

This library is known to work with the following versions of Ruby:
* 1.8.7 *
* 1.9.2
* 1.9.3 *
* jruby 1.6.4 (in Ruby 1.8 mode)

Those marked with an asterisk (*) are supported and bugs found against them
will be fixed. Other versions may work but are not supported.

== Usage

There are two entry points for the T2Server API:
* <tt>T2Server::Run</tt> - Use this for running single jobs on a server.
* <tt>T2Server::Server</tt> - Use this if you are providing a web interface to
  one or more Taverna 2 Server instances.

In both cases the gem should be initialized by requiring the top level ruby
file:
  require 't2-server.rb'

=== Configuring a Server connection

Setting up a connection to a secure server can be quite tricky and a secure
Taverna Server is no different. To make things slightly easier this library
provides some short cuts to providing various parameters for different types of
connection.

Connection configuration settings are passed in to various methods using the
+ConnectionParameters+ class. Parameters that can be set are:
* <tt>:ca_file</tt>
* <tt>:ca_path</tt>
* <tt>:verify_peer</tt>
* <tt>:client_certificate</tt>
* <tt>:client_password</tt>

And can be set like this for a standard https connection:

  conn_params = ConnectionParameters.new
  conn_params[:verify_peer] = true

This will ensure that the identity of the Taverna Server you are connecting to
will be verified using the set of certificates in <tt>/etc/ssl/certs</tt>.
<tt>:ca_path</tt> can also be set to a list of paths if required. You do not
need to include your platform's default certificate paths as these are included
automatically.

For convenience a number of standard sets of parameters have been defined. The
above example is available as +DefaultConnectionParameters+. Others available
are:
* +InsecureSSLConnectionParameters+ - to ignore SSL checks.
* +CustomCASSLConnectionParameters+ - for custom (self-signed) CAs.
* +ClientAuthSSLConnectionParameters+ - for client certificate authentication.

See the rdoc for more details on these classes.

=== Authenticating to a Taverna Server

Some calls to a server require that a set of user credentials are provided.
These are simple to set up:

  credentials = T2Server::HttpBasic.new("username", "password")

=== Server API example

The Server constructor can yield the newly created object. Simple supply a URI
and a set of connection parameters to connect to a server:

  T2Server::Server.new(uri, conn_params) do |server|
    ...
  end

Note that credentials are not required by default to simply connect to a
Taverna Server. Further operations (such as creating and starting runs) may
require authorization depending on how your server has been set up.

=== Run API example

You can bypass the Server API if you know you are only going to be dealing with
a couple of runs directly:

  T2Server::Run.create(uri, workflow, credentials, conn_params) do |run|
    ...
  end

Setting an input port to a run is very easy:

  run.input_port("port_name").value = 1
  run.input_port("port_name").value = "Hello!"
  run.input_port("port_name").value = ["list", "of", "values"]

Or you can use a local file as input:

  run.input_port("port_name").file = filename

Once all the inputs have been set the run can be started:

  run.start

And monitored to see if it has finished:

  run.finished?
  run.running?

Or just wait until the run has finished:

  run.wait

Then the outputs can be collected:

  result = run.output_port("port_name").value

If you have a lot of output you can grab the whole lot as a zip file:

  zip_data = run.zip_output

Using baclava documents for setting inputs and collecting outputs is also
supported:

  run.baclava_input = filename

But make sure you request baclava output *before* starting the run:

  run.request_baclava_output
  run.start
  run.wait
  output = run.baclava_output

See the rdoc for more information. Many methods and classes have much more
functionality than the defaults described above. Please note that anything
which does not appear in the documentation is not intended to be part of the
public API. Use of undocumented classes and methods is entirely at your own
risk! Such things might not have consistent behaviour and might be removed at
any time.

=== Example scripts

As well as rdoc there are also a couple of example scripts which
demonstrate good use of the T2Server API. These are available in the
<tt>bin</tt> directory but are also installed with the library code when the
gem is installed:
* t2-run-workflow
* t2-server-info
* t2-delete-runs
* t2-get-output
* t2-server-admin
Running any of these scripts with a <tt>-h</tt> or <tt>--help</tt>
switch will show how to use them, e.g.:
  t2-run-workflow --help

== Interacting with secure Web Services

This library can be used to run workflows that contain secure
services. Such services may be secured in a number of ways depending
on how the credentials are passed and whether they are REST, SOAP or Rshell
services.

Running workflows that contain secure services requires that you pass
your credentials to Taverna Server so that it can authenticate itself
as you on your behalf.

<b>It is essential that you trust the Taverna Server that you are
using!</b>

<b>Ideally, you should only pass sensitive information, such as
passwords, via https so that you can be sure that it is not being read
in transit.</b>

=== Username and password credentials
==== REST

REST services are commonly secured via HTTP Basic or HTTP Digest
authentication and Taverna treats these two schemes in the same
way. Simply pass in your username and password with the *host* name of
the server on which the service is running:

 run.add_password_credential("https://example.com:8443/", "username", "password")

The above example shows a https server running on port 8443. If the
service is on port 80 for http or port 443 for https then you don't
need to specify the port.

If there are services on the same host that require different credentials then
you will need to specify the realm for which each set of credentials applies.
This is done by adding the name of the realm to the end of the host name with
a # separating them:

 run.add_password_credential("https://example.com:8443/#realm", "username", "password")

==== SOAP

SOAP services are commonly secured via WS-Security. Simply pass in the
WSDL address of the service with your username and password:

 run.add_password_credential("https://example.com:8443/services/MyService?wsdl", "username", "password")

==== R Servers (via Rshells)

You can authenticate to R Servers in almost exactly the same as for
REST services - only the protocol scheme is different. So instead of
http or https it is rserve:

 run.add_password_credential("rserve://example.com:6311", "username", "password")

=== Keypair (certificate-based) credentials

Some https servers authenticate clients using certificates. If you
have services that require this type of authentication you can upload
a keypair:

 run.add_keypair_credential("https://example.com:8443/", "certificate.p12", "password")

=== Trusts (peer verification)

If the services in your workflows are on a https server then Taverna
requires that it can verify that the server is the one you expect it
to be. This is done by peer verification. In most cases this happens
automatically and transparently but if the remote server has a
non-standard or "self-signed" certificate then you will need to
provide Taverna with the corresponding public key for verification to
take place:

 run.add_trust("public-key.pem")

== Interacting with other Taverna Server users

Taverna Server is a multi-user system and as such insulates users from one
another as much as possible. Each run that a user creates can only be accessed
by that user by default. If you want to give another user permission to
perform certain actions on a run then you can do so:

 run.grant_permission("username", :permission)

Available permissions are:
* <tt>:none</tt> - No permissions.
* <tt>:read</tt> - Read the state of the run and get its outputs.
* <tt>:update</tt> - Set the state of the run (e.g. start it).
* <tt>:destroy</tt> - Delete the run.

Permissions are accumulative so giving a user the <tt>:destroy</tt> permission
also allows that user to read and set the run's state. Note that there is no
way for any user other than the owner of a run to perform any security related
actions on it. This means that only the owner may grant, query and revoke
permissions and only the owner may add, query and delete trusts and
credentials.

You can revoke a user's permission:

 run.revoke_permission("username")

You can get a list of the permissions you have granted for a run:

 run.permissions

And also see what permission you have granted a particular user:

 run.permission("username")

== Support

Please email mailto:support@mygrid.org.uk for any questions relating to
this Ruby gem.

== References

Taverna 2 Server::       http://www.taverna.org.uk/documentation/taverna-2-x/server/
REST API Documentation:: http://www.taverna.org.uk/documentation/taverna-2-x/server/rest-api/