t2-server 0.0.3 → 0.0.4

data/README.rdoc

@@ -1,21 +1,50 @@
 = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
 
-Authors::    Robert Haines
-Version::    0.1
-Contact::    mailto:rhaines@manchester.ac.uk
-URL::        http://taverna.sourceforge.net/
-Licence::    BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
-Copyright::  (c) 2010 The University of Manchester, UK
+Authors::     Robert Haines
+Gem Version:: 0.0.4
+API Version:: 2.2a1
+Contact::     mailto:rhaines@manchester.ac.uk
+URL::         http://taverna.sourceforge.net/
+Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
+Copyright::   (c) 2010 The University of Manchester, UK
 
 
 == Synopsis
 
-This is a Ruby library to interface with the Taverna 2 Server REST interface.
+This is a Ruby library to interface with the Taverna 2 Server REST API.
 
 == Installation
 
-[sudo] gem install t2-server
+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:
+http://rubygems.org/gems/t2-server
+
+You can also download the source code from here:
+http://github.com/myGrid/t2-server-gem
 
 == Usage
 
-TBC
+As well as the library 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:
+* run_workflow
+* server_info
+* delete_all_runs
+Running any of these scripts with a <tt>-h</tt> or <tt>--help</tt>
+switch will show how to use them, e.g.:
+  run_workflow --help
+
+== 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/

data/bin/run_workflow

@@ -38,23 +38,17 @@ require 'optparse'
 # out or save them to a file.
 # if the output is a list, it appears as a directory so
 # all the individual entries must be grabbed from there.
-# server seems to be rather sensitive to slashes, hence
-# all the [...] mucking about.
 def get_outputs(run, pout, dir="")
   dirs, files = run.ls("out#{dir}")
   dirs.each {|d| get_outputs(run, pout, "#{dir}/#{d}")}
   files.each do |out|
     print "          #{dir}/#{out} -> "
-    if dir == ""
-      output_name = out
-    else
-      output_name = "#{dir[1..-1]}/#{out}"
-    end
-    data = run.get_output(output_name)
+    data = run.get_output("#{dir}/#{out}")
     if pout
       p data
     else
-      filename = output_name.gsub('/', '-')
+      # remove leading slash
+      filename = "#{dir[1..-1]}/#{out}".gsub('/', '-')
       File.open(filename, "w") do |file|
         file.syswrite(data)
       end

data/bin/server_info

@@ -0,0 +1,75 @@
+#!/usr/bin/env ruby
+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 't2server'
+require 'optparse'
+
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: server_info [options] server-address"
+  opt.separator ""
+  opt.separator "  Where server-address is the full URI of the server to"
+  opt.separator "  connect to, e.g.: http://example.com:8080/taverna"
+  opt.separator "  and [options] can be:"
+  opt.on_tail("-h", "-?", "--help", "Show this message") do
+    puts opt
+    exit
+  end
+  opt.on_tail("-v", "--version", "Show the version") do
+    puts "Taverna 2 Server Ruby Gem version: #{T2Server::GEM_VERSION}"
+    puts "Taverna 2 Server REST API version: #{T2Server::API_VERSION}"
+    exit
+  end
+end
+
+# parse options
+opts.parse!
+
+# read and check server address
+uri = ARGV.shift
+if uri == nil
+  puts opts
+  exit 1
+end
+
+# connect to server and output information
+server = T2Server::Server.connect(uri)
+print "     Server: #{uri}\n"
+print "  Run limit: #{server.run_limit}\n"
+runs = server.runs
+print "No. of runs: #{runs.length}\n"
+if runs.length > 0
+  print "   Run list: #{runs[0].uuid} - #{runs[0].expiry}\n"
+  runs[1..-1].each do |run|
+    print "             #{run.uuid} - #{run.expiry}\n"
+  end
+end

data/lib/t2server.rb

@@ -35,6 +35,6 @@ require 't2server/server'
 require 't2server/run'
 
 module T2Server
-  GEM_VERSION = "0.0.3"
-  API_VERSION = "2.2.0a1"
+  GEM_VERSION = "0.0.4"
+  API_VERSION = "2.2a1"
 end

data/lib/t2server/server.rb

@@ -51,7 +51,7 @@ module T2Server
       @port = uri.port
       @base_path = uri.path
       @rest_path = uri.path + "/rest"
-      @links = get_server_description
+      @links = parse_description(get_attribute(@rest_path))
       #@links.each {|key, val| puts "#{key}: #{val}"}
       
       # get max runs
@@ -81,7 +81,7 @@ module T2Server
     end
     
     def initialize_run(workflow)
-      request = Net::HTTP::Post.new("#{@links[:runs]}")
+      request = Net::HTTP::Post.new("#{@links[:runs]}".gsub("//", "/"))
       request.content_type = "application/xml"
       response = Net::HTTP.new(@host, @port).start do |http|
         http.request(request, Fragments::WORKFLOW % workflow)
@@ -111,7 +111,7 @@ module T2Server
     end
 
     def delete_run(uuid)
-      request = Net::HTTP::Delete.new("#{@links[:runs]}/#{uuid}")
+      request = Net::HTTP::Delete.new("#{@links[:runs]}/#{uuid}".gsub("//", "/"))
       response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
       
       case response
@@ -133,7 +133,7 @@ module T2Server
     end
     
     def set_run_input(run, input, value)
-      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}")
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}".gsub("//", "/"))
       request.content_type = "application/xml"
       response = Net::HTTP.new(@host, @port).start do |http|
         http.request(request, Fragments::RUNINPUTVALUE % value)
@@ -149,7 +149,7 @@ module T2Server
     end
 
     def set_run_input_file(run, input, filename)
-      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}")
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}".gsub("//", "/"))
       request.content_type = "application/xml"
       response = Net::HTTP.new(@host, @port).start do |http|
         http.request(request, Fragments::RUNINPUTFILE % filename)
@@ -165,7 +165,7 @@ module T2Server
     end
 
     def make_run_dir(uuid, root, dir)
-      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{root}")
+      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{root}".gsub("//", "/"))
       request.content_type = "application/xml"
       response = Net::HTTP.new(@host, @port).start do |http|
         http.request(request,  Fragments::MKDIR % dir)
@@ -189,7 +189,7 @@ module T2Server
     def upload_run_file(uuid, filename, location, rename)
       contents = Base64.encode64(IO.read(filename))
       rename = filename.split('/')[-1] if rename == ""
-      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{location}")
+      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{location}".gsub("//", "/"))
       request.content_type = "application/xml"
       response = Net::HTTP.new(@host, @port).start do |http|
         http.request(request,  Fragments::UPLOAD % [rename, contents])
@@ -211,7 +211,7 @@ module T2Server
     end
 
     def set_run_attribute(uuid, path, value)
-      request = Net::HTTP::Put.new("#{@links[:runs]}/#{uuid}/#{path}")
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{uuid}/#{path}".gsub("//", "/"))
       request.content_type = "text/plain"
       response = Net::HTTP.new(@host, @port).start {|http| http.request(request, value)}
       
@@ -231,9 +231,9 @@ module T2Server
       end
     end
     
-    protected
+    private
     def get_attribute(path)
-      request = Net::HTTP::Get.new(path)
+      request = Net::HTTP::Get.new(path.gsub("//", "/"))
       response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
       
       case response
@@ -241,19 +241,8 @@ module T2Server
         return response.body
       when Net::HTTPNotFound
         puts "Cannot find attribute #{path}."
-      else
-        response_error(response)
-      end
-    end
-    
-    private
-    def get_server_description
-      request = Net::HTTP::Get.new(@rest_path)
-      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
-      
-      case response
-      when Net::HTTPOK
-        parse_description(response.body)
+      when Net::HTTPForbidden
+        puts "Verboten!"
       else
         response_error(response)
       end
@@ -269,20 +258,6 @@ module T2Server
         :permlisteners => URI.parse(XPath.first(doc, "//nsr:permittedListeners", nsmap).attributes["href"]).path
       }
     end
-
-    def get_run_description(uuid)
-      request = Net::HTTP::Get.new("#{@links[:runs]}/#{uuid}")
-      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
-      
-      case response
-      when Net::HTTPOK
-        return response.body
-      when Net::HTTPNotFound
-        puts "Cannot find run #{uuid}."
-      else
-        response_error(response)
-      end
-    end
     
     def response_error(response)
       puts "Unnexpected response from Taverna Server!"
@@ -296,36 +271,29 @@ module T2Server
     end
     
     def get_runs
-      request = Net::HTTP::Get.new("#{@links[:runs]}")
-      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
-      
-      case response
-      when Net::HTTPOK  
-        doc = Document.new(response.body)
-        
-        # get list of run uuids
-        uuids = []
-        XPath.each(doc, "//nsr:run", Namespaces::MAP) do |run|
-          uuids << run.attributes["href"].split('/')[-1]
-        end
-                
-        # add new runs
-        uuids.each do |uuid|
-          if !@runs.has_key? uuid
-            description = get_run_description(uuid)
-            @runs[uuid] = Run.create(self, "", uuid)
-          end
-        end
-        
-        # clear out the expired runs
-        if @runs.length > @run_limit
-          @runs.delete_if {|key, val| !uuids.member? key}
+      run_list = get_attribute("#{@links[:runs]}")
+
+      doc = Document.new(run_list)
+
+      # get list of run uuids
+      uuids = []
+      XPath.each(doc, "//nsr:run", Namespaces::MAP) do |run|
+        uuids << run.attributes["href"].split('/')[-1]
+      end
+
+      # add new runs
+      uuids.each do |uuid|
+        if !@runs.has_key? uuid
+          @runs[uuid] = Run.create(self, "", uuid)
         end
+      end
 
-        @runs
-      else
-        response_error(response)
+      # clear out the expired runs
+      if @runs.length > @run_limit
+        @runs.delete_if {|key, val| !uuids.member? key}
       end
+
+      @runs
     end
   end  
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-server
 version: !ruby/object:Gem::Version 
-  hash: 25
+  hash: 23
   prerelease: false
   segments: 
   - 0
   - 0
-  - 3
-  version: 0.0.3
+  - 4
+  version: 0.0.4
 platform: ruby
 authors: 
 - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-07-26 00:00:00 +01:00
+date: 2010-07-30 00:00:00 +01:00
 default_executable: 
 dependencies: []
 
@@ -29,6 +29,7 @@ extra_rdoc_files:
 - README.rdoc
 - LICENCE
 files: 
+- bin/server_info
 - bin/run_workflow
 - bin/delete_all_runs
 - lib/t2server.rb