t2-server 1.1.0 → 1.2.0

checksums.yaml

@@ -0,0 +1,15 @@
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+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
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+  data.tar.gz: !binary |-
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+SHA512:
+  metadata.gz: !binary |-
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+  data.tar.gz: !binary |-
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+    Yzk2MmE0YjVjZDAzMjc3ZGQyNjNkNzViNDNhODMxZTI1ODcxNDM=

data/.gitignore

@@ -1,6 +1,7 @@
 *~
 pkg/
 html/
+coverage/
 .buildpath
 .project
 .idea

data/.ruby-env

@@ -0,0 +1 @@
+RUBYLIB=./lib:../lib

data/.ruby-gemset

@@ -0,0 +1 @@
+t2-server

data/.ruby-version

@@ -0,0 +1 @@
+ruby-1.9.3-p484

data/.travis.yml

@@ -3,4 +3,10 @@ cache: bundler
 rvm:
   - 1.9.3
   - 2.0.0
-  - 2.1.0
+  - 2.1.2
+  - rbx-2
+  - ruby-head
+matrix:
+  allow_failures:
+    - rvm: rbx-2
+    - rvm: ruby-head

data/CHANGES.rdoc

@@ -1,5 +1,54 @@
 = Changes log for the T2 Ruby Gem
 
+== Version 1.2.0
+
+* Test provenance collection on version 2.5.4 and up only.
+* Only run tests against a live server if an address is supplied.
+* Add a test case to test the connection factory.
+* Set up mocking of Net::HTTP and mock creation of a run.
+* Mock testing server run limits and deleting all runs.
+* Add Coveralls integration to the tests.
+* Add tests for the credentials classes.
+* Add a simple check for parsing the server version.
+* Test a full run of a workflow.
+* Fix the parameters classes with initial parameters.
+* Test custom CA connection parameters.
+* Test a network timeout.
+* Catch Net::HTTP::Persistent::Error internally.
+* Net::HTTP::Persistent::Error is now wrapped internally.
+* Remove the unused RunNotFoundError.
+* Fix documentation for Run#upload_data.
+* Set minimum ruby version to be 1.9.3 in the spec.
+* Modernize the installation instructions.
+* Remove the unused workflow upload XML fragment.
+* Add XML generation methods for server messages.
+* Programmatic generation of mkdir server message.
+* Programmatic generation of the upload server message.
+* Streamline XML node generation methods.
+* Programmatically generate input server messages.
+* Generate permissions server message fragment.
+* Generate trusts server message fragment.
+* Generate credentials server messages.
+* Streamline the generation of hierarchical XML nodes.
+* Setup tests for the XML messages sent to server.
+* Factor out the common help and version CLI options.
+* Factor out the different SSL config options for HTTPS connections.
+* Neaten up the code to get a run's resource links.
+* Fix typo in Run#grant_permission.
+* Add a parse method to the credentials objects.
+* Found a way to better test the credentials objects.
+* Fix up the test suite driver code.
+* Update the public key of the secure remote services.
+* Update the client certificate for secure remote services.
+* Stop using a pre-cooked server reply for Run#status.
+* Only download a range of bytes if requested for outputs.
+* Streamline the OutputPort methods for getting data.
+* Remove unused private method (path) from OutputPort.
+* Factor out I/O Port processing.
+* Cache a run's finished state when it has finished.
+* Fix the client authentication connection settings.
+* Test InputPort and OutputPort.
+
 == Version 1.1.0
 
 * Remove hirb as a runtime dependency.

data/README.rdoc

@@ -6,9 +6,10 @@ URL::         http://www.taverna.org.uk/
 Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
 Copyright::   (c) 2010-2014 The University of Manchester, UK
 
-{<img src="https://badge.fury.io/rb/t2-server.png" alt="Gem Version" />}[http://badge.fury.io/rb/t2-server]
-{<img src="https://codeclimate.com/github/myGrid/t2-server-gem.png" />}[https://codeclimate.com/github/myGrid/t2-server-gem]
+{<img src="https://badge.fury.io/rb/t2-server.svg" alt="Gem Version" />}[http://badge.fury.io/rb/t2-server]
+{<img src="https://codeclimate.com/github/myGrid/t2-server-gem/badges/gpa.svg" />}[https://codeclimate.com/github/myGrid/t2-server-gem]
 {<img src="https://travis-ci.org/myGrid/t2-server-gem.svg?branch=master" alt="Build Status" />}[https://travis-ci.org/myGrid/t2-server-gem]
+{<img src="https://coveralls.io/repos/myGrid/t2-server-gem/badge.png?branch=master" alt="Coverage Status" />}[https://coveralls.io/r/myGrid/t2-server-gem?branch=master]
 
 == Synopsis
 
@@ -16,12 +17,13 @@ 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:
+Simply install as you would any other gem:
   [sudo] gem install t2-server
 
+Or use {Bundler}[http://bundler.io/], with
+  gem 't2-server', '~> 1.0'
+in your +Gemfile+, for example.
+
 In case of problems with the above the gem is available for download here:
 https://rubygems.org/gems/t2-server
 
@@ -57,10 +59,10 @@ version pairings:
 === Ruby
 
 This library is known to work with the following versions of Ruby:
-* 1.9.2
 * 1.9.3 +*
 * 2.0.0 +*
-* 2.1.0 +
+* 2.1.2 +*
+* rbx 2.2 +
 
 Those marked with an asterisk (*) are fully supported and bugs found against
 them will be fixed. Other versions may work but are not tested or supported.

data/bin/t2-delete-runs

@@ -88,9 +88,6 @@ for run in server_runs
         run.delete
       end
     end
-  rescue T2Server::RunNotFoundError => rnf
-    puts "Run '#{run.id}' not found - skipping."
-    next
   rescue T2Server::AuthorizationError => ae
     puts "You are not authorized to delete run '#{run.id}' - skipping."
     next

data/lib/t2-server-cli.rb

@@ -53,7 +53,7 @@ module T2Server
         ssl_auth_opts(opt, conn_params)
         ssl_transport_opts(opt, conn_params)
 
-        # common options
+        # Simple credential options
         opt.on_tail("-u", "--username=USERNAME", "The username to use for " +
           "server operations.") do |val|
             user = val.chomp
@@ -62,14 +62,9 @@ module T2Server
           "the supplied username.") do |val|
             pass = val.chomp
         end
-        opt.on_tail("-h", "-?", "--help", "Show this help message.") do
-          puts opt
-          exit
-        end
-        opt.on_tail("-v", "--version", "Show the version.") do
-          puts "Taverna 2 Server Ruby Gem version: #{T2Server::Version::STRING}"
-          exit
-        end
+
+        # Common options
+        common_opts(opt)
       end
 
       # parse options
@@ -96,6 +91,18 @@ module T2Server
 
     private
 
+    # The help and version options.
+    def common_opts(opt)
+      opt.on_tail("-h", "-?", "--help", "Show this help message.") do
+        puts opt
+        exit
+      end
+      opt.on_tail("-v", "--version", "Show the version.") do
+        puts "Taverna 2 Server Ruby Gem version: #{T2Server::Version::STRING}"
+        exit
+      end
+    end
+
     # The SSL authentication and peer verification options.
     def ssl_auth_opts(opt, conn_params)
       opt.on("-E CERT_FILE:PASSWORD", "--cert=CERT_FILE:PASSWORD", "Use " +

data/lib/t2-server/exceptions.rb

@@ -30,7 +30,7 @@
 #
 # Author: Robert Haines
 
-require 'net/http'
+require 'net/http/persistent'
 
 module T2Server
   # :stopdoc:
@@ -41,8 +41,10 @@ module T2Server
   module InternalHTTPError
   end
 
-  # These are the HTTP errors we want to catch.
-  # Add the above exception as an ancestor to them all.
+  # These are the HTTP errors we want to catch. Add the above exception as an
+  # ancestor to them all. Some are caught by Net::HTTP::Persistent and
+  # re-raised as a Net::HTTP::Persistent::Error but keep them listed here just
+  # in case.
   [
     EOFError,
     SocketError,
@@ -53,7 +55,8 @@ module T2Server
     Errno::ECONNREFUSED,
     Net::HTTPBadResponse,
     Net::HTTPHeaderSyntaxError,
-    Net::ProtocolError
+    Net::ProtocolError,
+    Net::HTTP::Persistent::Error
   ].each {|err| err.send(:include, InternalHTTPError)}
 
   # :startdoc:
@@ -112,21 +115,6 @@ module T2Server
     end
   end
 
-  # Raised when the run that is being operated on cannot be found. If the
-  # expectation is that the run exists then it could have been destroyed by
-  # a timeout or another user.
-  class RunNotFoundError < T2ServerError
-
-    # The identifier of the run that was not found on the server.
-    attr_reader :identifier
-
-    # Create a new RunNotFoundError with the specified identifier.
-    def initialize(id)
-      @identifier = id
-      super "Could not find run #{@identifier}"
-    end
-  end
-
   # Indicates that the attribute that the user is trying to read/change does
   # not exist. The attribute could be a server or run attribute.
   class AttributeNotFoundError < T2ServerError

data/lib/t2-server/net/connection.rb

@@ -306,7 +306,13 @@ module T2Server
         @http.ssl_version = @params[:ssl_version]
       end
 
-      # Peer verification
+      set_peer_verification
+      set_client_authentication
+    end
+
+    private
+
+    def set_peer_verification
       if @params[:verify_peer]
         if @params[:ca_file]
           @http.ca_file = @params[:ca_file]
@@ -328,14 +334,16 @@ module T2Server
       else
         @http.verify_mode = OpenSSL::SSL::VERIFY_NONE
       end
+    end
 
-      # Client authentication
+    def set_client_authentication
       if @params[:client_certificate]
-        pem = File.read(@params[:client_certificate])
-        @http.certificate = OpenSSL::X509::Certificate.new(pem)
-        @http.private_key = OpenSSL::PKey::RSA.new(pem,
-          @params[:client_password])
+        cert = File.read(@params[:client_certificate])
+        pkcs12 = OpenSSL::PKCS12.new(cert, @params[:client_password])
+        @http.certificate = pkcs12.certificate
+        @http.private_key = pkcs12.key
       end
     end
+
   end
 end

data/lib/t2-server/net/credentials.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2012 The University of Manchester, UK.
+# Copyright (c) 2010-2014 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -52,6 +52,17 @@ module T2Server
     end
     # :startdoc:
 
+    # :call-seq:
+    #   parse(userinfo) -> Credentials
+    #
+    # Parse a typical userinfo style string, such as "username:password", into
+    # a credentials object. In this case the credentials would have a username
+    # of "username" and a password of "password".
+    def self.parse(userinfo)
+      user, pass = userinfo.split(':', 2)
+      new(user, pass)
+    end
+
     # :call-seq:
     #   to_s -> string
     #

data/lib/t2-server/net/parameters.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2012 The University of Manchester, UK.
+# Copyright (c) 2010-2014 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -122,7 +122,7 @@ module T2Server
     # _path_ can either be a directory where the required certificate is stored
     # or the path to the certificate file itself.
     def initialize(path)
-      super
+      super()
 
       case path
       when String
@@ -147,7 +147,7 @@ module T2Server
     # encrypted. If _password_ is not specified, but needed, then the
     # underlying SSL implementation may ask for it if it can.
     def initialize(cert, password = nil)
-      super
+      super()
 
       case cert
       when String

data/lib/t2-server/port.rb

@@ -231,14 +231,9 @@ module T2Server
     #   run.output_port("port_name")[0].value(0..100)
     def value(range = nil, &block)
       if depth == 0
-        if range.nil?
-          @structure.value(&block)
-        else
-          @structure.value(range, &block)
-        end
+        @structure.value(range, &block)
       else
-        @values = strip(:value) if @values.nil?
-        @values
+        @values ||= strip(:value)
       end
     end
 
@@ -261,11 +256,7 @@ module T2Server
         "Stream passed in must provide a write method" unless
           stream.respond_to? :write
 
-      if range.nil?
-        @structure.stream_value(stream)
-      else
-        @structure.stream_value(stream, range)
-      end
+      @structure.stream_value(stream, range)
     end
 
     # :call-seq:
@@ -282,11 +273,7 @@ module T2Server
     def write_value_to_file(filename, range = nil)
       return 0 unless depth == 0
 
-      if range.nil?
-        @structure.write_value_to_file(filename)
-      else
-        @structure.write_value_to_file(filename, range)
-      end
+      @structure.write_value_to_file(filename, range)
     end
 
     # :call-seq:
@@ -407,12 +394,6 @@ module T2Server
       end
     end
 
-    # Generate the path to the actual data for a data value.
-    def path(ref)
-      parts = ref.split('/')
-      @depth == 0 ? parts[-1] : "/" + parts[-(@depth + 1)..-1].join('/')
-    end
-
     # Strip the requested attribute from the raw values structure.
     def strip(attribute, struct = @structure)
       if struct.instance_of? Array
@@ -477,22 +458,24 @@ module T2Server
     # This method does not cache any data.
     #
     # If this port is an error then this value will be the error message.
-    def value(range = 0...@size, &block)
+    def value(range = nil, &block)
       # The following block is a workaround for Taverna Server versions prior
       # to 2.4.1 and can be removed when support for those versions is no
       # longer required.
       if error? && @size == 0
         value = @port.download(@reference)
         @size = value.size
-        range = 0...@size if range.min.nil?
+        range = 0...@size if range.nil? || range.min.nil?
         return value[range]
       end
 
       return "" if @type == EMPTY_TYPE
 
       # Check that the range provided is sensible
-      range = 0..range.max if range.min < 0
-      range = range.min...@size if range.max >= @size
+      unless range.nil?
+        range = 0..range.max if range.min < 0
+        range = range.min...@size if range.max >= @size
+      end
 
       @port.download(@reference, range, &block)
     end
@@ -506,7 +489,7 @@ module T2Server
     # File, for example. No data is cached by this method.
     #
     # The number of bytes written to the stream is returned.
-    def stream_value(stream, range = 0...@size)
+    def stream_value(stream, range = nil)
       raise ArgumentError,
         "Stream passed in must provide a write method" unless
           stream.respond_to? :write
@@ -527,7 +510,7 @@ module T2Server
     # Stream this port value directly to a file. If a range is supplied then
     # just that range of data is downloaded from the server. No data is cached
     # by this method.
-    def write_value_to_file(filename, range = 0...@size)
+    def write_value_to_file(filename, range = nil)
       File.open(filename, "wb") do |file|
         stream_value(file, range)
       end

data/lib/t2-server/run.rb

@@ -115,6 +115,9 @@ module T2Server
 
       @credentials = credentials
 
+      # Has this Run finished executing on the server?
+      @finished = false
+
       # Has this Run object been deleted from the server?
       @deleted = false
 
@@ -320,7 +323,13 @@ module T2Server
     # :running or :finished.
     def status
       return :deleted if @deleted
-      Status.to_sym(@server.read(links[:status], "text/plain", @credentials))
+      return :finished if @finished
+
+      state = Status.to_sym(@server.read(links[:status], "text/plain",
+        @credentials))
+
+      @finished = (state == :finished)
+      state
     end
 
     # :call-seq:
@@ -441,11 +450,14 @@ module T2Server
     end
 
     # :call-seq:
-    #   upload_data(data, remote_name, remote_directory = "") -> true or false
+    #   upload_data(data, remote_name, remote_directory = "") -> URI
     #
     # Upload data to the server and store it in <tt>remote_file</tt>. The
     # remote directory to put this file in can also be specified, but if it is
     # it must first have been created by a call to Run#mkdir.
+    #
+    # Returns the URI of the file on the server in which the data has been
+    # stored.
     def upload_data(data, remote_name, remote_directory = "")
       location_uri = Util.append_to_uri_path(links[:wdir], remote_directory)
       @server.upload_data(data, remote_name, location_uri, @credentials)
@@ -730,7 +742,7 @@ module T2Server
     def grant_permission(username, permission)
       return unless owner?
 
-      value = XML::Fragments::PERM_UPDATE % [username, permission.to_s]
+      value = xml_permissions_fragment(username, permission.to_s)
       @server.create(links[:sec_perms], value, "application/xml", @credentials)
     end
 
@@ -797,8 +809,7 @@ module T2Server
       # basic uri checks
       uri = _check_cred_uri(uri)
 
-      cred = XML::Fragments::USERPASS_CRED % [uri, username, password]
-      value = XML::Fragments::CREDENTIAL % cred
+      value = xml_password_cred_fragment(uri, username, password)
 
       if cred_uri.nil?
         @server.create(links[:sec_creds], value, "application/xml",
@@ -829,9 +840,7 @@ module T2Server
       # basic uri checks
       uri = _check_cred_uri(uri)
 
-      cred = XML::Fragments::KEYPAIR_CRED % [uri, name, contents,
-        type, password]
-      value = XML::Fragments::CREDENTIAL % cred
+      value = xml_keypair_cred_fragment(uri, name, contents, type, password)
 
       @server.create(links[:sec_creds], value, "application/xml", @credentials)
     end
@@ -908,7 +917,7 @@ module T2Server
 
       contents = Base64.encode64(IO.read(filename))
 
-      value = XML::Fragments::TRUST % [contents, type]
+      value = xml_trust_fragment(contents, type)
       @server.create(links[:sec_trusts], value, "application/xml", @credentials)
     end
 
@@ -1060,9 +1069,9 @@ module T2Server
           # use a remote file.
           port.remote_file = upload_file(port.file) unless port.remote_file?
 
-          xml_value = XML::Fragments::RUNINPUTFILE % xml_text_node(port.file)
+          xml_value = xml_input_fragment(port.file, :file)
         else
-          xml_value = XML::Fragments::RUNINPUTVALUE % xml_text_node(port.value)
+          xml_value = xml_input_fragment(port.value)
         end
 
         @server.update(uri, xml_value, "application/xml", @credentials)
@@ -1112,33 +1121,35 @@ module T2Server
     end
 
     def _get_input_port_info
-      ports = {}
       port_desc = @server.read(links[:inputexp], "application/xml",
         @credentials)
 
       doc = xml_document(port_desc)
 
-      xpath_find(doc, @@xpaths[:port_in]).each do |inp|
-        port = InputPort.new(self, inp)
-        ports[port.name] = port
-      end
-
-      ports
+      _get_port_info(doc, :port_in)
     end
 
     def _get_output_port_info
-      ports = {}
-
       begin
         port_desc = @server.read(links[:output], "application/xml", @credentials)
       rescue AttributeNotFoundError => anfe
-        return ports
+        return {}
       end
 
       doc = xml_document(port_desc)
 
-      xpath_find(doc, @@xpaths[:port_out]).each do |out|
-        port = OutputPort.new(self, out)
+      _get_port_info(doc, :port_out)
+    end
+
+    def _get_port_info(doc, type)
+      ports = {}
+
+      xpath_find(doc, @@xpaths[type]).each do |desc|
+        port = if type == :port_out
+                 OutputPort.new(self, desc)
+               else
+                 InputPort.new(self, desc)
+               end
         ports[port.name] = port
       end
 
@@ -1177,20 +1188,12 @@ module T2Server
 
       links.merge! get_uris_from_doc(doc, [:baclava, :inputexp])
 
-      # set io properties
-      links[:io]       = Util.append_to_uri_path(links[:listeners], "io")
-      [:stdout, :stderr, :exitcode].each do |res|
-        links[res] = Util.append_to_uri_path(links[:io], "properties/#{res}")
-      end
+      # IO properties links
+      _get_io_properties_links(links)
 
-      # security properties - only available to the owner of a run
+      # Security properties links - only available to the owner of a run
       if owner?
-        securectx = @server.read(links[:securectx], "application/xml",
-          @credentials)
-        doc = xml_document(securectx)
-
-        links.merge! get_uris_from_doc(doc,
-          [:sec_creds, :sec_perms, :sec_trusts])
+        _get_security_links(links)
       end
 
       links
@@ -1209,6 +1212,22 @@ module T2Server
       end
     end
 
+    def _get_io_properties_links(links)
+      links[:io] = Util.append_to_uri_path(links[:listeners], "io")
+      [:stdout, :stderr, :exitcode].each do |res|
+        links[res] = Util.append_to_uri_path(links[:io], "properties/#{res}")
+      end
+    end
+
+    def _get_security_links(links)
+      securectx = @server.read(links[:securectx], "application/xml",
+        @credentials)
+      doc = xml_document(securectx)
+
+      links.merge! get_uris_from_doc(doc,
+        [:sec_creds, :sec_perms, :sec_trusts])
+    end
+
     def download_or_stream(param, uri, type, &block)
       if param.respond_to? :write
         @server.read_to_stream(param, uri, type, @credentials)