taverna-player 0.1.0

data/Rakefile

@@ -0,0 +1,65 @@
+#!/usr/bin/env rake
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+begin
+  require 'bundler/setup'
+rescue LoadError
+  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
+end
+begin
+  require 'rdoc/task'
+rescue LoadError
+  require 'rdoc/rdoc'
+  require 'rake/rdoctask'
+  RDoc::Task = Rake::RDocTask
+end
+
+RDoc::Task.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.main     = 'README.rdoc'
+  rdoc.title    = 'Taverna Player'
+  rdoc.options << '--line-numbers'
+  rdoc.options << "--tab-width=2"
+
+  files = [
+    "README.rdoc",
+    "LICENCE.rdoc",
+    "app/helpers/taverna_player/application_helper.rb",
+    "app/models/taverna_player/run.rb",
+    "app/models/taverna_player/run_port.rb",
+    "app/models/taverna_player/service_credential.rb",
+    "lib/taverna-player.rb",
+    "lib/taverna_player/output_renderer.rb"
+    ]
+
+  rdoc.rdoc_files.include(files)
+end
+
+APP_RAKEFILE = File.expand_path("../test/dummy/Rakefile", __FILE__)
+load 'rails/tasks/engine.rake'
+
+
+
+Bundler::GemHelper.install_tasks
+
+require 'rake/testtask'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = false
+end
+
+
+task :default => :test

data/app/assets/javascripts/taverna_player/application.js

@@ -0,0 +1,14 @@
+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or vendor/assets/javascripts of plugins, if any, can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// the compiled file.
+//
+// WARNING: THE FIRST BLANK LINE MARKS THE END OF WHAT'S TO BE PROCESSED, ANY BLANK LINE SHOULD
+// GO AFTER THE REQUIRES BELOW.
+//
+//= require pmrpc
+//= require_tree .

data/app/assets/javascripts/taverna_player/runs.js

@@ -0,0 +1,42 @@
+//-----------------------------------------------------------------------------
+// Copyright (c) 2013 The University of Manchester, UK.
+//
+// BSD Licenced. See LICENCE.rdoc for details.
+//
+// Taverna Player was developed in the BioVeL project, funded by the European
+// Commission 7th Framework Programme (FP7), through grant agreement
+// number 283359.
+//
+// Author: Robert Haines
+//-----------------------------------------------------------------------------
+
+// Copied from http://www.netlobo.com/url_query_string_javascript.html
+function getParameterValue(name) {
+  name = name.replace(/[\[]/, "\\\[").replace(/[\]]/, "\\\]");
+  var regexS = "[\\?&]" + name + "=([^&#]*)";
+  var regex = new RegExp(regexS);
+  var results = regex.exec(window.location.href);
+
+  if (results == null)
+    return "";
+  else
+    return results[1];
+}
+
+function interaction_reply(url, status, results) {
+  var outputData = JSON.stringify(results);
+
+  jQuery.ajax({
+    url: url,
+    type: "POST",
+    async: false,
+    data: outputData,
+    headers: {
+      "Content-Type": "application/json",
+      "X-Taverna-Interaction-Reply": escape(status),
+      "X-CSRF-Token": jQuery('meta[name="csrf-token"]').attr("content")
+    }
+  });
+
+  return false;
+}

data/app/assets/stylesheets/scaffold.css

@@ -0,0 +1,56 @@
+body { background-color: #fff; color: #333; }
+
+body, p, ol, ul, td {
+  font-family: verdana, arial, helvetica, sans-serif;
+  font-size:   13px;
+  line-height: 18px;
+}
+
+pre {
+  background-color: #eee;
+  padding: 10px;
+  font-size: 11px;
+}
+
+a { color: #000; }
+a:visited { color: #666; }
+a:hover { color: #fff; background-color:#000; }
+
+div.field, div.actions {
+  margin-bottom: 10px;
+}
+
+#notice {
+  color: green;
+}
+
+.field_with_errors {
+  padding: 2px;
+  background-color: red;
+  display: table;
+}
+
+#error_explanation {
+  width: 450px;
+  border: 2px solid red;
+  padding: 7px;
+  padding-bottom: 0;
+  margin-bottom: 20px;
+  background-color: #f0f0f0;
+}
+
+#error_explanation h2 {
+  text-align: left;
+  font-weight: bold;
+  padding: 5px 5px 5px 15px;
+  font-size: 12px;
+  margin: -7px;
+  margin-bottom: 0px;
+  background-color: #c00;
+  color: #fff;
+}
+
+#error_explanation ul li {
+  font-size: 12px;
+  list-style: square;
+}

data/app/assets/stylesheets/taverna_player/application.css

@@ -0,0 +1,13 @@
+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
+ * or vendor/assets/stylesheets of plugins, if any, can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the top of the
+ * compiled file, but it's generally better to create a new file per style scope.
+ *
+ *= require_self
+ *= require_tree .
+ */

data/app/assets/stylesheets/taverna_player/coderay.css

@@ -0,0 +1,120 @@
+.CodeRay {
+  background-color: hsl(0,0%,95%);
+  border: 1px solid silver;
+  color: black;
+}
+.CodeRay pre {
+  margin: 0px;
+}
+
+span.CodeRay { white-space: pre; border: 0px; padding: 2px; }
+
+table.CodeRay { border-collapse: collapse; width: 100%; padding: 2px; }
+table.CodeRay td { padding: 2px 4px; vertical-align: top; }
+
+.CodeRay .line-numbers {
+  background-color: hsl(100,65%,90%);
+  color: gray;
+  text-align: right;
+  -webkit-user-select: none;
+  -moz-user-select: none;
+  user-select: none;
+}
+.CodeRay .line-numbers a {
+  background-color: hsl(100,65%,90%) !important;
+  color: gray !important;
+  text-decoration: none !important;
+}
+.CodeRay .line-numbers a:target { color: blue !important; }
+.CodeRay .line-numbers .highlighted { color: red !important; }
+.CodeRay .line-numbers .highlighted a { color: red !important; }
+.CodeRay span.line-numbers { padding: 0px 4px; }
+.CodeRay .line { display: block; float: left; width: 100%; }
+.CodeRay .code { width: 100%; }
+
+.CodeRay .debug { color: white !important; background: blue !important; }
+
+.CodeRay .annotation { color:#007 }
+.CodeRay .attribute-name { color:#b48 }
+.CodeRay .attribute-value { color:#700 }
+.CodeRay .binary { color:#509 }
+.CodeRay .char .content { color:#D20 }
+.CodeRay .char .delimiter { color:#710 }
+.CodeRay .char { color:#D20 }
+.CodeRay .class { color:#B06; font-weight:bold }
+.CodeRay .class-variable { color:#369 }
+.CodeRay .color { color:#0A0 }
+.CodeRay .comment { color:#777 }
+.CodeRay .comment .char { color:#444 }
+.CodeRay .comment .delimiter { color:#444 }
+.CodeRay .complex { color:#A08 }
+.CodeRay .constant { color:#036; font-weight:bold }
+.CodeRay .decorator { color:#B0B }
+.CodeRay .definition { color:#099; font-weight:bold }
+.CodeRay .delimiter { color:black }
+.CodeRay .directive { color:#088; font-weight:bold }
+.CodeRay .doc { color:#970 }
+.CodeRay .doc-string { color:#D42; font-weight:bold }
+.CodeRay .doctype { color:#34b }
+.CodeRay .entity { color:#800; font-weight:bold }
+.CodeRay .error { color:#F00; background-color:#FAA }
+.CodeRay .escape  { color:#666 }
+.CodeRay .exception { color:#C00; font-weight:bold }
+.CodeRay .float { color:#60E }
+.CodeRay .function { color:#06B; font-weight:bold }
+.CodeRay .global-variable { color:#d70 }
+.CodeRay .hex { color:#02b }
+.CodeRay .imaginary { color:#f00 }
+.CodeRay .include { color:#B44; font-weight:bold }
+.CodeRay .inline { background-color: hsla(0,0%,0%,0.07); color: black }
+.CodeRay .inline-delimiter { font-weight: bold; color: #666 }
+.CodeRay .instance-variable { color:#33B }
+.CodeRay .integer  { color:#00D }
+.CodeRay .key .char { color: #60f }
+.CodeRay .key .delimiter { color: #404 }
+.CodeRay .key { color: #606 }
+.CodeRay .keyword { color:#080; font-weight:bold }
+.CodeRay .label { color:#970; font-weight:bold }
+.CodeRay .local-variable { color:#963 }
+.CodeRay .namespace { color:#707; font-weight:bold }
+.CodeRay .octal { color:#40E }
+.CodeRay .operator { }
+.CodeRay .predefined { color:#369; font-weight:bold }
+.CodeRay .predefined-constant { color:#069 }
+.CodeRay .predefined-type { color:#0a5; font-weight:bold }
+.CodeRay .preprocessor { color:#579 }
+.CodeRay .pseudo-class { color:#00C; font-weight:bold }
+.CodeRay .regexp .content { color:#808 }
+.CodeRay .regexp .delimiter { color:#404 }
+.CodeRay .regexp .modifier { color:#C2C }
+.CodeRay .regexp { background-color:hsla(300,100%,50%,0.06); }
+.CodeRay .reserved { color:#080; font-weight:bold }
+.CodeRay .shell .content { color:#2B2 }
+.CodeRay .shell .delimiter { color:#161 }
+.CodeRay .shell { background-color:hsla(120,100%,50%,0.06); }
+.CodeRay .string .char { color: #b0b }
+.CodeRay .string .content { color: #D20 }
+.CodeRay .string .delimiter { color: #710 }
+.CodeRay .string .modifier { color: #E40 }
+.CodeRay .string { background-color:hsla(0,100%,50%,0.05); }
+.CodeRay .symbol .content { color:#A60 }
+.CodeRay .symbol .delimiter { color:#630 }
+.CodeRay .symbol { color:#A60 }
+.CodeRay .tag { color:#070 }
+.CodeRay .type { color:#339; font-weight:bold }
+.CodeRay .value { color: #088; }
+.CodeRay .variable  { color:#037 }
+
+.CodeRay .insert { background: hsla(120,100%,50%,0.12) }
+.CodeRay .delete { background: hsla(0,100%,50%,0.12) }
+.CodeRay .change { color: #bbf; background: #007; }
+.CodeRay .head { color: #f8f; background: #505 }
+.CodeRay .head .filename { color: white; }
+
+.CodeRay .delete .eyecatcher { background-color: hsla(0,100%,50%,0.2); border: 1px solid hsla(0,100%,45%,0.5); margin: -1px; border-bottom: none; border-top-left-radius: 5px; border-top-right-radius: 5px; }
+.CodeRay .insert .eyecatcher { background-color: hsla(120,100%,50%,0.2); border: 1px solid hsla(120,100%,25%,0.5); margin: -1px; border-top: none; border-bottom-left-radius: 5px; border-bottom-right-radius: 5px; }
+
+.CodeRay .insert .insert { color: #0c0; background:transparent; font-weight:bold }
+.CodeRay .delete .delete { color: #c00; background:transparent; font-weight:bold }
+.CodeRay .change .change { color: #88f }
+.CodeRay .head .head { color: #f4f }

data/app/controllers/taverna_player/application_controller.rb

@@ -0,0 +1,16 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class ApplicationController < ApplicationController
+  end
+end

data/app/controllers/taverna_player/runs_controller.rb

@@ -0,0 +1,18 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class RunsController < TavernaPlayer::ApplicationController
+    # See lib/taverna_player/concerns/controllers/runs_controller.rb
+    include TavernaPlayer::Concerns::Controllers::RunsController
+  end
+end

data/app/controllers/taverna_player/service_credentials_controller.rb

@@ -0,0 +1,18 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class ServiceCredentialsController < TavernaPlayer::ApplicationController
+    # See lib/taverna_player/concerns/controllers/service_credentials_controller.rb
+    include TavernaPlayer::Concerns::Controllers::ServiceCredentialsController
+  end
+end

data/app/helpers/taverna_player/application_helper.rb

@@ -0,0 +1,55 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+
+  # These helpers will be available in the main application when you use
+  # Taverna Player.
+  module ApplicationHelper
+
+    # :call-seq:
+    #   new_embedded_run_path(workflow) -> string
+    #
+    # Given a workflow instance, or workflow id, this method returns the URI
+    # path to a new embedded run of that workflow.
+    def new_embedded_run_path(id_or_model)
+      id = workflow_id(id_or_model)
+
+      raw(taverna_player.new_run_path(:workflow_id => id, :embedded => true))
+    end
+
+    # :call-seq:
+    #   new_embedded_run_url(workflow) -> string
+    #
+    # Given a workflow instance, or workflow id, this method returns the full
+    # URI to a new embedded run of that workflow.
+    def new_embedded_run_url(id_or_model)
+      id = workflow_id(id_or_model)
+
+      raw(taverna_player.new_run_url(:workflow_id => id, :embedded => true))
+    end
+
+    private
+
+    def workflow_id(id_or_model)
+      case id_or_model
+      when TavernaPlayer::Run
+        id_or_model.workflow_id
+      when TavernaPlayer.workflow_proxy.class_name
+        id_or_model.id
+      else
+        id_or_model
+      end
+    end
+
+  end
+end

data/app/helpers/taverna_player/runs_helper.rb

@@ -0,0 +1,84 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  module RunsHelper
+
+    def interaction_redirect(interaction)
+      if interaction.page_uri.blank?
+        run_url(interaction.run) + "/interaction/#{interaction.unique_id}"
+      else
+        interaction.page_uri
+      end
+    end
+
+    def show_output(run, output)
+      if output.depth == 0
+        if output.value.blank?
+          content = run_path(output.run_id) + "/output/#{output.name}"
+        else
+          if output.metadata[:size] < 255
+            content = output.value
+          else
+            Zip::ZipFile.open(run.results.path) do |zip|
+              content = zip.read(output.name)
+            end
+          end
+        end
+        raw(TavernaPlayer.output_renderer.render(content, output.metadata[:type]))
+      else
+        parse_port_list(run, output)
+      end
+    end
+
+    private
+
+    def parse_port_list(run, output)
+      types = output.metadata[:type]
+      content = String.new
+
+      Zip::ZipFile.open(run.results.path) do |zip|
+        content = deep_parse(types, output, zip)
+      end
+
+      content
+    end
+
+    def deep_parse(types, output, zip, index = [])
+      content = "<ol>"
+      i = 0
+      types.each do |type|
+        if type.is_a?(Array)
+          content += "<li><br />" +
+            deep_parse(type, output, zip, index + [i]) + "</li>"
+        else
+          # Text outputs are inlined here by us. Other types are linked and
+          # inlined by the browser.
+          content += "<li>(#{type})<p>"
+          if type.starts_with?("text")
+            path = (index + [i]).map { |j| j += 1 }.join("/")
+            data = zip.read("#{output.name}/#{path}")
+          else
+            path = (index + [i]).join("/")
+            data = run_path(output.run_id) + "/output/#{output.name}/#{path}"
+          end
+          content += TavernaPlayer.output_renderer.render(data, type)
+          content += "</p></li>"
+        end
+        i += 1
+      end
+
+      raw(content += "</ol>")
+    end
+
+  end
+end