t2-server 1.0.0 → 1.1.0

data/t2-server.gemspec

@@ -1,128 +1,66 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
+# Copyright (c) 2010-2014 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
 
-Gem::Specification.new do |s|
-  s.name = "t2-server"
-  s.version = "1.0.0"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Robert Haines", "Finn Bacall"]
-  s.date = "2013-11-05"
-  s.description = "This gem provides access to the Taverna 2 Server REST interface from Ruby."
-  s.email = ["support@mygrid.org.uk"]
-  s.executables = ["t2-delete-runs", "t2-run-workflow", "t2-server-info", "t2-get-output", "t2-server-admin"]
-  s.extra_rdoc_files = [
-    "CHANGES.rdoc",
-    "LICENCE.rdoc",
-    "README.rdoc"
-  ]
-  s.files = [
-    "CHANGES.rdoc",
-    "LICENCE.rdoc",
-    "README.rdoc",
-    "Rakefile",
-    "bin/t2-delete-runs",
-    "bin/t2-get-output",
-    "bin/t2-run-workflow",
-    "bin/t2-server-admin",
-    "bin/t2-server-info",
-    "extras/t2-server-stress",
-    "lib/t2-server-cli.rb",
-    "lib/t2-server.rb",
-    "lib/t2-server/admin.rb",
-    "lib/t2-server/exceptions.rb",
-    "lib/t2-server/interaction.rb",
-    "lib/t2-server/net/connection.rb",
-    "lib/t2-server/net/credentials.rb",
-    "lib/t2-server/net/parameters.rb",
-    "lib/t2-server/port.rb",
-    "lib/t2-server/run-cache.rb",
-    "lib/t2-server/run.rb",
-    "lib/t2-server/server.rb",
-    "lib/t2-server/util.rb",
-    "lib/t2-server/xml/libxml.rb",
-    "lib/t2-server/xml/nokogiri.rb",
-    "lib/t2-server/xml/rexml.rb",
-    "lib/t2-server/xml/xml.rb",
-    "lib/t2-server/xml/xpath_cache.rb",
-    "t2-server.gemspec",
-    "test/tc_admin.rb",
-    "test/tc_misc.rb",
-    "test/tc_params.rb",
-    "test/tc_perms.rb",
-    "test/tc_run.rb",
-    "test/tc_secure.rb",
-    "test/tc_server.rb",
-    "test/tc_util.rb",
-    "test/ts_t2server.rb",
-    "test/workflows/always_fail.t2flow",
-    "test/workflows/empty_list.t2flow",
-    "test/workflows/empty_list_input.baclava",
-    "test/workflows/in.txt",
-    "test/workflows/list_and_value.t2flow",
-    "test/workflows/list_with_errors.t2flow",
-    "test/workflows/missing_outputs.t2flow",
-    "test/workflows/no-ports.t2flow",
-    "test/workflows/pass_through.t2flow",
-    "test/workflows/secure/basic-http.t2flow",
-    "test/workflows/secure/basic-https.t2flow",
-    "test/workflows/secure/client-https.t2flow",
-    "test/workflows/secure/digest-http.t2flow",
-    "test/workflows/secure/digest-https.t2flow",
-    "test/workflows/secure/heater-pk.pem",
-    "test/workflows/secure/user-cert.p12",
-    "test/workflows/secure/ws-http.t2flow",
-    "test/workflows/secure/ws-https.t2flow",
-    "test/workflows/strings.txt",
-    "test/workflows/xml_xpath.t2flow",
-    "version.yml"
-  ]
-  s.homepage = "http://www.taverna.org.uk/"
-  s.rdoc_options = ["-N", "--tab-width=2", "--main=README.rdoc"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.21"
-  s.summary = "Support for interacting with Taverna 2 Server."
-  s.test_files = ["test/ts_t2server.rb"]
-
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "t2-server/version"
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<rake>, ["~> 0.9.2"])
-      s.add_development_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-      s.add_development_dependency(%q<nokogiri>, [">= 1.5.0"])
-      s.add_development_dependency(%q<rdoc>, [">= 3.9.4"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_development_dependency(%q<launchy>, ["~> 2.2.0"])
-      s.add_runtime_dependency(%q<net-http-persistent>, ["~> 2.6"])
-      s.add_runtime_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
-      s.add_runtime_dependency(%q<ratom>, ["~> 0.8.2"])
-      s.add_runtime_dependency(%q<hirb>, [">= 0.4.0"])
-    else
-      s.add_dependency(%q<rake>, ["~> 0.9.2"])
-      s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-      s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
-      s.add_dependency(%q<rdoc>, [">= 3.9.4"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_dependency(%q<launchy>, ["~> 2.2.0"])
-      s.add_dependency(%q<net-http-persistent>, ["~> 2.6"])
-      s.add_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
-      s.add_dependency(%q<ratom>, ["~> 0.8.2"])
-      s.add_dependency(%q<hirb>, [">= 0.4.0"])
-    end
-  else
-    s.add_dependency(%q<rake>, ["~> 0.9.2"])
-    s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
-    s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
-    s.add_dependency(%q<rdoc>, [">= 3.9.4"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-    s.add_dependency(%q<launchy>, ["~> 2.2.0"])
-    s.add_dependency(%q<net-http-persistent>, ["~> 2.6"])
-    s.add_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
-    s.add_dependency(%q<ratom>, ["~> 0.8.2"])
-    s.add_dependency(%q<hirb>, [">= 0.4.0"])
-  end
+Gem::Specification.new do |s|
+  s.name             = "t2-server"
+  s.version          = T2Server::Version::STRING
+  s.authors          = ["Robert Haines", "Finn Bacall"]
+  s.email            = ["support@mygrid.org.uk"]
+  s.homepage         = "http://www.taverna.org.uk/"
+  s.platform         = Gem::Platform::RUBY
+  s.summary          = "Support for interacting with Taverna 2 Server."
+  s.description      = "This gem provides access to the Taverna 2 Server " +
+                         "REST interface from Ruby."
+  s.license          = "BSD"
+  s.require_path     = "lib"
+  s.bindir           = "bin"
+  s.files            = `git ls-files`.split($/)
+  s.executables      = ["t2-delete-runs", "t2-run-workflow", "t2-server-info",
+                          "t2-get-output", "t2-server-admin"]
+  s.test_file        = "test/ts_t2server.rb"
+  s.has_rdoc         = true
+  s.extra_rdoc_files = ["README.rdoc", "LICENCE.rdoc", "CHANGES.rdoc"]
+  s.rdoc_options     = ["-N", "--tab-width=2", "--main=README.rdoc"]
+  s.add_development_dependency('rake', '~> 10.0')
+  s.add_development_dependency('bundler', '~> 1.5')
+  s.add_development_dependency('rdoc', '~> 4.1')
+  s.add_development_dependency('launchy', '~> 2.2')
+  s.add_development_dependency('hirb', '~> 0.7')
+  s.add_runtime_dependency('net-http-persistent', '~> 2.6')
+  s.add_runtime_dependency('taverna-baclava', '~> 1.0')
+  s.add_runtime_dependency('ratom', '~> 0.8.2')
+  s.add_runtime_dependency('libxml-ruby', '~> 2.6')
 end
-

data/test/tc_run.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.
 #
@@ -124,10 +124,8 @@ class TestRun < Test::Unit::TestCase
   # Test run naming. This is different for different versions of server.
   def test_run_naming
     T2Server::Server.new($uri, $conn_params) do |server|
-      vc = server.version_components
-      v250plus = vc[0] > 2 || (vc[0] == 2 && vc[1] >= 5)
       server.create_run($wkf_no_io, $creds) do |run|
-        if v250plus
+        if server.version >= "2.5.0"
           # Read initial name.
           assert(run.name.length > 0)
           assert_equal("Workflow1", run.name[0...9])
@@ -202,7 +200,7 @@ class TestRun < Test::Unit::TestCase
     end
   end
 
-  # Test run with a list and file input
+  # Test run with a list and file input, and check that provenance is not on
   def test_run_list_and_file
     T2Server::Run.create($uri, $wkf_l_v, $creds, $conn_params) do |run|
       list = ["one", 2, :three]
@@ -228,6 +226,10 @@ class TestRun < Test::Unit::TestCase
         assert_not_equal(log_cache.size, 0)
       end
 
+      assert_raise(T2Server::AccessForbiddenError) do
+        run.provenance
+      end
+
       assert(run.delete)
     end
   end
@@ -245,7 +247,8 @@ class TestRun < Test::Unit::TestCase
     end
   end
 
-  # Test run with file input. Also pass workflow as File object.
+  # Test run with file input. Also pass workflow as File object. Also test
+  # toggling provenance on and then off again.
   def test_run_file_input
     workflow = File.open($wkf_pass, "r")
 
@@ -253,12 +256,20 @@ class TestRun < Test::Unit::TestCase
 
       assert_nothing_raised(T2Server::AttributeNotFoundError) do
         run.input_port("IN").file = $file_input
+        run.generate_provenance
+        run.generate_provenance(false)
       end
+      refute run.generate_provenance?
 
       run.start
       assert(run.running?)
       assert_nothing_raised(T2Server::RunStateError) { run.wait }
       assert_equal(run.output_port("OUT").value, "Hello, World!")
+
+      assert_raise(T2Server::AccessForbiddenError) do
+        run.provenance
+      end
+
       assert(run.delete)
     end
 
@@ -266,10 +277,18 @@ class TestRun < Test::Unit::TestCase
   end
 
   # Test run that returns list of lists, some empty, using baclava for input
+  # Also test provenance output works with baclava input
   def test_baclava_input
     T2Server::Run.create($uri, $wkf_lists, $creds, $conn_params) do |run|
       assert_nothing_raised(T2Server::AttributeNotFoundError) do
         run.baclava_input = $list_input
+        run.generate_provenance
+      end
+
+      if run.server.version >= "2.5.3"
+        assert(run.generate_provenance?)
+      else
+        refute(run.generate_provenance?)
       end
 
       assert_equal(run.input_ports.keys.sort, ["MANY_IN", "SINGLE_IN"])
@@ -291,6 +310,20 @@ class TestRun < Test::Unit::TestCase
       assert(run.output_port("MANY")[1][0][0].empty?)
       assert_equal(run.output_port("MANY")[1][0][1].value(1..3), "ell")
       assert_raise(NoMethodError) { run.output_port("SINGLE")[0].value }
+
+      # Grab provenance
+      if run.server.version >= "2.5.3"
+        assert_nothing_raised(T2Server::AccessForbiddenError) do
+          prov = run.provenance
+          assert_not_equal(prov, "")
+        end
+      else
+        assert_raise(T2Server::AccessForbiddenError) do
+          prov = run.provenance
+          assert_equal(prov, "")
+        end
+      end
+
       assert(run.delete)
     end
   end
@@ -300,9 +333,9 @@ class TestRun < Test::Unit::TestCase
     T2Server::Run.create($uri, $wkf_pass, $creds, $conn_params) do |run|
       run.input_port("IN").value = "Some input..."
       assert_nothing_raised(T2Server::AttributeNotFoundError) do
-        run.request_baclava_output
+        run.generate_baclava_output
       end
-      assert(run.baclava_output?)
+      assert(run.generate_baclava_output?)
 
       run.start
       assert(run.running?)
@@ -323,12 +356,19 @@ class TestRun < Test::Unit::TestCase
     end
   end
 
-  # Test partial result download
+  # Test partial result download and provenance streaming
   def test_result_download
     T2Server::Run.create($uri, $wkf_pass, $creds, $conn_params) do |run|
       assert_nothing_raised(T2Server::AttributeNotFoundError) do
         file = run.upload_file($file_strs)
         run.input_port("IN").remote_file = file
+        run.generate_provenance(true)
+      end
+
+      if run.server.version >= "2.5.3"
+        assert(run.generate_provenance?)
+      else
+        refute(run.generate_provenance?)
       end
 
       run.start
@@ -371,6 +411,23 @@ class TestRun < Test::Unit::TestCase
       out = run.output_port("OUT").value
       assert_equal(out.length, 100)
 
+      # test streaming provenance data
+      if run.server.version >= "2.5.3"
+        assert_nothing_raised(T2Server::AccessForbiddenError) do
+          prov_cache = TestCache.new
+          prov_size = run.provenance(prov_cache)
+          assert_not_equal(prov_size, 0)
+          assert_not_equal(prov_cache.data, "")
+        end
+      else
+        assert_raise(T2Server::AccessForbiddenError) do
+          prov_cache = TestCache.new
+          prov_size = run.provenance(prov_cache)
+          assert_equal(prov_size, 0)
+          assert_equal(prov_cache.data, "")
+        end
+      end
+
       assert(run.delete)
     end
   end

data/test/tc_server_version.rb

@@ -0,0 +1,82 @@
+# Copyright (c) 2014 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 't2-server'
+
+class TestServerVersion < Test::Unit::TestCase
+
+  TWO_FOUR = "2.4"
+  TWO_FOUR_ZERO = "2.4.0"
+  TWO_FOUR_ONE = "2.4.1"
+  TWO_FIVE_ZERO = "2.5.0"
+  TWO_FIVE_ONE = "2.5.1"
+
+  TWO_FOUR_ZERO_SNAP = "2.4.0-SNAPSHOT"
+  TWO_FOUR_ZERO_ALPHA = "2.4.0alpha99"
+
+  def setup
+    @v24 = T2Server::Server::Version.new(TWO_FOUR)
+    @v240 = T2Server::Server::Version.new(TWO_FOUR_ZERO)
+    @v241 = T2Server::Server::Version.new(TWO_FOUR_ONE)
+    @v250 = T2Server::Server::Version.new(TWO_FIVE_ZERO)
+    @v251 = T2Server::Server::Version.new(TWO_FIVE_ONE)
+
+    @v240s = T2Server::Server::Version.new(TWO_FOUR_ZERO_SNAP)
+    @v240a = T2Server::Server::Version.new(TWO_FOUR_ZERO_ALPHA)
+  end
+
+  def test_version_parsing
+    assert_equal TWO_FOUR_ZERO, @v24.to_s
+    assert_equal TWO_FOUR_ZERO, @v240.to_s
+    assert_equal TWO_FOUR_ZERO, @v240s.to_s
+    assert_equal TWO_FOUR_ZERO, @v240a.to_s
+    assert_equal @v24.to_s, @v240.to_s
+  end
+
+  def test_version_comparison
+    assert @v24 == @v240
+    assert @v240 < @v250
+    assert @v240 < @v241
+    assert @v251 > @v241
+    assert @v251 > @v250
+  end
+
+  def test_version_components
+    assert_equal [2, 4, 0], @v24.to_a
+    assert_equal [2, 4, 0], @v240.to_a
+    assert_equal [2, 5, 0], @v250.to_a
+
+    assert_equal [2, 4, 0], @v240s.to_a
+    assert_equal [2, 4, 0], @v240a.to_a
+  end
+
+end

data/test/ts_t2server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2013 The University of Manchester, UK.
+# Copyright (c) 2010-2014 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -53,8 +53,8 @@ if ARGV.size != 0
 
   # Clear the commandline arguments so that we don't confuse runit.
   ARGV.clear
-else
-  # get a server address to test - 30 second timeout
+elsif !ENV["TRAVIS"]
+  # get a server address to test if not in travis - 30 second timeout
   print "\nPlease supply a valid Taverna 2 Server address.\n\nNOTE that " +
     "these tests will fully load the server and then delete all the runs " +
     "that it has permission to do so - if you are not using security ALL " +
@@ -62,16 +62,17 @@ else
   $stdout.flush
   if select([$stdin], [], [], 30)
     address = $stdin.gets.chomp
-  else
-    puts "\nSkipping tests that require a Taverna 2 Server instance..."
-    address = ""
   end
 end
 
+# If address is still unset then set it to something.
+address ||= ""
+
 # the testcases to run
 require 'tc_util'
 require 'tc_params'
-if address != ""
+require 'tc_server_version'
+unless address == ""
   $uri, $creds = T2Server::Util.strip_uri_credentials(address)
 
   # override creds if passed in on the command line