t2-server 0.9.3 → 1.0.0

data/bin/t2-run-workflow

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010-2012 The University of Manchester, UK.
+# Copyright (c) 2010-2013 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -39,18 +39,18 @@ include T2Server::CLI
 # set up options
 inputs  = {}
 files = {}
-options = {}
-conn_params, creds = register_options("Usage: t2-run-workflow [options] " +
+options = {:screds => [], :interactions => :show}
+conn_params, creds = register_options("Usage: t2-run-workflow [options] "\
     "server-address") do |opt|
   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("-w WORKFLOW", "--workflow=WORKFLOW", "The workflow to run. If " +
-    "this is not specified then the workflow is read from standard " +
+  opt.on("-w WORKFLOW", "--workflow=WORKFLOW", "The workflow to run. If "\
+    "this is not specified then the workflow is read from standard "\
     "input") do |val|
       options[:wkf_file] = val.chomp
   end
-  opt.on("-i INPUT:VALUE", "--input=INPUT:VALUE", "Set input port INPUT to " +
+  opt.on("-i INPUT:VALUE", "--input=INPUT:VALUE", "Set input port INPUT to "\
     "VALUE") do |val|
       input, value = val.chomp.split(':', 2)
       inputs[input] = value
@@ -60,35 +60,78 @@ conn_params, creds = register_options("Usage: t2-run-workflow [options] " +
       input, filename = val.chomp.split(':', 2)
       files[input] = filename
   end
-  opt.on("-e EXPIRY", "--expiry=EXPIRY", "Set the expiry date/time of this " +
+  opt.on("-I LEVEL", "--interactions=LEVEL", "Show, open or ignore any "\
+    "workflow interactions. LEVEL can be 'show' (the default), which simply "\
+    "lists the interaction URI in the terminal; 'open', which will open the "\
+    "interaction in a Web browser; or 'none', which will not check for "\
+    "interactions from the workflow at all. This should only be set to "\
+    "'none' if you are sure the workflow has no interactions or if you will "\
+    "be handling them in some other way.") do |val|
+      levels = [:show, :open, :none]
+      level = val.downcase.to_sym
+      options[:interactions] = levels.include?(level) ? level : :show
+  end
+  opt.on("-e EXPIRY", "--expiry=EXPIRY", "Set the expiry date/time of this "\
     "run") do |val|
       options[:expiry] = Time.parse(val.chomp)
   end
-  opt.on("-b BACLAVA", "--baclava-in=BACLAVA", "Set baclava file for input " +
+  opt.on("-N NAME", "--name=NAME", "Give this run a name. Supported in "\
+    "Taverna Server versions 2.5.0 and up") do |val|
+      options[:name] = val.chomp
+  end
+  opt.on("-c URI::USER:PASS", "--credential=URI::USER:PASS",
+    "Provide a credential for a secure remote service. NOTE :: between URI "\
+    "and credential") do |val|
+      uri, cred = val.chomp.split('::', 2)
+      user, pass = cred.chomp.split(':', 2)
+      options[:screds] << [uri, user, pass]
+  end
+  opt.on("-b BACLAVA", "--baclava-in=BACLAVA", "Set baclava file for input "\
     "port values") do |val|
       inputs[:baclava] = val
   end
-  opt.on("-o", "--baclava-out=BACLAVA", "Return outputs in baclava format." +
+  opt.on("-o", "--baclava-out=BACLAVA", "Return outputs in baclava format."\
     " A filename may be specified or 'out.xml' is used") do |val|
       options[:baclava_out] = val.chomp
   end
-  opt.on("-n", "--no-wait", "Do not wait for workflow to finish, return " +
+  opt.on("-n", "--no-wait", "Do not wait for workflow to finish, return "\
     "once it has started running") do |val|
       options[:no_wait] = true
   end
-  opt.on("-r", "--output-refs", "Return URIs that point to the data items " +
+  opt.on("-r", "--output-refs", "Return URIs that point to the data items "\
     "of the output rather than the data items themselves.") do |val|
       options[:output_refs] = val
   end
-  opt.on("-D", "--delete", "Delete the run from the server when it is " +
-    "complete. By default the run and its results are preserved. Note that " +
+  opt.on("-D", "--delete", "Delete the run from the server when it is "\
+    "complete. By default the run and its results are preserved. Note that "\
     "the run will still be deleted when its expiry time is reached") do |val|
       options[:delete] = val
   end
-  opt.on("-z", "--zip=FILE", "Get the entire working directory of the run " +
+  opt.on("-z", "--zip=FILE", "Get the entire working directory of the run "\
     "in zip format and save it to the provided filename.") do |val|
       options[:zip_out] = val.chomp
   end
+  opt.on("-x", "--exitcode", "Return the exitcode of the run.") do
+    options[:exitcode] = true
+  end
+  opt.on("--stderr", 'Return the "standard error" output of the run.') do
+    options[:stderr] = true
+  end
+  opt.on("--stdout", 'Return the "standard out" output of the run.') do
+    options[:stdout] = true
+  end
+end
+
+if options[:interactions] == :open
+  begin
+    require 'launchy'
+  rescue LoadError
+    puts "\n****\nTo support opening interactions in your Web browser the "\
+      "launchy gem must be installed:\n\n$ gem install launchy\n\n"\
+      "Interaction URIs will be listed here instead. Please copy and paste "\
+      "them into your Web browser to display them.\n****\n\n"
+    options[:interactions] = :show
+  end
 end
 
 # read and check server address
@@ -107,6 +150,12 @@ begin
     puts "Created run with identifier: #{run.identifier}"
     puts "Created at #{run.create_time}"
 
+    # set run name
+    if options[:name]
+      run.name = options[:name]
+      puts "Run name set to '#{run.name}'"
+    end
+
     # set run expiry
     if options[:expiry]
       run.expiry=(options[:expiry])
@@ -135,43 +184,56 @@ begin
       end
     end
 
+    # set remote service credentials
+    options[:screds].each do |list|
+      run.add_password_credential(list[0], list[1], list[2])
+    end
+
     # output baclava?
     run.request_baclava_output if options[:baclava_out]
 
-    # start run and wait until it is finished
-    run.start
+    # try to start run
+    unless run.start
+      puts "Run could not be started because the server is already running "\
+        "its configured maximum number of runs. Please try again later."
+      run.delete
+      exit 1
+    end
     puts "Started at #{run.start_time}"
 
     # bail out if user doesn't want to wait
     exit 0 if options[:no_wait]
 
-    # otherwise wait
-    print "Running"
+    # otherwise wait, but list or open notifications if there are any
+    print "Running."
     until run.finished?
       sleep(1)
+      unless options[:interactions] == :none
+        run.notifications(:new_requests).each do |note|
+          if options[:interactions] == :open
+            Launchy.open note.uri
+          else
+            puts "\n#{note.uri}\n"
+          end
+        end
+      end
       print "."
       $stdout.flush
     end
     puts "\nFinished at #{run.finish_time}"
 
     # get outputs
-    stdout = run.stdout
-    stderr = run.stderr
     exitcd = run.exitcode
-    puts "Exitcode: #{exitcd}"
-    if stdout != "" then puts "Stdout:\n#{stdout}" end
-    if stderr != "" then puts "Stderr:\n#{stderr}" end
+    puts "Exitcode: #{exitcd}" if options[:exitcode] || exitcd != 0
+    puts "Stdout:\n#{run.stdout}" if options[:stdout]
+    puts "Stderr:\n#{run.stderr}" if options[:stderr]
 
     if exitcd == 0
       if options[:baclava_out]
-        File.open(options[:baclava_out], "w") do |file|
-          file.syswrite(run.baclava_output)
-        end
+        run.baclava_output(options[:baclava_out])
         puts "Baclava file written to '#{options[:baclava_out]}'"
       elsif options[:zip_out]
-        File.open(options[:zip_out],"w") do |file|
-          file.syswrite(run.zip_output)
-        end
+        run.zip_output(options[:zip_out])
         puts "Zip file written to '#{options[:zip_out]}'"
       else
         # go through the outputs and print them out

data/bin/t2-server-info

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010-2012 The University of Manchester, UK.
+# Copyright (c) 2010-2013 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -38,15 +38,16 @@ require 'hirb'
 include T2Server::CLI
 
 # set up options
-options = {}
+options = { :list => 0 }
 conn_params, creds = register_options("Usage: t2-server-info [options] " +
   "server-address") do |opt|
   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("-l", "--list", "List details for the runs on this server.") do
-    options[:list] = true
+  opt.on("-l", "--list", "List details for the runs on this server. Repeat "\
+    "(e.g. -ll or -lll) to increase the amount of detail shown.") do
+    options[:list] += 1
   end
 end
 
@@ -61,14 +62,30 @@ begin
     puts "  Run limit: #{server.run_limit(creds)}"
     runs = server.runs(creds)
     puts "No. of runs: #{runs.length}"
-    if options[:list] && runs.length > 0
-      puts (Hirb::Helpers::ObjectTable.render runs,
-        :fields=>[:identifier, :status, :expiry],
-        :headers=>{:identifier=>'Run ID', :status=>'Status',
-          :expiry=>'Expiry time (local)'},
-        :filters=>{:expiry=>[:strftime, "%H:%M:%S %d/%m/%Y"]},
-        :max_fields=>{:expiry=>19},
-        :description=>false)
+    if options[:list] > 0 && runs.length > 0
+      if options[:list] == 1
+        fields = [:identifier]
+        headers = {:identifier => 'Run ID'}
+        lengths = {}
+      elsif options[:list] == 2
+        fields = [:identifier, :status, :expiry]
+        headers = {:identifier => 'Run ID', :status => 'Status',
+          :expiry => 'Expiry time (local)'}
+        lengths = {:status => 11, :expiry => 19}
+      else
+        fields = [:identifier, :name, :status, :expiry]
+        headers = {:identifier => 'Run ID', :name => "Name",
+          :status => 'Status', :expiry => 'Expiry time (local)'}
+        lengths = {:identifier => 11, :name => 25, :status => 11,
+          :expiry => 19}
+      end
+
+      puts Hirb::Helpers::ObjectTable.render(runs,
+        :fields => fields,
+        :headers => headers,
+        :filters => {:expiry => [:strftime, "%H:%M:%S %d/%m/%Y"]},
+        :max_fields => lengths,
+        :description => false)
     end
   end
 rescue RuntimeError => e

data/extras/t2-server-stress

@@ -0,0 +1,184 @@
+#!/usr/bin/env ruby
+# Copyright (c) 2010-2013 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 'rubygems'
+require 't2-server-cli'
+require 'hirb'
+
+include T2Server::CLI
+
+# Set up options and workflow inputs.
+inputs  = {}
+files = {}
+options = {:number => 5, :backoff => 0, :screds => []}
+conn_params, creds = register_options("Usage: t2-server-stress [options] "\
+  "server-address") do |opt|
+  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("-n NUMBER", "--number=NUMBER", "Number of concurrent runs. "\
+    "Default 5") do |val|
+      options[:number] = val.chomp.to_i
+  end
+  opt.on("-b NUMBER", "--backoff=NUMBER", "Time (in seconds) to back off "\
+    "before starting next run. Default 0") do |val|
+      options[:backoff] = val.chomp.to_i
+  end
+  opt.on("-w WORKFLOW", "--workflow=WORKFLOW", "The workflow to run. If "\
+    "this is not specified then the workflow is read from standard "\
+    "input") do |val|
+      options[:wkf_file] = val.chomp
+  end
+  opt.on("-i INPUT:VALUE", "--input=INPUT:VALUE", "Set input port INPUT to "\
+    "VALUE") do |val|
+      input, value = val.chomp.split(':', 2)
+      inputs[input] = value
+  end
+  opt.on("-f INPUT:FILE", "--input-file=INPUT:FILE",
+    "Set input port INPUT to use the contents of FILE as its input") do |val|
+      input, filename = val.chomp.split(':', 2)
+      files[input] = filename
+  end
+  opt.on("-K", "--keep-runs",
+    "Do not delete the runs at the end of the test") do
+      options[:keep] = true
+  end
+  opt.on("-c URI::USER:PASS", "--credential=URI::USER:PASS",
+    "Provide a credential for a secure remote service. NOTE :: between URI "\
+    "and credential") do |val|
+      uri, cred = val.chomp.split('::', 2)
+      user, pass = cred.chomp.split(':', 2)
+      options[:screds] << [uri, user, pass]
+  end
+end
+
+# Read and check server address and credentials.
+uri, creds = parse_address(ARGV.shift, creds)
+
+# Read workflow and ensure that it is not empty.
+if options[:wkf_file]
+  wkf = IO.read(options[:wkf_file])
+else
+  wkf = ARGF.read
+end
+exit 1 if wkf == ""
+
+# Connect to server and check it's in a good state.
+server = T2Server::Server.new(uri, conn_params)
+puts "\nConnected to server at #{server.uri}"
+
+current_runs = server.runs(creds)
+unless current_runs.length == 0
+  puts "\nServer already has runs on it. Please clear out all runs before "\
+    "running the stress tests."
+  exit 1
+end
+
+run_limit = server.run_limit(creds)
+unless run_limit >= options[:number]
+  puts "\nYou have asked for more concurrent runs than this server has been "\
+    "configured to allow. Please set the number to #{run_limit} or less."
+  exit 1
+end
+
+puts "\nInitializing #{options[:number]} runs and setting inputs."
+runs = []
+options[:number].times do
+  server.create_run(wkf, creds) do |run|
+    # Set inputs.
+    run.input_ports.each_value do |port|
+      input = port.name
+      if inputs.include? input
+        port.value = inputs[input]
+      elsif files.include? input
+        port.file = files[input]
+      else
+        puts "Input '#{input}' has not been given, exiting."
+        run.delete
+        exit 1
+      end
+    end
+
+    options[:screds].each do |list|
+      run.add_password_credential(list[0], list[1], list[2])
+    end
+
+    runs << run
+  end
+end
+
+puts "\nStarting runs with #{options[:backoff]} seconds back-off time between."
+
+w_start = Time.now
+runs.each do |run|
+  r_start = Time.now
+  while !run.start
+    puts "Server has reached configured maximum of concurrently running "\
+      "runs. Backing off for 10 seconds before retrying..."
+      sleep(10)
+  end
+  r_started = Time.now
+  puts "Run started at #{r_started} and took #{r_started - r_start} seconds to start."
+  sleep options[:backoff] if options[:backoff] > 0  
+end
+
+puts "\nWaiting for runs to finish."
+
+while runs.count { |run| run.finished? } < options[:number] do
+  sleep(5)
+end
+w_end = Time.now
+
+puts "\nRuns finished.\n\nRun times:"
+
+total = 0
+runs.each do |run|
+  time = run.finish_time - run.start_time
+  total += time
+  puts time
+end
+
+average = total / options[:number]
+puts "\nAverage time: #{average}"
+w_time = w_end - w_start
+puts "Wallclock time: #{w_time}"
+
+unless options[:keep]
+  puts "\nDeleting runs."
+  runs.each do |run|
+    run.delete
+  end
+end
+
+puts "\nDone."