t2-server 0.6.1 → 0.9.0

data/bin/t2-delete-runs

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010, 2011 The University of Manchester, UK.
+# Copyright (c) 2010-2012 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -15,7 +15,7 @@
 #
 #  * 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. 
+#    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
@@ -32,34 +32,24 @@
 # Author: Robert Haines
 
 require 'rubygems'
-require 't2-server'
-require 'optparse'
+require 't2-server-cli'
+
+include T2Server::CLI
 
 # set up options
-delete_all = false
-opts = OptionParser.new do |opt|
-  opt.banner = "Usage: t2-delete-runs [options] server-address [run-ids...]"
-  opt.separator ""
-  opt.separator "  Where server-address is the full URI of the server to connect to,"
-  opt.separator "  e.g.: http://example.com:8080/taverna, run-ids are the id numbers"
+options = {}
+conn_params, creds = register_options("Usage: t2-delete-runs [options] " +
+    "server-address [run-ids...]") do |opt|
+  opt.separator "  Where server-address is the full URI of the server to " +
+    "connect to,"
+  opt.separator "  e.g.: http://example.com:8080/taverna, run-ids are the " +
+    "id numbers"
   opt.separator "  of the runs you want to delete and [options] can be:"
   opt.on("--all", "Delete all runs on the server") do
-    delete_all = true
-  end
-  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
+    options[:all] = true
   end
 end
 
-# parse options
-opts.parse!
-
 # get runs and server address from the arguments
 runs = []
 address = ""
@@ -71,33 +61,30 @@ for arg in ARGV
   end
 end
 
-# can't do anything without a server address
-if address == ""
-  puts opts
-  exit 1
-end
+uri, creds = parse_address(address, creds)
 
 # connect...
 begin
-  server = T2Server::Server.connect(ARGV[0])
-rescue T2Server::T2ServerError => e
+  server = T2Server::Server.new(uri, conn_params)
+rescue RuntimeError => e
   puts e
   exit 1
 end
 
 # ...and delete them!
-if delete_all
+if options[:all]
   begin
-    server.delete_all_runs
+    server.delete_all_runs(creds)
   rescue T2Server::AuthorizationError => ae
     puts "You are not authorized to delete runs on this server."
   rescue T2Server::T2ServerError => e
-    puts "There was a problem while deleting runs. Some may remain on the server."
+    puts "There was a problem while deleting runs. " +
+      "Some may remain on the server."
   end
 else
   for run in runs
     begin
-      server.delete_run(run)
+      server.delete_run(run, creds)
     rescue T2Server::RunNotFoundError => rnf
       puts "Run '#{run}' not found - skipping."
       next

data/bin/t2-get-output

@@ -0,0 +1,134 @@
+#!/usr/bin/env ruby
+# Copyright (c) 2010-2012 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'
+
+include T2Server::CLI
+
+# set up options
+options = {}
+ports = []
+conn_params, creds = register_options("Usage: t2-get-output [options] " +
+    "server-address run-id") 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, run-ids"
+  opt.separator "  are the id numbers of the runs you want to collect output"
+  opt.separator "  from and [options] can be:"
+  opt.on("-r", "--refs", "Return references to the output data rather than " +
+    "the data itself.") do
+    options[:refs] = true
+  end
+  opt.on("-o", "--output=OUTPUT", "Return the named output port. If none " +
+    "are specified then list all the output ports.") do |val|
+    ports << val.chomp
+  end
+  opt.on("-x", "--exitcode", "Return the exitcode of the run.") do
+    options[:exitcode] = true
+  end
+  opt.on("-e", "--stderr", 'Return the "standard error" output of the run.') do
+    options[:stderr] = true
+  end
+  opt.on("-s", "--stdout", 'Return the "standard out" output of the run.') do
+    options[:stdout] = true
+  end
+  opt.on("-t", "--total-size", "Return the total size of the data in the " +
+    "output.") do
+    options[:tsize] = true
+  end
+  opt.on("-T", "--types", "Return the mime types of singleton ports.") do
+    options[:types] = true
+  end
+end
+
+# get run id and server address from the arguments
+run_id = ""
+address = ""
+for arg in ARGV
+  argc = arg.chomp
+  if argc.match(/https?:\/\//).nil?
+    run_id = argc
+  else
+    address = argc
+  end
+end
+
+uri, creds = parse_address(address, creds)
+
+if run_id.empty?
+  puts opts
+  exit 1
+end
+
+# connect...
+begin
+  server = T2Server::Server.new(uri, conn_params)
+  run = server.run(run_id, creds)
+
+  ports = run.output_ports.keys if ports.empty?
+  ports.each do |p|
+    port = run.output_port(p)
+    puts "#{port.name}"
+    if options[:refs]
+      print "  Reference: "
+      p port.reference
+    else
+      print "  Value: "
+      p port.value
+    end
+
+    if options[:types]
+      print "   Type: "
+      p port.type
+    end
+
+    if options[:tsize]
+      puts "  Total data size: #{port.total_size}"
+    end
+  end
+
+  if options[:exitcode]
+    puts "Exitcode: #{run.exitcode}"
+  end
+
+  if options[:stdout]
+    puts "Stdout: #{run.stdout}"
+  end
+
+  if options[:stderr]
+    puts "Stderr: #{run.stderr}"
+  end
+rescue RuntimeError => e
+  puts e
+  exit 1
+end

data/bin/t2-run-workflow

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010, 2011 The University of Manchester, UK.
+# Copyright (c) 2010-2012 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -15,7 +15,7 @@
 #
 #  * 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. 
+#    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
@@ -32,156 +32,168 @@
 # Author: Robert Haines
 
 require 'rubygems'
-require 't2-server'
-require 'optparse'
+require 't2-server-cli'
+
+include T2Server::CLI
 
 # set up options
 inputs  = {}
 files = {}
-wkf_file = ""
-output_refs = false
-baclava_out = ""
-delete_run = false
-no_wait = false
-opts = OptionParser.new do |opt|
-  opt.banner = "Usage: t2-run-workflow [options] server-address"
-  opt.separator ""
+options = {}
+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 input") do |val|
-    wkf_file = val
+  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
+  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("-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("-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 " +
+    "port values") do |val|
+      inputs[:baclava] = val
+  end
+  opt.on("-o", "--baclava-out=BACLAVA", "Return outputs in baclava format." +
     " A filename may be specified or 'out.xml' is used") do |val|
-    if val != nil and val.include? "."
-      baclava_out = val
-    else
-      baclava_out = "out.xml"
-    end
+      options[:baclava_out] = val.chomp
   end
   opt.on("-n", "--no-wait", "Do not wait for workflow to finish, return " +
     "once it has started running") do |val|
-      no_wait = true
+      options[:no_wait] = true
   end
   opt.on("-r", "--output-refs", "Return URIs that point to the data items " +
     "of the output rather than the data items themselves.") do |val|
-    output_refs = 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 " +
     "the run will still be deleted when its expiry time is reached") do |val|
-    delete_run = val    
+      options[:delete] = val
   end
-  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
+  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
 end
 
-# parse options
-opts.parse!
-
 # read and check server address
-uri = ARGV.shift
-if uri == nil
-  puts opts
-  exit 1
-end
+uri, creds = parse_address(ARGV.shift, creds)
 
-# read workflow
-if wkf_file == ""
-  wkf = ARGF.read
+# read workflow and ensure that it is not empty
+if options[:wkf_file]
+  wkf = IO.read(options[:wkf_file])
 else
-  wkf = IO.read(wkf_file)
+  wkf = ARGF.read
 end
+exit 1 if wkf == ""
 
-# create run
 begin
-  run = T2Server::Run.create(uri, wkf)
-rescue T2Server::T2ServerError => e
-  puts e
-  exit 1
-end
-puts "Created run with uuid: #{run.uuid}"
-puts "Created at #{run.create_time}"
+  T2Server::Run.create(uri, wkf, creds, conn_params) do |run|
+    puts "Created run with identifier: #{run.identifier}"
+    puts "Created at #{run.create_time}"
 
-# set inputs
-if inputs.has_key?(:baclava)
-  run.upload_baclava_file(inputs[:baclava])
-  puts "Uploaded baclava input file"
-else
-  inputs.each do |input, value|
-    puts "Set input '#{input}' to #{value}"
-    run.set_input(input, value)
-  end
-  
-  files.each do |input, file|
-    name = file.split("/")[-1];
-    puts "Set input '#{input}' to use file '#{name}'"
-    run.upload_input_file(input, file)
-  end
-end
+    # set run expiry
+    if options[:expiry]
+      run.expiry=(options[:expiry])
+      puts "Expiry time set to #{run.expiry}"
+    end
+
+    # set inputs
+    in_ports = run.input_ports
+    if inputs.has_key?(:baclava)
+      run.baclava_input = inputs[:baclava]
+      puts "Uploaded baclava input file"
+    else
+      in_ports.each_value do |port|
+        input = port.name
+        if inputs.include? input
+          port.value = inputs[input]
+          puts "Input '#{input}' set to #{port.value}"
+        elsif files.include? input
+          port.file = files[input]
+          puts "Input '#{input}' set to use file '#{port.file}'"
+        else
+          puts "Input '#{input}' has not been set."
+          run.delete
+          exit 1
+        end
+      end
+    end
 
-# output baclava?
-run.set_baclava_output(baclava_out) unless baclava_out == ""
+    # output baclava?
+    run.request_baclava_output if options[:baclava_out]
 
-# start run and wait until it is finished
-run.start
-puts "Started at #{run.start_time}"
+    # start run and wait until it is finished
+    run.start
+    puts "Started at #{run.start_time}"
 
-# bail out if user doesn't want to wait
-exit 0 if no_wait
+    # bail out if user doesn't want to wait
+    exit 0 if options[:no_wait]
 
-# otherwise wait
-print "Running"
-run.wait(:progress => true)
-puts "Finished at #{run.finish_time}"
+    # otherwise wait
+    print "Running"
+    until run.finished?
+      sleep(1)
+      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
+    # 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
 
-if exitcd == 0
-  if baclava_out != ""
-    File.open(baclava_out, "w") do |file|
-      file.syswrite(run.get_baclava_output)
+    if exitcd == 0
+      if options[:baclava_out]
+        File.open(options[:baclava_out], "w") do |file|
+          file.syswrite(run.baclava_output)
+        end
+        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
+        puts "Zip file written to '#{options[:zip_out]}'"
+      else
+        # go through the outputs and print them out
+        puts "Outputs:"
+        run.output_ports.each_value do |port|
+          print "    #{port.name} (#{port.depth}) -> "
+          if options[:output_refs]
+            p port.reference
+          else
+            p port.value
+          end
+        end
+      end
     end
-    puts "Baclava file written to '#{baclava_out}'"
-  else
-    # go through the outputs and print them out
-    puts "Outputs:"
-    run.get_output_ports.each do |o|
-      print "          #{o} -> "
-      p run.get_output("#{o}", output_refs)
+
+    # delete run?
+    if options[:delete]
+      run.delete
+      puts "Run deleted"
     end
   end
-end
-
-# delete run?
-if delete_run
-  run.delete
-  puts "Run deleted"
+rescue RuntimeError => e
+  puts e
+  exit 1
 end