t2-server 0.1.0 → 0.1.1

data/README.rdoc

@@ -1,7 +1,7 @@
 = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
 
 Authors::     Robert Haines
-Gem Version:: 0.1.0
+Gem Version:: 0.1.1
 API Version:: 2.2a1
 Contact::     mailto:rhaines@manchester.ac.uk
 URL::         http://taverna.sourceforge.net/

data/bin/run_workflow

@@ -61,6 +61,7 @@ end
 inputs  = {}
 wkf_file = ""
 print_output = true
+baclava_out = ""
 opts = OptionParser.new do |opt|
   opt.banner = "Usage: run_workflow [options] server-address"
   opt.separator ""
@@ -75,7 +76,19 @@ opts = OptionParser.new do |opt|
     input, value = val.chomp.split(':')
     inputs[input] = value
   end
-  opt.on("-p", "--[no-]print", "Print outputs to the console. On by default") do |val|
+  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
+  end
+  opt.on("-p", "--[no-]print", "Print outputs to the console. On by default " +
+    "unless baclava output is selected") do |val|
     print_output = val
   end
   opt.on_tail("-h", "-?", "--help", "Show this message") do
@@ -117,11 +130,19 @@ puts "Created run with uuid: #{run.uuid}"
 puts "Created at #{run.create_time}"
 
 # set inputs
-inputs.each do |input, value|
-  puts "Set input '#{input}' to #{value}"
-  run.set_input(input, value)
+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
 end
 
+# output baclava?
+run.set_baclava_output(baclava_out) unless baclava_out == ""
+
 # start run and wait until it is finished
 run.start
 puts "Started at #{run.start_time}"
@@ -138,8 +159,15 @@ if stdout != "" then puts "Stdout:\n#{stdout}" end
 if stderr != "" then puts "Stderr:\n#{stderr}" end
 
 if exitcd == 0
-  puts "Outputs:"
-  get_outputs(run, print_output)
+  if baclava_out != ""
+    File.open(baclava_out, "w") do |file|
+      file.syswrite(run.get_baclava_output)
+    end
+    puts "Baclava file written to '#{baclava_out}'"
+  else
+    puts "Outputs:"
+    get_outputs(run, print_output)
+  end
 end
 
 # delete run

data/lib/t2server/run.rb

@@ -46,6 +46,9 @@ module T2Server
   #   download.
   class Run
     private_class_method :new
+
+    # The identifier of this run on the server. It is currently a UUID
+    # (version 4).
     attr_reader :uuid
 
     # :stopdoc:
@@ -61,7 +64,8 @@ module T2Server
       @server = server
       @uuid = uuid
       @workflow = ""
-      @baclava = false
+      @baclava_in = false
+      @baclava_out = ""
       
       @links = get_attributes(@server.get_run_attribute(uuid, ""))
       #@links.each {|key, val| puts "#{key}: #{val}"}
@@ -315,11 +319,39 @@ module T2Server
       state = status
       raise RunStateError.new(state, STATE[:initialized]) if state != STATE[:initialized]
 
-      @baclava = true
+      @baclava_in = true
       rename = upload_file(filename)
       @server.set_run_attribute(@uuid, @links[:baclava], rename)
     end
 
+    # :call-seq:
+    #   run.set_baclava_output(name="out.xml") -> bool
+    #
+    # Set the server to save the outputs of this run in baclava format. The
+    # filename can be specified with the _name_ parameter otherwise a default
+    # of 'out.xml' is used. This must be done before the run is started.
+    def set_baclava_output(name="out.xml")
+      state = status
+      raise RunStateError.new(state, STATE[:initialized]) if state != STATE[:initialized]
+      
+      @baclava_out = name.strip_path
+      @server.set_run_attribute(@uuid, @links[:output], @baclava_out)
+    end
+
+    # :call-seq:
+    #   run.get_baclava_output -> string
+    #
+    # Get the outputs of this run in baclava format. This can only be done if
+    # the output has been requested in baclava format by #set_baclava_output
+    # before starting the run.
+    def get_baclava_output
+      state = status
+      raise RunStateError.new(state, STATE[:finished]) if state != STATE[:finished]
+      
+      raise AttributeNotFoundError.new("#{@links[:wdir]}/#{@baclava_out}") if @baclava_out == ""
+      @server.get_run_attribute(@uuid, "#{@links[:wdir]}/#{@baclava_out}")
+    end
+
     # :call-seq:
     #   run.ls(dir="") -> [[dirs], [objects]]
     #

data/lib/t2server/server.rb

@@ -42,7 +42,14 @@ module T2Server
   # instances.
   class Server
     private_class_method :new
-    attr_reader :uri, :run_limit
+
+    # The URI of this server instance as a String.
+    attr_reader :uri
+    
+    # The maximum number of runs that this server will allow at any one time.
+    # Runs in any state (+Initialized+, +Running+ and +Finished+) are counted
+    # against this maximum.
+    attr_reader :run_limit
     
     # list of servers we know about
     @@servers = []

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-server
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 25
   prerelease: false
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-09-02 00:00:00 +01:00
+date: 2010-09-03 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -26,10 +26,12 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 49
         segments: 
         - 0
-        version: "0"
+        - 8
+        - 7
+        version: 0.8.7
   type: :development
   version_requirements: *id001
 description: This gem provides access to the Taverna 2 Server REST interface from Ruby.