rbbt-util 5.26.134 → 5.26.135

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ba54901fafef6428fe96583512b3760909f9d0f535575bc26da5bc590ec8d832
-  data.tar.gz: 7d6468ffda01e175ab48dd0f1a622cc00b9abc01624006c133c26950c1ac7225
+  metadata.gz: 909dfa474d2b8e4b75c1eef7083175b77f4851af9d73ce08fd133c4113b278d6
+  data.tar.gz: 6090421ae9f31d4aeebab5f830213449417739c715f2f69d441de0fb2ff9c76a
 SHA512:
-  metadata.gz: 468dfc192067e76b71c73d73b0d2e6b6fb468a24452054edc791337886366630484a4bd43c8fe045334c1bdf46da3ebd19b3e18c6b1a3f236395336b1bc26ab7
-  data.tar.gz: ba8710edc5ec1033d5bd0eca18eff9bd36f2443bc4363a2eee1a94a5fa156be4c1a841a10854a1b86c831a7e61df5d13f00feee9812d76662c6dab90a9842cf4
+  metadata.gz: 26dfe891c7d16718b1c8ea261c24156ba9c8225646ecddbea77f912f4319070dcfbd18fd02906c1801ede7389817406e74b89d27fb939b1c4bdd33f0a6fc4ffe
+  data.tar.gz: 2db91525e84a01390b190b50b9b9f3ffe7689660266d2909bf319bf42c3bcdceb9d03c49e3e591814be485eba85dbd333045f167f18e9d53424cfd10fdb72f15

data/lib/rbbt/workflow/remote/client.rb

@@ -29,12 +29,12 @@ class WorkflowRemoteClient
     end
     init_remote_tasks
   end
-  
+
   def to_s
     name
   end
 
-  def job(task, name, inputs)
+  def job(task, name = nil, inputs = {})
     task_info = task_info(task)
     fixed_inputs = {}
     input_types = IndiferentHash.setup(task_info[:input_types])

data/lib/rbbt/workflow/remote/remote_step.rb

@@ -22,26 +22,33 @@ class WorkflowRemoteClient
       @base_name
     end
 
+    def cache_file
+      digest = Misc.obj2digest([url, task, base_name, inputs])
+      Rbbt.var.cache.REST[digest].find
+    end
+
     def run(no_load = false)
       no_load = @is_stream ? :stream : true if no_load
 
       @mutex.synchronize do
-        @result ||= begin
-                      if @is_exec
-                        exec(no_load)
-                      elsif no_load == :stream
-                        _run_job(:stream)
-                      elsif no_load
-                        init_job 
-                        nil
-                      else
-                        init_job 
-                        join
-                        self.load
-                      end
-                    ensure
-                      @started = true
-                    end
+        @result ||= Persist.persist("REST persist", result_type, :file => cache_file) do
+          begin
+            if @is_exec
+              exec(no_load)
+            elsif no_load == :stream
+              _run_job(:stream)
+            elsif no_load
+              init_job 
+              nil
+            else
+              init_job 
+              join
+              self.load
+            end
+          ensure
+            @started = true
+          end
+        end
       end
 
       return @result if no_load == :stream

data/lib/rbbt/workflow/remote/rest/get.rb

@@ -231,6 +231,7 @@ module WorkflowRESTClient
   def _clean
     begin
       _restart
+      Open.rm cache_file
       params = {:_update => :clean}
       @adaptor.clean_url(url, params) if @url
     rescue Exception

data/lib/rbbt/workflow/util/archive.rb

@@ -211,7 +211,7 @@ puts resource[path].find(search_path)
         end
       end
 
-      TmpFile.with_file(files_and_dirs.sort_by{|l| l.length}.to_a * "\n", false) do |tmp_include_file|
+      TmpFile.with_file(files_and_dirs.sort_by{|l| l.length}.to_a * "\n") do |tmp_include_file|
         test_str = options[:test] ? '-nv' : ''
 
         cmd = "rsync -avztAXHP --progress #{test_str} --files-from='#{tmp_include_file}' #{source}/ #{target}/ #{other_rsync_args}"

data/test/rbbt/workflow/remote/test_client.rb

@@ -1,13 +1,57 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/workflow'
 require 'rbbt/workflow/remote/client'
 
+class TestWFRest
+  extend Workflow
+
+  input :name, :string, "Name to greet", "World"
+  task :hi => :string do |name|
+    "Hello #{name}"
+  end
+
+  dep :hi
+  task :intro => :string do 
+    step(:hi).load + ", nice to meet you"
+  end
+end
+
 class TestRemote < Test::Unit::TestCase
-  def test_ssh
+
+  def _test_ssh
     Log.severity = 0
     client = WorkflowRemoteClient.new "ssh://localhost:Translation", "Translation"
     job = client.job("translate", "SSH-TEST", :genes => ["TP53","KRAS"])
     iii job.url
     puts job.run
   end
+
+  def test_rest
+    Log.with_severity 0 do
+
+      workflow_server(TestWFRest) do |client|
+        assert_equal "Hello World", client.job(:hi, nil, {}).run
+        assert_equal "Hello Miguel", client.job(:hi, nil, {:name => :Miguel}).run
+        assert_equal "Hello Miguel, nice to meet you", client.job(:intro, nil, {:name => :Miguel}).run
+      end
+
+      workflow_server(TestWFRest, :Port => 1902) do |client|
+        assert_equal "Hello World", client.job(:hi, nil, {}).run
+        assert_equal "Hello Miguel", client.job(:hi, nil, {:name => :Miguel}).run
+        assert_equal "Hello Miguel, nice to meet you", client.job(:intro, nil, {:name => :Miguel}).run
+      end
+    end
+  end
+
+  def test_rest_clean
+    real_job = TestWFRest.job(:hi)
+    real_job.run
+    first_time = File.ctime(real_job.path)
+    workflow_server(TestWFRest) do |client|
+      assert File.ctime(real_job.path) == first_time
+      assert_equal "Hello World", client.job(:hi, nil, {}).clean.run
+      assert File.ctime(real_job.path) > first_time
+    end
+  end
 end
 

data/test/test_helper.rb

@@ -12,6 +12,8 @@ require 'rbbt'
 require 'rbbt/resource/path'
 
 
+class TestServerLoaded < Exception; end
+
 class Test::Unit::TestCase
   include FileUtils
 
@@ -44,4 +46,40 @@ class Test::Unit::TestCase
   def datafile_test(file)
     Test::Unit::TestCase.datafile_test(file)
   end
+
+  def workflow_server(workflow, options = {}, &block)
+    trap(:USR1){ raise TestServerLoaded}
+
+    pid = Process.fork do 
+      TmpFile.with_file do |app_dir|
+        Misc.in_dir(app_dir) do
+          require 'rack'
+          ENV["RBBT_WORKFLOW_EXPORT_ALL"] = 'true'
+
+          app_dir = Path.setup(app_dir.dup)
+          Open.write(app_dir.etc.target_workflow.find, workflow.to_s)
+
+          config_ru_file = File.exist?('./workflow_config.ru') ? './workflow_config.ru' : Rbbt.share['workflow_config.ru'].find
+          options[:config] = config_ru_file
+          app = Rack::Server.new(options)
+          app.start do
+            Process.kill :USR1, Process.ppid
+          end
+        end
+      end
+    end
+
+    begin
+      sleep 1 while true
+    rescue TestServerLoaded
+    end
+
+    client = WorkflowRemoteClient.new "http://localhost:#{options[:Port] || 9292}/#{workflow.to_s}", workflow.to_s
+
+    yield client
+
+    Process.kill :INT, pid
+    Process.wait pid
+  end
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.134
+  version: 5.26.135
 platform: ruby
 authors:
 - Miguel Vazquez