scout-gear 7.2.0 → 8.0.0

data/test/scout/workflow/test_task.rb

@@ -21,38 +21,6 @@ class TestTask < Test::Unit::TestCase
     assert_equal 2, s.run
   end
 
-  def test_override_inputs
-    wf = Workflow.annonymous_workflow "TaskInputs" do
-      input :input1, :string
-      task :step1 => :string do |i| i end
-
-      dep :step1, :input1 => 1
-      input :input2, :string
-      task :step2 => :string do |i| i end
-    end
-
-    job = wf.job(:step2, :input1 => 2)
-    assert_equal Task::DEFAULT_NAME, job.name
-    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
-  end
-
-  def test_override_inputs_block
-    wf = Workflow.annonymous_workflow "TaskInputs" do
-      input :input1, :string
-      task :step1 => :string do |i| i end
-
-      dep :step1 do |id,options|
-        {:inputs => {:input1 => 1}}
-      end
-      input :input2, :string
-      task :step2 => :string do |i| i end
-    end
-
-    job = wf.job(:step2, :input1 => 2)
-    assert_equal Task::DEFAULT_NAME, job.name
-    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
-  end
-
   def test_task_override_dep
     wf = Workflow.annonymous_workflow "TaskInputs" do
       input :input1, :integer
@@ -108,11 +76,13 @@ class TestTask < Test::Unit::TestCase
     assert_equal Task::DEFAULT_NAME, job.name
 
     step1 = wf.job(:step1, :input1 => 3)
+    assert_equal 3, step1.run
     job = wf.job(:double, "TaskInputs#step1" => step1)
     assert_equal 12, job.run
     assert_not_equal Task::DEFAULT_NAME, job.name
 
     step1 = wf.job(:step1, :input1 => 4)
+    assert_equal 4, step1.run
     job = wf.job(:double, "TaskInputs#step1" => step1)
     assert_equal 14, job.run
     assert_not_equal Task::DEFAULT_NAME, job.name
@@ -172,5 +142,171 @@ class TestTask < Test::Unit::TestCase
     job = wf.job(:my_sum, :vv1 => 2, :vv2 => 3)
     assert_equal 5, job.run
   end
+
+  def test_defaults_in_dep_block
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :v1, :integer
+      input :v2, :integer
+      task :sum => :integer do |v1,v2|
+        v1 + v2
+      end
+
+      input :vv1, :integer
+      input :vv2, :integer, nil, 3
+      dep :sum, :v1 => :placeholder, :v2 => :placeholder do |jobname,options,dependencies|
+        raise "Non-numeric value where integer expected" unless Numeric === options[:vv1]
+        {inputs: {v1: options[:vv1], v2: options[:vv2]} }
+      end
+      task :my_sum => :integer do
+        dependencies.last.load
+      end
+    end
+
+    job = wf.job(:my_sum, :vv1 => "2")
+    assert_equal 5, job.run
+  end
+
+  def test_dependency_jobname
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :v1, :integer
+      input :v2, :integer
+      task :sum => :integer do |v1,v2|
+        v1 + v2
+      end
+
+      input :vv1, :integer
+      input :vv2, :integer
+      dep :sum, :v1 => :vv1, :v2 => :vv2, :jobname => "OTHER_NAME"
+      task :my_sum => :integer do
+        dependencies.last.load
+      end
+    end
+
+    job = wf.job(:my_sum, "TEST_NAME", :vv1 => 2, :vv2 => 3)
+    assert_equal 5, job.run
+    assert_equal "TEST_NAME", job.clean_name
+    assert_equal "OTHER_NAME", job.step(:sum).clean_name
+  end
+
+  def test_no_param_last_job
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :v1, :integer
+      input :v2, :integer
+      task :sum => :integer do |v1,v2|
+        v1 + v2
+      end
+
+      dep :sum
+      task :my_sum => :integer do
+        dependencies.last.load
+      end
+    end
+
+    job = wf.job(:my_sum, :v1 => 2, :v2 => "3")
+    assert_equal 5, job.run
+    refute_equal Task::DEFAULT_NAME, job.name
+  end
+
+  def test_no_param_last_job_block
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :v1, :integer
+      input :v2, :integer
+      task :sum => :integer do |v1,v2|
+        v1 + v2
+      end
+
+      dep :sum do |jobname,options|
+        {inputs: options}
+      end
+      task :my_sum => :integer do
+        dependencies.last.load
+      end
+    end
+
+    job = wf.job(:my_sum, :v1 => 2, :v2 => "3")
+    assert_equal 5, job.run
+    refute_equal Task::DEFAULT_NAME, job.name
+  end
+
+
+  def test_override_inputs_block
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :input1, :string
+      task :step1 => :string do |i| i end
+
+      dep :step1, :input1 => 1  do |id,options|
+        {:inputs => options}
+      end
+      input :input2, :string
+      task :step2 => :string do |i| step(:step1).load end
+    end
+
+    job = wf.job(:step2, :input1 => 2)
+    assert_equal 1, job.run
+    assert_equal Task::DEFAULT_NAME, job.name
+    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
+  end
+
+  def test_override_inputs_block_array
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :input1, :string
+      task :step1 => :string do |i| i end
+
+      dep :step1, :input1 => 1  do |id,options|
+        [{:inputs => options}]
+      end
+      input :input2, :string
+      task :step2 => :string do |i| step(:step1).load end
+    end
+
+    job = wf.job(:step2, :input1 => 2)
+    assert_equal 1, job.run
+    assert_equal Task::DEFAULT_NAME, job.name
+    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
+  end
+
+  def test_override_inputs
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :input1, :string
+      task :step1 => :string do |i| i end
+
+      dep :step1, :input1 => 1
+      input :input2, :string
+      task :step2 => :string do |i| step(:step1).load end
+    end
+
+    job = wf.job(:step2, :input1 => 2)
+    assert_equal 1, job.run
+    assert_equal Task::DEFAULT_NAME, job.name
+    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
+  end
+
+  def test_non_default_inputs
+    wf = Workflow.annonymous_workflow "TaskInputs" do
+      input :input1, :integer, "", 1
+      input :input2, :integer, "", 0
+      task :step1 => :string do |i1,i2| i1 + i2 end
+
+      dep :step1, :input2 => 1
+      task :step2 => :string do |i| step(:step1).load end
+
+      dep :step2
+      task :step3 => :string do |i| step(:step1).load end
+    end
+
+    job = wf.job(:step3, :input1 => 1)
+    assert_equal Task::DEFAULT_NAME, job.name
+    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
+    assert_equal 2, job.run
+
+    job = wf.job(:step3, :input1 => 2)
+    assert_equal 3, job.run
+
+
+    job = wf.job(:step3)
+    assert_equal Task::DEFAULT_NAME, job.name
+    assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
+  end
+
 end
 

data/test/scout/workflow/test_usage.rb

@@ -9,27 +9,54 @@ class TestWorkflowUsage < Test::Unit::TestCase
     self.name = "UsageWorkflow"
 
     self.title = "Workflow to test documentation"
-    self.description = "Use this workflow to test if the documentation is correctly presented."
+    self.description = "Use this workflow to evaluate if the documentation is correctly presented."
 
     desc "Desc"
     input :array, :array, "Array"
-    task :step1 => :string do
+    task :step1 => :string do |a|
+      a * ", "
     end
 
-    dep :step1
     desc "Desc2"
+    dep :step1
+    input :float, :float, "Float"
+    task :step2 => :string do |f|
+      step(:step1).load + " " + f.to_s
+    end
+
+    desc "Desc2_fixed"
+    dep :step1, :array => %w(a b)
     input :float, :float, "Float"
-    task :step2 => :string do
+    task :step2_fixed => :string do
+    end
+
+    desc 'Desc3'
+    task_alias :step3, UsageWorkflow, :step2
+
+    desc "Desc3"
+    dep :step3, :array => %w(a b)
+    task :step3_fixed => :string do
     end
   end
 
 
   def test_workflow_usage
-    assert_match "test if the documentation", UsageWorkflow.usage
+    assert_match "evaluate if the documentation", UsageWorkflow.usage
   end
 
   def test_task_usage
-    assert_match "Desc2", UsageWorkflow.tasks[:step2].usage
+    assert_match /Desc2/, UsageWorkflow.tasks[:step2].usage(UsageWorkflow)
+    assert_match /--array/, UsageWorkflow.tasks[:step2].usage(UsageWorkflow)
+    assert_match /Desc2_fixed/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
+    assert_match /Desc3/, UsageWorkflow.tasks[:step3].usage(UsageWorkflow)
+    assert_match /--array/, UsageWorkflow.tasks[:step3].usage(UsageWorkflow)
+  end
+
+  def test_task_input_fixed
+    assert_match /Desc2_fixed/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
+    refute_match /--array/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
+    assert_match /Desc3/, UsageWorkflow.tasks[:step3_fixed].usage(UsageWorkflow)
+    refute_match /--array/, UsageWorkflow.tasks[:step3_fixed].usage(UsageWorkflow)
   end
 end
 

data/test/test_helper.rb

@@ -33,12 +33,14 @@ class Test::Unit::TestCase
   end
 
   def tmpdir
-    @tmpdir = Path.setup('tmp/test_tmpdir').find
+    @tmpdir ||= Path.setup('tmp/test_tmpdir').find
   end
 
   setup do
+    TmpFile.tmpdir = tmpdir.tmpfiles
     Log::ProgressBar.default_severity = 0
     Persist.cache_dir = tmpdir.var.cache
+    Persist::MEMORY_CACHE.clear
     Open.remote_cache_dir = tmpdir.var.cache
     Workflow.directory = tmpdir.var.jobs
     Workflow.workflows.each{|wf| wf.directory = Workflow.directory[wf.name] }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 7.2.0
+  version: 8.0.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-05-09 00:00:00.000000000 Z
+date: 2023-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: term-ansicolor
@@ -114,17 +114,20 @@ files:
 - lib/scout/log/progress.rb
 - lib/scout/log/progress/report.rb
 - lib/scout/log/progress/util.rb
+- lib/scout/log/trap.rb
 - lib/scout/meta_extension.rb
 - lib/scout/misc.rb
 - lib/scout/misc/digest.rb
 - lib/scout/misc/filesystem.rb
 - lib/scout/misc/format.rb
+- lib/scout/misc/helper.rb
 - lib/scout/misc/insist.rb
 - lib/scout/misc/monitor.rb
 - lib/scout/misc/system.rb
 - lib/scout/named_array.rb
 - lib/scout/open.rb
 - lib/scout/open/lock.rb
+- lib/scout/open/lock/lockfile.rb
 - lib/scout/open/remote.rb
 - lib/scout/open/stream.rb
 - lib/scout/open/util.rb
@@ -152,15 +155,26 @@ files:
 - lib/scout/simple_opt/setup.rb
 - lib/scout/tmpfile.rb
 - lib/scout/tsv.rb
+- lib/scout/tsv/attach.rb
+- lib/scout/tsv/change_id.rb
 - lib/scout/tsv/dumper.rb
 - lib/scout/tsv/index.rb
+- lib/scout/tsv/open.rb
 - lib/scout/tsv/parser.rb
 - lib/scout/tsv/path.rb
 - lib/scout/tsv/persist.rb
 - lib/scout/tsv/persist/adapter.rb
+- lib/scout/tsv/persist/fix_width_table.rb
+- lib/scout/tsv/persist/serialize.rb
 - lib/scout/tsv/persist/tokyocabinet.rb
+- lib/scout/tsv/transformer.rb
 - lib/scout/tsv/traverse.rb
 - lib/scout/tsv/util.rb
+- lib/scout/tsv/util/filter.rb
+- lib/scout/tsv/util/process.rb
+- lib/scout/tsv/util/reorder.rb
+- lib/scout/tsv/util/select.rb
+- lib/scout/tsv/util/unzip.rb
 - lib/scout/work_queue.rb
 - lib/scout/work_queue/socket.rb
 - lib/scout/work_queue/worker.rb
@@ -173,7 +187,9 @@ files:
 - lib/scout/workflow/step/file.rb
 - lib/scout/workflow/step/info.rb
 - lib/scout/workflow/step/load.rb
+- lib/scout/workflow/step/progress.rb
 - lib/scout/workflow/step/provenance.rb
+- lib/scout/workflow/step/status.rb
 - lib/scout/workflow/task.rb
 - lib/scout/workflow/task/inputs.rb
 - lib/scout/workflow/usage.rb
@@ -234,19 +250,30 @@ files:
 - test/scout/test_work_queue.rb
 - test/scout/test_workflow.rb
 - test/scout/tsv/persist/test_adapter.rb
+- test/scout/tsv/persist/test_fix_width_table.rb
 - test/scout/tsv/persist/test_tokyocabinet.rb
+- test/scout/tsv/test_attach.rb
+- test/scout/tsv/test_change_id.rb
 - test/scout/tsv/test_dumper.rb
 - test/scout/tsv/test_index.rb
+- test/scout/tsv/test_open.rb
 - test/scout/tsv/test_parser.rb
 - test/scout/tsv/test_persist.rb
+- test/scout/tsv/test_transformer.rb
 - test/scout/tsv/test_traverse.rb
 - test/scout/tsv/test_util.rb
+- test/scout/tsv/util/test_filter.rb
+- test/scout/tsv/util/test_process.rb
+- test/scout/tsv/util/test_reorder.rb
+- test/scout/tsv/util/test_select.rb
+- test/scout/tsv/util/test_unzip.rb
 - test/scout/work_queue/test_socket.rb
 - test/scout/work_queue/test_worker.rb
 - test/scout/workflow/step/test_dependencies.rb
 - test/scout/workflow/step/test_info.rb
 - test/scout/workflow/step/test_load.rb
 - test/scout/workflow/step/test_provenance.rb
+- test/scout/workflow/step/test_status.rb
 - test/scout/workflow/task/test_inputs.rb
 - test/scout/workflow/test_definition.rb
 - test/scout/workflow/test_documentation.rb