rbbt-util 5.32.10 → 5.32.16

data/test/rbbt/util/test_python.rb

@@ -2,6 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/util/python'
 
 class TestPython < Test::Unit::TestCase
+
   def test_python
     TmpFile.with_file do |tmpdir|
       code =<<-EOF
@@ -67,7 +68,7 @@ def python_print():
 
   def test_keras
     defined = RbbtPython.run do
-      pyimport "keras.models", as: :km
+      pyimport "tensorflow.keras.models", as: :km
       defined?(km.Sequential)
     end
     assert defined
@@ -75,7 +76,7 @@ def python_print():
 
   def test_keras_import
     defined = RbbtPython.run do
-      pyfrom "keras.models", import: :Sequential
+      pyfrom "tensorflow.keras.models", import: :Sequential
       defined?(self::Sequential)
     end
     assert defined

data/test/rbbt/util/test_simpleDSL.rb

@@ -35,12 +35,12 @@ class TestDSL < Test::Unit::TestCase
 
   def test_config
     config = <<-EOC
-  action1("Hello")
-  action2("Good bye")
+  action1 "Hello"  
+  action2 "Good bye" 
     EOC
 
     begin
-      assert(@parser.config(:action) == config)
+      assert_equal config.split("\n").collect{|l| l.strip}, @parser.config(:action).split("\n").collect{|l| l.strip}
     rescue SimpleDSL::NoRuby2Ruby
     end
   end

data/test/rbbt/workflow/util/test_data.rb

@@ -0,0 +1,48 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/workflow/util/data'
+
+module TestDataWF
+  extend Workflow
+  extend Workflow::Data
+
+  input :salutation, :string
+  task :salute_luis => :string do |name,salutation|
+    "Hi Luis: #{salutation}"
+  end
+
+  input :name, :string
+  input :salutation, :string
+  task :salute => :string do |name,salutation|
+    "Hi #{name}: #{salutation}"
+  end
+
+  data_task :salute_data, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
+    options.merge({:salutation => directory.salutation.read})
+  end
+
+  data_task :salute_data2, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
+    {:task => :salute_luis, :inputs => options.merge({:salutation => directory.salutation.read})}
+  end
+end
+
+class TestWorkflowData < Test::Unit::TestCase
+  def test_workflow_data
+    TmpFile.with_file do |tmpdir|
+      tmpdir = Path.setup(tmpdir.dup)
+
+      Open.write(tmpdir.TestDir.options.name, "Miguel")
+      Open.write(tmpdir.TestDir.salutation, "My salutations")
+
+      TestDataWF.data tmpdir
+
+      job = TestDataWF.job(:salute_data, "TestDir")
+      job.recursive_clean.run
+      assert job.run.include? "Miguel"
+
+      job = TestDataWF.job(:salute_data2, "TestDir")
+      job.recursive_clean.run
+      assert job.run.include? "Luis"
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.10
+  version: 5.32.16
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-04 00:00:00.000000000 Z
+date: 2021-07-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -344,9 +344,11 @@ files:
 - lib/rbbt/workflow/task.rb
 - lib/rbbt/workflow/usage.rb
 - lib/rbbt/workflow/util/archive.rb
+- lib/rbbt/workflow/util/data.rb
 - lib/rbbt/workflow/util/orchestrator.rb
 - lib/rbbt/workflow/util/provenance.rb
 - lib/rbbt/workflow/util/trace.rb
+- python/rbbt.py
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R
@@ -549,13 +551,14 @@ files:
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/util/test_archive.rb
+- test/rbbt/workflow/util/test_data.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -570,104 +573,104 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.7.6
-signing_key:
+rubygems_version: 3.1.4
+signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/test_packed_index.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
 - test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
-- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_data.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/test_step.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_concurrency.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/resource/test_path.rb
 - test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_procpath.rb
+- test/rbbt/util/misc/test_development.rb
 - test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_format.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_config.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_R.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_hpc.rb
-- test/rbbt/test_persist.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/test_association.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/test_helper.rb