rbbt-util 5.42.0 → 5.43.0

data/test/rbbt/util/test_misc.rb

@@ -471,7 +471,7 @@ eum fugiat quo voluptas nulla pariatur?"
   end
 
   def test_snake_case
-    ppp Misc.snake_case("KinaseSARfari")
+    assert_equal "kinase_SAR_fari", Misc.snake_case("KinaseSARFari")
   end
 
   def test_bootstrap
@@ -676,7 +676,7 @@ Commands:
     assert_equal "1.10.2-dirty", Misc.scan_version_text(txt, "bcftools")
 
     txt =<<-EOF
-The Genome Analysis Toolkit (GATK) v4.1.4.1
+The Genome Analysis Toolkit (GATK) 4.1.4.1
 HTSJDK Version: 2.21.0
 Picard Version: 2.21.2
     EOF
@@ -719,5 +719,10 @@ Written by Mike Haertel and others, see <http://git.sv.gnu.org/cgit/grep.git/tre
     end
 
   end
+
+  def test_tokenize
+    iii Misc.tokenize("One Two 'this is Three'")
+    iii Misc.tokenize("some - 'Ex t=tr'")
+  end
 end
 

data/test/rbbt/util/test_procpath.rb

@@ -3,7 +3,7 @@ require 'rbbt/util/procpath'
 
 class TestProcPath < Test::Unit::TestCase
   def test_record_and_plot
-    Log.with_severity 0 do
+    keyword_test :procpath do
       pid = Process.fork do
         a = ""
         (0..1000).each do 

data/test/rbbt/util/test_python.rb

@@ -67,19 +67,23 @@ def python_print():
   end
 
   def test_keras
-    defined = RbbtPython.run do
-      pyimport "tensorflow.keras.models", as: :km
-      defined?(km.Sequential)
+    keyword_test :tensorflow do
+      defined = RbbtPython.run do
+        pyimport "tensorflow.keras.models", as: :km
+        defined?(km.Sequential)
+      end
+      assert defined
     end
-    assert defined
   end
 
   def test_keras_import
-    defined = RbbtPython.run do
-      pyfrom "tensorflow.keras.models", import: :Sequential
-      defined?(self::Sequential)
+    keyword_test :tensorflow do
+      defined = RbbtPython.run do
+        pyfrom "tensorflow.keras.models", import: :Sequential
+        defined?(self::Sequential)
+      end
+      assert defined
     end
-    assert defined
   end
 
   def test_iterate

data/test/rbbt/workflow/step/test_dependencies.rb

@@ -169,7 +169,6 @@ class TestWorkflowDependency < Test::Unit::TestCase
 
   def test_task4
     size = 100000
-    Log.severity = 0
     content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
     last_line = nil
     TmpFile.with_file(content) do |input_file|
@@ -227,7 +226,6 @@ class TestWorkflowDependency < Test::Unit::TestCase
     size = 100000
     content = (1..size).to_a.collect{|num| "Line #{num}" } * "\n"
     last_line = nil
-    Log.severity = 0
     TmpFile.with_file(content) do |input_file|
       begin
         job = DepWorkflow.job(:task6, "TEST", :input_file => input_file)
@@ -250,7 +248,6 @@ class TestWorkflowDependency < Test::Unit::TestCase
     size = 10000
     content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
     last_line = nil
-    Log.severity = 0
     TmpFile.with_file(content) do |input_file|
       begin
       job = DepWorkflow.job(:task8, "TEST", :input_file => input_file)
@@ -285,7 +282,6 @@ class TestWorkflowDependency < Test::Unit::TestCase
   end
 
   def test_resume
-    Log.severity = 0
     job = ResumeWorkflow.job(:reverse)
     job.recursive_clean
     assert_raise do

data/test/rbbt/workflow/test_remote_workflow.rb

@@ -59,7 +59,7 @@ class TestRemoteWorkflow < Test::Unit::TestCase
   end
 
   def test_rest
-    Log.with_severity 0 do
+    keyword_test :rest do
 
       remote_workflow_server(TestWFRest) do |client|
         job = client.job(:hi, nil, {})
@@ -89,10 +89,11 @@ class TestRemoteWorkflow < Test::Unit::TestCase
 
 
   def test_ssh
-    Log.severity = 0
-    client = RemoteWorkflow.new "ssh://#{ENV["HOSTNAME"]}:Translation", "Translation"
-    job = client.job("translate", "SSH-TEST-1", :genes => ["TP53","KRAS"])
-    assert_equal 2, job.run.select{|l| l =~ /ENSG/}.length
+    keyword_test :ssh do
+      client = RemoteWorkflow.new "ssh://#{ENV["HOSTNAME"] || 'localhost'}:Translation", "Translation"
+      job = client.job("translate", "SSH-TEST-1", :genes => ["TP53","KRAS"])
+      assert_equal 2, job.run.select{|l| l =~ /ENSG/}.length
+    end
   end
 end
 

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

@@ -16,16 +16,12 @@ class TestClass < Test::Unit::TestCase
     job = ArchiveTestWF.job(:test_archive)
     job.run
 
-    Log.with_severity 0 do
-      TmpFile.with_file do |tmpdir|
-        Misc.in_dir tmpdir do
-          Step.migrate(job.path, :current, :delete => false, :print => false)
-        end
-        assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
+    TmpFile.with_file do |tmpdir|
+      Misc.in_dir tmpdir do
+        Step.migrate(job.path, :current, :delete => false, :print => false)
       end
+      assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
     end
-
-
   end
 end
 

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

@@ -66,9 +66,7 @@ TestWF:
     EOF
 
     orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
-    Log.with_severity 0 do
-      orchestrator.process(rules, jobs)
-    end
+    orchestrator.process(rules, jobs)
 
     data = Workflow.trace jobs, :plot_data => true
     eend = data.column("End.second").values.collect{|v| v.to_f}.max
@@ -120,9 +118,7 @@ TestWF:
     EOF
 
     orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
-    Log.with_severity 3 do
-      orchestrator.process(rules, jobs)
-    end
+    orchestrator.process(rules, jobs)
 
     jobs.each do |job|
       assert job.step(:c).dependencies.empty?
@@ -167,9 +163,7 @@ TestWF:
     EOF
 
     orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
-    Log.with_severity 3 do
-      orchestrator.process(rules, jobs)
-    end
+    orchestrator.process(rules, jobs)
 
     jobs.each do |job|
       assert job.step(:c).dependencies.empty?
@@ -212,9 +206,7 @@ TestWF:
     EOF
 
     orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
-    Log.with_severity 3 do
-      orchestrator.process(rules, jobs)
-    end
+    orchestrator.process(rules, jobs)
 
     jobs.each do |job|
       next unless job.task_name.to_s == 'd'
@@ -258,9 +250,7 @@ TestWF:
     EOF
 
     orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
-    Log.with_severity 3 do
-      orchestrator.process(rules, jobs)
-    end
+    orchestrator.process(rules, jobs)
 
     jobs.each do |job|
       next unless job.task_name.to_s == 'd' || job.task_name.to_s == 'e'

data/test/test_helper.rb

@@ -10,6 +10,7 @@ require 'rubygems'
 
 require 'rbbt'
 require 'rbbt/resource/path'
+require 'rbbt/util/config'
 
 
 class TestServerLoaded < Exception; end
@@ -41,10 +42,33 @@ class Test::Unit::TestCase
     #end
   end
 
+  def config(*args)
+    Rbbt::Config.get *args
+  end
+
+  def keyword_test(key, &block)
+    test = config(:test, key)
+    if %w(true yes).include?(test.to_s.downcase)
+      block.call
+    else
+      Log.high "Not testing for #{key}"
+    end
+  end
+
+  def self.datadir_test
+    #Rbbt.root.test.data
+    Path.setup(File.join(File.dirname(__FILE__), 'data'))
+  end
+
   def self.datafile_test(file)
-    Path.setup(File.join(File.dirname(__FILE__), 'data', file.to_s))
+    datadir_test[file.to_s]
   end
 
+  def datadir_test
+    Test::Unit::TestCase.datadir_test
+  end
+
+
   def datafile_test(file)
     Test::Unit::TestCase.datafile_test(file)
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.42.0
+  version: 5.43.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-23 00:00:00.000000000 Z
+date: 2024-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -468,6 +468,7 @@ files:
 - test/rbbt/hpc/orchestrate/test_chains.rb
 - test/rbbt/hpc/orchestrate/test_rules.rb
 - test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_hpc_test_workflows.rb
 - test/rbbt/hpc/test_orchestrate.rb
 - test/rbbt/hpc/test_pbs.rb
 - test/rbbt/hpc/test_slurm.rb
@@ -489,7 +490,6 @@ files:
 - test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_hpc.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_monitor.rb
 - test/rbbt/test_packed_index.rb
@@ -584,7 +584,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.0.dev
+rubygems_version: 3.5.6
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
@@ -600,6 +600,7 @@ test_files:
 - test/rbbt/hpc/orchestrate/test_chains.rb
 - test/rbbt/hpc/orchestrate/test_rules.rb
 - test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_hpc_test_workflows.rb
 - test/rbbt/hpc/test_orchestrate.rb
 - test/rbbt/hpc/test_pbs.rb
 - test/rbbt/hpc/test_slurm.rb
@@ -621,7 +622,6 @@ test_files:
 - test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_hpc.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_monitor.rb
 - test/rbbt/test_packed_index.rb

data/test/rbbt/test_hpc.rb

@@ -1,16 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.rb')
-require 'rbbt/hpc'
-require 'rbbt/workflow'
-
-
-class TestHPC < Test::Unit::TestCase
-  def test_relay
-
-    Log.severity = 0
-    Workflow.require_workflow "Translation"
-    job = Translation.job(:translate, nil, :genes => %w(TP53 KRAS))
-    Marenostrum.relay job
-
-  end
-end
-