rbbt-util 5.32.12 → 5.32.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 26e430d330e39371b8fb59f3508b3e1eb215bf042bf2faa5262040fd19369e24
+  metadata.gz: 4c61ee9aa98e617b2cd43ea3c57b71439cbb5c2c65282ed7695fafd5c46ccbf3
+  data.tar.gz: e30e12b162f86ee74b4a4c33e44c7e976612a11e8219b2afd9c6cc0ea520fe24
 SHA512:
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+  metadata.gz: abee1a9322982a9da1cca62f7c36e47a7517a6c8066177f5155f8bfc17e6bc19054bfc1b8068c67e58fb0bf4a1c7585c3d493c2ca70d600391348e03f61ebab6
+  data.tar.gz: 80e3f811802c5e33cefd1c7c9561a9bdfcc2cfbfa97f300babd3c095de1d5bfb14a88e2e52918c4be9e869f9bf2722df68a493895077101e42b2f4ee57e9427c

data/lib/rbbt/tsv/manipulate.rb

@@ -174,6 +174,8 @@ module TSV
         if Hash === @monitor
           desc = @monitor[:desc] if @monitor.include? :desc 
           step = @monitor[:step] if @monitor.include? :step 
+        elsif String === @monitor
+          desc = @monitor
         end
         progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
       end

data/lib/rbbt/util/R.rb

@@ -41,7 +41,7 @@ source('#{UTIL}');
 
     if monitor
       #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
-      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => true))
+      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => options[:xvfb]))
       while line = io.gets
         case monitor
         when Proc
@@ -52,7 +52,7 @@ source('#{UTIL}');
       end
       nil
     else
-      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => true))
+      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => options[:xvfb]))
     end
   end
 

data/lib/rbbt/util/python.rb

@@ -3,10 +3,17 @@ require 'pycall/import'
 
 module RbbtPython
   extend PyCall::Import
+
+  def self.exec(script)
+    PyCall.exec(script)
+  end
+
   def self.run(mod = nil, imports = nil, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -17,8 +24,10 @@ module RbbtPython
 
   def self.run_log(mod = nil, imports = nil, severity = 0, severity_err = nil, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -31,8 +40,10 @@ module RbbtPython
 
   def self.run_log_stderr(mod = nil, imports = nil, severity = 0, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -49,4 +60,14 @@ module RbbtPython
     end
   end
 
+  def self.add_paths(paths)
+    self.run 'sys' do
+      paths.each do |path|
+        sys.path.append path
+      end
+    end
+  end
+
+  RbbtPython.add_paths Rbbt.python.find_all
+  RbbtPython.pyimport "rbbt"
 end

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

@@ -0,0 +1,31 @@
+require 'rbbt/workflow'
+require 'rbbt/workflow/examples'
+
+module Workflow
+  module Data
+    def data(directory)
+      @@data_directory = directory
+    end
+
+    def get_datadir(clean_name)
+      data_dir = File.join(@@data_directory, clean_name)
+      raise "Data dir not found #{data_dir}" unless File.directory?(data_dir)
+      if Path === @@data_directory
+        @@data_directory.annotate data_dir
+      else
+        Path.setup(data_dir)
+      end
+    end
+
+    def data_task(name, workflow, oname, *rest, &block)
+      dep_task(name, workflow, oname, *rest) do |jobname, options|
+        data_dir = self.get_datadir(jobname)
+        task_info = workflow.task_info(oname)
+        dir_options = Workflow.load_inputs(data_dir.options, task_info[:inputs], task_info[:input_types])
+        data_options = block.call data_dir, dir_options, task_info
+        {:inputs => data_options.merge(options)}
+      end
+    end
+  end
+
+end

data/python/rbbt.py

@@ -0,0 +1,3 @@
+def rbbt():
+    print("Rbbt")
+

data/share/install/software/lib/install_helpers

@@ -499,7 +499,7 @@ install_jar(){
     local url="$2"
 
     [ -d  "$OPT_DIR/$name/" ] || mkdir -p  "$OPT_DIR/$name/"
-    wget "$url" -O "$OPT_DIR/jars/$name.jar" || wget "$url" -O "$OPT_DIR/jars/$name.jar" --no-check-certificate || (rm "$OPT_DIR/jars/$name.jar"; exit -1)
+    wget "$url" -O "$OPT_DIR/$name/$name.jar" || wget "$url" -O "$OPT_DIR/$name/$name.jar" --no-check-certificate || (rm "$OPT_DIR/$name/$name.jar"; exit -1)
     link "$OPT_DIR/$name/$name.jar" "$OPT_JAR_DIR/$name.jar" 
 }
 

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/workflow/util/test_data.rb

@@ -0,0 +1,35 @@
+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 :name, :string
+  input :salutation, :string
+  task :salute => :string do |name,salutation|
+    "Hi #{name}: #{salutation}"
+  end
+
+  data_task :salute_data, TestDataWF, :salute do |directory,options|
+    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
+      ppp job.run
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.12
+  version: 5.32.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-25 00:00:00.000000000 Z
+date: 2021-05-26 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
@@ -549,6 +551,7 @@ 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
@@ -579,6 +582,7 @@ test_files:
 - test/rbbt/workflow/test_remote_workflow.rb
 - test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.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