rbbt-util 5.40.3 → 5.40.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 92ab9d09861bb5569f70b13f1cc444158f87141c0024e5c3c623f06c1387745e
+  metadata.gz: bc59a09644d58c21eb59f643cd04bd50d4fc81a494f024cef8af1ea26197a0e7
+  data.tar.gz: 84c1669d61fce9e4a239ec7865aee04b67684f99911cc9e378b569517b819388
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+  data.tar.gz: 3e5c396193a6423d7c8afbb381c623844bf457d0a34ef329b7bfe6ac29f6a13841f23b9ce7c3bb051fdeeb35a2e72bfed16279aff52fb3a0ff1484b1587bb841

data/bin/rbbt

@@ -75,7 +75,7 @@ end
 Log.ignore_stderr do
   begin
     require "nokogiri"
-  rescue
+  rescue Exception
   end
 end
 

data/lib/rbbt/resource/path.rb

@@ -359,7 +359,16 @@ module Path
   end
 
   def list
-    Open.read(self.produce.find).split "\n"
+    begin
+      path = self.produce
+    rescue Resource::ResourceNotFound => e
+      begin
+        path = self.set_extension('list').produce
+      rescue Resource::ResourceNotFound 
+        raise e
+      end
+    end
+    Open.read(path).split("\n")
   end
 
   def keys(field = 0, sep = "\t")

data/lib/rbbt/util/migrate.rb

@@ -26,6 +26,7 @@ puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
       if original_path.located?
         paths = [original_path]
       else
+        path = Path.setup(path) unless Path === path
         paths = (path.directory? ? path.glob_all : path.find_all)
       end
 

data/lib/rbbt/workflow/dependencies.rb

@@ -165,7 +165,8 @@ module Workflow
                    workflow, dep_task, options = dependency
 
                    if override_dependencies[workflow.to_s] && value = override_dependencies[workflow.to_s][dep_task]
-                     overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                      setup_override_dependency(value, workflow, dep_task)
                    else
 
@@ -189,21 +190,23 @@ module Workflow
                      job = workflow._job(dep_task, jobname, _inputs)
                      ComputeDependency.setup(job, compute) if compute
 
-                     overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                     overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
 
                      job
                    end
                  when Step
                    job = dependency
-                   overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                   overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                    job
                  when Symbol
                    if override_dependencies[self.to_s] && value = override_dependencies[self.to_s][dependency]
-                     overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                      setup_override_dependency(value, self, dependency)
                    else
                      job = _job(dependency, jobname, _inputs)
-                     overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                     overriden = true if Symbol === job.overriden && (options.nil? || ! options[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
+
                      job
                    end
                  when Proc
@@ -212,7 +215,8 @@ module Workflow
                      wf, task_name, options = orig_dep
 
                      if override_dependencies[wf.to_s] && value = override_dependencies[wf.to_s][task_name]
-                       overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                       overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                       #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                        dep = setup_override_dependency(value, wf, task_name)
                      else
 
@@ -243,7 +247,8 @@ module Workflow
                            d[:task] ||= task_name
                            _override_dependencies = override_dependencies.merge(override_dependencies(d[:inputs] || {}))
                            d = if _override_dependencies[d[:workflow].to_s] && value = _override_dependencies[d[:workflow].to_s][d[:task]]
-                                 overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                                 overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                                 #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                                  setup_override_dependency(value, d[:workflow], d[:task])
                                else
                                  task_info = d[:workflow].task_info(d[:task])
@@ -251,7 +256,7 @@ module Workflow
                                  _inputs = assign_dep_inputs({}, options.merge(d[:inputs] || {}), real_dependencies, task_info) 
                                  _jobname = d.include?(:jobname) ? d[:jobname] : jobname
                                  job = d[:workflow]._job(d[:task], _jobname, _inputs) 
-                                 overriden = true if TrueClass === job.overriden && (d.nil? || ! d[:not_overriden])
+                                 overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                                  job
                                end
                          end
@@ -267,14 +272,15 @@ module Workflow
                        dep[:workflow] ||= wf || self
                        _override_dependencies = override_dependencies.merge(override_dependencies(dep[:inputs] || {}))
                        if _override_dependencies[dep[:workflow].to_s] && value = _override_dependencies[dep[:workflow].to_s][dep[:task]]
-                         overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                         overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                         #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                          setup_override_dependency(value, dep[:workflow], dep[:task])
                        else
                          task_info = (dep[:task] && dep[:workflow]) ? dep[:workflow].task_info(dep[:task]) : nil
                          _inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, task_info)
                          _jobname = dep.include?(:jobname) ? dep[:jobname] : jobname
                          job = dep[:workflow]._job(dep[:task], _jobname, _inputs)
-                         overriden = true if TrueClass === job.overriden && (d.nil? || ! d[:not_overriden])
+                         overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                          job
                        end
                      end

data/lib/rbbt/workflow/step/accessor.rb

@@ -16,6 +16,17 @@ class Step
                        end
                      end
 
+  def relocated
+    if @relocated.nil?
+      if Open.exists?(info_file) and (info[:path] != path)
+        @relocated = true
+      else
+        @relocated = false
+      end
+    end
+    @relocated
+  end
+
   def self.serialize_info(info)
     info = info.clean_version if IndiferentHash === info
     INFO_SERIALIZER.dump(info)

data/lib/rbbt/workflow/step/info.rb

@@ -48,7 +48,11 @@ class Step
         IndiferentHash.setup info_inputs
         @inputs = NamedArray.setup info_inputs.values_at(*task.inputs.collect{|name| name.to_s}), task.inputs
       else
-        @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
+        if Hash === info_inputs
+          @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
+        else
+          @inputs = info_inputs
+        end
       end
     else
       nil

data/lib/rbbt/workflow/step.rb

@@ -51,9 +51,6 @@ class Step
     @info_mutex = Mutex.new
     @inputs = inputs 
     NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs
-    if Open.exists?(info_file) and (info[:path] != path)
-      @relocated = true
-    end
   end
 
   def workflow

data/lib/rbbt/workflow.rb

@@ -495,7 +495,8 @@ module Workflow
       end
     end
 
-    overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
+    #overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
+    overriden = true if dependencies.select{|d| Symbol === d.overriden }.any?
 
     input_values = task.take_input_values(inputs)
     if real_inputs.empty? && Workflow::TAG != :inputs && ! overriden #&& ! dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
@@ -665,6 +666,7 @@ module Workflow
     step = Step.new path
     relocated = false
     dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
+      dep_path = task if dep_path.nil?
       if Open.exists?(dep_path) || Open.exists?(dep_path + '.info') || Open.remote?(dep_path) || Open.ssh?(dep_path)
         Workflow._load_step dep_path
       else

data/share/rbbt_commands/tsv/write_excel

@@ -7,11 +7,12 @@ $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_c
 
 options = SOPT.setup <<EOF
 
-Description
+Write a Excel file with the contents of a TSV
 
-$ rbbt tsv write_excel [options] <filename.tsv|-> <filename.xls|filename.xlsx>
+$ rbbt tsv write_excel [options] <filename.tsv|-> [<filename.xls|filename.xlsx>]
 
-Use - to read from STDIN
+If no target file is specified it uses the same input files but replaces extension. Specifying
+the extension of the excel file select the excel format to use.
 
 -k--key_field* Key field
 -f--fields* Fields

data/share/rbbt_commands/workflow/cmd

@@ -70,9 +70,14 @@ begin
       exit 0
     else
       if command == 'bootstrap'
-        Log.info "No bootstrap for #{ workflow }, running examples instead"
-        puts `rbbt workflow example #{ workflow }`
-        exit 0
+        if wf.libdir["test_workflow.rb"].exists?
+          Log.info "No bootstrap for #{ workflow }, running test_workflow.rb instead"
+          CMD.cmd_log('ruby', wf.libdir["test_workflow.rb"].find)
+        else
+          Log.info "No bootstrap for #{ workflow }, running examples instead"
+          CMD.cmd_log("rbbt workflow example #{ workflow }")
+          exit 0
+        end
       end
 
       raise ParameterException, "Error: Command not understood: #{command}"

data/share/rbbt_commands/workflow/info

@@ -114,6 +114,7 @@ end
 if dependencies and dependencies.any?
   puts Log.color(:magenta, "Dependencies") << ": "
   dependencies.each do |name,task,file|
+    file = name if file.nil?
     puts "  " << file
   end 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.40.3
+  version: 5.40.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-18 00:00:00.000000000 Z
+date: 2023-10-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -584,7 +584,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.19
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)