rbbt-util 5.28.5 → 5.28.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 0e5cf607bd69452be51bf21d36ceeef49ab3d0cb2821728900547e7db60a03af
+  metadata.gz: 900106fb1799c857a482187c7cb7d18a40c35dbeb5dd231bf8e1851235e28c63
+  data.tar.gz: e5ec2271b3ada0b282963f4ffc7e2b623d8bb84fcb72867a6848b93a80052463
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+  metadata.gz: 1a418d5b4fe4369f7c25dd063c60a65c2b6c0bd7e3dbf9fd156fe875f85ef1b2eeb4d2eb1a03472e191de98bbfbae20abdb86877d381193f86fe4c8325d2f391
+  data.tar.gz: 5225d6dbdbab08d0ed5239eba91bbe3d2a8dd16c92c24fe177b66ed3b9d4baef4e24818057de8bf694edf715aabd72b481926a2466c76492c27b75be25634b27

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -377,6 +377,7 @@ module TSV
         obj.run(true) unless obj.done? || obj.started? || obj.result
 
         stream = obj.get_stream
+        options = {:type => :array}.merge(options) if obj.result_type == :array
 
         if stream
           traverse_obj(stream, options, &block)

data/lib/rbbt/util/misc/inspect.rb

@@ -292,7 +292,7 @@ module Misc
                 files = obj.glob("**/*")
                 "directory: #{Misc.fingerprint(files)}"
               else
-                "file: " << obj << "--" << mtime_str(obj)
+                "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
               end
             else
               obj + " (file missing)"

data/lib/rbbt/workflow.rb

@@ -364,6 +364,7 @@ module Workflow
       raise ParameterException, "Inputs #{Misc.humanize_list(missing_inputs)} are required but were not provided or are nil"
     end
 
+    # jobname => true sets the value of the input to the name of the job
     if task.input_options
       jobname_input = task.input_options.select{|i,o| o[:jobname]}.collect{|i,o| i }.first
     else

data/lib/rbbt/workflow/accessor.rb

@@ -26,105 +26,106 @@ module Workflow
     raise "No '#{name}' task in '#{self.to_s}' Workflow" if task.nil?
     id = File.join(self.to_s, name.to_s)
     @task_info ||= {}
-    @task_info[id] ||= begin description = task.description
-                           result_description = task.result_description
-                           result_type = task.result_type
-                           inputs = rec_inputs(name).uniq
-                           input_types = rec_input_types(name)
-                           input_descriptions = rec_input_descriptions(name)
-                           input_use = rec_input_use(name)
-                           input_defaults = rec_input_defaults(name)
-                           input_options = rec_input_options(name)
-                           extension = task.extension
-                           export = case
-                                    when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
-                                      :synchronous
-                                    when (asynchronous_exports.include?(name.to_sym) or asynchronous_exports.include?(name.to_s))
-                                      :asynchronous
-                                    when (exec_exports.include?(name.to_sym) or exec_exports.include?(name.to_s))
-                                      :exec
-                                    when (stream_exports.include?(name.to_sym) or stream_exports.include?(name.to_s))
-                                      :stream
-                                    else
-                                      :none
-                                    end
+    @task_info[id] ||= begin 
+                         description = task.description
+                         result_description = task.result_description
+                         result_type = task.result_type
+                         inputs = rec_inputs(name).uniq
+                         input_types = rec_input_types(name)
+                         input_descriptions = rec_input_descriptions(name)
+                         input_use = rec_input_use(name)
+                         input_defaults = rec_input_defaults(name)
+                         input_options = rec_input_options(name)
+                         extension = task.extension
+                         export = case
+                                  when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
+                                    :synchronous
+                                  when (asynchronous_exports.include?(name.to_sym) or asynchronous_exports.include?(name.to_s))
+                                    :asynchronous
+                                  when (exec_exports.include?(name.to_sym) or exec_exports.include?(name.to_s))
+                                    :exec
+                                  when (stream_exports.include?(name.to_sym) or stream_exports.include?(name.to_s))
+                                    :stream
+                                  else
+                                    :none
+                                  end
 
-                           dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
-                           info = { :id => id,
-                             :description => description,
-                             :export => export,
-                             :inputs => inputs,
-                             :input_types => input_types,
-                             :input_descriptions => input_descriptions,
-                             :input_defaults => input_defaults,
-                             :input_options => input_options,
-                             :input_use => input_use,
-                             :result_type => result_type,
-                             :result_description => result_description,
-                             :dependencies => dependencies,
-                             :extension => extension
-                           }
-                         end
+                         dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
+                         { :id => id,
+                           :description => description,
+                           :export => export,
+                           :inputs => inputs,
+                           :input_types => input_types,
+                           :input_descriptions => input_descriptions,
+                           :input_defaults => input_defaults,
+                           :input_options => input_options,
+                           :input_use => input_use,
+                           :result_type => result_type,
+                           :result_description => result_description,
+                           :dependencies => dependencies,
+                           :extension => extension
+                         }
+                       end
   end
 
   def rec_dependencies(taskname)
     @rec_dependencies ||= {}
     @rec_dependencies[taskname] ||= begin
-                            if task_dependencies.include? taskname
-
-                              deps = task_dependencies[taskname]
-
-                              #all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}
-
-                              all_deps = []
-                              deps.each do |dep| 
-                                if DependencyBlock === dep
-                                  all_deps << dep.dependency if dep.dependency
-                                else
-                                  all_deps << dep unless Proc === dep
-                                end
-
-                                begin
-                                  case dep
-                                  when Array
-                                    wf, t, o = dep
-
-                                    wf.rec_dependencies(t.to_sym).each do |d|
-                                      if Array === d
-                                        new = d.dup
-                                      else
-                                        new = [dep.first, d]
-                                      end
-
-                                      if Hash === o and not o.empty? 
-                                        if Hash === new.last
-                                          hash = new.last.dup
-                                          o.each{|k,v| hash[k] ||= v}
-                                          new[new.length-1] = hash
-                                        else
-                                          new.push o.dup
+                                      if task_dependencies.include? taskname
+
+                                        deps = task_dependencies[taskname]
+
+                                        #all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}
+
+                                        all_deps = []
+                                        deps.each do |dep| 
+                                          if DependencyBlock === dep
+                                            all_deps << dep.dependency if dep.dependency
+                                          else
+                                            all_deps << dep unless Proc === dep
+                                          end
+
+                                          begin
+                                            case dep
+                                            when Array
+                                              wf, t, o = dep
+
+                                              wf.rec_dependencies(t.to_sym).each do |d|
+                                                if Array === d
+                                                  new = d.dup
+                                                else
+                                                  new = [dep.first, d]
+                                                end
+
+                                                if Hash === o and not o.empty? 
+                                                  if Hash === new.last
+                                                    hash = new.last.dup
+                                                    o.each{|k,v| hash[k] ||= v}
+                                                    new[new.length-1] = hash
+                                                  else
+                                                    new.push o.dup
+                                                  end
+                                                end
+
+                                                all_deps << new
+                                              end if wf && t
+
+                                            when String, Symbol
+                                              rec_deps = rec_dependencies(dep.to_sym)
+                                              all_deps.concat rec_deps
+                                            when DependencyBlock
+                                              dep = dep.dependency
+                                              raise TryAgain
+                                            end
+                                          rescue TryAgain
+                                            retry
+                                          end
                                         end
+                                        all_deps.uniq
+                                      else
+                                        []
                                       end
-
-                                      all_deps << new
-                                    end if wf && t
-
-                                  when String, Symbol
-                                    rec_deps = rec_dependencies(dep.to_sym)
-                                    all_deps.concat rec_deps
-                                  when DependencyBlock
-                                    dep = dep.dependency
-                                    raise TryAgain
-                                  end
-                                rescue TryAgain
-                                  retry
-                                end
-                              end
-                              all_deps.uniq
-                            else
-                              []
-                            end
-                          end
+                                    end
   end
 
   def task_from_dep(dep)
@@ -182,7 +183,7 @@ module Workflow
       acc
     }.tap{|h| IndiferentHash.setup(h)}
   end
-  
+
   def rec_input_use(taskname)
     task = task_from_dep(taskname)
     deps = rec_dependencies(taskname)
@@ -474,7 +475,7 @@ module Workflow
     else
       workdir_find = workdir
     end
- 
+
     workdir_find = File.expand_path(workdir_find)
     path = File.expand_path(path)
     dir = File.dirname(path)

data/lib/rbbt/workflow/remote_workflow/driver/rest.rb

@@ -85,7 +85,11 @@ class RemoteWorkflow
 
       RemoteWorkflow::REST.__prepare_inputs_for_restclient(params)
       name = RemoteWorkflow.capture_exception do
-        RestClient.post(self.encode(url), params)
+        begin
+          RestClient.post(self.encode(url), params)
+        rescue RestClient::MovedPermanently, RestClient::Found, RestClient::TemporaryRedirect
+          raise RbbtException, "REST end-point moved to: #{$!.response.headers[:location]}"
+        end
       end
 
       Log.debug{ "RestClient jobname returned for #{ url } - #{Misc.fingerprint params}: #{name}" }

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

@@ -93,8 +93,8 @@ class Step
         else
           Open.write(path + '.read', value.to_s)
         end
-      when Step === v
-        v = v.produce.load 
+      when Step === value
+        value = value.produce.load 
       else
         Open.write(path, value.to_s)
       end
@@ -110,12 +110,14 @@ class Step
     task_info = workflow.task_info(task_name)
     input_types = task_info[:input_types]
     task_inputs = task_info[:inputs]
+    input_defaults = task_info[:input_defaults]
 
     inputs = {}
     job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
       next unless task_inputs.include? name.to_sym
       next if options and ! options.include?(name)
       next if value.nil?
+      next if input_defaults[name] == value
       inputs[name] = value
     end
 
@@ -125,7 +127,7 @@ class Step
     end
     save_inputs(inputs, input_types, dir)
 
-    inputs.any?
+    inputs.keys
   end
 
   def name

data/lib/rbbt/workflow/usage.rb

@@ -240,7 +240,7 @@ module Workflow
 
           inputs.each do |input, type, file|
             case type
-            when :tsv, :array, :text
+            when :tsv, :array, :text, :file
               lines = file.read.split("\n")
               head = lines[0..5].compact * "\n\n"
               head = head[0..500]

data/share/rbbt_commands/workflow/server

@@ -25,6 +25,7 @@ $ rbbt workflow server [options] <Workflow>
 --stream Activate streaming of workflow tasks
 -fs--file_server Activate file serving for resources
 -mj--monitor_jobs Monitor jobs (UNSAFE)
+-a--app_dir* Application execution directory
 --export_all Export all workflow tasks (use with caution!)
 --export* Export workflow tasks (asynchronous)
 --export_asynchronous* Export workflow tasks as asynchronous
@@ -74,6 +75,7 @@ sync_exports = options[:export_synchronous].split(/\s*,/) if options[:export_syn
 exec_exports = options[:export_exec].split(/\s*,/) if options[:export_exec]
 
 TmpFile.with_file do |app_dir|
+  app_dir = options[:app_dir] if options[:app_dir]
   Misc.in_dir(app_dir) do
     app_dir = Path.setup(app_dir.dup)
     Open.write(app_dir.etc.target_workflow.find, workflow)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.5
+  version: 5.28.6
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-09-30 00:00:00.000000000 Z
+date: 2020-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake