rbbt-util 5.27.8 → 5.27.9

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 88040e654ed6cb7818930897c0d66763e7f7834e7ea530ac0ef45e2b318ed078
+  data.tar.gz: b4813ae7c39189b7a17af4bd958a15823b506a293a03234c7f4cd7af773d37a4
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+  data.tar.gz: 0d17a7e040af5a666d21a8a6db880ede4a50a7491e59476fe0288e6f9c444e174e34a27eec09aa15c6bccfb81e7348e1bb17b2f5ed5b9c115ea88b1321cf8265

data/lib/rbbt/entity.rb

@@ -261,7 +261,7 @@ module Entity
 
         define_method method_name do |*args|
           id = self.id
-          persist_name = orig_method_name.to_s << ":" << (Array === id ? Misc.obj2digest(id) : id)
+          persist_name = orig_method_name.to_s + ":" << (Array === id ? Misc.obj2digest(id) : id)
 
           persist_options = options
           persist_options = persist_options.merge(:other => {:args => args}) if args and args.any?

data/lib/rbbt/fix_width_table.rb

@@ -28,7 +28,7 @@ class FixWidthTable
     else
       Log.debug "FixWidthTable up-to-date: #{ filename } - (in_memory:#{in_memory})"
       if in_memory
-        @file        = Open.open(@filename, :mode => 'r:ASCII-ASCII'){|f| StringIO.new f.read}
+        @file        = Open.open(@filename, :mode => 'r:ASCII-8BIT'){|f| StringIO.new f.read}
       else
         @file        = File.open(@filename, 'r:ASCII-8BIT')
       end

data/lib/rbbt/persist.rb

@@ -365,12 +365,12 @@ module Persist
     type ||= :marshal
 
     persist_options ||= {}
-    if type == :memory and persist_options[:file] and persist_options[:persist] 
+    if type == :memory && persist_options[:file] && persist_options[:persist] 
       repo = persist_options[:repo] || Persist::MEMORY
       if persist_options[:persist] == :update || persist_options[:update]
         repo.delete persist_options[:file]
       end
-      return repo[persist_options[:file]] ||= yield 
+      return repo[persist_options[:file]] ||= yield
     end
 
     if FalseClass === persist_options[:persist]

data/lib/rbbt/util/tmpfile.rb

@@ -17,14 +17,14 @@ module TmpFile
 
   # Creates a random file name, with the given suffix and a random number
   # up to +max+
-  def self.random_name(s = "tmp-", max = 10000000)
+  def self.random_name(s = "tmp-", max = 1_000_000_000)
     n = rand(max)
     s + n.to_s
   end
 
   # Creates a random filename in the temporary directory
-  def self.tmp_file(s = "tmp-", max=10000000, dir = TMPDIR)
-    File.expand_path(File.join(dir, random_name(s,max)))
+  def self.tmp_file(s = "tmp-", max=1_000_000_000, dir = TMPDIR)
+    File.expand_path(File.join(dir, random_name(s, max)))
   end
 
   def self.with_file(content = nil, erase = true, options = {})
@@ -33,7 +33,7 @@ module TmpFile
 
     prefix = options[:prefix] || "tmp-"
     tmpdir = options[:tmpdir] || TMPDIR
-    max = options[:max] || 10000000
+    max = options[:max] || 1_000_000_000
     tmpfile = tmp_file prefix, max, tmpdir
     if options[:extension]
       tmpfile += ".#{options[:extension]}"

data/lib/rbbt/workflow.rb

@@ -10,9 +10,6 @@ require 'rbbt/workflow/util/provenance'
 
 module Workflow
 
-  STEP_CACHE = {}
-  LOAD_STEP_CACHE = {}
-
   class TaskNotFoundException < Exception 
     def initialize(workflow, task = nil)
       if task
@@ -264,11 +261,11 @@ module Workflow
   end
 
   def step_cache
-    @step_cache ||= Workflow::STEP_CACHE
+    Thread.current[:step_cache] ||= {}
   end
 
   def self.load_step_cache
-    @load_step_cache ||= Workflow::LOAD_STEP_CACHE
+    Thread.current[:load_step_cache] ||= {}
   end
 
 

data/lib/rbbt/workflow/accessor.rb

@@ -418,7 +418,7 @@ module Workflow
                        when :hash
                          clean_inputs = Annotated.purge(inputs)
                          clean_inputs = clean_inputs.collect{|i| Symbol === i ? i.to_s : i }
-                         deps_str = dependencies.collect{|d| Step === d ? d.short_path : d }
+                         deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep === Step)) ? "Step: " << d.short_path : d }
                          key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
                          key_str = Misc.obj2str(key_obj)
                          hash_str = Misc.digest(key_str)

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

@@ -137,14 +137,16 @@ class RemoteWorkflow
 
         post_thread = Thread.new(Thread.current) do |parent|
           bl = lambda do |rok|
-            if Net::HTTPOK === rok 
+            case rok
+            when Net::HTTPOK
               _url = rok["RBBT-STREAMING-JOB-URL"]
               @url = File.join(task_url, File.basename(_url)) if _url
               rok.read_body do |c,_a, _b|
                 sin.write c
               end
               sin.close
-            elsif Net::HTTPSeeOther === rok
+            when Net::HTTPRedirection, Net::HTTPAccepted
+              Thread.current.report_on_exception = false
               raise TryThis.new(rok)
             else
               err = StringIO.new
@@ -178,7 +180,8 @@ class RemoteWorkflow
           begin
             RestClient::Request.execute(:method => :post, :url => task_url, :payload => task_params, :block_response => bl)
           rescue TryThis
-            RestClient::Request.execute(:method => :get, :url => $!.payload.header[:location], :block_response => bl)
+            url = $!.payload["location"]
+            RestClient::Request.execute(:method => :get, :url => url, :block_response => bl)
           end
         end
 

data/lib/rbbt/workflow/remote_workflow/remote_step.rb

@@ -26,8 +26,8 @@ class RemoteStep < Step
 
   def cache_file
     begin
-      digest = Misc.obj2digest([base_url, task, base_name, inputs])
-      Rbbt.var.cache.REST[[task, clean_name, digest].compact * "."].find
+      digest = Misc.obj2digest([base_url, task.to_s, base_name, inputs])
+      Rbbt.var.cache.REST[task.to_s][[clean_name, digest].compact * "."].find
     rescue
       Log.exception $!
       raise $!
@@ -143,7 +143,11 @@ class RemoteStep < Step
     @info = Persist.memory("RemoteSteps Info", :url => @url, :persist => true, :update => update) do
       @last_info_time = Time.now
       init_job unless @url
-      info = @adaptor.get_json(File.join(@url, 'info'))
+      info = begin
+               @adaptor.get_json(File.join(@url, 'info'))
+             rescue
+               {:status => :noinfo}
+             end
       info = RemoteWorkflow.fix_hash(info)
       info[:status] = info[:status].to_sym if String === info[:status]
       info
@@ -243,6 +247,7 @@ class RemoteStep < Step
   def join
     return true if cache_files.any?
     init_job unless @url
+    produce unless @started
     Log.debug{ "Joining RemoteStep: #{path}" }
 
     if IO === @result
@@ -258,7 +263,6 @@ class RemoteStep < Step
       sleep 1 unless self.done? || self.aborted? || self.error?
       while not (self.done? || self.aborted? || self.error?)
         sleep 3
-        iif [self.done?, self.status, self.info]
       end
     end
 
@@ -311,6 +315,10 @@ class RemoteStep < Step
     end
   end
 
+  def short_path
+    init_job unless @url
+    [@task, @name] * "/"
+  end
 
   def input_checks
     []

data/share/rbbt_commands/system/clean

@@ -97,7 +97,7 @@ TSV.traverse jobs do |file,i|
   else
     info = begin
              Open.open(i[:info_file]) do |f|
-               Step::INFO_SERIALIAZER.load(f)
+               Step::INFO_SERIALIZER.load(f)
              end
            rescue
              {:status => :noinfo}
@@ -134,7 +134,7 @@ TSV.traverse jobs do |file,i|
     end
   end
 
-  if (force and status !~ /done/) or 
+  if (force && status !~ /done/) or 
     status =~ /\b(old|dirty|nopid|error|missing|aborted|dead|sync)$/ or
     (status == "noinfo" and not done) or
     status == "" 

data/share/rbbt_commands/tsv/uncollapse

@@ -0,0 +1,29 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.setup <<EOF
+Read a TSV file and dump it
+
+$ rbbt tsv read [options] <filename.tsv|->
+
+Use - to read from STDIN
+
+-k--key_field* Key field
+-f--fields* Fields
+-t--type* Type
+-m--merge* Merge from multiple rows
+-h--help Print this help
+
+EOF
+rbbt_usage and exit 0 if options[:help]
+
+file = ARGV.shift
+
+file = STDIN if file == '-'
+
+tsv = TSV.open file, :merge => true, :type => :double
+
+
+puts tsv.to_unmerged_expanded_s

data/share/rbbt_commands/workflow/info

@@ -153,7 +153,7 @@ if recursive
     dep = deps.shift
     inputs = {} if inputs.nil?
     inputs = inputs.merge(dep.info[:inputs] || {})
-    deps = deps.concat dep.dependencies
+    deps = deps.concat dep.dependencies if dep.dependencies
   end
 
   inputs = inputs.merge step.archived_inputs

data/share/rbbt_commands/workflow/task

@@ -337,6 +337,8 @@ if clean_task
       dep.clean 
       dep.set_info :status, :cleaned
     end
+
+    job.clean if job.task_name.to_s == clean_task.to_s
   end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.8
+  version: 5.27.9
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-01 00:00:00.000000000 Z
+date: 2020-07-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -403,6 +403,7 @@ files:
 - share/rbbt_commands/tsv/sort
 - share/rbbt_commands/tsv/subset
 - share/rbbt_commands/tsv/transpose
+- share/rbbt_commands/tsv/uncollapse
 - share/rbbt_commands/tsv/unzip
 - share/rbbt_commands/tsv/values
 - share/rbbt_commands/tsv/write_excel