rbbt-util 5.25.33 → 5.25.34

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5224ee57ce9c9356d168864d1457989ab094b579
-  data.tar.gz: ee950dc591700be501b2d1f84e23bae4492cea1d
+  metadata.gz: 5a19151d029e95e791eb078a3674524810940988
+  data.tar.gz: 828a0fadafa776b7e8b78dc44463fc506414205c
 SHA512:
-  metadata.gz: 64f17229abeefc9faecec3519b347c069f2fd387205f59513fd5d2cf1b38d71eb8352dabefa9fc08c968cf76f0c6e544b061a8841d17ef9a7825930c7553b214
-  data.tar.gz: 76975c93b0151e609959817f158130d0db5e57235cc4f5a6850f3d879912b09d7a3996b6fde0da1f1435ea769ebcd921050d1a54d40c08d99118576218063e6f
+  metadata.gz: 869494e15e50643fbf9f5256af85d7632ce8874ccb648b620db68ced62f27ae845d5d0ec0a8cbe447affae8ab7c1679317df8919d6f1f2e4b6458ba61d1bdb04
+  data.tar.gz: 282f5414814f58c91ba166ba8bf78e74051720a87983b29d482cb19b69c03c6dc56d80b98e5f43b85aaf7abd10115e9dc12c653b8e7f0f1d6b72bee43ee21345

data/lib/rbbt.rb

@@ -3,3 +3,5 @@ module Rbbt
   extend Resource
   pkgdir = 'rbbt'
 end
+
+require 'rbbt/util/version'

data/lib/rbbt/tsv/accessor.rb

@@ -672,7 +672,7 @@ module TSV
     peek
   end
 
-  def head(times=10)
+  def head_str(times=10)
     stream = dumper_stream
     str = ""
     times.times do |i|
@@ -682,6 +682,19 @@ module TSV
     str
   end
 
+  def head_tsv(times = 10)
+    new = self.annotate({})
+    i = 0
+    self.each do |k,v|
+      return new if i == times
+      new[k] = v
+      i += 1
+    end
+    new
+  end
+
+  alias head head_tsv
+
   def summary
 
     key = nil

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

@@ -1,6 +1,8 @@
 module Misc
   ARRAY_MAX_LENGTH = 1000
   STRING_MAX_LENGTH = ARRAY_MAX_LENGTH * 100
+  TSV_MAX_FIELDS=100
+  TSV_MAX_ROWS=100
 
   def self.break_lines(text, char_size=80)
     text = text.gsub("\n", " ")
@@ -120,7 +122,28 @@ module Misc
       filename = "STDIN(rand-#{rand(10000000)})" if filename == '-'
       remove_long_items("TSV Stream: " + filename + " -- " << Misc.fingerprint(obj.options))
     when TSV === obj
-      remove_long_items((obj.all_fields || []) + obj.keys.sort)
+      tsv = obj
+      fields = tsv.fields
+
+      if obj.size > TSV_MAX_ROWS
+        tsv = obj.head(TSV_MAX_ROWS)
+        tsv["Truncated rows at #{TSV_MAX_ROWS} (#{obj.size})"] = nil
+      end
+
+      if fields && fields.length > TSV_MAX_FIELDS
+        tsv = obj.slice(fields[0..TSV_MAX_ROWS-1])
+        tsv.add_field "Truncated at #{TSV_MAX_ROWS} (#{fields.length})" do
+          nil
+        end
+      elsif fields.nil?
+        new = tsv.annotate({})
+        tsv.each do |k,v|
+          new[k] = Misc.remove_long_items(v)
+        end
+        tsv = new
+      end
+
+      tsv
     when (Array === obj and obj.length > ARRAY_MAX_LENGTH)
       remove_long_items(obj[0..ARRAY_MAX_LENGTH-2] << "TRUNCATED at #{ ARRAY_MAX_LENGTH }/#{obj.length}")
     when (Hash === obj and obj.length > ARRAY_MAX_LENGTH)

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

@@ -173,7 +173,7 @@ module Misc
 
     muts = muts.collect do |m|
       case
-      when ref.empty?
+      when (ref.empty? or ref == '-')
         "+" << m
       when (m.length < ref.length and (m.empty? or ref.index(m)))
         "-" * (ref.length - m.length)

data/lib/rbbt/util/version.rb

@@ -0,0 +1,45 @@
+module Rbbt
+  VERSIONS = IndiferentHash.setup({})
+
+  def self.add_version(file)
+    dir = Path.caller_lib_dir(file)
+    libname = File.basename(dir).sub('rbbt-','')
+    return if VERSIONS.include? libname
+
+    version = if dir.VERSION.exists?
+      dir.VERSION.read
+    elsif dir[".git"].exists?
+      head = dir[".git"]["HEAD"].read.split(" ").last.strip
+      dir[".git"][head].read.strip
+    elsif libname.include?("-")
+      name,_sep, v = libname.partition("-")
+      if v =~ /^\d+\.\d+\.\d+$/
+        libname = name
+        v
+      else
+        nil
+      end
+    else
+      nil
+    end
+    return if version.nil?
+
+    VERSIONS[libname] = version
+  end
+
+  def self.versions
+    versions = Rbbt::VERSIONS
+    Gem.loaded_specs.keys.each do |gem|
+      next unless gem.include? 'rbbt'
+      iii gem
+      name = gem.sub('rbbt-','')
+      next if versions.include? name
+      version =  Gem.loaded_specs[gem].version.version
+      versions[name] = version
+    end
+    versions
+  end
+
+  Rbbt.add_version(__FILE__)
+end
+

data/lib/rbbt/workflow.rb

@@ -63,6 +63,8 @@ module Workflow
 
       filename = File.expand_path(filename)
 
+      Rbbt.add_version(filename)
+
       require filename
       Log.debug{"Workflow loaded from: #{ filename }"}
       return true

data/lib/rbbt/workflow/accessor.rb

@@ -184,8 +184,8 @@ class Step
     end
   end
 
-  def init_info
-    return nil if @exec or info_file.nil? or Open.exists?(info_file)
+  def init_info(force = false)
+    return nil if @exec or info_file.nil? or (Open.exists?(info_file) and ! force)
     Open.lock(info_file, :lock => info_lock) do
       i = {:status => :waiting, :pid => Process.pid, :path => path}
       i[:dependencies] = dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies

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

@@ -220,7 +220,7 @@ class Step
           Open.write(pid_file, Process.pid.to_s) unless Open.exists? pid_file
 
           @exec = false
-          init_info
+          init_info(true)
 
           log :setup, "#{Log.color :green, "Setup"} step #{Log.color :yellow, task.name.to_s || ""}"
 
@@ -234,7 +234,8 @@ class Step
             :task_name => @task.name,
             :result_type => @task.result_type,
             :result_description => @task.result_description,
-            :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
+            :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]},
+            :versions => Rbbt.versions
           })
 
 

data/test/rbbt/util/test_misc.rb

@@ -609,4 +609,16 @@ EOF
     assert_equal 60*60*24, Misc.timespan('1d')
     assert_equal 60*60*24, Misc.timespan('1d')
   end
+
+  def test_remove_long_items
+    tsv = TSV.setup({}, "key~value1,value2#:type=:list")
+    tsv["a"] = [2,3]
+    tsv["b"] = [6,7]
+    iii Misc.remove_long_items(tsv)
+    1000.times do |n|
+      tsv[n] = [n*2, n*3]
+    end
+    iii Misc.remove_long_items(tsv)
+  end
 end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.33
+  version: 5.25.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-15 00:00:00.000000000 Z
+date: 2019-03-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -315,6 +315,7 @@ files:
 - lib/rbbt/util/task/job.rb
 - lib/rbbt/util/tc_cache.rb
 - lib/rbbt/util/tmpfile.rb
+- lib/rbbt/util/version.rb
 - lib/rbbt/workflow.rb
 - lib/rbbt/workflow/accessor.rb
 - lib/rbbt/workflow/annotate.rb