rbbt-util 5.21.81 → 5.21.83

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: ef2edb51a1ea3d2591ba43aa3350162a043724ac
+  metadata.gz: 9a9203165804c6c7d43397d02aada2d6b9c99649
+  data.tar.gz: f8e2c8ed913e3a01cb27bbc8d2d9751a213ca78e
 SHA512:
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-  data.tar.gz: 9cb934bec141ad0870e3644d25bf5c31f19ea26427ce1a74f1991fcc56e0ea7fac3961b2f455ddcb838dac74ad3549f8155ecb5b5fd2576d7139e552624f702a
+  metadata.gz: 54ab5caf41e7e0b8e3b6d98cd0016f043161e137c3cf78596cc94239797a41d09fdb23fc41d0851e42c250c0422560c850b2c6b18679ad7cb859cfc2441bd20c
+  data.tar.gz: 0057b7bf24c1506791b26b071ea94f5366f242b405464a6fc24c3c4e0307650fbb71fee4c3534f68c383a5bb8b942fc22db9cad929834df63937207a7b5630d3

data/lib/rbbt/rest/client/step.rb

@@ -53,7 +53,7 @@ class WorkflowRESTClient
       end
 
       return @result if no_load == :stream
-      no_load ? path + '?_format=raw' : @result
+      no_load ? Misc.add_GET_param(path, "_format", "raw") : @result
     end
 
 
@@ -220,7 +220,7 @@ class WorkflowRESTClient
 
     def path
       if @url
-        @url + '?_format=raw'
+        Misc.add_GET_param(@url, "_format", "raw")
       else
         [base_url, task, @base_name + '-' +  Misc.fingerprint(inputs)] * "/"
       end

data/lib/rbbt/tsv/excel.rb

@@ -116,7 +116,10 @@ module TSV
             f.puts "#" + header * "\t"
           end
 
-          rows.each do |row| f.puts row * "\t" end
+          rows.each do |row| 
+            values =  row.collect{|c| c.respond_to?(:value) ? c.value : c }
+            f.puts values * "\t"
+          end
         end
 
         TSV.open(filename, options)

data/lib/rbbt/util/R.rb

@@ -121,7 +121,7 @@ source('#{UTIL}');
     when Array
       "c(#{object.collect{|e| ruby2R(e) } * ", "})"
     when Hash
-      object.collect{|k,v| [k, ruby2R(v)] * "="} * ", "
+      "list(" << object.collect{|k,v| [k, ruby2R(v)] * "="} * ", " << ")"
     else
       raise "Type of object not known: #{ object.inspect }"
     end

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

@@ -352,8 +352,8 @@ module Misc
           pos2 = f2.pos
 
           sline2, schr2, sstart2, seend2, srest2 = line2, chr2, start2, eend2, rest2
-          while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2))
-            out.puts line1 + "\t" + line2
+          while chr1 == chr2 and eend1 >= start2
+            out.puts line1 + "\t" + line2 if start1 <= eend2
             if f2.eof?
               chr2 = 'next2'
             else

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

@@ -75,6 +75,14 @@ module Misc
     }.compact * "&"
   end
 
+  def self.add_GET_param(url, param, value)
+    clean_url, param_str = url.split("?")
+    hash = param_str.nil? ? {} : self.GET_params2hash(param_str)
+    IndiferentHash.setup hash
+    hash[param] = value
+    clean_url << "?" << hash2GET_params(hash)
+  end
+
   def self.hash_to_html_tag_attributes(hash)
     return "" if hash.nil? or hash.empty?
     hash.collect{|k,v| 

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

@@ -656,8 +656,8 @@ module Misc
     end
   end
 
-  def self.sort_mutation_stream(stream)
-    CMD.cmd('grep ":" | sort -u | sed "s/^M:/MT:/" | env LC_ALL=C sort -k1,1 -k2,2n -k3,3n -t:', :in => stream, :pipe => true, :no_fail => true)
+  def self.sort_mutation_stream(stream, sep=":")
+    CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
   end
 
 

data/lib/rbbt/util/named_array.rb

@@ -208,5 +208,14 @@ module NamedArray
     end * "\n"
   end
 
+  def to_hash
+    hash = {}
+    self.fields.zip(self) do |field,value|
+      hash[field] = value
+    end
+    IndiferentHash.setup hash
+    hash
+  end
+
 end
 

data/lib/rbbt/workflow/accessor.rb

@@ -689,83 +689,103 @@ module Workflow
     }.tap{|h| IndiferentHash.setup(h)}
   end
 
-  def real_dependencies(task, jobname, inputs, dependencies)
-    real_dependencies = []
-    path_deps = {}
-    dependencies.each do |dependency|
-      real_dep = case dependency
-      when Array
-        workflow, dep_task, options = dependency
-
-        _inputs = IndiferentHash.setup(inputs.dup)
-        compute = options[:compute] if options
-        options.each{|i,v|
-          next if i == :compute or i == "compute"
-          case v
-          when :compute
-            compute = v
-          when Symbol
-            all_d = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
-            rec_dependency = all_d.select{|d| d.task_name.to_sym == v }.first
-
-            if rec_dependency.nil?
-              if inputs.include? v
-                _inputs[i] = _inputs.delete(v)
-              else
-                _inputs[i] = v unless _inputs.include? i
-              end
-            else
-              input_options = workflow.task_info(dep_task)[:input_options][i] || {}
-              if input_options[:stream] or true
-                #rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
-                _inputs[i] = rec_dependency
-              else
-                rec_dependency.abort if rec_dependency.streaming? and not rec_dependency.running?
-                rec_dependency.clean if rec_dependency.error? or rec_dependency.aborted?
-                if rec_dependency.streaming? and rec_dependency.running?
-                  _inputs[i] = rec_dependency.join.load
-                else
-                  rec_dependency.run(true)
-                  rec_dependency.join
-                  _inputs[i] = rec_dependency.load
-                end
-              end
-            end
+  def assign_dep_inputs(_inputs, options, all_d, task_info)
+    options.each{|i,v|
+      next if i == :compute or i == "compute"
+      case v
+      when :compute
+        compute = v
+      when Symbol
+        rec_dependency = all_d.select{|d| d.task_name.to_sym == v }.first
+
+        if rec_dependency.nil?
+          if inputs.include? v
+            _inputs[i] = _inputs.delete(v)
           else
-            _inputs[i] = v
+            _inputs[i] = v unless _inputs.include? i
           end
-        } if options
-
-        job = workflow.job(dep_task, jobname, _inputs)
-        ComputeDependency.setup(job, compute) if compute
-        job
-      when Step
-        dependency
-      when Symbol
-        _inputs = IndiferentHash.setup(inputs.dup)
-        job(dependency, jobname, _inputs)
-      when Proc
-        _inputs = IndiferentHash.setup(inputs.dup)
-        dep = dependency.call jobname, _inputs, real_dependencies
-
-        if DependencyBlock === dependency
-          orig_dep = dependency.dependency 
-          if Hash === orig_dep.last
-            options = orig_dep.last
-            compute = options[:compute]
-
-            if Array === dep
-              dep.each{|d| ComputeDependency.setup(d, compute)}
-            elsif dep
-              ComputeDependency.setup(dep, compute)
-            end if compute
+        else
+          input_options = task_info[:input_options][i] || {}
+          if input_options[:stream] or true
+            #rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
+            _inputs[i] = rec_dependency
+          else
+            rec_dependency.abort if rec_dependency.streaming? and not rec_dependency.running?
+            rec_dependency.clean if rec_dependency.error? or rec_dependency.aborted?
+            if rec_dependency.streaming? and rec_dependency.running?
+              _inputs[i] = rec_dependency.join.load
+            else
+              rec_dependency.run(true)
+              rec_dependency.join
+              _inputs[i] = rec_dependency.load
+            end
           end
         end
-
-        dep
       else
-        raise "Dependency for #{task.name} not understood: #{Misc.fingerprint dependency}"
+        _inputs[i] = v
       end
+    } if options
+
+    _inputs
+  end
+
+  def real_dependencies(task, jobname, inputs, dependencies)
+    real_dependencies = []
+    path_deps = {}
+    dependencies.each do |dependency|
+      _inputs = IndiferentHash.setup(inputs.dup)
+      real_dep = case dependency
+                 when Array
+                   workflow, dep_task, options = dependency
+
+                   compute = options[:compute] if options
+
+                   all_d = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
+                   
+                   _inputs = assign_dep_inputs(_inputs, options, all_d, workflow.task_info(dep_task))
+
+                   job = workflow.job(dep_task, jobname, _inputs)
+                   ComputeDependency.setup(job, compute) if compute
+                   job
+                 when Step
+                   dependency
+                 when Symbol
+                   job(dependency, jobname, _inputs)
+                 when Proc
+                   if DependencyBlock === dependency
+                     orig_dep = dependency.dependency 
+                     if Hash === orig_dep.last
+                       options = orig_dep.last
+                       compute = options[:compute]
+                     else
+                       options = {}
+                       compute = nil
+                     end
+
+                     dep = dependency.call jobname, options.merge(_inputs), real_dependencies
+
+                     dep = [dep] unless Array === dep
+
+                     new_=[]
+                     dep.each{|d| 
+                       inputs = assign_dep_inputs({}, options.merge(d[:inputs]), real_dependencies, d[:workflow].task_info(d[:task]))
+                       d = d[:workflow].job(d[:task], d[:jobname], inputs) if Hash === d
+                       ComputeDependency.setup(d, compute) if compute
+                       new_ << d
+                     }
+                     dep = new_
+                   else
+                     dep = dependency.call jobname, _inputs, real_dependencies
+                     if Hash === dep
+                       inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, dep[:workflow].task_info(dep[:task]))
+                       dep = dep[:workflow].job(dep[:task], dep[:jobname], inputs)
+                     end
+                   end
+
+                   dep
+                 else
+                   raise "Dependency for #{task.name} not understood: #{Misc.fingerprint dependency}"
+                 end
 
       real_dependencies << real_dep
     end

data/lib/rbbt/workflow/usage.rb

@@ -46,7 +46,7 @@ module Task
     if selects.any?
       puts Log.color(:magenta, "Input select options")
       puts
-      selects.each do |input,options|
+      selects.collect{|p| p}.uniq.each do |input,options|
         puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| o.to_s} * ", ") << "\n"
         puts
       end

data/share/Rlib/util.R

@@ -621,3 +621,8 @@ rbbt.plot.text_scatter <- function(formula, data) {
     plot(formula, data=data, cex = 0)
     text(formula, data=data, cex = 0.6, labels=rownames(data))
 }
+
+install.bioc <-function(pkg){
+    source("http://bioconductor.org/biocLite.R")
+    biocLite(pkg)
+}

data/share/install/software/lib/install_helpers

@@ -171,7 +171,7 @@ build(){
 
 versioned?(){
     local name="$1"
-    echo $name | grep ':' &>/dev/null
+    [[ $name =~ : ]]
 }
 
 opt_dir(){

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.81
+  version: 5.21.83
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-05-11 00:00:00.000000000 Z
+date: 2017-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake