rbbt-util 5.34.13 → 5.34.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9481e1e7a7e7341b95824a48c314d2316a7283e356ea916b424edb2f15886616
-  data.tar.gz: 5012fb19a8cb88d1e9764a2b6ab049e203c38bc2daf758e112c8e256dca68565
+  metadata.gz: 7eff409b235c1e08141d4c3c4f30600e91d3c033598731ff6457f1e826389597
+  data.tar.gz: 279844e3cda015f07db9429faf3e9941f12080be28b21bafa2f8472d784969b8
 SHA512:
-  metadata.gz: e72b2d6f831128ace58d54e62fdad1f180acdd74d9c73304cc315760dd66c7705b733d024b62794c165a2ea00cdbf6b1d67569f1b40a8e19822424a1638ecd1f
-  data.tar.gz: f8ffee23f77ac7024a06b50d7b48ba6db900080fa06e78d44e61dd4274b4843d6fd203644a5c9be0b730e1728a3b0550e32fc503401744737dcc2bed7401ce8d
+  metadata.gz: 1047b4a4449dd169bb572790f7dec2ac15f3ee99a6ed45a81108a102f00870d16f0c07776addd9746bf7656d86285e472234f880308ce8ca8c1d5c8fb3df2ad7
+  data.tar.gz: 227c22590c7d08d4e47121c1f814af71d11b9afa7f5fd71aabed014a8e857b6ebd7424b70ed669b8bc3aa993461339209ca1a67a15c3ab9cf81ac9fd85a83cbe

data/lib/rbbt/persist/tsv.rb

@@ -146,9 +146,22 @@ module Persist
           data.serializer = :type 
         end
 
-        data.write_and_read do
-          yield data
+        if persist_options[:persist] == :preload
+          tmp_tsv = yield({})
+          tmp_tsv.annotate data
+          data.serializer = tmp_tsv.type
+          data.write_and_read do
+            tmp_tsv.each do |k,v|
+              data[k] = v
+            end
+          end
+        else
+          data.write_and_read do
+            yield data
+          end
+        end
 
+        data.write_and_read do
           FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
           tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
           tsv.persistence_path = path
@@ -165,6 +178,7 @@ module Persist
       end
     end
   end
+
 end
 
 require 'rbbt/persist/tsv/sharder'

data/lib/rbbt/resource.rb

@@ -204,6 +204,10 @@ module Resource
             case type
             when :string
               Misc.sensiblewrite(final_path, content)
+            when :csv
+              require 'rbbt/tsv/csv'
+              tsv = TSV.csv Open.open(content)
+              Misc.sensiblewrite(final_path, tsv.to_s)
             when :url
               options = {}
               options[:noz] = true if Open.gzip?(final_path) || Open.bgzip?(final_path) || Open.zip?(final_path)

data/lib/rbbt/tsv/csv.rb

@@ -25,7 +25,9 @@ module TSV
           when Path
             CSV.read obj.find.open, options
           when String
-            if Misc.is_filename?(obj)
+            if Open.remote?(obj)
+              CSV.read Open.open(obj), options
+            elsif Misc.is_filename?(obj)
               CSV.read obj, options
             else
               CSV.new obj, **options

data/lib/rbbt/tsv/excel.rb

@@ -266,7 +266,7 @@ module TSV
 
   def self.xls(filename, options ={})
     if Open.remote? filename
-      TmpFile.with_file do |tmp|
+      TmpFile.with_file nil, :extension => 'xls' do |tmp|
         Open.download(filename, tmp)
         TSV::XLS.read(tmp, options)
       end
@@ -278,7 +278,7 @@ module TSV
   def self.xlsx(filename, options ={})
     if Open.remote? filename
 
-      TmpFile.with_file do |tmp|
+      TmpFile.with_file nil, :extension => 'xlsx' do |tmp|
         Open.download(filename, tmp)
         TSV::XLSX.read(tmp, options)
       end

data/lib/rbbt/tsv/manipulate.rb

@@ -360,7 +360,7 @@ module TSV
     new = TSV.setup({}, :key_field => key_field, :fields => fields, :type => type, :filename => filename, :identifiers => identifiers)
     self.with_unnamed do
       keys.each do |k|
-        new[k] = self[k]
+        new[k] = self[k] if self.include?(k)
       end
     end
     new

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

@@ -193,6 +193,16 @@ def self.add_libdir(dir=nil)
     insist(3, &block)
   end
 
+  def self.chunk(array, num)
+    total = array.length
+    current = 0
+    while current < total
+      last = current + num - 1
+      yield array[current..last]
+      current = last + 1
+    end
+  end
+
   # Divides the array into +num+ chunks of the same size by placing one
   # element in each chunk iteratively.
   def self.divide(array, num)

data/lib/rbbt/util/misc.rb

@@ -71,6 +71,9 @@ module Misc
   end
 
   def self.timespan(str, default = "s")
+
+    return - timespan(str[1..-1], default) if str[0] == "-"
+    
     if str.include?(":")
       seconds, minutes, hours = str.split(":").reverse
       return seconds.to_i + minutes.to_i * 60 + hours.to_i * 60 * 60
@@ -86,7 +89,7 @@ module Misc
       "h" => (60 * 60),
       "d" => (60 * 60 * 24),
       "w" => (60 * 60 * 24 * 7),
-      "mo" => (60 * 60 * 24 * 30),
+      "mo" => (60 * 60 * 24 * 31),
       "y" => (60 * 60 * 24 * 365),
     }
 

data/lib/rbbt/util/open.rb

@@ -640,7 +640,7 @@ module Open
     io
   end
 
-  def self.download(url, file)
+  def self.download_old(url, file)
     Open.open(url, :mode => 'rb', :noz => true) do |sin|
       Open.open(file, :mode => 'wb') do |sout|
         Misc.consume_stream(sin, false, sout)
@@ -648,6 +648,10 @@ module Open
     end
   end
 
+  def self.download(url, path)
+    Open.wget(url, "--output-document" => path, :pipe => false)
+  end
+
   def self.can_open?(file)
     String === file and (Open.exist?(file) or remote?(file))
   end
@@ -841,7 +845,4 @@ module Open
     File.symlink?(path) && ! File.exist?(File.readlink(path))
   end
 
-  def self.download(url, path)
-    Open.wget(url, "--output-document" => path)
-  end
 end

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

@@ -203,7 +203,7 @@ class Step
     files
   end
 
-  def file(name)
+  def file(name=nil)
     Path.setup(File.join(files_dir, name.to_s), workflow, self)
   end
 

data/share/Rlib/plot.R

@@ -39,3 +39,9 @@ geom_entity <- function (real.geom = NULL, mapping = NULL, data = NULL, stat = "
 }
 
 rbbt.ggplot2.rotate_x_labels <- function(){ theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1)) }
+
+rbbt.ggplot2.theme <- function(plot){
+
+    plot + theme_classic() + scale_y_continuous(labels=scales::comma) + scale_x_continuous(labels=scales::comma) + rbbt.ggplot2.rotate_x_labels()
+
+}

data/share/Rlib/util.R

@@ -812,7 +812,7 @@ rbbt.plot.text_scatter <- function(formula, data) {
 rbbt.install.CRAN <- function(pkg){
     cat("Try CRAN install:", pkg, "\n")
     res = FALSE
-    tryCatch({ install.packages(pkg); library(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
+    tryCatch({ install.packages(pkg); library(pkg, character.only=T); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
     return(res)
 }
 

data/share/rbbt_commands/tsv/info

@@ -18,6 +18,7 @@ Display summary information. Works with Tokyocabinet HDB and BDB as well.
 -hh--header_hash* Change the character used to mark the header line (defaults to #)
 -k--key_field* Change the key field
 -f--fields* Change the fields to load
+-fp--fingerprint Fingerprint values
 -s--sep* Change the fields separator (default TAB)
 -h--help Help
 EOF
@@ -70,7 +71,11 @@ else
   
   puts "Rows: #{Log.color :blue, rows}" 
   parts = []
-  header.first_line.split(header.sep, -1).each_with_index{|p,i| parts << (Log.color(:cyan, "(#{i}) ") << p.strip) }
+  header.first_line.split(header.sep, -1).each_with_index do |p,i| 
+   p.strip!
+   p = Misc.fingerprint p.split("|") if %w(double flat).include?(header.options[:type].to_s) && options[:fingerprint]
+   parts << (Log.color(:cyan, "(#{i}) ") << p.strip) 
+  end
   puts parts * "\t"
   puts
 end

data/test/rbbt/util/test_misc.rb

@@ -610,6 +610,8 @@ EOF
     assert_equal 60*60*24, Misc.timespan('1d')
     assert_equal 60*60*24, Misc.timespan('1d')
     assert_equal 60*60*24, Misc.timespan('24:00:00')
+
+    assert_equal Misc.timespan('1min'), - Misc.timespan('-1min')
   end
 
   def test_remove_long_items

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.13
+  version: 5.34.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-09-19 00:00:00.000000000 Z
+date: 2022-10-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake