rbbt-util 5.34.13 → 5.34.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9481e1e7a7e7341b95824a48c314d2316a7283e356ea916b424edb2f15886616
-  data.tar.gz: 5012fb19a8cb88d1e9764a2b6ab049e203c38bc2daf758e112c8e256dca68565
+  metadata.gz: b2e50428f936aab209874c5f26e7504aa14da9a30bc7e2b13575432527a5b6a4
+  data.tar.gz: e522b76bb910b477e303e2cfc323c8708fa4d3bbecc0a7c46de473fe81f1ef6a
 SHA512:
-  metadata.gz: e72b2d6f831128ace58d54e62fdad1f180acdd74d9c73304cc315760dd66c7705b733d024b62794c165a2ea00cdbf6b1d67569f1b40a8e19822424a1638ecd1f
-  data.tar.gz: f8ffee23f77ac7024a06b50d7b48ba6db900080fa06e78d44e61dd4274b4843d6fd203644a5c9be0b730e1728a3b0550e32fc503401744737dcc2bed7401ce8d
+  metadata.gz: e73a4ceda5eca11497ea4f0fe91fda7275375aaf8aeb6f9f70a45a46d4c71022527d7cd32c0cb30700a6bc2724bd1e2d2e0bd808a553ee3c8d6e729baa1dc2c0
+  data.tar.gz: a050c5defff3e3d36fe5682c117802d54cfeb930e3e61ff96da29e326719bf97af6fe85b5c30812dd91c5c6a447201164c15a3e1714aa1226690a0c49782ba9a

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/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/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: 5.34.14
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-09-19 00:00:00.000000000 Z
+date: 2022-09-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake