miga-base 0.3.2.3 → 0.3.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 83a243d552f8c0f850cd46e827069e2a0b6abb5b8ed3f2cda41cec21a5b93c85
-  data.tar.gz: 85d9838dc0f9708d50e7d4375b8e641bc85ef096d95c88fcc43e8b5d1421e449
+  metadata.gz: 518860e2b5fbd03ec6887055a40f1d3fe5761f2bbab7550ccf575fa6a2b7b5bf
+  data.tar.gz: 620c88f6eca40d4f054191a871b52d1ec35bd0caf7dc580a8e27f2fcec7fa19f
 SHA512:
-  metadata.gz: 7705f7987ae8a13a6664d8d3a9ca586bbbebc5447c5858fb5c9980c9d31d97a57e779e6987d4ca49dc06b7ccbb8602f22a2747cb1f55acfda3a5bf4edaa1798f
-  data.tar.gz: 3920ee4cdbd9b6666e0d0233c3557218ad30abe4a4e9276de8db9532da628626ba764080766bf27ca5cee335c892cf7c72d610d2fc356dd2da464b24c881c228
+  metadata.gz: 957cf133b881d048a1804b276a331fa9f459275290b8108685e9338173f80300d145c01dc0e0c4ec6f1504248c26651799ebc4fb00bbee94ffc0be01247b051e
+  data.tar.gz: 338cf79cd3dd467b0997b51d6a4677b63eda00f55e957dd85b723b358eb9f207836b1e2df0d8258e2fef1db44081fd08289471b6e872a7f82e94712c844d8ec4

data/actions/about.rb

@@ -3,7 +3,7 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true, info:false, processing:false}
+o = {q:true, info:false, processing:false, tabular:false}
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project])
@@ -12,6 +12,8 @@ OptionParser.new do |opt|
   opt.on("-m", "--metadata STRING",
     "Print name and metadata field only."
     ){ |v| o[:datum]=v }
+  opt.on("--tab STRING",
+    "Returns a tab-delimited table."){ |v| o[:tabular] = v }
   opt_common(opt, o)
 end.parse!
 
@@ -30,12 +32,12 @@ elsif o[:processing]
   keys = MiGA::Project.DISTANCE_TASKS + MiGA::Project.INCLADE_TASKS
   puts MiGA::MiGA.tabulate([:task, :status], keys.map do |k|
     [k, p.add_result(k, false).nil? ? "queued" : "done"]
-  end)
+  end, o[:tabular])
 else
   puts MiGA::MiGA.tabulate([:key, :value], p.metadata.data.keys.map do |k|
     v = p.metadata[k]
     [k, k==:datasets ? v.size : v]
-  end)
+  end, o[:tabular])
 end
 
 $stderr.puts "Done." unless o[:q]

data/actions/ls.rb

@@ -3,7 +3,7 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true, info:false, processing:false, silent:false}
+o = {q:true, info:false, processing:false, silent:false, tabular:false}
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset_opt])
@@ -15,6 +15,8 @@ OptionParser.new do |opt|
   opt.on("-m", "--metadata STRING",
     "Print name and metadata field only. If set, ignores -i."
     ){ |v| o[:datum]=v }
+  opt.on("--tab STRING",
+    "Returns a tab-delimited table."){ |v| o[:tabular] = v }
   opt.on("-s", "--silent",
     "No output and exit with non-zero status if the dataset list is empty."
     ){ |v| o[:silent] = v }
@@ -43,11 +45,12 @@ exit(1) if o[:silent] and ds.empty?
 if not o[:datum].nil?
   ds.each{|d| puts "#{d.name}\t#{d.metadata[ o[:datum] ] || "?"}"}
 elsif o[:info]
-  puts MiGA::MiGA.tabulate(MiGA::Dataset.INFO_FIELDS, ds.map{ |d| d.info })
+  puts MiGA::MiGA.tabulate(
+        MiGA::Dataset.INFO_FIELDS, ds.map{ |d| d.info }, o[:tabular])
 elsif o[:processing]
   comp = ["-","done","queued"]
   puts MiGA::MiGA.tabulate([:name] + MiGA::Dataset.PREPROCESSING_TASKS,
-    ds.map{ |d| [d.name] + d.profile_advance.map{ |i| comp[i] } })
+    ds.map{ |d| [d.name] + d.profile_advance.map{ |i| comp[i] } }, o[:tabular])
 else
   ds.each{|d| puts d.name}
 end

data/actions/summary.rb

@@ -0,0 +1,55 @@
+#!/usr/bin/env ruby
+
+# @package MiGA
+# @license Artistic-2.0
+
+o = {q:true, units:false, tabular:false}
+opts = OptionParser.new do |opt|
+  opt_banner(opt)
+  opt_object(opt, o, [:project, :dataset_opt, :result_dataset])
+  opt.on("--tab STRING",
+    "Returns a tab-delimited table."){ |v| o[:tabular] = v }
+  opt.on("--key STRING",
+    "Returns only the value of the requested key."){ |v| o[:key] = v }
+  opt.on("--with-units",
+    "Includes units in each cell."){ |v| o[:units] = v }
+  opt_common(opt, o)
+end.parse!
+
+##=> Main <=
+opts.parse!
+opt_require(o, project:"-P", name:"-r")
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Listing datasets." unless o[:q]
+if o[:dataset].nil?
+  ds = p.datasets
+elsif MiGA::Dataset.exist? p, o[:dataset]
+  ds = [p.dataset(o[:dataset])]
+else
+  ds = []
+end
+ds = filter_datasets!(ds, o)
+
+$stderr.puts "Loading results." unless o[:q]
+stats = ds.map do |d|
+  r = d.add_result(o[:name].to_sym, false)
+  s = r.nil? ? {} : r[:stats]
+  s.tap{ |i| i[:dataset] = d.name }
+end
+keys = o[:key].nil? ? stats.map(&:keys).flatten.uniq :
+      [:dataset, o[:key].downcase.miga_name.to_sym]
+keys.delete :dataset
+keys.unshift :dataset
+
+table = o[:units] ?
+      stats.map{ |s| keys.map{ |k|
+            s[k].is_a?(Array) ? s[k].map(&:to_s).join('') : s[k] } } :
+      stats.map{ |s| keys.map{ |k| s[k].is_a?(Array) ? s[k].first : s[k] } }
+puts MiGA::MiGA.tabulate(keys, table, o[:tabular])
+
+$stderr.puts "Done." unless o[:q]
+

data/bin/miga

@@ -29,6 +29,7 @@ $task_desc = {
   stats: "Extracts statistics for the given result.",
   files: "Lists all registered files from the results of a dataset or project.",
   run: "Executes locally one step analysis producing the given result.",
+  summary: "Generates a summary table for the statistics of all datasets.",
   # System
   init: "Initialize MiGA to process new projects.",
   daemon: "Controls the daemon of a MiGA project.",
@@ -56,6 +57,7 @@ $task_alias = {
   result_stats: :stats,
   list_files: :files,
   run_local: :run,
+  sum_stats: :summary,
   # System
   c: :console,
   # Taxonomy
@@ -114,6 +116,10 @@ def opt_object(opt, o, what=[:project, :dataset])
     "Recognized names for project-wide results include:",
     *MiGA::Project.RESULT_DIRS.keys.map{|n| " ~ #{n}"}
     ){ |v| o[:name]=v.downcase.to_sym } if what.include? :result
+  opt.on("-r", "--result STRING",
+    "(Mandatory) Name of the result to add. One of:",
+    *MiGA::Dataset.RESULT_DIRS.keys.map{|n| " ~ #{n}"}
+    ){ |v| o[:name]=v.downcase.to_sym } if what.include? :result_dataset
 end
 
 # OptParse flags common to all actions.

data/lib/miga/common/format.rb

@@ -6,15 +6,16 @@ module MiGA::Common::Format
   ##
   # Tabulates an +values+, and Array of Arrays, all with the same number of
   # entries as +header+. Returns an Array of String, one per line.
-  def tabulate(header, values)
+  def tabulate(header, values, tabular=false)
     fields = [header.map(&:to_s)]
-    fields << fields.first.map { |h| h.gsub(/\S/, '-') }
+    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
     fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
-    clen = fields.map { |r| r.map(&:length) }.transpose.map(&:max)
+    clen = tabular ? Array.new(header.size, 0) :
+          fields.map { |r| r.map(&:length) }.transpose.map(&:max)
     fields.map do |r|
       (0 .. clen.size - 1).map do |col_n|
         col_n == 0 ? r[col_n].rjust(clen[col_n]) : r[col_n].ljust(clen[col_n])
-      end.join('  ')
+      end.join(tabular ? "\t" : '  ')
     end
   end
 

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.3, 2, 3]
+  VERSION = [0.3, 3, 0]
   
   ##
   # Nickname for the current major.minor version.

data/scripts/distances.bash

@@ -15,6 +15,5 @@ miga date > "$DATASET.start"
 ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"
 
 # Finalize
-rm -R "$TMPDIR"
 miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f

data/utils/distance/pipeline.rb

@@ -81,6 +81,8 @@ module MiGA::DistanceRunner::Pipeline
     end
     # Save test
     File.open(File.expand_path("#{dataset.name}.intax.txt", home), "w") do |fh|
+      fh.puts "Closest relative: #{cr[0][0]} with AAI: #{cr[0][1]}."
+      fh.puts ""
       fh.puts MiGA::MiGA.tabulate(%w[Rank Taxonomy P-value Signif.], r)
       fh.puts ""
       fh.puts "Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01."

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.2.3
+  version: 0.3.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-31 00:00:00.000000000 Z
+date: 2018-08-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -136,6 +136,7 @@ files:
 - actions/rm.rb
 - actions/run.rb
 - actions/stats.rb
+- actions/summary.rb
 - actions/tax_dist.rb
 - actions/tax_index.rb
 - actions/tax_set.rb