miga-base 0.3.0.1 → 0.3.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 20d84d5171a208f02d6278778c7967ff7d1ec3e5
-  data.tar.gz: 7f92d205fb8058af84b15c96d158049889efa0ca
+  metadata.gz: 128dc675d7890680368567d6d20d4fc37f746852
+  data.tar.gz: f58156b654b1463670d48c613c552e55b14d1b18
 SHA512:
-  metadata.gz: 3d78f1bf02243234a668e91cd2bafe608a7ca48fd41a11bcee77f6a7164d0222841a0b54ed8c3076f38d47268ff671ac128519d6433284f7fef8286d638c77b4
-  data.tar.gz: 21ae7b9c7514d542496197541a14ddc3d19dd424f97c04ec1a1913f34dadf93f4b25f76c7d54d2c3c79b4ccb67cf567bb552ea35c263dc62f0db4ab235757ffd
+  metadata.gz: 9431dc3c5ce79996bdaf77d9a2bffe06cb32645a95ebbe397164de0706825c50c8da54fdd0574b4ba4123226cbbd3dd7a322a9a5d87d8dd40ced955c618f59ae
+  data.tar.gz: 24e4ba089124116c4a12b67df9be0930c11a60af8d70dac3a2525061ffddf195e20b4f130d94de391a474af7782222066f2a41552de5f078234af7f3d03f0972

data/actions/create_dataset.rb

@@ -12,8 +12,6 @@ OptionParser.new do |opt|
     ){ |v| o[:ref]=!v }
   opt.on("-d", "--description STRING",
     "Description of the dataset."){ |v| o[:description]=v }
-  opt.on("-u", "--user STRING",
-    "Owner of the dataset."){ |v| o[:user]=v }
   opt.on("-c", "--comments STRING",
     "Comments on the dataset."){ |v| o[:comments]=v }
   opt.on("-m", "--metadata STRING",
@@ -43,9 +41,7 @@ end.parse!
 
 ##=> Main <=
 opt_require(o)
-opt_require(o, type:"-t") unless o[:update]
-raise "Unrecognized dataset type: #{o[:type]}." if
-  (not o[:update]) and MiGA::Dataset.KNOWN_TYPES[o[:type]].nil?
+opt_require_type(o, MiGA::Dataset) unless o[:update]
 
 $stderr.puts "Loading project." unless o[:q]
 p = MiGA::Project.load(o[:project])
@@ -55,7 +51,7 @@ raise "Dataset already exists, aborting." unless
   o[:update] or not MiGA::Dataset.exist?(p, o[:dataset])
 $stderr.puts "Loading dataset." unless o[:q]
 d = o[:update] ? p.dataset(o[:dataset]) :
-  MiGA::Dataset.new(p, o[:dataset], o[:ref], {})
+  MiGA::Dataset.new(p, o[:dataset], o[:ref])
 raise "Dataset does not exist." if d.nil?
 
 in_files = [:raw_reads, :trimmed_fasta_s, :trimmed_fasta_c, :assembly]
@@ -83,21 +79,7 @@ if in_files.any? { |i| not o[i].nil? }
   cp_result(o, d, p, :assembly, :assembly, %w[.LargeContigs.fna])
 end
 
-unless o[:metadata].nil?
-  o[:metadata].split(",").each do |pair|
-    (k,v) = pair.split("=")
-    case v
-      when "true";  v = true
-      when "false"; v = false
-      when "nil";   v = nil
-    end
-    d.metadata[k] = v
-  end
-end
-[:type, :description, :user, :comments].each do |k|
-  d.metadata[k]=o[k] unless o[k].nil?
-end
-
+d = add_metadata(o, d)
 d.save
 p.add_dataset(o[:dataset]) unless o[:update]
 res = d.first_preprocessing(true)

data/actions/create_project.rb

@@ -11,9 +11,12 @@ OptionParser.new do |opt|
     "Name of the project."){ |v| o[:name]=v }
   opt.on("-d", "--description STRING",
     "Description of the project."){ |v| o[:description]=v }
-  opt.on("-u", "--user STRING", "Owner of the project."){ |v| o[:user]=v }
   opt.on("-c", "--comments STRING",
     "Comments on the project."){ |v| o[:comments]=v }
+  opt.on("-m", "--metadata STRING",
+    "Metadata as key-value pairs separated by = and delimited by comma.",
+    "Values are saved as strings except for booleans (true / false) or nil."
+    ){ |v| o[:metadata]=v }
   opt.on("--update",
     "Updates the project if it already exists."){ o[:update]=true }
   opt_common(opt, o)
@@ -21,14 +24,12 @@ end.parse!
 
 ##=> Main <=
 opt_require(o, project:"-P")
-opt_require(o, type:"-t") unless o[:update]
+opt_require_type(o, MiGA::Project) unless o[:update]
 
 unless File.exist? "#{ENV["HOME"]}/.miga_rc" and
       File.exist? "#{ENV["HOME"]}/.miga_daemon.json"
-  puts "You must initialize MiGA before creating the first project.\n" +
-    "Do you want to initialize MiGA now? (yes / no)"
-  `'#{File.dirname(__FILE__)}/../scripts/init.bash'` if
-    $stdin.gets.chomp == 'yes'
+  raise "You must initialize MiGA before creating the first project.\n" +
+    "Please use miga init."
 end
 
 $stderr.puts "Creating project." unless o[:q]
@@ -37,11 +38,8 @@ raise "Project already exists, aborting." unless
 p = MiGA::Project.new(o[:project], o[:update])
 # The following check is redundant with MiGA::Project#create,
 # but allows upgrading projects from (very) early code versions
-o[:name] = File.basename(p.path) if
-  o[:update] and o[:name].nil?
-[:name, :description, :user, :comments, :type].each do |k|
-  p.metadata[k] = o[k] unless o[k].nil?
-end
+o[:name] = File.basename(p.path) if o[:update] and o[:name].nil?
+p = add_metadata(o, p)
 p.save
 
 $stderr.puts "Done." unless o[:q]

data/actions/init.rb

@@ -7,7 +7,7 @@ require "shellwords"
 
 o = {q:true, mytaxa:nil, config:File.expand_path(".miga_modules", ENV["HOME"]),
   ask: false, auto:false, dtype: "bash"}
-opts = OptionParser.new do |opt|
+OptionParser.new do |opt|
   opt_banner(opt)
   opt.on("-c","--config PATH",
     "Path to the Bash configuration file.",
@@ -83,7 +83,7 @@ unless File.exist? o[:config]
   o[:config] = ask_user(
     "Is there a script I need to load at startup?", o[:config])
 end
-if File.exists? o[:config]
+if File.exist? o[:config]
   o[:config] = File.expand_path o[:config]
   $stderr.puts "Found bash configuration script: #{o[:config]}."
   rc_fh.puts "MIGA_STARTUP='#{o[:config]}'"

data/actions/run_local.rb

@@ -6,7 +6,7 @@
 require "shellwords"
 
 o = {q:true, try_load:false, thr:1}
-opts = OptionParser.new do |opt|
+OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset_opt, :result])
   opt.on("-t", "--threads INT",

data/bin/miga

@@ -71,7 +71,7 @@ def opt_object(opt, o, what=[:project, :dataset])
       what.include? :dataset_type_req
   opt.on("-t", "--type STRING",
     (what.include?(:project_type_req) ? "(Mandatory) " : "") +
-    "Type of dataset. Recognized types include:", 
+    "Type of project. Recognized types include:", 
     *MiGA::Project.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
     ){ |v| o[:type]=v.to_sym } if what.include? :project_type or
       what.include? :project_type_req
@@ -116,6 +116,11 @@ def opt_require(o, req={project:"-P", dataset:"-D"})
   end
 end
 
+def opt_require_type(o, klass)
+  opt_require(o, type:"-t")
+  raise "Unrecognized type: #{o[:type]}." if klass.KNOWN_TYPES[o[:type]].nil?
+end
+
 # Filters datasets by keys set in +opt_filter_datasets+.
 def filter_datasets!(ds, o)
   ds.select!{|d| d.is_ref? == o[:ref] } unless o[:ref].nil?
@@ -128,6 +133,22 @@ def filter_datasets!(ds, o)
   ds
 end
 
+def add_metadata(o, obj)
+  o[:metadata].split(",").each do |pair|
+    (k,v) = pair.split("=")
+    case v
+      when "true";  v = true
+      when "false"; v = false
+      when "nil";   v = nil
+    end
+    obj.metadata[k] = v
+  end
+  [:type, :name, :user, :description, :comments].each do |k|
+    obj.metadata[k] = o[k] unless o[k].nil?
+  end
+  obj
+end
+
 ##=> Main <=
 
 execs = $task_desc.keys.map{ |k| k.to_s }

data/lib/miga/project.rb

@@ -283,16 +283,26 @@ class MiGA::Project < MiGA::MiGA
   ##
   # Get the next distances task, saving intermediate results if +save+. Returns
   # a Symbol.
-  def next_distances(save=true)
-    @@DISTANCE_TASKS.find{ |t| add_result(t, save).nil? }
-  end
+  def next_distances(save=true) ; next_task(@@DISTANCE_TASKS, save) ; end
   
   ##
   # Get the next inclade task, saving intermediate results if +save+. Returns a
   # Symbol.
-  def next_inclade(save=true)
-    return nil unless metadata[:type]==:clade
-    @@INCLADE_TASKS.find{ |t| add_result(t, save).nil? }
+  def next_inclade(save=true) ; next_task(@@INCLADE_TASKS, save) ; end
+
+  ##
+  # Get the next task from +tasks+, saving intermediate results if +save+.
+  # Returns a Symbol.
+  def next_task(tasks=@@DISTANCE_TASKS+@@INCLADE_TASKS, save=true)
+    tasks.find do |t|
+      if metadata["run_#{t}"]==false or
+            (!is_clade? and @@INCLADE_TASKS.include?(t) and
+                  metadata["run_#{t}"]!=true)
+        false
+      else
+        add_result(t, save).nil?
+      end
+    end
   end
   
   ##

data/lib/miga/result.rb

@@ -114,7 +114,7 @@ class MiGA::Result < MiGA::MiGA
     json = File.read(path)
     @data = JSON.parse(json, {:symbolize_names=>true})
     @data[:files] ||= {}
-    @results = self[:results].map{ |rs| MiGA::Result.new rs }
+    @results = (self[:results] || []).map{ |rs| MiGA::Result.new rs }
   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, 0, 1]
+  VERSION = [0.3, 0, 2]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2017, 6, 6)
+  VERSION_DATE = Date.new(2017, 6, 14)
   
   ##
   # Reference of MiGA.

data/test/project_test.rb

@@ -86,6 +86,16 @@ class ProjectTest < Test::Unit::TestCase
     assert_equal(MiGA::Result, p1.add_result(:haai_distances).class)
   end
 
+  def test_result
+    p1 = $p1
+    assert_nil(p1.result :n00b)
+    assert_nil(p1.result :project_stats)
+    File.open(File.expand_path("data/90.stats/miga-project.json",p1.path),
+      "w"){ |fh| fh.puts "{}" }
+    assert_not_nil(p1.result :project_stats)
+    assert_equal(1, p1.results.size)
+  end
+
   def test_preprocessing
     p1 = $p1
     assert(p1.done_preprocessing?)
@@ -142,6 +152,7 @@ class ProjectTest < Test::Unit::TestCase
         "Impossible to add #{r} result.")
     end
     assert_nil(p1.next_inclade)
+
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.0.1
+  version: 0.3.0.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-06-06 00:00:00.000000000 Z
+date: 2017-06-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client