miga-base 1.3.10.0 → 1.3.10.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: '0239e39a0588b73d042da7d970925d2d93a5334c858453e032d51b0af760fa27'
-  data.tar.gz: 81e6903e1feba6571d76fe5d113a60414bd0d3b1b3090d6e26367a93cf8d0da7
+  metadata.gz: e3a7f2c88342fa48b9b5a1485c3b371bdff02e2e5bf19af7c24ab9b19b3fd373
+  data.tar.gz: cffaf705081cb22a9c3834e91a6ed46ccd86d138433d65a4e78269c6698f73be
 SHA512:
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-  data.tar.gz: 8d27c2f580106c0d1f74e6daaf1cb81ffd7c6fbabf86e7569342027ff9e09b1810c245ad560eff0179c3d06a88b2d1a087344c56e34a2d54c799004e2f6370c0
+  metadata.gz: '093441822af4f362f210d0bbb0b4ade917757a5a5ba6938dec60038fdbdb73f75b0a479d2c930e223a54e81fce0ba9ab83b7f42ccc6a77944f33b66b53ad91a8'
+  data.tar.gz: 688e9925740ac96b258dd25521c5c5d63be05c2f0ebdf82a0b669bac0bd0d5c4def96537bcd4e1d411aeb03e6662b631447a5ed748c7de6c3631ea23f0d1021b

data/lib/miga/cli/action/download/ncbi.rb

@@ -29,7 +29,7 @@ module MiGA::Cli::Action::Download::Ncbi
     opt.on(
       '--ncbi-taxonomy-dump STRING',
       'Path to an NCBI Taxonomy dump directory to query instead of API calls'
-    ) { |v| MiGA::RemoteDataset.use_ncbi_taxonomy_dump(v) }
+    ) { |v| cli[:ncbi_taxonomy_dump] = v }
   end
 
   def cli_name_modifiers(opt)
@@ -55,6 +55,11 @@ module MiGA::Cli::Action::Download::Ncbi
   end
 
   def remote_list
+    if cli[:ncbi_taxonomy_dump]
+      cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
+      MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump])
+    end
+
     if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
       cli.say "Reusing remote list: #{cli[:ncbi_list_json]}"
       return MiGA::Json.parse(cli[:ncbi_list_json])

data/lib/miga/dataset/status.rb

@@ -20,7 +20,10 @@ module MiGA::Dataset::Status
     old_status = metadata[:status]
     metadata[:status] =
       !active? ? 'inactive' : done_preprocessing? ? 'complete' : 'incomplete'
-    self.save if save && (old_status.nil? || old_status != metadata[:status])
+    if save && (old_status.nil? || old_status != metadata[:status])
+      self.save
+      MiGA::MiGA.DEBUG "Status changed: #{old_status} -> #{metadata[:status]}"
+    end
     metadata[:status].to_sym
   end
 end

data/lib/miga/dataset.rb

@@ -61,6 +61,7 @@ class MiGA::Dataset < MiGA::MiGA
     @project, @name, @metadata = project, name, nil
     metadata[:ref] = is_ref
     metadata[:type] ||= :empty
+    metadata[:status] ||= 'incomplete'
     @metadata_future = [
       File.join(project.path, 'metadata', "#{name}.json"),
       metadata
@@ -84,15 +85,18 @@ class MiGA::Dataset < MiGA::MiGA
   ##
   # Save any changes you've made in the dataset
   def save
-    MiGA.DEBUG "Dataset.metadata: #{metadata.data}"
+    MiGA.DEBUG "Dataset.save: #{name}"
     metadata.save
     pull_hook :on_save
   end
 
   ##
-  # Currently +save!+ is simply an alias of +save+, for compatibility with the
-  # +Project+ interface
-  alias :save! :save
+  # Forces a save even if nothing has changed in the metadata
+  def save!
+    MiGA.DEBUG "Dataset.save!: #{name}"
+    metadata.save!
+    pull_hook :on_save
+  end
 
   ##
   # Delete the dataset with all it's contents (including results) and returns
@@ -148,7 +152,7 @@ class MiGA::Dataset < MiGA::MiGA
   ##
   # Is this dataset active?
   def active?
-    metadata[:inactive].nil? or !metadata[:inactive]
+    metadata[:inactive].nil? || !metadata[:inactive]
   end
 
   ##

data/lib/miga/metadata.rb

@@ -26,12 +26,17 @@ class MiGA::Metadata < MiGA::MiGA
   # Path to the JSON file describing the metadata
   attr_reader :path
 
+  ##
+  # Hash (Integer) of the last saved data Hash (object)
+  attr_reader :saved_hash
+
   ##
   # Initiate a MiGA::Metadata object with description in +path+.
   # It will create it if it doesn't exist.
   def initialize(path, defaults = {})
     @data = nil
     @path = File.absolute_path(path)
+    @saved_hash = nil
     unless File.exist? path
       @data = {}
       defaults.each { |k, v| self[k] = v }
@@ -57,35 +62,41 @@ class MiGA::Metadata < MiGA::MiGA
   # Save the metadata into #path
   def save
     return if self[:never_save]
+    return if !saved_hash.nil? && saved_hash == data.hash
 
     MiGA::MiGA.DEBUG "Metadata.save #{path}"
+    path_tmp = "#{path}.tmp"
     self[:updated] = Time.now.to_s
+    @saved_hash = data.hash
     json = to_json
     wait_for_lock
     FileUtils.touch(lock_file)
-    ofh = File.open("#{path}.tmp", 'w')
-    ofh.puts json
-    ofh.close
+    File.open(path_tmp, 'w') { |ofh| ofh.puts json }
 
-    unless File.exist?("#{path}.tmp") && File.exist?(lock_file)
+    unless File.exist?(path_tmp) && File.exist?(lock_file)
       raise "Lock-racing detected for #{path}"
     end
 
-    File.rename("#{path}.tmp", path)
+    File.rename(path_tmp, path)
     File.unlink(lock_file)
   end
 
+  ##
+  # Force +save+ even if nothing has changed since the last save
+  # or load. However, it doesn't save if +:never_save+ is true.
+  def save!
+    @saved_hash = nil
+    save
+  end
+
   ##
   # (Re-)load metadata stored in #path
   def load
-    sleeper = 0.0
-    while File.exist? lock_file
-      sleeper += 0.1 if sleeper <= 10.0
-      sleep(sleeper.to_i)
-    end
+    wait_for_lock
     tmp = MiGA::Json.parse(path, additions: true)
     @data = {}
     tmp.each { |k, v| self[k] = v }
+    @saved_hash = data.hash
   end
 
   ##

data/lib/miga/project.rb

@@ -67,7 +67,7 @@ class MiGA::Project < MiGA::MiGA
   ##
   # Save any changes persistently, regardless of +do_not_save+
   def save!
-    metadata.save
+    metadata.save!
     pull_hook :on_save
     self.load
   end

data/lib/miga/remote_dataset.rb

@@ -20,6 +20,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
       raise "Directory doesn't exist: #{path}" unless File.directory?(path)
 
       # Structure: { TaxID => ["name", "rank", parent TaxID] }
+      MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
       @ncbi_taxonomy_names = {}
 
       # Read names.dmp

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 10, 0].freeze
+  VERSION = [1.3, 10, 1].freeze
 
   ##
   # Nickname for the current major.minor version.

data/test/metadata_test.rb

@@ -13,7 +13,7 @@ class MetadataTest < Test::Unit::TestCase
       File.unlink(md1.lock_file)
     end
     t1 = Time.new
-    md1.save
+    md1.save!
     t2 = Time.new
     assert_path_not_exist(md1.lock_file)
     assert_ge(t2 - t1, 1.0)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.10.0
+  version: 1.3.10.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R