miga-base 0.2.0.6 → 0.2.0.7
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- checksums.yaml +4 -4
- data/Gemfile +3 -0
- data/LICENSE +201 -0
- data/README.md +17 -335
- data/Rakefile +31 -0
- data/actions/add_result +2 -5
- data/actions/add_taxonomy +4 -7
- data/actions/create_dataset +5 -6
- data/actions/create_project +2 -5
- data/actions/daemon +2 -5
- data/actions/download_dataset +88 -58
- data/actions/find_datasets +36 -38
- data/actions/import_datasets +2 -5
- data/actions/index_taxonomy +2 -5
- data/actions/list_datasets +47 -49
- data/actions/list_files +7 -11
- data/actions/unlink_dataset +2 -5
- data/bin/miga +1 -1
- data/lib/miga/common.rb +132 -0
- data/lib/miga/daemon.rb +229 -168
- data/lib/miga/dataset.rb +354 -277
- data/lib/miga/gui.rb +346 -269
- data/lib/miga/metadata.rb +115 -71
- data/lib/miga/project.rb +361 -259
- data/lib/miga/remote_dataset.rb +200 -148
- data/lib/miga/result.rb +150 -99
- data/lib/miga/tax_index.rb +124 -67
- data/lib/miga/taxonomy.rb +129 -100
- data/lib/miga/version.rb +57 -0
- data/lib/miga.rb +2 -77
- data/scripts/_distances_noref_nomulti.bash +2 -0
- data/scripts/_distances_ref_nomulti.bash +2 -0
- data/scripts/aai_distances.bash +1 -0
- data/scripts/ani_distances.bash +1 -0
- data/scripts/assembly.bash +1 -0
- data/scripts/cds.bash +1 -0
- data/scripts/clade_finding.bash +17 -1
- data/scripts/distances.bash +1 -0
- data/scripts/essential_genes.bash +1 -0
- data/scripts/haai_distances.bash +1 -0
- data/scripts/init.bash +2 -0
- data/scripts/mytaxa.bash +1 -0
- data/scripts/mytaxa_scan.bash +1 -0
- data/scripts/ogs.bash +1 -0
- data/scripts/read_quality.bash +1 -0
- data/scripts/ssu.bash +1 -0
- data/scripts/subclades.bash +1 -0
- data/scripts/trimmed_fasta.bash +1 -0
- data/scripts/trimmed_reads.bash +1 -0
- data/test/common_test.rb +82 -0
- data/test/daemon_test.rb +53 -0
- data/test/dataset_test.rb +156 -0
- data/test/jruby_gui_test.rb +20 -0
- data/test/metadata_test.rb +48 -0
- data/test/project_test.rb +54 -0
- data/test/remote_dataset_test.rb +41 -0
- data/test/tax_index_test.rb +44 -0
- data/test/taxonomy_test.rb +36 -0
- data/test/test_helper.rb +32 -0
- metadata +53 -38
data/lib/miga/metadata.rb
CHANGED
@@ -1,74 +1,118 @@
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# @package MiGA
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# @
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# @license artistic license 2.0
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# @update Jul-06-2015
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#
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# @license Artistic-2.0
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end
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##
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# Metadata associated to objects like MiGA::Project, MiGA::Dataset, and
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# MiGA::Result.
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class MiGA::Metadata < MiGA::MiGA
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# Class-level
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##
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# Does the metadata described in +path+ already exist?
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def self.exist?(path) File.size? path end
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##
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# Load the metadata described in +path+ and return MiGA::Metadata if it
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# exists, or nil otherwise.
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def self.load(path)
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return nil unless Metadata.exist? path
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MiGA::Metadata.new(path)
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end
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# Instance-level
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##
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# Path to the JSON file describing the metadata.
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attr_reader :path
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##
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# Parsed data as a Hash.
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attr_reader :data
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##
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# Initiate a MiGA::Metadata object with description in +path+. It will create
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# it if it doesn't exist.
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def initialize(path, defaults={})
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@path = File.absolute_path(path)
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@data = {}
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defaults.each_pair{ |k,v| self[k]=v }
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self.create unless File.size? self.path
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self.load
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end
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##
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# Reset :created field and save the current data.
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def create
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@data[:created] = Time.now.to_s
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self.save
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end
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##
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# Save the metadata into #path.
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def save
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MiGA.DEBUG "Metadata.save #{path}"
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@data[:updated] = Time.now.to_s
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json = JSON.pretty_generate(data)
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sleeper = 0.0
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while File.exist?(lock_file)
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sleeper += 0.1 if sleeper <= 10.0
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sleep(sleeper.to_i)
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end
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FileUtils.touch lock_file
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ofh = File.open(path + ".tmp", "w")
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ofh.puts json
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ofh.close
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raise "Lock-racing detected for #{path}." unless
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File.exist?(path + ".tmp") and File.exist?(lock_file)
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File.rename(path + ".tmp", path)
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File.unlink(lock_file)
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end
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##
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# (Re-)load metadata stored in #path.
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def load
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sleeper = 0.0
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while File.exist? lock_file
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sleeper += 0.1 if sleeper <= 10.0
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sleep(sleeper.to_i)
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end
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# :symbolize_names does not play nicely with :create_additions
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tmp = JSON.parse(File.read(path),
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{:symbolize_names=>false, :create_additions=>true})
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@data = {}
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tmp.each_pair{ |k,v| self[k] = v }
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end
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##
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# Delete file at #path.
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def remove!
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MiGA.DEBUG "Metadata.remove! #{self.path}"
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File.unlink(self.path)
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nil
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end
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##
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# Lock file for the metadata.
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def lock_file ; path + ".lock" ; end
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##
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# Return the value of +k+ in #data.
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def [](k) data[k.to_sym] end
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##
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# Set the value of +k+ to +v+.
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def []=(k,v)
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k = k.to_sym
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# Protect the special field :name
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v=v.miga_name if k==:name
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# Symbolize the special field :type
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v=v.to_sym if k==:type
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# Register and return
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@data[k]=v
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end
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##
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# Iterate +blk+ for each data with 2 arguments key and value.
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def each(&blk) data.each{ |k,v| blk.call(k,v) } ; end
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end
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