Class: MiGA::Metadata
Overview
Metadata associated to objects like MiGA::Project, MiGA::Dataset, and MiGA::Result.
Constant Summary
Constants included from MiGA
CITATION, VERSION, VERSION_DATE, VERSION_NAME
Instance Attribute Summary collapse
-
#path ⇒ Object
readonly
Path to the JSON file describing the metadata.
Class Method Summary collapse
-
.exist?(path) ⇒ Boolean
Does the metadata described in
path
already exist?. -
.load(path) ⇒ Object
Load the metadata described in
path
and return MiGA::Metadata if it exists, or nil otherwise.
Instance Method Summary collapse
-
#[](k) ⇒ Object
Return the value of
k
in #data. -
#[]=(k, v) ⇒ Object
Set the value of
k
tov
. -
#create ⇒ Object
Reset :created field and save the current data.
-
#data ⇒ Object
Parsed data as a Hash.
-
#each(&blk) ⇒ Object
Iterate
blk
for each data with 2 arguments key and value. -
#initialize(path, defaults = {}) ⇒ Metadata
constructor
Initiate a MiGA::Metadata object with description in
path
. -
#load ⇒ Object
(Re-)load metadata stored in #path.
-
#lock_file ⇒ Object
Lock file for the metadata.
-
#remove! ⇒ Object
Delete file at #path.
-
#save ⇒ Object
Save the metadata into #path.
Methods inherited from MiGA
CITATION, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, clean_fasta_file, initialized?, #result_files_exist?, root_path, script_path, seqs_length, tabulate
Constructor Details
#initialize(path, defaults = {}) ⇒ Metadata
Initiate a MiGA::Metadata object with description in path
. It will create it if it doesn’t exist.
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# File 'lib/miga/metadata.rb', line 31 def initialize(path, defaults={}) @data = nil @path = File.absolute_path(path) unless File.exist? path @data = {} defaults.each_pair{ |k,v| self[k]=v } create end end |
Instance Attribute Details
#path ⇒ Object (readonly)
Path to the JSON file describing the metadata.
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# File 'lib/miga/metadata.rb', line 26 def path @path end |
Class Method Details
.exist?(path) ⇒ Boolean
Does the metadata described in path
already exist?
12 |
# File 'lib/miga/metadata.rb', line 12 def self.exist?(path) File.exist? path end |
Instance Method Details
#[](k) ⇒ Object
Return the value of k
in #data.
105 |
# File 'lib/miga/metadata.rb', line 105 def [](k) data[k.to_sym] end |
#[]=(k, v) ⇒ Object
Set the value of k
to v
.
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# File 'lib/miga/metadata.rb', line 109 def []=(k,v) self.load if @data.nil? k = k.to_sym # Protect the special field :name v=v.miga_name if k==:name # Symbolize the special field :type v=v.to_sym if k==:type # Delete if nil, register, and return v.nil? ? @data.delete(k) : (@data[k]=v) end |
#create ⇒ Object
Reset :created field and save the current data.
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# File 'lib/miga/metadata.rb', line 50 def create self[:created] = Time.now.to_s save end |
#data ⇒ Object
Parsed data as a Hash.
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# File 'lib/miga/metadata.rb', line 43 def data self.load if @data.nil? @data end |
#each(&blk) ⇒ Object
Iterate blk
for each data with 2 arguments key and value.
122 |
# File 'lib/miga/metadata.rb', line 122 def each(&blk) data.each{ |k,v| blk.call(k,v) } ; end |
#load ⇒ Object
(Re-)load metadata stored in #path.
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# File 'lib/miga/metadata.rb', line 78 def load sleeper = 0.0 while File.exist? lock_file sleeper += 0.1 if sleeper <= 10.0 sleep(sleeper.to_i) end # :symbolize_names does not play nicely with :create_additions tmp = JSON.parse(File.read(path), {:symbolize_names=>false, :create_additions=>true}) @data = {} tmp.each_pair{ |k,v| self[k] = v } end |
#lock_file ⇒ Object
Lock file for the metadata.
101 |
# File 'lib/miga/metadata.rb', line 101 def lock_file ; "#{path}.lock" ; end |
#remove! ⇒ Object
Delete file at #path.
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# File 'lib/miga/metadata.rb', line 93 def remove! MiGA.DEBUG "Metadata.remove! #{path}" File.unlink(path) nil end |
#save ⇒ Object
Save the metadata into #path.
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# File 'lib/miga/metadata.rb', line 57 def save MiGA.DEBUG "Metadata.save #{path}" self[:updated] = Time.now.to_s json = JSON.pretty_generate(data) sleeper = 0.0 while File.exist?(lock_file) sleeper += 0.1 if sleeper <= 10.0 sleep(sleeper.to_i) end FileUtils.touch lock_file ofh = File.open("#{path}.tmp", "w") ofh.puts json ofh.close raise "Lock-racing detected for #{path}." unless File.exist?("#{path}.tmp") and File.exist?(lock_file) File.rename("#{path}.tmp", path) File.unlink(lock_file) end |