Module: GnCrossmap
- Defined in:
- lib/gn_crossmap.rb,
lib/gn_crossmap/stats.rb,
lib/gn_crossmap/reader.rb,
lib/gn_crossmap/writer.rb,
lib/gn_crossmap/version.rb,
lib/gn_crossmap/resolver.rb,
lib/gn_crossmap/collector.rb,
lib/gn_crossmap/column_collector.rb,
lib/gn_crossmap/result_processor.rb,
lib/gn_crossmap/sci_name_collector.rb
Overview
Namespace module for crossmapping checklists to GN sources
Defined Under Namespace
Classes: Collector, ColumnCollector, Reader, Resolver, ResultProcessor, SciNameCollector, Stats, Writer
Constant Summary collapse
- INPUT_MODE =
"r:utf-8"
- OUTPUT_MODE =
"w:utf-8"
- MATCH_TYPES =
{ 0 => "No match", 1 => "Exact string match", 2 => "Canonical form exact match", 3 => "Canonical form fuzzy match", 4 => "Partial canonical form match", 5 => "Partial canonical form fuzzy match", 6 => "Genus part match", 7 => "Error in matching" }.freeze
- VERSION =
"3.1.3"
Class Attribute Summary collapse
-
.logger ⇒ Object
rubocop:enable all.
Class Method Summary collapse
- .find_id(row, name) ⇒ Object
- .log(message) ⇒ Object
-
.run(opts) ⇒ Object
rubocop:disable Metrics/AbcSize.
- .version ⇒ Object
Class Attribute Details
.logger ⇒ Object
rubocop:enable all
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# File 'lib/gn_crossmap.rb', line 55 def logger @logger ||= Logger.new(STDERR) end |
Class Method Details
.find_id(row, name) ⇒ Object
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# File 'lib/gn_crossmap.rb', line 63 def find_id(row, name) row.key?(:taxonid) ? row[:taxonid].strip : GnUUID.uuid(name) end |
.log(message) ⇒ Object
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# File 'lib/gn_crossmap.rb', line 59 def log() logger.info() end |
.run(opts) ⇒ Object
rubocop:disable Metrics/AbcSize
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# File 'lib/gn_crossmap.rb', line 42 def run(opts) opts = opts_struct(opts) input_io, output_io = io(opts.input, opts.output) reader = create_reader(input_io, opts) data = block_given? ? reader.read(&Proc.new) : reader.read writer = create_writer(reader, output_io, opts) resolver = create_resolver(writer, opts) block_given? ? resolver.resolve(data, &Proc.new) : resolver.resolve(data) resolver.stats end |
.version ⇒ Object
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# File 'lib/gn_crossmap/version.rb', line 7 def self.version VERSION end |