dwc-archive 0.9.6 → 1.1.1
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- checksums.yaml +7 -0
- data/.gitignore +31 -0
- data/.rspec +3 -0
- data/.rubocop.yml +23 -0
- data/.ruby-version +1 -0
- data/.travis.yml +4 -5
- data/CHANGELOG +15 -7
- data/Gemfile +3 -15
- data/LICENSE +1 -1
- data/README.md +135 -111
- data/Rakefile +13 -54
- data/dwc-archive.gemspec +37 -0
- data/features/step_definitions/dwc-creator_steps.rb +5 -5
- data/features/step_definitions/dwc-reader_steps.rb +47 -28
- data/features/support/env.rb +1 -1
- data/lib/dwc_archive.rb +121 -0
- data/lib/dwc_archive/archive.rb +59 -0
- data/lib/dwc_archive/classification_normalizer.rb +382 -0
- data/lib/dwc_archive/core.rb +25 -0
- data/lib/{dwc-archive → dwc_archive}/errors.rb +2 -0
- data/lib/dwc_archive/expander.rb +85 -0
- data/lib/{dwc-archive → dwc_archive}/extension.rb +5 -3
- data/lib/dwc_archive/generator.rb +90 -0
- data/lib/dwc_archive/generator_eml_xml.rb +116 -0
- data/lib/dwc_archive/generator_meta_xml.rb +72 -0
- data/lib/dwc_archive/gnub_taxon.rb +14 -0
- data/lib/dwc_archive/ingester.rb +106 -0
- data/lib/dwc_archive/metadata.rb +56 -0
- data/lib/dwc_archive/taxon_normalized.rb +23 -0
- data/lib/dwc_archive/version.rb +6 -0
- data/lib/dwc_archive/xml_reader.rb +89 -0
- data/spec/files/file with characters(3).gz b/data/spec/files/file with → characters(3).tar.gz +0 -0
- data/spec/files/generator_eml.xml +47 -0
- data/spec/files/generator_meta.xml +19 -0
- data/spec/lib/classification_normalizer_spec.rb +214 -0
- data/spec/lib/core_spec.rb +100 -0
- data/spec/lib/darwin_core_spec.rb +249 -0
- data/spec/lib/generator_eml_xml_spec.rb +22 -0
- data/spec/lib/generator_meta_xml_spec.rb +22 -0
- data/spec/lib/generator_spec.rb +124 -0
- data/spec/lib/gnub_taxon_spec.rb +32 -0
- data/spec/lib/metadata_spec.rb +89 -0
- data/spec/lib/taxon_normalized_spec.rb +142 -0
- data/spec/lib/xml_reader_spec.rb +11 -11
- data/spec/spec_helper.rb +78 -6
- metadata +180 -92
- data/.rvmrc +0 -1
- data/Gemfile.lock +0 -155
- data/VERSION +0 -1
- data/lib/dwc-archive.rb +0 -95
- data/lib/dwc-archive/.expander.rb.swo +0 -0
- data/lib/dwc-archive/archive.rb +0 -37
- data/lib/dwc-archive/classification_normalizer.rb +0 -424
- data/lib/dwc-archive/core.rb +0 -17
- data/lib/dwc-archive/expander.rb +0 -80
- data/lib/dwc-archive/generator.rb +0 -75
- data/lib/dwc-archive/generator_eml_xml.rb +0 -84
- data/lib/dwc-archive/generator_meta_xml.rb +0 -50
- data/lib/dwc-archive/ingester.rb +0 -101
- data/lib/dwc-archive/metadata.rb +0 -42
- data/lib/dwc-archive/utf_regex_ruby18.rb +0 -10
- data/lib/dwc-archive/xml_reader.rb +0 -64
- data/spec/lib/dwc-archive_spec.rb +0 -250
- data/spec/spec.opts +0 -1
checksums.yaml
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---
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SHA256:
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metadata.gz: a5d4e174cb4ec6df2328fe99abb52b13587c74f22f01efb2a9017db4d9f1d7ba
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data.tar.gz: e341038db2a23282173cf2e4671750739464dca6076f7560694cc40251bdd036
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SHA512:
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metadata.gz: 8b51b82724e21acab76e1763dc2375658080a16dc440c9913fd632aff195a45c34e7bf9446cf5d4afc9fc397c8ee562763ab36532ab5992421e5ed3f2df64273
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data.tar.gz: 04cbcc92c8b565b2c5f8e8bf082d284b65c55520d91f19c16bc63789519ea374f5ed0466c176ce69907a83566caa8efd2f834399f7b57a26801603455cf2b118
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data/.gitignore
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## MAC OS
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.DS_Store
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## TEXTMATE
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*.tmproj
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tmtags
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## EMACS
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*~
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\#*
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.\#*
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## VIM
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*.swp
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## PROJECT::GENERAL
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coverage
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rdoc
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pkg
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install
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Gemfile.lock
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## PROJECT::SPECIFIC
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tags
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bin
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.bundle
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bundle_bin
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Gemfile.lock
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.byebug_history
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data/.rspec
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data/.rubocop.yml
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AllCops:
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TargetRubyVersion: 2.6
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Exclude:
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- features/**/*
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- .bundle/**/*
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- bundle_bin/**/*
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- lib/dwc_archive/ingester.rb
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- lib/dwc_archive/generator_meta_xml.rb
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- lib/dwc_archive/generator_eml_xml.rb
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- lib/dwc_archive/classification_normalizer.rb
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Style/StringLiterals:
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EnforcedStyle: double_quotes
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Layout/DotPosition:
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EnforcedStyle: trailing
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Metrics/BlockLength:
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Exclude:
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- 'Rakefile'
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- '*.gemspec'
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- '**/*.rake'
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- 'spec/**/*spec.rb'
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data/.ruby-version
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2.7.1
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data/.travis.yml
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rvm:
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-
-
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- 2.
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- 2.5
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- 2.6
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- 2.7
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before_install:
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- sudo apt-get update
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-
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bundler_args: --without development
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- gem install bundler
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script:
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- bundle exec cucumber
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- bundle exec rake
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branches:
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only:
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- master
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-
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data/CHANGELOG
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1.1.0 Update name parser to go-based biodiversity
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0.
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1.0.1 Cleanup and gems update
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0.9.
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0.9.11 Removed VERSION duplicate
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0.
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0.9.7 Refactoring and tests improvements
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0.
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0.9.6 Added support for GNUB DwCA files
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0.9.4 Gem dependencies updated, added travis support
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0.9.0 Migrated code to ruby 1.9.3
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0.8.3 Updated outdated exception rasing
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0.8.2 Removed species info from linnean classification path
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0.8.1 Linnean classification path is now only for species and infraspecies with canonical forms. It ends with a canonical form of the taxon
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0.8.0 Added linnean classification path to normalized data from DwCA. It consists of data associated with clades like 'kingdom', 'order' etc.
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data/Gemfile
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# frozen_string_literal: true
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gem 'parsley-store', '~> 0.3.2'
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gem 'archive-tar-minitar', '~> 0.5'
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source "https://rubygems.org"
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gem 'debugger', '~> 1.3'
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end
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group :test do
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gem 'rspec', '~> 2.13'
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gem 'cucumber', '~> 1.3'
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gem 'bundler', '~> 1.3'
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gem 'jeweler', '~> 1.8'
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gem 'jazz_hands', '~> 0.5'
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end
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gemspec
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data/LICENSE
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data/README.md
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[![Gem Version][1]][2]
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[![Continuous Integration Status][3]][4]
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[![
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[![Coverage Status][5]][6]
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[![CodePolice][7]][8]
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[![Dependency Status][9]][10]
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Darwin Core Archive format is a current standard for information exchange
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between Global Names Architecture modules. This gem allows to work with
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Darwin Core Archive data compressed to either zip or tar.gz files.
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More information about Darwing Core Archive can be found on a [GBIF page:][
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More information about Darwing Core Archive can be found on a [GBIF page:][11]
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Installation
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------------
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sudo gem install dwc-archive
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### System Requirements
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You need [Redis Server][12] and unzip library installed
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Usage
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-----
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-
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```ruby
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require 'rubygems'
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require 'dwc_archive'
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dwc = DarwinCore.new('/path_to_file/archive_file.tar.gz')
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dwc.archive.files # the archive file list
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dwc.metadata.data # summary of metadata from eml.xml if it exists
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dwc.metadata.authors # authors of the archive
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dwc.core.data # summary of DarwinCore main file
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dwc.core.file_path # path to the DarwinCore main file
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dwc.extensions # array of DarwinCore Star extensions
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dwc.extensions[0].data # summary for an extension
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-
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# read content of the core data file into memory or used with a block
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# it returns array of arrays of data
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# rows that had a wrong encoding will be collected into errors array
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data, errors = dwc.core.read
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# read content using a block, getting back results in sets of 100 rows each
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results = []
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tail_data, tail_errors = dwc.core.read(100) do |data, errors|
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results << [data, errors]
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end
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results << [tail_data, tail_errors]
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-
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-
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# read content of an extension data file into memory
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data, errors = dwc.core.extensions[0].read
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# read content of an extension data using block
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results = []
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tail_data, tail_errors = dwc.core.extensions[0](100) do |data, errors|
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results << [data, errors]
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end
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results << [tail_data, tail_errors]
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-
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-
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# normalize names in classification collecting together synonyms,
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# canonical names, vernacular names and associating paths to taxons
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# in a classification distributed as DwCA file
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-
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result = dwc.normalize_classification
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# for a finer control over normalization:
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cn = DarwinCore::ClassificationNormalizer.new(dwc)
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cn.normalize
|
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# if you don't want to generate path consisting of canonical forms
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# of ancestors to a taxon
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cn.normalize(:with_canonical_names => false)
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-
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# if you don't want to ingest information from extensions
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cn.normalize(:with_extensions => false)
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-
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-
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# to get a flat hash of nodes with attached vernacular names and synonyms
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normalized_data = cn.normalized_data
|
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-
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-
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# to get a representation of tree organization as a hash
|
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classification_tree = cn.tree
|
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-
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-
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# to get list of all name strings used as scientific or vernacular names
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all_name_strings = cn.name_strings
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-
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# to get list of errors generated during the normalization
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errors = cn.error_names
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84
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-
|
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+
DarwinCore.clean_all # remove all expanded archives
|
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```
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Creating a DarwinCore Archive file
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----------------------------------
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```ruby
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gen = DarwinCore::Generator.new('/tmp/dwc_birches.tar.gz')
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|
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core = [
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["http://rs.tdwg.org/dwc/terms/taxonID",
|
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"http://rs.tdwg.org/dwc/terms/parentNameUsageID",
|
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"http://rs.tdwg.org/dwc/terms/scientificName",
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"http://rs.tdwg.org/dwc/terms/taxonRank"],
|
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[1, 0, "Plantae", "kingdom"],
|
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[2, 1, "Betula", "genus"],
|
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[3, 2, "Betula verucosa", "species"]
|
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]
|
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|
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vernacular_names = [
|
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["http://rs.tdwg.org/dwc/terms/TaxonID",
|
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"http://rs.tdwg.org/dwc/terms/vernacularName"],
|
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[1, "Plants"],
|
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[1, "Растения"],
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[2, "Birch"],
|
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[2, "Береза"],
|
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[3, "Wheeping Birch"],
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[3, "Береза плакучая"]
|
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]
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|
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eml = {
|
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:id => '1234',
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:license => 'http://creativecommons.org/licenses/by-sa/3.0/',
|
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:title => 'Test Classification',
|
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:authors => [
|
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{ :first_name => 'John',
|
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:last_name => 'Doe',
|
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:email => 'jdoe@example.com',
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:organization => 'Example',
|
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:position => 'Assistant Professor',
|
132
|
+
:url => 'http://example.org' },
|
133
|
+
{ :first_name => 'Jane',
|
134
|
+
:last_name => 'Doe',
|
135
|
+
:email => 'jane@example.com' }
|
136
|
+
],
|
137
|
+
:metadata_providers => [
|
138
|
+
{ :first_name => 'Jim',
|
139
|
+
:last_name => 'Doe',
|
140
|
+
:email => 'jimdoe@example.com',
|
141
|
+
:url => 'http://aggregator.example.org' }],
|
142
|
+
:abstract => 'test classification',
|
143
|
+
:citation =>
|
144
|
+
'Test classification: Doe John, Doe Jane, Taxnonmy, 10, 1, 2010',
|
145
|
+
:url => 'http://example.com'
|
146
|
+
}
|
147
|
+
|
148
|
+
gen.add_core(core, 'core.txt')
|
149
|
+
gen.add_extension(vernacular_names,
|
150
|
+
'vernacular_names.txt',
|
151
|
+
true, 'http://rs.gbif.org/terms/1.0/VernacularName')
|
152
|
+
gen.add_meta_xml
|
153
|
+
gen.add_eml_xml(eml)
|
154
|
+
gen.pack
|
155
|
+
```
|
145
156
|
|
146
157
|
Logging
|
147
158
|
-------
|
@@ -168,12 +179,25 @@ Note on Patches/Pull Requests
|
|
168
179
|
Copyright
|
169
180
|
---------
|
170
181
|
|
171
|
-
|
182
|
+
Author -- [@dimus][13]
|
183
|
+
|
184
|
+
Contributors -- [@mjy][14], [@LocoDelAssembly][16]
|
185
|
+
|
186
|
+
Copyright (c) 2010-2020 [@dimus][15]. See LICENSE for details.
|
172
187
|
|
173
188
|
[1]: https://badge.fury.io/rb/dwc-archive.png
|
174
189
|
[2]: http://badge.fury.io/rb/dwc-archive
|
175
190
|
[3]: https://secure.travis-ci.org/GlobalNamesArchitecture/dwc-archive.png
|
176
191
|
[4]: http://travis-ci.org/GlobalNamesArchitecture/dwc-archive
|
177
|
-
[5]: https://
|
178
|
-
[6]: https://
|
179
|
-
[7]:
|
192
|
+
[5]: https://coveralls.io/repos/GlobalNamesArchitecture/dwc-archive/badge.png
|
193
|
+
[6]: https://coveralls.io/r/GlobalNamesArchitecture/dwc-archive
|
194
|
+
[7]: https://codeclimate.com/github/GlobalNamesArchitecture/dwc-archive.png
|
195
|
+
[8]: https://codeclimate.com/github/GlobalNamesArchitecture/dwc-archive
|
196
|
+
[9]: https://gemnasium.com/GlobalNamesArchitecture/dwc-archive.png
|
197
|
+
[10]: https://gemnasium.com/GlobalNamesArchitecture/dwc-archive
|
198
|
+
[11]: http://bit.ly/2IxcBA
|
199
|
+
[12]: http://redis.io/topics/quickstart
|
200
|
+
[13]: https://github.com/dimus
|
201
|
+
[14]: https://github.com/mjy
|
202
|
+
[15]: http://mbl.edu
|
203
|
+
[16]: https://github.com/LocoDelAssembly
|
data/Rakefile
CHANGED
@@ -1,62 +1,21 @@
|
|
1
|
-
|
2
|
-
require 'rake'
|
1
|
+
# frozen_string_literal: true
|
3
2
|
|
4
|
-
|
5
|
-
|
6
|
-
|
7
|
-
gem.name = "dwc-archive"
|
8
|
-
gem.summary = %Q{Handler of Darwin Core Archive files}
|
9
|
-
gem.description = 'Darwin Core Archive is the current standard exchange ' +
|
10
|
-
'format for GLobal Names Architecture modules. ' +
|
11
|
-
'This gem makes it easy to incorporate files in ' +
|
12
|
-
'Darwin Core Archive format into a ruby project.'
|
13
|
-
gem.email = "dmozzherin at gmail dot com"
|
14
|
-
gem.homepage = "http://github.com/GlobalNamesArchitecture/dwc-archive"
|
15
|
-
gem.authors = ["Dmitry Mozzherin"]
|
16
|
-
#gem.add_dependency "fastercsv" if RUBY_VERSION.match /^1.8/
|
17
|
-
gem.add_dependency 'parsley-store', ">= 0.3.0"
|
18
|
-
gem.add_development_dependency "rspec", ">= 1.2.9"
|
19
|
-
gem.add_development_dependency "cucumber", ">= 0"
|
20
|
-
end
|
21
|
-
Jeweler::GemcutterTasks.new
|
22
|
-
rescue LoadError
|
23
|
-
puts 'Jeweler (or a dependency) not available. ' +
|
24
|
-
'Install it with: gem install jeweler'
|
25
|
-
end
|
26
|
-
|
27
|
-
require 'rspec/core/rake_task'
|
28
|
-
RSpec::Core::RakeTask.new(:spec) do |spec|
|
29
|
-
spec.pattern = 'spec/**/*_spec.rb'
|
30
|
-
end
|
31
|
-
|
32
|
-
RSpec::Core::RakeTask.new(:rcov) do |spec|
|
33
|
-
spec.pattern = 'spec/**/*_spec.rb'
|
34
|
-
spec.rcov = true
|
35
|
-
end
|
36
|
-
|
37
|
-
# task :spec => :check_dependencies
|
38
|
-
|
39
|
-
begin
|
40
|
-
require 'cucumber/rake/task'
|
41
|
-
Cucumber::Rake::Task.new(:features)
|
3
|
+
require "bundler/gem_tasks"
|
4
|
+
require "rspec/core/rake_task"
|
5
|
+
require "cucumber/rake/task"
|
42
6
|
|
43
|
-
|
44
|
-
|
45
|
-
task :features do
|
46
|
-
abort 'Cucumber is not available. In order to run features, ' +
|
47
|
-
'you must: sudo gem install cucumber'
|
48
|
-
end
|
7
|
+
RSpec::Core::RakeTask.new(:rspec) do |rspec|
|
8
|
+
rspec.pattern = "spec/**/*_spec.rb"
|
49
9
|
end
|
50
10
|
|
51
|
-
|
52
|
-
task :irb, [:script] do |t, args|
|
53
|
-
ARGV.clear
|
11
|
+
Cucumber::Rake::Task.new(:features)
|
54
12
|
|
55
|
-
|
56
|
-
|
13
|
+
# task rspec: :check_dependencies
|
14
|
+
task features: :check_dependencies
|
57
15
|
|
58
|
-
|
59
|
-
|
16
|
+
desc "open an irb session preloaded with this library"
|
17
|
+
task :console do
|
18
|
+
sh "irb -I lib -I extra -r dwc_archive.rb"
|
60
19
|
end
|
61
20
|
|
62
|
-
task :
|
21
|
+
task default: :rspec
|