dwc-archive 0.1.4 → 0.1.5
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- data/.gitignore +1 -0
- data/README.rdoc +10 -8
- data/VERSION +1 -1
- data/features/dwc-archive.feature +10 -0
- data/features/step_definitions/dwc-archive_steps.rb +32 -1
- data/lib/dwc-archive.rb +17 -2
- data/lib/dwc-archive/archive.rb +2 -2
- data/lib/dwc-archive/errors.rb +6 -0
- data/lib/dwc-archive/expander.rb +5 -3
- data/lib/dwc-archive/metadata.rb +2 -2
- data/spec/files/broken.tar.gz +0 -0
- data/spec/files/eml.xml +36 -36
- data/spec/files/invalid.tar.gz +0 -0
- data/spec/files/minimal.tar.gz +0 -0
- data/spec/files/uncompressed +1 -0
- data/spec/lib/dwc-archive_spec.rb +33 -0
- data/spec/lib/ruby_extenstions_spec.rb +1 -1
- data/spec/spec_helper.rb +2 -0
- metadata +10 -7
- data/dwc-archive.gemspec +0 -75
- data/spec/dwc-archive_spec.rb +0 -7
- data/t +0 -74
data/.gitignore
CHANGED
data/README.rdoc
CHANGED
@@ -13,14 +13,16 @@ Update to latest rubygems (v >= 1.3.6) which adds gemcutter sources by default.
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require 'rubygems'
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require 'dwc-archive'
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-
dwc =
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-
dwc.archive.files
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-
dwc.metadata.data
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-
dwc.metadata.authors
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-
dwc.core.data
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-
dwc.core.file_path
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-
dwc.
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-
dwc.
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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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DarwinCore.clean_all # remove all expanded archives
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== Note on Patches/Pull Requests
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.5
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@@ -12,6 +12,11 @@ Feature: Creation of a Darwing Core Archive
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12
12
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When I delete expanded files
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Then they should disappear
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15
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+
Scenario: Instantiating DarwinCore with a file without "eml.xml"
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Given path to a dwc file "minimal.tar.gz"
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+
When I create a new DarwinCore instance
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+
Then "DarwinCore_instance.metadata.data" should send instance of "NilClass" back
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+
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Scenario: Instantiating DarwinCore with tar.gz file
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Given path to a dwc file "data.tar.gz"
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When I create a new DarwinCore instance
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@@ -32,3 +37,8 @@ Feature: Creation of a Darwing Core Archive
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Given path to a dwc file "data.zip"
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When I create a new DarwinCore instance
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Then instance should have a valid archive
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+
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+
Scenario: Cleaning temporary directory from expanded archives
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+
Given acces to DarwinCore gem
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+
When I use DarwinCore.clean_all method
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+
Then all temporary directories created by DarwinCore are deleted
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@@ -26,7 +26,12 @@ Then /^they should disappear$/ do
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26
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end
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When /^I create a new DarwinCore instance$/ do
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-
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29
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+
begin
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@dwc = DarwinCore.new(@dwca_file)
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rescue
|
32
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@dwca_broken_file = @dwca_file
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33
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@dwc_error = $!
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34
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end
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35
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end
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Then /^instance should have a valid archive$/ do
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@@ -93,3 +98,29 @@ Then /^extension should have properties, data, file_path, coreid, fields$/ do
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ext.coreid.should == {:index=>0}
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ext.fields.should == [{:term=>"http://rs.gbif.org/ecat/terms/vernacularName", :index=>1}, {:term=>"http://rs.gbif.org/thesaurus/languageCode", :index=>2}]
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end
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+
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102
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Given /^acces to DarwinCore gem$/ do
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end
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104
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+
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105
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When /^I use DarwinCore\.clean_all method$/ do
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Dir.entries("/tmp").select {|e| e.match(/^dwc_/) }.size.should > 0
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DarwinCore.clean_all
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+
end
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Then /^all temporary directories created by DarwinCore are deleted$/ do
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+
Dir.entries("/tmp").select {|e| e.match(/^dwc_/) }.should == []
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+
end
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+
|
114
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+
Then /^I receive "([^\"]*)" exception with "([^\"]*)" message$/ do |arg1, arg2|
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@dwc_error.class.to_s.should == arg1
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116
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+
@dwc_error.message.should == arg2
|
117
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+
@dwca_broken_file.should == @dwca_file
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118
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+
@dwc_error = nil
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119
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+
@dwca_broken_file = nil
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+
end
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121
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+
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+
Then /^"([^\"]*)" should send instance of "([^\"]*)" back$/ do |arg1, arg2|
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res = eval(arg1.gsub(/DarwinCore_instance/, "@dwc"))
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res.class.to_s.should == arg2
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end
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+
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data/lib/dwc-archive.rb
CHANGED
@@ -2,6 +2,8 @@
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2
2
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$:.unshift(File.dirname(__FILE__)) unless
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$:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
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require 'ruby_extensions'
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+
require 'fileutils'
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+
require 'dwc-archive/errors'
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require 'dwc-archive/expander'
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require 'dwc-archive/archive'
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require 'dwc-archive/core'
|
@@ -11,12 +13,25 @@ require 'dwc-archive/metadata'
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class DarwinCore
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attr_reader :archive, :core, :metadata, :extensions
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alias :eml :metadata
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-
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+
|
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+
DEFAULT_TMP_DIR = "/tmp"
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+
|
19
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+
def initialize(dwc_path, tmp_dir = DEFAULT_TMP_DIR)
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@archive = DarwinCore::Archive.new(dwc_path, tmp_dir)
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@core = DarwinCore::Core.new(@archive)
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@metadata = DarwinCore::Metadata.new(@archive)
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18
23
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@extensions = get_extensions
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24
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end
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25
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+
|
26
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+
def self.clean_all(tmp_dir = DEFAULT_TMP_DIR)
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Dir.entries(tmp_dir).each do |entry|
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path = File.join(tmp_dir, entry)
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29
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if FileTest.directory?(path) && entry.match(/^dwc_[\d]+$/)
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30
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+
FileUtils.rm_rf(path)
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31
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+
end
|
32
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+
end
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33
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+
end
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34
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+
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35
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private
|
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36
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def get_extensions
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22
37
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res = []
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@@ -24,6 +39,6 @@ class DarwinCore
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24
39
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ext = @archive.meta[root_key][:extension]
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25
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return [] unless ext
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41
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ext = [ext] unless ext.class == Array
|
27
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-
ext.map {|e| DarwinCore::Extension.new(@archive, e)}
|
42
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+
ext.map { |e| DarwinCore::Extension.new(@archive, e) }
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28
43
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end
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44
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end
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data/lib/dwc-archive/archive.rb
CHANGED
@@ -12,13 +12,13 @@ class DarwinCore
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12
12
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@eml = files.include?("eml.xml") ? Hash.from_xml(open(File.join(@expander.path, 'eml.xml'))) : nil
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else
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clean
|
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-
raise
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+
raise InvalidArchiveError
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16
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end
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17
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end
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18
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19
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def valid?
|
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20
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valid = true
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21
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-
valid = valid && FileTest.exists?(@
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21
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+
valid = valid && @expander.path && FileTest.exists?(@expander.path)
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22
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valid = valid && files && files.include?('meta.xml')
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23
23
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end
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24
24
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data/lib/dwc-archive/expander.rb
CHANGED
@@ -9,7 +9,9 @@ class DarwinCore
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9
9
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10
10
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def unpack
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11
11
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clean
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12
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-
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12
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+
raise FileNotFoundError unless File.exists?(@archive_path)
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13
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+
success = @unpacker.call(@path, @archive_path) if @unpacker
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(@unpacker && success && $?.exitstatus == 0) ? success : (clean; raise UnpackingError)
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15
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end
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15
17
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def path
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@@ -32,12 +34,12 @@ class DarwinCore
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|
32
34
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if file_type.match(/tar.*gzip/i)
|
33
35
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return proc do |tmp_path, archive_path|
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34
36
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FileUtils.mkdir tmp_path
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35
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-
system
|
37
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+
system("tar -zxf #{archive_path} -C #{tmp_path} > /dev/null 2>&1")
|
36
38
|
end
|
37
39
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end
|
38
40
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|
39
41
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if file_type.match(/Zip/)
|
40
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-
return proc { |tmp_path, archive_path| system
|
42
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+
return proc { |tmp_path, archive_path| system("unzip -qq -d #{tmp_path} #{archive_path} > /dev/null 2>&1") }
|
41
43
|
end
|
42
44
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|
43
45
|
return nil
|
data/lib/dwc-archive/metadata.rb
CHANGED
@@ -10,11 +10,11 @@ class DarwinCore
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|
10
10
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end
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11
11
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12
12
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def id
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13
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-
@metadata[:eml][:dataset][:attributes][:id]
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13
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+
@metadata[:eml][:dataset][:attributes][:id] rescue nil
|
14
14
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end
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15
15
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|
16
16
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def title
|
17
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-
@metadata[:eml][:dataset][:title]
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17
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+
@metadata[:eml][:dataset][:title] rescue nil
|
18
18
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end
|
19
19
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|
20
20
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def authors
|
Binary file
|
data/spec/files/eml.xml
CHANGED
@@ -5,42 +5,42 @@ xmlns:eml="eml://ecoinformatics.org/eml-2.1.0"
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|
5
5
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
6
6
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xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.0 eml.xsd">
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7
7
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<dataset id="leptogastrinae:version:2.5">
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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39
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-
|
8
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+
<title>Leptogastrinae (Diptera: Asilidae) Classification</title>
|
9
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+
<creator id="10" scope="document">
|
10
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+
<individualName>
|
11
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+
<givenName>Keith</givenName>
|
12
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<surName>Bayless</surName>
|
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</individualName>
|
14
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<electronicMailAddress>keith.bayless@gmail.com</electronicMailAddress>
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</creator>
|
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<creator id="5" scope="document">
|
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<individualName>
|
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<givenName>Torsten</givenName>
|
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<surName>Dikow</surName>
|
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+
</individualName>
|
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<electronicMailAddress>dshorthouse@eol.org</electronicMailAddress>
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</creator>
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<metadataProvider>
|
24
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+
<organizationName>Encyclopedia of Life: LifeDesks (http://www.lifedesks.org)</organizationName>
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+
</metadataProvider>
|
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+
<pubDate>2010-02-03T01:09:41-05:00</pubDate>
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<abstract>These are all the names in the Leptogastrinae classification.</abstract>
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28
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+
<intellectualRights>Creative Commons: publicdomain</intellectualRights>
|
29
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+
<distribution>
|
30
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+
<online>
|
31
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+
<url function="download">http://leptogastrinae.lifedesks.org/files/leptogastrinae/classification_export/shared/leptogastrinae.tar.gz</url>
|
32
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+
</online>
|
33
|
+
</distribution>
|
34
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+
<contact>
|
35
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+
<references>5</references>
|
36
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+
</contact>
|
37
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+
<publisher>
|
38
|
+
<organizationName>The Marine Biological Laboratory</organizationName>
|
39
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+
</publisher>
|
40
40
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</dataset>
|
41
41
|
<additionalMetadata>
|
42
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-
|
43
|
-
|
44
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-
|
42
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+
<metadata>
|
43
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+
<citation>Dikow, Torsten. 2010. The Leptogastrinae classification.</citation>
|
44
|
+
</metadata>
|
45
45
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</additionalMetadata>
|
46
|
-
</eml:eml>
|
46
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+
</eml:eml>
|
Binary file
|
Binary file
|
@@ -0,0 +1 @@
|
|
1
|
+
an example of uncompressed file
|
@@ -0,0 +1,33 @@
|
|
1
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+
require File.dirname(__FILE__) + "/../spec_helper"
|
2
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+
|
3
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+
describe DarwinCore do
|
4
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+
before(:all) do
|
5
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+
@file_dir = File.join(File.dirname(__FILE__), '..', 'files')
|
6
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+
end
|
7
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+
|
8
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+
describe ".new" do
|
9
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+
|
10
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+
it "should create DarwinCore instance out of archive file" do
|
11
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+
['data.zip', 'data.tar.gz', 'minimal.tar.gz'].each do |file|
|
12
|
+
file = File.join(@file_dir, file)
|
13
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+
dwc = DarwinCore.new(file)
|
14
|
+
dwc.archive.valid?.should be_true
|
15
|
+
end
|
16
|
+
end
|
17
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+
|
18
|
+
it "should raise error if archive file does not exist" do
|
19
|
+
file = 'not_a_file'
|
20
|
+
lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::FileNotFoundError)
|
21
|
+
end
|
22
|
+
|
23
|
+
it "should raise error if archive is broken" do
|
24
|
+
file = File.join(@file_dir, 'broken.tar.gz')
|
25
|
+
lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::UnpackingError)
|
26
|
+
end
|
27
|
+
|
28
|
+
it "should raise error if archive is invalid" do
|
29
|
+
file = File.join(@file_dir, 'invalid.tar.gz')
|
30
|
+
lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::InvalidArchiveError)
|
31
|
+
end
|
32
|
+
end
|
33
|
+
end
|
@@ -2,7 +2,7 @@ require File.dirname(__FILE__) + "/../spec_helper"
|
|
2
2
|
|
3
3
|
describe "Hash" do
|
4
4
|
it "should parse xml to hash" do
|
5
|
-
Hash.public_methods.include?("from_xml").should be_true
|
5
|
+
Hash.public_methods.map { |i| i.to_s }.include?("from_xml").should be_true
|
6
6
|
end
|
7
7
|
|
8
8
|
it "should parse xml" do
|
data/spec/spec_helper.rb
CHANGED
@@ -1,8 +1,10 @@
|
|
1
1
|
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
2
2
|
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
3
|
+
require 'rubygems'
|
3
4
|
require 'dwc-archive'
|
4
5
|
require 'spec'
|
5
6
|
require 'spec/autorun'
|
7
|
+
require 'ruby-debug'
|
6
8
|
|
7
9
|
Spec::Runner.configure do |config|
|
8
10
|
|
metadata
CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
|
|
5
5
|
segments:
|
6
6
|
- 0
|
7
7
|
- 1
|
8
|
-
-
|
9
|
-
version: 0.1.
|
8
|
+
- 5
|
9
|
+
version: 0.1.5
|
10
10
|
platform: ruby
|
11
11
|
authors:
|
12
12
|
- Dmitry Mozzherin
|
@@ -14,7 +14,7 @@ autorequire:
|
|
14
14
|
bindir: bin
|
15
15
|
cert_chain: []
|
16
16
|
|
17
|
-
date: 2010-
|
17
|
+
date: 2010-04-28 00:00:00 -04:00
|
18
18
|
default_executable:
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
|
@@ -59,7 +59,6 @@ files:
|
|
59
59
|
- README.rdoc
|
60
60
|
- Rakefile
|
61
61
|
- VERSION
|
62
|
-
- dwc-archive.gemspec
|
63
62
|
- features/dwc-archive.feature
|
64
63
|
- features/step_definitions/dwc-archive_steps.rb
|
65
64
|
- features/support/env.rb
|
@@ -67,19 +66,23 @@ files:
|
|
67
66
|
- lib/dwc-archive/.expander.rb.swo
|
68
67
|
- lib/dwc-archive/archive.rb
|
69
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|
- lib/dwc-archive/core.rb
|
69
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+
- lib/dwc-archive/errors.rb
|
70
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- lib/dwc-archive/expander.rb
|
71
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- lib/dwc-archive/extension.rb
|
72
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|
- lib/dwc-archive/metadata.rb
|
73
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- lib/ruby_extensions.rb
|
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-
- spec/
|
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+
- spec/files/broken.tar.gz
|
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- spec/files/data.tar.gz
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- spec/files/data.zip
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- spec/files/eml.xml
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- spec/files/invalid.tar.gz
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- spec/files/minimal.tar.gz
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- spec/files/uncompressed
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- spec/lib/dwc-archive_spec.rb
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- spec/spec.opts
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- spec/spec_helper.rb
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- t
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has_rdoc: true
|
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homepage: http://github.com/dimus/dwc-archive
|
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licenses: []
|
@@ -111,6 +114,6 @@ signing_key:
|
|
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specification_version: 3
|
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summary: Handler of Darwin Core Archive files
|
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test_files:
|
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-
- spec/dwc-archive_spec.rb
|
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+
- spec/lib/dwc-archive_spec.rb
|
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- spec/lib/ruby_extenstions_spec.rb
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|
data/dwc-archive.gemspec
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{dwc-archive}
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s.version = "0.1.4"
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9
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-
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-
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Dmitry Mozzherin"]
|
12
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-
s.date = %q{2010-03-18}
|
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s.description = %q{Darwin Core Archive is the current standard exchange format for GLobal Names Architecture modules. This gem makes it easy to incorporate files in Darwin Core Archive format into a ruby project.}
|
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s.email = %q{dmozzherin at gmail dot com}
|
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s.extra_rdoc_files = [
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"LICENSE",
|
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"README.rdoc"
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]
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s.files = [
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".document",
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-
".gitignore",
|
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-
"LICENSE",
|
23
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-
"README.rdoc",
|
24
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-
"Rakefile",
|
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"VERSION",
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"dwc-archive.gemspec",
|
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"features/dwc-archive.feature",
|
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"features/step_definitions/dwc-archive_steps.rb",
|
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"features/support/env.rb",
|
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"lib/dwc-archive.rb",
|
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"lib/dwc-archive/.expander.rb.swo",
|
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"lib/dwc-archive/archive.rb",
|
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"lib/dwc-archive/core.rb",
|
34
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"lib/dwc-archive/expander.rb",
|
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"lib/dwc-archive/extension.rb",
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"lib/dwc-archive/metadata.rb",
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"lib/ruby_extensions.rb",
|
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-
"spec/dwc-archive_spec.rb",
|
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"spec/files/data.tar.gz",
|
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-
"spec/files/data.zip",
|
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"spec/files/eml.xml",
|
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"spec/files/meta.xml",
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"spec/lib/ruby_extenstions_spec.rb",
|
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"spec/spec.opts",
|
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-
"spec/spec_helper.rb",
|
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"t"
|
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-
]
|
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s.homepage = %q{http://github.com/dimus/dwc-archive}
|
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s.rdoc_options = ["--charset=UTF-8"]
|
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s.require_paths = ["lib"]
|
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s.rubygems_version = %q{1.3.6}
|
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s.summary = %q{Handler of Darwin Core Archive files}
|
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s.test_files = [
|
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-
"spec/dwc-archive_spec.rb",
|
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-
"spec/lib/ruby_extenstions_spec.rb",
|
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"spec/spec_helper.rb"
|
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]
|
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|
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if s.respond_to? :specification_version then
|
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
|
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|
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|
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
|
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s.add_development_dependency(%q<rspec>, [">= 1.2.9"])
|
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|
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s.add_development_dependency(%q<cucumber>, [">= 0"])
|
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else
|
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|
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s.add_dependency(%q<rspec>, [">= 1.2.9"])
|
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s.add_dependency(%q<cucumber>, [">= 0"])
|
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end
|
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else
|
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s.add_dependency(%q<rspec>, [">= 1.2.9"])
|
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s.add_dependency(%q<cucumber>, [">= 0"])
|
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-
end
|
74
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end
|
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|
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|
data/spec/dwc-archive_spec.rb
DELETED
data/t
DELETED
@@ -1,74 +0,0 @@
|
|
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# Generated by jeweler
|
2
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# DO NOT EDIT THIS FILE DIRECTLY
|
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# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
|
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
|
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s.name = %q{dwc-archive}
|
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s.version = "0.1.2"
|
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|
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
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s.authors = ["Dmitry Mozzherin"]
|
12
|
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s.date = %q{2010-03-18}
|
13
|
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s.description = %q{Darwin Core Archive is the current standard exchange format for GLobal Names Architecture modules. This gem makes it easy to incorporate files in Darwin Core Archive format into a ruby project.}
|
14
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s.email = %q{dmozzherin at gmail dot com}
|
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s.extra_rdoc_files = [
|
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"LICENSE",
|
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-
"README.rdoc"
|
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]
|
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s.files = [
|
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".document",
|
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".gitignore",
|
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|
-
"LICENSE",
|
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"README.rdoc",
|
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"Rakefile",
|
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|
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"VERSION",
|
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|
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"dwc-archive.gemspec",
|
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|
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"features/step_definitions/dwc-archive_steps.rb",
|
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"features/support/env.rb",
|
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|
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"lib/dwc-archive.rb",
|
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"lib/dwc-archive/.expander.rb.swo",
|
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"lib/dwc-archive/archive.rb",
|
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"lib/dwc-archive/core.rb",
|
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"lib/dwc-archive/expander.rb",
|
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|
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"lib/dwc-archive/extension.rb",
|
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"lib/dwc-archive/metadata.rb",
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"lib/ruby_extensions.rb",
|
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"spec/dwc-archive_spec.rb",
|
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"spec/files/data.tar.gz",
|
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"spec/files/data.zip",
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"spec/files/eml.xml",
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"spec/files/meta.xml",
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"spec/lib/ruby_extenstions_spec.rb",
|
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"spec/spec.opts",
|
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"spec/spec_helper.rb"
|
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|
-
]
|
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s.homepage = %q{http://github.com/dimus/dwc-archive}
|
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|
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s.require_paths = ["lib"]
|
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|
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|
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s.test_files = [
|
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"spec/dwc-archive_spec.rb",
|
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|
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"spec/lib/ruby_extenstions_spec.rb",
|
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|
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"spec/spec_helper.rb"
|
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|
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]
|
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|
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|
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if s.respond_to? :specification_version then
|
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
|
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s.specification_version = 3
|
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|
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|
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
|
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|
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s.add_development_dependency(%q<rspec>, [">= 1.2.9"])
|
64
|
-
s.add_development_dependency(%q<cucumber>, [">= 0"])
|
65
|
-
else
|
66
|
-
s.add_dependency(%q<rspec>, [">= 1.2.9"])
|
67
|
-
s.add_dependency(%q<cucumber>, [">= 0"])
|
68
|
-
end
|
69
|
-
else
|
70
|
-
s.add_dependency(%q<rspec>, [">= 1.2.9"])
|
71
|
-
s.add_dependency(%q<cucumber>, [">= 0"])
|
72
|
-
end
|
73
|
-
end
|
74
|
-
|