rbbt 1.2.5 → 2.0.0
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- checksums.yaml +7 -0
- data/README.rdoc +2 -138
- metadata +69 -214
- data/LICENSE +0 -20
- data/bin/rbbt_config +0 -245
- data/install_scripts/classifier/R/classify.R +0 -36
- data/install_scripts/classifier/Rakefile +0 -140
- data/install_scripts/get_abner.sh +0 -2
- data/install_scripts/get_banner.sh +0 -25
- data/install_scripts/get_biocreative.sh +0 -72
- data/install_scripts/get_crf++.sh +0 -26
- data/install_scripts/get_entrez.sh +0 -4
- data/install_scripts/get_go.sh +0 -4
- data/install_scripts/get_polysearch.sh +0 -8
- data/install_scripts/ner/Rakefile +0 -206
- data/install_scripts/ner/config/default.rb +0 -52
- data/install_scripts/norm/Rakefile +0 -219
- data/install_scripts/norm/config/cue_default.rb +0 -10
- data/install_scripts/norm/config/tokens_default.rb +0 -86
- data/install_scripts/norm/functions.sh +0 -23
- data/install_scripts/organisms/Ath.Rakefile +0 -55
- data/install_scripts/organisms/Cal.Rakefile +0 -84
- data/install_scripts/organisms/Cel.Rakefile +0 -109
- data/install_scripts/organisms/Hsa.Rakefile +0 -140
- data/install_scripts/organisms/Mmu.Rakefile +0 -77
- data/install_scripts/organisms/Rakefile +0 -43
- data/install_scripts/organisms/Rno.Rakefile +0 -88
- data/install_scripts/organisms/Sce.Rakefile +0 -66
- data/install_scripts/organisms/Spo.Rakefile +0 -40
- data/install_scripts/organisms/rake-include.rb +0 -252
- data/install_scripts/wordlists/consonants +0 -897
- data/install_scripts/wordlists/stopwords +0 -1
- data/lib/rbbt.rb +0 -83
- data/lib/rbbt/bow/bow.rb +0 -88
- data/lib/rbbt/bow/classifier.rb +0 -116
- data/lib/rbbt/bow/dictionary.rb +0 -187
- data/lib/rbbt/ner/abner.rb +0 -34
- data/lib/rbbt/ner/banner.rb +0 -73
- data/lib/rbbt/ner/dictionaryNER.rb +0 -98
- data/lib/rbbt/ner/regexpNER.rb +0 -70
- data/lib/rbbt/ner/rner.rb +0 -227
- data/lib/rbbt/ner/rnorm.rb +0 -143
- data/lib/rbbt/ner/rnorm/cue_index.rb +0 -80
- data/lib/rbbt/ner/rnorm/tokens.rb +0 -217
- data/lib/rbbt/sources/biocreative.rb +0 -75
- data/lib/rbbt/sources/biomart.rb +0 -105
- data/lib/rbbt/sources/entrez.rb +0 -211
- data/lib/rbbt/sources/go.rb +0 -85
- data/lib/rbbt/sources/gscholar.rb +0 -74
- data/lib/rbbt/sources/organism.rb +0 -241
- data/lib/rbbt/sources/polysearch.rb +0 -117
- data/lib/rbbt/sources/pubmed.rb +0 -248
- data/lib/rbbt/util/arrayHash.rb +0 -266
- data/lib/rbbt/util/filecache.rb +0 -72
- data/lib/rbbt/util/index.rb +0 -47
- data/lib/rbbt/util/misc.rb +0 -106
- data/lib/rbbt/util/open.rb +0 -251
- data/lib/rbbt/util/rake.rb +0 -183
- data/lib/rbbt/util/simpleDSL.rb +0 -87
- data/lib/rbbt/util/tmpfile.rb +0 -35
- data/tasks/install.rake +0 -124
- data/test/rbbt/bow/test_bow.rb +0 -33
- data/test/rbbt/bow/test_classifier.rb +0 -72
- data/test/rbbt/bow/test_dictionary.rb +0 -91
- data/test/rbbt/ner/rnorm/test_cue_index.rb +0 -57
- data/test/rbbt/ner/rnorm/test_tokens.rb +0 -70
- data/test/rbbt/ner/test_abner.rb +0 -17
- data/test/rbbt/ner/test_banner.rb +0 -17
- data/test/rbbt/ner/test_dictionaryNER.rb +0 -122
- data/test/rbbt/ner/test_regexpNER.rb +0 -33
- data/test/rbbt/ner/test_rner.rb +0 -126
- data/test/rbbt/ner/test_rnorm.rb +0 -47
- data/test/rbbt/sources/test_biocreative.rb +0 -38
- data/test/rbbt/sources/test_biomart.rb +0 -31
- data/test/rbbt/sources/test_entrez.rb +0 -49
- data/test/rbbt/sources/test_go.rb +0 -24
- data/test/rbbt/sources/test_organism.rb +0 -59
- data/test/rbbt/sources/test_polysearch.rb +0 -27
- data/test/rbbt/sources/test_pubmed.rb +0 -39
- data/test/rbbt/util/test_arrayHash.rb +0 -257
- data/test/rbbt/util/test_filecache.rb +0 -37
- data/test/rbbt/util/test_index.rb +0 -31
- data/test/rbbt/util/test_misc.rb +0 -20
- data/test/rbbt/util/test_open.rb +0 -110
- data/test/rbbt/util/test_simpleDSL.rb +0 -57
- data/test/rbbt/util/test_tmpfile.rb +0 -21
- data/test/test_helper.rb +0 -4
- data/test/test_rbbt.rb +0 -11
data/lib/rbbt/sources/biomart.rb
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require 'rbbt/util/open'
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require 'rbbt'
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# This module interacts with BioMart. It performs queries to BioMart and
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# synthesises a hash with the results. Note that this module connects to the
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# online BioMart WS using the Open in 'rbbt/util/open' module which offers
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# caching by default. To obtain up to date results you may need to clear the
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# cache from previous queries.
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module BioMart
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class BioMart::QueryError < StandardError; end
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private
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@@biomart_query_xml = <<-EOT
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE Query>
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<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6" >
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<Dataset name = "<!--DATABASE-->" interface = "default" >
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<!--FILTERS-->
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<!--MAIN-->
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<!--ATTRIBUTES-->
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</Dataset>
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</Query>
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EOT
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def self.get(database, main, attrs = nil, filters = nil, data = nil)
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attrs ||= []
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filters ||= ["with_#{main}"]
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data ||= {}
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query = @@biomart_query_xml.clone
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query.sub!(/<!--DATABASE-->/,database)
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query.sub!(/<!--FILTERS-->/, filters.collect{|name| "<Filter name = \"#{ name }\" excluded = \"0\"/>"}.join("\n") )
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query.sub!(/<!--MAIN-->/,"<Attribute name = \"#{main}\" />")
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query.sub!(/<!--ATTRIBUTES-->/, attrs.collect{|name| "<Attribute name = \"#{ name }\"/>"}.join("\n") )
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response = Open.read('http://www.biomart.org/biomart/martservice?query=' + query.gsub(/\n/,' '))
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if response =~ /Query ERROR:/
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raise BioMart::QueryError, response
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end
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response.each_line{|l|
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parts = l.chomp.split(/\t/)
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main = parts.shift
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next if main.nil? || main.empty?
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data[main] ||= {}
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attrs.each{|name|
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value = parts.shift
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data[main][name] ||= []
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next if value.nil?
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data[main][name] << value
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}
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}
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data
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end
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public
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# This method performs a query in biomart for a datasets and a given set of
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# attributes, there must be a main attribute that will be used as the key in
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# the result hash, optionally there may be a list of additional attributes
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# and filters. The data parameter at the end is used internally to
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# incrementally building the result, due to a limitation of the BioMart WS
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# that only allows 3 external arguments, users normally should leave it
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# unspecified or nil. The result is a hash, where the keys are the different
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# values for the main attribute, and the value is a hash with every other
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# attribute as key, and as value and array with all possible values (Note
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# that for a given value of the main attribute, there may be more than one
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# value for another attribute). If filters is left a nil it adds a filter to
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# the BioMart query to remove results with the main attribute empty, this may
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# cause an error if the BioMart WS does not allow filtering with that
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# attribute.
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def self.query(database, main, attrs = nil, filters = nil, data = nil)
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attrs ||= []
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data ||= {}
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chunks = []
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chunk = []
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attrs.each{|a|
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chunk << a
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if chunk.length == 2
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chunks << chunk
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chunk = []
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end
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}
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chunks << chunk if chunk.any?
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chunks.each{|chunk|
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data = get(database,main,chunk, filters, data)
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}
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data
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end
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end
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data/lib/rbbt/sources/entrez.rb
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require 'rbbt'
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require 'rbbt/util/open'
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require 'rbbt/util/tmpfile'
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require 'rbbt/util/filecache'
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require 'rbbt/bow/bow.rb'
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require 'set'
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# This module is used to parse and extract information from the
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# gene_info file at Entrez Gene, as well as from the gene2pubmed file.
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# Both need to be downloaded and accesible for Rbbt, which is done as
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# part of a normal installation.
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module Entrez
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class NoFileError < StandardError; end
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# Given a taxonomy, or set of taxonomies, it returns an inverse hash,
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# where each key is the entrez id of a gene, and the value is an array
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# of possible synonyms in other databases. Is mostly used to translate
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# entrez ids to the native database id of the organism. The parameter
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# +native+ specifies the position of the key containing synonym, the
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# fifth by default, +fix+ and +check+ are Procs used, if present, to
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# pre-process lines and to check if they should be processed.
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def self.entrez2native(taxs, native = nil, fix = nil, check = nil)
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raise NoFileError, "Install the Entrez gene_info file" unless File.exists? File.join(Rbbt.datadir, 'dbs/entrez/gene_info')
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native ||= 5
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taxs = [taxs] unless taxs.is_a?(Array)
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taxs = taxs.collect{|t| t.to_s}
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lexicon = {}
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tmp = TmpFile.tmp_file("entrez-")
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system "cat '#{File.join(Rbbt.datadir, 'dbs/entrez/gene_info')}' |grep '^\\(#{taxs.join('\\|')}\\)[[:space:]]' > #{tmp}"
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File.open(tmp).each{|l|
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parts = l.chomp.split(/\t/)
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next if parts[native] == '-'
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entrez = parts[1]
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parts[native].split(/\|/).each{|id|
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id = fix.call(id) if fix
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next if check && !check.call(id)
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lexicon[entrez] ||= []
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lexicon[entrez] << id
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}
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}
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FileUtils.rm tmp
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lexicon
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end
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# For a given taxonomy, or set of taxonomies, it returns a hash with
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# genes as keys and arrays of related PubMed ids as values, as
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# extracted from the gene2pubmed file from Entrez Gene.
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def self.entrez2pubmed(taxs)
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raise NoFileError, "Install the Entrez gene2pubmed file" unless File.exists? File.join(Rbbt.datadir, 'dbs/entrez/gene2pubmed')
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taxs = [taxs] unless taxs.is_a?(Array)
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taxs = taxs.collect{|t| t.to_s}
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data = {}
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tmp = TmpFile.tmp_file("entrez-")
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system "cat '#{File.join(Rbbt.datadir, 'dbs/entrez/gene2pubmed')}' |grep '^\\(#{taxs.join('\\|')}\\)[[:space:]]' > #{tmp}"
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data = Open.to_hash(tmp, :native => 1, :extra => 2).each{|code, value_lists| value_lists.flatten!}
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FileUtils.rm tmp
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data
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end
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# This class parses an xml containing the information for a particular
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# gene as served by Entrez Gene, and hold some of its information.
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class Gene
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attr_reader :organism, :symbol, :description, :aka, :protnames, :summary, :comentaries
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def initialize(xml)
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return if xml.nil?
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@organism = xml.scan(/<Org-ref_taxname>(.*)<\/Org-ref_taxname>/s)
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@symbol = xml.scan(/<Gene-ref_locus>(.*)<\/Gene-ref_locus>/s)
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@description = xml.scan(/<Gene-ref_desc>(.*)<\/Gene-ref_desc>/s)
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@aka = xml.scan(/<Gene-ref_syn_E>(.*)<\Gene-ref_syn_E>/s)
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@protnames = xml.scan(/<Prot-ref_name_E>(.*)<\/Prot-ref_name_E>/s)
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@summary = xml.scan(/<Entrezgene_summary>(.*)<\/Entrezgene_summary>/s)
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@comentaries = xml.scan(/<Gene-commentary_text>(.*)<\/Gene-commentary_text>/s)
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end
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# Joins the text from symbol, description, aka, protnames, and
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# summary
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def text
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#[@organism, @symbol, @description, @aka, @protnames, @summary,@comentaries.join(". ")].join(". ")
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[@symbol, @description, @aka, @protnames, @summary].flatten.join(". ")
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end
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end
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private
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@@last = Time.now
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@@entrez_lag = 1
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def self.get_online(geneids)
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geneids_list = ( geneids.is_a?(Array) ? geneids.join(',') : geneids.to_s )
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url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&retmode=xml&id=#{geneids_list}"
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diff = Time.now - @@last
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sleep @@entrez_lag - diff unless diff > @@entrez_lag
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xml = Open.read(url, :quiet => true, :nocache => true)
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@@last = Time.now
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genes = xml.scan(/(<Entrezgene>.*?<\/Entrezgene>)/sm).flatten
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if geneids.is_a? Array
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list = {}
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genes.each_with_index{|gene,i|
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#geneid = gene.scan(/<Gene-track_geneid>(.*?)<\/Gene-track_geneid>/).flatten.first
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geneid = geneids[i]
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list[geneid ] = gene
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}
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return list
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else
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return genes.first
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end
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end
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public
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# Build a file name for a gene based on the id. Prefix the id by 'gene-',
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# substitute the slashes with '_SLASH_', and add a '.xml' extension.
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def self.gene_filename(id)
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FileCache.clean_path('gene-' + id.to_s + '.xml')
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end
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# Returns a Gene object for the given Entrez Gene id. If an array of
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# ids is given instead, a hash is returned. This method uses the
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# caching facilities from Rbbt.
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def self.get_gene(geneid)
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return nil if geneid.nil?
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if Array === geneid
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missing = []
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list = {}
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geneid.each{|p|
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next if p.nil?
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filename = gene_filename p
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if File.exists? FileCache.path(filename)
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list[p] = Gene.new(Open.read(FileCache.path(filename)))
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else
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missing << p
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end
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}
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return list unless missing.any?
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genes = get_online(missing)
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genes.each{|p, xml|
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filename = gene_filename p
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FileCache.add_file(filename,xml) unless File.exist? FileCache.path(filename)
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list[p] = Gene.new(xml)
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}
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return list
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else
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filename = gene_filename geneid
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if File.exists? FileCache.path(filename)
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return Gene.new(Open.read(FileCache.path(filename)))
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else
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-
xml = get_online(geneid)
|
181
|
-
FileCache.add_file(filename,xml)
|
182
|
-
|
183
|
-
return Gene.new(xml)
|
184
|
-
end
|
185
|
-
end
|
186
|
-
end
|
187
|
-
|
188
|
-
# Counts the words in common between a chunk of text and the text
|
189
|
-
# found in Entrez Gene for that particular gene. The +gene+ may be a
|
190
|
-
# gene identifier or a Gene class instance.
|
191
|
-
def self.gene_text_similarity(gene, text)
|
192
|
-
|
193
|
-
case
|
194
|
-
when Entrez::Gene === gene
|
195
|
-
gene_text = gene.text
|
196
|
-
when String === gene || Fixnum === gene
|
197
|
-
gene_text = get_gene(gene).text
|
198
|
-
else
|
199
|
-
return 0
|
200
|
-
end
|
201
|
-
|
202
|
-
|
203
|
-
gene_words = gene_text.words.to_set
|
204
|
-
text_words = text.words.to_set
|
205
|
-
|
206
|
-
return 0 if gene_words.empty? || text_words.empty?
|
207
|
-
|
208
|
-
common = gene_words.intersection(text_words)
|
209
|
-
common.length / (gene_words.length + text_words.length).to_f
|
210
|
-
end
|
211
|
-
end
|
data/lib/rbbt/sources/go.rb
DELETED
@@ -1,85 +0,0 @@
|
|
1
|
-
require 'rbbt'
|
2
|
-
|
3
|
-
|
4
|
-
# This module holds helper methods to deal with the Gene Ontology files. Right
|
5
|
-
# now all it does is provide a translation form id to the actual names.
|
6
|
-
module GO
|
7
|
-
|
8
|
-
@@info = nil
|
9
|
-
MULTIPLE_VALUE_FIELDS = %w(is_a)
|
10
|
-
|
11
|
-
# This method needs to be called before any translations can be made, it is
|
12
|
-
# called automatically the first time the id2name method is called. It loads
|
13
|
-
# the gene_ontology.obo file and extracts all the fields, although right now,
|
14
|
-
# only the name field is used.
|
15
|
-
def self.init
|
16
|
-
@@info = {}
|
17
|
-
File.open(File.join(Rbbt.datadir, 'dbs/go/gene_ontology.obo')).read.
|
18
|
-
split(/\[Term\]/).
|
19
|
-
each{|term|
|
20
|
-
term_info = {}
|
21
|
-
term.split(/\n/).
|
22
|
-
select{|l| l =~ /:/}.
|
23
|
-
each{|l|
|
24
|
-
key, value = l.chomp.match(/(.*?):(.*)/).values_at(1,2)
|
25
|
-
if MULTIPLE_VALUE_FIELDS.include? key.strip
|
26
|
-
term_info[key.strip] ||= []
|
27
|
-
term_info[key.strip] << value.strip
|
28
|
-
else
|
29
|
-
term_info[key.strip] = value.strip
|
30
|
-
end
|
31
|
-
}
|
32
|
-
@@info[term_info["id"]] = term_info
|
33
|
-
}
|
34
|
-
end
|
35
|
-
|
36
|
-
def self.info
|
37
|
-
self.init unless @@info
|
38
|
-
@@info
|
39
|
-
end
|
40
|
-
|
41
|
-
def self.goterms
|
42
|
-
self.init unless @@info
|
43
|
-
@@info.keys
|
44
|
-
end
|
45
|
-
|
46
|
-
def self.id2name(id)
|
47
|
-
self.init unless @@info
|
48
|
-
if id.kind_of? Array
|
49
|
-
@@info.values_at(*id).collect{|i| i['name'] if i}
|
50
|
-
else
|
51
|
-
return nil if @@info[id].nil?
|
52
|
-
@@info[id]['name']
|
53
|
-
end
|
54
|
-
end
|
55
|
-
|
56
|
-
def self.id2ancestors(id)
|
57
|
-
self.init unless @@info
|
58
|
-
if id.kind_of? Array
|
59
|
-
@@info.values_at(*id).
|
60
|
-
select{|i| ! i['is_a'].nil?}.
|
61
|
-
collect{|i| i['is_a'].collect{|id|
|
62
|
-
id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/)
|
63
|
-
}.compact
|
64
|
-
}
|
65
|
-
else
|
66
|
-
return [] if @@info[id].nil? || @@info[id]['is_a'].nil?
|
67
|
-
@@info[id]['is_a'].
|
68
|
-
collect{|id|
|
69
|
-
id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/)
|
70
|
-
}.compact
|
71
|
-
end
|
72
|
-
end
|
73
|
-
|
74
|
-
def self.id2namespace(id)
|
75
|
-
self.init unless @@info
|
76
|
-
if id.kind_of? Array
|
77
|
-
@@info.values_at(*id).collect{|i| i['namespace'] if i}
|
78
|
-
else
|
79
|
-
return nil if @@info[id].nil?
|
80
|
-
@@info[id]['namespace']
|
81
|
-
end
|
82
|
-
end
|
83
|
-
|
84
|
-
|
85
|
-
end
|
@@ -1,74 +0,0 @@
|
|
1
|
-
require 'mechanize'
|
2
|
-
|
3
|
-
|
4
|
-
module GoogleScholar
|
5
|
-
def self.user_agent
|
6
|
-
@@a ||= Mechanize.new
|
7
|
-
end
|
8
|
-
|
9
|
-
def self.citation_link(title)
|
10
|
-
citation_link = nil
|
11
|
-
|
12
|
-
# Get citation page
|
13
|
-
user_agent.get("http://scholar.google.es/scholar?q='#{ title }'&hl=es&lr=&lr=") do |page|
|
14
|
-
article = page.search('div[@class=gs_r]').first
|
15
|
-
return nil if article.nil?
|
16
|
-
|
17
|
-
return article.search('a').select{|link| link['href'] =~ /scholar\?cites/ && link.inner_html =~ /\d+$/ }.first
|
18
|
-
end
|
19
|
-
end
|
20
|
-
|
21
|
-
def self.full_text_url(title)
|
22
|
-
full_text_link = nil
|
23
|
-
|
24
|
-
# Get page
|
25
|
-
user_agent.get("http://scholar.google.es/scholar?q='#{ title }'&hl=es&lr=&lr=") do |page|
|
26
|
-
article = page.search('div[@class=gs_r]').first
|
27
|
-
return nil if article.nil?
|
28
|
-
|
29
|
-
link = article.search('a').select{ |link|
|
30
|
-
link['href'] =~ /\.pdf$/ || link['href'] =~ /type=pdf/
|
31
|
-
}.first
|
32
|
-
|
33
|
-
return nil if link.nil?
|
34
|
-
|
35
|
-
return link['href']
|
36
|
-
end
|
37
|
-
end
|
38
|
-
|
39
|
-
|
40
|
-
def self.number_cites(title)
|
41
|
-
|
42
|
-
link = citation_link title
|
43
|
-
return 0 if link.nil?
|
44
|
-
|
45
|
-
link.inner_html =~ /(\d+)$/
|
46
|
-
|
47
|
-
return $1.to_i
|
48
|
-
end
|
49
|
-
|
50
|
-
end
|
51
|
-
|
52
|
-
|
53
|
-
#def get_citers(title)
|
54
|
-
# puts title
|
55
|
-
# citation_link = nil
|
56
|
-
#
|
57
|
-
# # Get citation page
|
58
|
-
# $a.get("http://scholar.google.es/scholar?q='#{ title }'&hl=es&lr=&lr=") do |page|
|
59
|
-
# citation_link = page.search('div[@class=gs_r]').first.search('a').select{|link| link['href'] =~ /scholar\?cites/ && link.inner_html =~ /\d+$/ }.first
|
60
|
-
# end
|
61
|
-
#
|
62
|
-
# return [] if citation_link.nil?
|
63
|
-
#
|
64
|
-
# # Parse citations
|
65
|
-
#
|
66
|
-
# citers = []
|
67
|
-
# $a.get("http://scholar.google.es" + citation_link['href']) do |page|
|
68
|
-
# citers = page.search('div[@class=gs_r]').collect do |entry|
|
69
|
-
# entry.search('h3').first.search('a').first.inner_html
|
70
|
-
# end
|
71
|
-
# end
|
72
|
-
#
|
73
|
-
# return citers
|
74
|
-
#end
|