From 9bef583d759fc2ba9d381293805f0daae06b1bdf Mon Sep 17 00:00:00 2001 From: Scott Chamberlain Date: Wed, 15 Apr 2020 15:52:26 -0700 Subject: [PATCH] dont gitignore doc anymore --- .gitignore | 1 - doc/Array.html | 205 +++++++ doc/Configuration.html | 296 +++++++++ doc/Extcite.html | 1122 ++++++++++++++++++++++++++++++++++ doc/Hash.html | 380 ++++++++++++ doc/String.html | 289 +++++++++ doc/Textminer.html | 601 ++++++++++++++++++ doc/Textminer/Fetch.html | 447 ++++++++++++++ doc/Textminer/Mined.html | 509 +++++++++++++++ doc/Textminer/Miner.html | 385 ++++++++++++ doc/Textminer/Request.html | 669 ++++++++++++++++++++ doc/Textminer/Response.html | 923 ++++++++++++++++++++++++++++ doc/_index.html | 135 ++++ doc/class_list.html | 51 ++ doc/css/common.css | 1 + doc/css/full_list.css | 58 ++ doc/css/style.css | 496 +++++++++++++++ doc/file.README.html | 139 +++++ doc/file_list.html | 56 ++ doc/frames.html | 17 + doc/index.html | 139 +++++ doc/js/app.js | 314 ++++++++++ doc/js/full_list.js | 216 +++++++ doc/js/jquery.js | 4 + doc/method_list.html | 155 +++++ doc/top-level-namespace.html | 397 ++++++++++++ 26 files changed, 8004 insertions(+), 1 deletion(-) create mode 100644 doc/Array.html create mode 100644 doc/Configuration.html create mode 100644 doc/Extcite.html create mode 100644 doc/Hash.html create mode 100644 doc/String.html create mode 100644 doc/Textminer.html create mode 100644 doc/Textminer/Fetch.html create mode 100644 doc/Textminer/Mined.html create mode 100644 doc/Textminer/Miner.html create mode 100644 doc/Textminer/Request.html create mode 100644 doc/Textminer/Response.html create mode 100644 doc/_index.html create mode 100644 doc/class_list.html create mode 100644 doc/css/common.css create mode 100644 doc/css/full_list.css create mode 100644 doc/css/style.css create mode 100644 doc/file.README.html create mode 100644 doc/file_list.html create mode 100644 doc/frames.html create mode 100644 doc/index.html create mode 100644 doc/js/app.js create mode 100644 doc/js/full_list.js create mode 100644 doc/js/jquery.js create mode 100644 doc/method_list.html create mode 100644 doc/top-level-namespace.html diff --git a/.gitignore b/.gitignore index e6999b5..c7fdcb0 100644 --- a/.gitignore +++ b/.gitignore @@ -17,7 +17,6 @@ build/ ## Documentation cache and generated files: /.yardoc/ /_yardoc/ -/doc/ /rdoc/ ## Environment normalisation: diff --git a/doc/Array.html b/doc/Array.html new file mode 100644 index 0000000..902eb10 --- /dev/null +++ b/doc/Array.html @@ -0,0 +1,205 @@ + + + + + + + Class: Array + + — Documentation by YARD 0.9.24 + + + + + + + + + + + + + + + + + +
+ +
+
+ +
+ + +

Class: Array + + + +

+
+ +
+
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+
+ + + + + + + + + + + +
+
Defined in:
+
lib/extcite/methods_array.rb
+
+ +
+ +

Overview

+
+ +

Array methods

+ + +
+
+
+ + +
+ + + + + + + +

+ Instance Method Summary + collapse +

+ + + + + + +
+

Instance Method Details

+ + +
+

+ + #write_bib(file) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+3
+4
+5
+6
+7
+ 		+ 
# File 'lib/extcite/methods_array.rb', line 3
+
+def write_bib(file)
+  File.open(file, 'a') do |f|
+    f.puts self
+  end
+end
+
+
+ +
+ +
+ + + +
+ + \ No newline at end of file diff --git a/doc/Configuration.html b/doc/Configuration.html new file mode 100644 index 0000000..f38a222 --- /dev/null +++ b/doc/Configuration.html @@ -0,0 +1,296 @@ + + + + + + Module: Configuration + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Module: Configuration + + + +

+ +
+ + + + + + + +
Included in:
+
Textminer
+ + + +
Defined in:
+
lib/textminer/helpers/configuration.rb
+ +
+
+ +

Overview

+
+ +

taken from: viget.com/extend/easy-gem-configuration-variables-with-defaults

+ + +
+
+
+ + +
+ + + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + + + +
+

Instance Method Details

+ + +
+

+ + - (Object) configuration {|_self| ... } + + + + + +

+
+ + +
+
+
+ +

Yields:

+
    + +
  • + + + (_self) + + + +
    • + +
+

Yield Parameters:

+
    + +
  • + + _self + + + (Configuration) + + + + — +
    +

    the object that the method was called on

    +
    + +
    • + +
+ +
+ + + + +
+ 
+
+
+4
+5
+6
+ 		+ 
# File 'lib/textminer/helpers/configuration.rb', line 4
+
+def configuration
+  yield self
+end
+
+
+ +
+

+ + - (Object) define_setting(name, default = nil) + + + + + +

+ + + + +
+ 
+
+
+8
+9
+10
+11
+12
+13
+14
+15
+16
+ 		+ 
# File 'lib/textminer/helpers/configuration.rb', line 8
+
+def define_setting(name, default = nil)
+  class_variable_set("@@#{name}", default)
+  define_class_method "#{name}=" do |value|
+    class_variable_set("@@#{name}", value)
+  end
+  define_class_method name do
+    class_variable_get("@@#{name}")
+  end
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Extcite.html b/doc/Extcite.html new file mode 100644 index 0000000..91f6254 --- /dev/null +++ b/doc/Extcite.html @@ -0,0 +1,1122 @@ + + + + + + + Module: Extcite + + — Documentation by YARD 0.9.24 + + + + + + + + + + + + + + + + + +
+ +
+
+ +
+ + +

Module: Extcite + + + +

+
+ + + + + + + + + + + +
+
Defined in:
+
lib/extcite.rb,
+ lib/extcite/version.rb +
+
+ +
+ + + +

+ Constant Summary + collapse +

+ +
+ +
VERSION = + +
+ 
"0.4.0"
+ +
+ + + + + + + + + +

+ Class Method Summary + collapse +

+ + + + + + +
+

Class Method Details

+ + +
+

+ + .cont_neg(ids:) ⇒ Object + + + + + +

+
+ +

Get citation(s) using Crossref content negotation

+ +

Return: an string of bib data

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+Extcite.cont_neg(ids: "10.1016/j.dendro.2014.01.004")
+ +
+

Parameters:

+
    + +
  • + + ids + + + (Array[String]) + + + + — +
    +

    One or more DOIs in an array

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+296
+297
+298
+299
+ 		+ 
# File 'lib/extcite.rb', line 296
+
+def self.cont_neg(ids:)
+  out = Serrano.content_negotiation(ids: ids)
+  return out
+end
+
+
+ +
+

+ + .extract(path:, file: "out.bib", output: "bib") ⇒ Object + + + + + +

+
+ +

Extract DOIs from one or more PDFs

+ +

Return: writes bib files to a .bib file or an array if file is nil

+ +
When writing to a file, `extract` by default appends to the end
+of the file so you can build up your bibtex file with your
+citations
+
+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+require 'faraday'# get a paper in pdf format
+
+path = '2068.pdf'
+res = Faraday.new(:url => "https://peerj.com/articles/2068.pdf").get;
+f = File.new(path, "wb");
+f.write(res.body);
+f.close()# extract doi from the pdf
+
+Extcite.extract(path: path)
+Extcite.extract(path: path, file: nil)
+ +
+

Parameters:

+
    + +
  • + + path + + + (String) + + + + — +
    +

    Path to a pdf file, or a folder of PDF files

    +
    + +
    • + +
  • + + file + + + (String) + + + (defaults to: "out.bib") + + + — +
    +

    File name to write data to - or nil to stdout

    +
    + +
    • + +
  • + + output + + + (String) + + + (defaults to: "bib") + + + — +
    +

    Typeo of output. only bibtex for now

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+38
+39
+40
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+114
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+116
+117
+ 		+ 
# File 'lib/extcite.rb', line 38
+
+def self.extract(path:, file: "out.bib", output: "bib")
+  path = make_paths(path)
+  path.each do |x|
+    # try PDF metadata first
+    ids = nil
+    rr = PDF::Reader.new(x);
+    pdfmeta = rr.metadata
+    if !pdfmeta.nil?
+      xml = Oga.parse_xml(pdfmeta);
+      begin
+        tt = xml.xpath('//rdf:Description')        # try dc:identifier attribute
+
+        ss = tt.attr('dc:identifier')[0]
+        if !ss.nil?
+          ids = ss.text.sub(/doi:/, '')
+        else
+          # try prism:doi node
+          pdoi = xml.xpath('//rdf:Description//prism:doi')
+          if pdoi.length == 1
+            ids = pdoi.text
+          else
+            # try pdf:WPS-ARTICLEDOI node
+            wpsdoi = xml.xpath('//rdf:Description//pdf:WPS-ARTICLEDOI')
+            if wpsdoi.length == 1
+              ids = wpsdoi.text
+            else
+              # try pdfx:WPS-ARTICLEDOI node
+              pdfxwpsdoi = xml.xpath('//rdf:Description//pdfx:WPS-ARTICLEDOI')
+              if pdfxwpsdoi.length == 1
+                ids = pdfxwpsdoi.text
+              else
+                ids = nil
+              end
+            end
+          end
+        end
+      rescue
+        ids = nil
+      end
+    end
+
+    # if not found, try regexing for DOI
+    if ids.nil?
+      ids = Extcite.get_ids(txt: Extcite.extract_text_one(x))
+    end
+
+    if ids.length == 0
+      puts "no DOI found in " + x
+    else
+      if !ids.match(/arxiv/i).nil? && ids.length < 200
+        conn = Faraday.new(:url => 'http://export.arxiv.org/api/query?id_list=' + ids.gsub(/arxiv:/i, '')).get
+        bibs = conn.body.make_bib_arxiv(ids.gsub(/arxiv:/i, ''))
+      else
+        bibs = Extcite.cont_neg(ids: ids)
+      end
+
+      # if an error or not found, skip
+      bibstest = nil
+      if bibs.class == Array
+        bibstest = bibs[0]
+      else
+        bibstest = bibs
+      end
+
+      if !bibstest.nil?
+        if !bibstest.match(/error|not found/i).nil? || !bibstest.match(/<\/html>/i).nil?
+          puts "DOI found: " + ids + " ; but citation not found via content negotation - passing"          # do something else?
+
+        else
+          if file.nil?
+            return bibstest
+          else
+            puts "writing " + ids + " to " + file
+            bibs.write_bib(file)
+          end
+        end
+      end
+    end
+  end
+end
+
+
+ +
+

+ + .extract_dois(path:) ⇒ Object + + + + + +

+
+ +

Extract DOIs from one or more PDFs after extracting text

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+require 'faraday'# get a paper in pdf format
+
+path = '2068.pdf'
+res = Faraday.new(:url => "https://peerj.com/articles/2068.pdf").get
+f = File.new(path, "wb")
+f.write(res.body)
+f.close()# extract doi from the pdf
+
+Extcite.extract_dois(path: path)
+ +
+

Parameters:

+
    + +
  • + + path + + + (String) + + + + — +
    +

    Path to a pdf file, or a folder of PDF files

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+210
+211
+212
+213
+214
+ 		+ 
# File 'lib/extcite.rb', line 210
+
+def self.extract_dois(path:)
+  txt = Extcite.extract_text(path: path)  # return txt.map { |z| z.match("[0-9]+\\.[0-9]+/.+").to_s.gsub(/\s.+/, '') }
+
+  return Extcite.get_ids(txt: txt)
+end
+
+
+ +
+

+ + .extract_from_metadata(path:) ⇒ Object + + + + + +

+
+ +

Try to extract DOIs from one or more PDF metadata sections

+ +

Return: DOI string

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+require 'faraday'# get a paper in pdf format
+
+path = '2068.pdf'
+res = Faraday.new(:url => "https://peerj.com/articles/2068.pdf").get;
+f = File.new(path, "wb");
+f.write(res.body)
+f.close()# extract doi from the pdf
+
+Extcite.extract_from_metadata(path: path)
+ +
+

Parameters:

+
    + +
  • + + path + + + (String) + + + + — +
    +

    Path to a pdf file, or a folder of PDF files

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+137
+138
+139
+140
+141
+142
+143
+144
+145
+146
+147
+148
+149
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+187
+188
+189
+190
+191
+192
+ 		+ 
# File 'lib/extcite.rb', line 137
+
+def self.extract_from_metadata(path:)
+  path = make_paths(path)
+  path.each do |x|
+    # try PDF metadata first
+    ids = nil
+    rr = PDF::Reader.new(x)
+    pdfmeta = rr.metadata
+    if !pdfmeta.nil?
+      begin
+        xml = Oga.parse_xml(pdfmeta);
+      rescue Exception => e
+        xml = nil
+      end
+
+      if !xml.nil?
+        begin
+          tt = xml.xpath('//rdf:Description')          # try dc:identifier attribute
+
+          ss = tt.attr('dc:identifier')[0]
+          if !ss.nil?
+            ids = ss.text.sub(/doi:/, '')
+          else
+            # try prism:doi node
+            pdoi = xml.xpath('//rdf:Description//prism:doi')
+            if pdoi.length == 1
+              ids = pdoi.text
+            else
+              # try pdf:WPS-ARTICLEDOI node
+              wpsdoi = xml.xpath('//rdf:Description//pdf:WPS-ARTICLEDOI')
+              if wpsdoi.length == 1
+                ids = wpsdoi.text
+              else
+                # try pdfx:WPS-ARTICLEDOI node
+                pdfxwpsdoi = xml.xpath('//rdf:Description//pdfx:WPS-ARTICLEDOI')
+                if pdfxwpsdoi.length == 1
+                  ids = pdfxwpsdoi.text
+                else
+                  ids = nil
+                end
+              end
+            end
+          end
+        rescue
+          ids = nil
+        end
+      end
+    end
+
+    # if not found, try regexing for DOI
+    if ids.nil?
+      ids = Extcite.get_ids(txt: Extcite.extract_text_one(x))
+    end
+
+    return ids
+  end
+end
+
+
+ +
+

+ + .extract_text(path:) ⇒ Object + + + + + +

+
+ +

Extract text from a pdf, or many pdfs

+ +

This method is used internally within fetch to parse PDFs.

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+require 'faraday'# get a paper in pdf format
+
+path = '2068.pdf'
+res = Faraday.new(:url => "https://peerj.com/articles/2068.pdf").get
+f = File.new(path, "wb")
+f.write(res.body)
+f.close()# extract doi from the pdf
+
+Extcite.extract_text(path: path)
+ +
+

Parameters:

+
    + +
  • + + path + + + (String) + + + + — +
    +

    Path to a pdf file, or a folder of PDF files

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+263
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+273
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+278
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+280
+281
+282
+283
+284
+ 		+ 
# File 'lib/extcite.rb', line 263
+
+def self.extract_text(path:)
+  path = Array(path)
+  if path.length == 1
+    if File.directory?(path[0])      # keep only files with .pdf extension
+
+      path = dir_files(path[0]).keep_if { |z| !!z.match(/.pdf/) }
+    end
+  end
+
+  out = []
+  path.each do |x|
+    begin
+      rr = PDF::Reader.new(x)
+      txt = rr.pages.map { |page| page.text }.join("\n")
+    rescue Exception => e
+      warn e
+      txt = ""
+    end
+    out << txt
+  end
+  return out
+end
+
+
+ +
+

+ + .get_ids(txt:) ⇒ Object + + + + + +

+
+ +

Get DOIs from a String or Array of String's

+ +

Return: Array of DOIs

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'extcite'
+Extcite.get_ids(txt: '10.1016/j.dendro.2014.01.004 adfasdf asd fas df asdfsd')
+ +
+

Parameters:

+
    + +
  • + + txt + + + (String) + + + + — +
    +

    String or Array of String's

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+226
+227
+228
+229
+230
+231
+232
+233
+234
+235
+236
+237
+238
+239
+240
+241
+242
+243
+ 		+ 
# File 'lib/extcite.rb', line 226
+
+def self.get_ids(txt:)
+  # see if there's
+
+  return Array(txt).map { |z|
+    # detect if is an arxiv paper
+    if !z.match(/arxiv:[0-9]+\.[0-9A-Za-z]+/i).nil?      # if so, return arxiv id for later extraction of arxiv citation via their API
+
+      z = z.match(/arxiv:[0-9]+\.[0-9A-Za-z]+/i).to_s
+    else
+      doi_pattern = '(10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?![%"#? ])\\S)+)'
+      z = z.match(doi_pattern).to_s.gsub(/\s.+/, '')      # z = z.match("10\\.[0-9]+/.+").to_s.gsub(/\s.+/, '')
+
+    end    # clean up doi
+
+    z = z.gsub(/\.$|\.;$|\.\]$|\.\}$|\.\)$|,$/, '')
+    return z.gsub(/;$|\]$|\}$|\)$/, '')
+  }[0]
+end
+
+
+ +
+ +
+ + + +
+ + \ No newline at end of file diff --git a/doc/Hash.html b/doc/Hash.html new file mode 100644 index 0000000..d5afaed --- /dev/null +++ b/doc/Hash.html @@ -0,0 +1,380 @@ + + + + + + Class: Hash + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Hash + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/link_methods_hash.rb,
+ lib/textminer/link_methods_hash.rb,
lib/textminer/link_methods_hash.rb,
lib/textminer/link_methods_hash.rb +
+ +
+
+ +

Overview

+
+ +

Hash methods

+ + +
+
+
+ + +
+ + + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + + + +
+

Instance Method Details

+ + +
+ + + + + +
+ 
+
+
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+ 		+ 
# File 'lib/textminer/link_methods_hash.rb', line 3
+
+def links(just_urls = true)
+  if self['message']['items'].nil?
+    tmp = self['message']['link']
+    if tmp.nil?
+      tmp = nil
+    else
+      tmp = tmp.reject { |c| c.empty? }
+    end
+  else
+    tmp = self['message']['items'].collect { |x| x['link'] }.reject { |c| c.empty? }
+  end
+
+	return parse_links(tmp, just_urls)
+end
+
+
+ +
+

+ + - (Object) links_pdf(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+26
+27
+28
+ 		+ 
# File 'lib/textminer/link_methods_hash.rb', line 26
+
+def links_pdf(just_urls = true)
+	return parse_links(pull_links(self, '^application\/pdf$'), just_urls)
+end
+
+
+ +
+

+ + - (Object) links_plain(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+32
+33
+34
+ 		+ 
# File 'lib/textminer/link_methods_hash.rb', line 32
+
+def links_plain(just_urls = true)
+	return parse_links(pull_links(self, '^application\/plain$|^text\/plain$'), just_urls)
+end
+
+
+ +
+

+ + - (Object) links_xml(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+20
+21
+22
+ 		+ 
# File 'lib/textminer/link_methods_hash.rb', line 20
+
+def links_xml(just_urls = true)
+	return parse_links(pull_links(self, '^application\/xml$|^text\/xml$'), just_urls)
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/String.html b/doc/String.html new file mode 100644 index 0000000..c7d78d0 --- /dev/null +++ b/doc/String.html @@ -0,0 +1,289 @@ + + + + + + + Class: String + + — Documentation by YARD 0.9.24 + + + + + + + + + + + + + + + + + +
+ +
+
+ +
+ + +

Class: String + + + +

+
+ +
+
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+
+ + + + + + + + + + + +
+
Defined in:
+
lib/extcite/methods_string.rb,
+ lib/extcite/methods_string.rb +
+
+ +
+ +

Overview

+
+ +

String methods

+ + +
+
+
+ + +
+ + + + + + + +

+ Instance Method Summary + collapse +

+ + + + + + +
+

Instance Method Details

+ + +
+

+ + #make_bib_arxiv(id) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+ 		+ 
# File 'lib/extcite/methods_string.rb', line 14
+
+def make_bib_arxiv(id)
+	# prep xml
+	xml = Oga.parse_xml(self)	# author = xml.xpath('//author//name')[0].text.downcase.gsub(/\s|\./, '_')
+
+	year = DateTime.strptime(xml.xpath('//updated')[0].text).year
+
+	# make bib citation
+	bib = BibTeX::Bibliography.new
+	bib << BibTeX::Entry.new({
+	  :bibtex_type => :article,
+	  :url => xml.xpath('//entry/id').text,
+	  :author => xml.xpath('//author//name').collect { |x| x.text }.join(' and '),
+	  :eprint => id,
+	  :title => xml.xpath('//entry//title').text,
+	  :year => year
+	})
+	return bib.to_s
+end
+
+
+ +
+

+ + #write_bib(file) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+6
+7
+8
+9
+10
+ 		+ 
# File 'lib/extcite/methods_string.rb', line 6
+
+def write_bib(file)
+  File.open(file, 'a') do |f|
+    f.puts self
+  end
+end
+
+
+ +
+ +
+ + + +
+ + \ No newline at end of file diff --git a/doc/Textminer.html b/doc/Textminer.html new file mode 100644 index 0000000..5766857 --- /dev/null +++ b/doc/Textminer.html @@ -0,0 +1,601 @@ + + + + + + Module: Textminer + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Module: Textminer + + + +

+ +
+ + + +
Extended by:
+
Configuration
+ + + + + + + +
Defined in:
+
lib/textminer/mined.rb,
+ lib/textminer.rb,
lib/textminer/miner.rb,
lib/textminer/request.rb,
lib/textminer/version.rb,
lib/textminer/response.rb +
+ +
+
+ +

Overview

+
+ +

Textminer::Miner

+ +

Class to give back text mining object

+ + +
+
+
+ + +

Defined Under Namespace

+

+ + + + + Classes: Mined, Miner, Request, Response + + +

+ +

Constant Summary

+ +
+ +
VERSION = + +
+ 
"0.1.5"
+ +
+ + + + + + + + + +

+ Class Method Summary + (collapse) +

+ + + + + + + + + + + + + +

Methods included from Configuration

+

configuration, define_setting

+ + +
+

Class Method Details

+ + +
+

+ + + (Object) extract(path) + + + + + +

+
+ +

Thin layer around pdf-reader gem's PDF::Reader

+ +

This method is used internally within fetch to parse PDFs.

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'textminer'
+res = Textminer.search(member: 2258, filter: {has_full_text: true});
+links = res.links_pdf(true);
+# Get full text for an article
+out = Textminer.fetch(url: links[0]);
+# extract pdf to text
+Textminer.extract(out.path)
+ +
+

Parameters:

+
    + +
  • + + path + + + (String) + + + + — +
    +

    Path to a pdf file downloaded via fetch, or another way.

    +
    + +
    • + +
+ + +
+ + + + +
+ 
+
+
+140
+141
+142
+143
+ 		+ 
# File 'lib/textminer.rb', line 140
+
+def self.extract(path)
+  rr = PDF::Reader.new(path)
+  rr.pages.map { |page| page.text }.join("\n")
+end
+
+
+ +
+

+ + + (Mined) fetch(url) + + + + + +

+
+ +

Get full text

+ +

Work easily for open access papers, but for closed. For non-OA papers, use +Crossref's Text and Data Mining service, which requires authentication +and pre-authorized IP address. Go to apps.crossref.org/clickthrough/researchers +to sign up for the TDM service, to get your key. The only publishers taking +part at this time are Elsevier and Wiley.

+ +

the url requested, the file path, and parsing the plain text, XML, or +extracting text from the pdf.

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'textminer'
+# Set authorization
+Textminer.configuration do |config|
+  config.tdm_key = "<your key>"
+end
+# Get some elsevier works
+res = Textminer.search(member: 78, filter: {has_full_text: true});
+links = res.links_xml(true);
+# Get full text for an article
+out = Textminer.fetch(url: links[0]);
+out.url
+out.path
+out.type
+xml = out.parse()
+puts xml
+xml.xpath('//xocs:cover-date-text', xml.root.namespaces).text
+# Get lots of articles
+links = links[1..3]
+out = links.collect{ |x| Textminer.fetch(url: x) }
+out.collect{ |z| z.path }
+out.collect{ |z| z.parse }
+zz = out[0].parse
+zz.xpath('//xocs:cover-date-text', zz.root.namespaces).text
+
+## plain text
+# get full text links, here doing xml
+links = res.links_plain(true);
+# Get full text for an article
+res = Textminer.fetch(url: links[0]);
+res.url
+res.parse
+
+# With open access content - using Pensoft
+res = Textminer.search(member: 2258, filter: {has_full_text: true});
+links = res.links_xml(true);
+# Get full text for an article
+res = Textminer.fetch(url: links[0]);
+res.url
+res.parse
+
+# OA content - pdfs, using pensoft again
+res = Textminer.search(member: 2258, filter: {has_full_text: true});
+links = res.links_pdf(true);
+# Get full text for an article
+res = Textminer.fetch(url: links[0]);
+# url used
+res.url
+# document type
+res.type
+# document path on your machine
+res.path
+# get text
+res.parse
+ +
+

Parameters:

+
    + +
  • + + url + + + (String) + + + + — +
    +

    A url for full text

    +
    + +
    • + +
+ +

Returns:

+
    + +
  • + + + (Mined) + + + + — +
    +

    An object of class Mined, with methods for extracting

    +
    + +
    • + +
+ +
+ + + + +
+ 
+
+
+120
+121
+122
+ 		+ 
# File 'lib/textminer.rb', line 120
+
+def self.fetch(url)
+  Miner.new(url).perform
+end
+
+
+ +
+

+ + + (Array) search(doi: nil, member: nil, filter: nil, limit: nil, options: nil) + + + + + +

+
+ +

Search for papers and get full text links

+ + +
+
+
+ +
+

Examples:

+ + + 
require 'textminer'
+# link to full text available
+Textminer.search(doi: '10.3897/phytokeys.42.7604')
+# no link to full text available
+Textminer.search(doi: "10.1371/journal.pone.0000308")
+# many DOIs at once
+require 'serrano'
+dois = Serrano.random_dois(sample: 6)
+res = Textminer.search(doi: dois)
+res = Textminer.search(doi: ["10.3897/phytokeys.42.7604", "10.3897/zookeys.516.9439"])
+res.links
+res.links_pdf
+res.links_xml
+res.links_plain
+# only full text available
+x = Textminer.search(doi: '10.3816/clm.2001.n.006')
+x.links_xml
+x.links_plain
+x.links_pdf
+# no dois
+x = Textminer.search(filter: {has_full_text: true})
+x.links_xml
+x.links_plain
+x = Textminer.search(member: 311, filter: {has_full_text: true})
+x.links_pdf
+ +
+

Parameters:

+
    + +
  • + + doi + + + (Array) + + + + — +
    +

    A DOI, digital object identifier

    +
    + +
    • + +
  • + + options + + + (Array) + + + + — +
    +

    Curl request options

    +
    + +
    • + +
+ +

Returns:

+
    + +
  • + + + (Array) + + + + — +
    +

    the output

    +
    + +
    • + +
+ +
+ + + + +
+ 
+
+
+48
+49
+50
+ 		+ 
# File 'lib/textminer.rb', line 48
+
+def self.search(doi: nil, member: nil, filter: nil, limit: nil, options: nil)
+  Request.new(doi, member, filter, limit, options).perform
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Textminer/Fetch.html b/doc/Textminer/Fetch.html new file mode 100644 index 0000000..1dc4fcc --- /dev/null +++ b/doc/Textminer/Fetch.html @@ -0,0 +1,447 @@ + + + + + + Class: Textminer::Fetch + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Textminer::Fetch + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/fetch.rb
+ +
+
+ +

Overview

+
+ +

:nodoc:

+ + +
+
+
+ + +
+ + + +

Instance Attribute Summary (collapse)

+ + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + +
+

Constructor Details

+ +
+

+ + - (Fetch) initialize(doi, type) + + + + + +

+
+ +

Returns a new instance of Fetch

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+5
+6
+7
+8
+ 		+ 
# File 'lib/textminer/fetch.rb', line 5
+
+def initialize(doi, type)
+  self.doi = doi
+  self.type = type
+end
+
+
+ +
+ +
+

Instance Attribute Details

+ + + +
+

+ + - (Object) doi + + + + + +

+
+ +

Returns the value of attribute doi

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+3
+4
+5
+ 		+ 
# File 'lib/textminer/fetch.rb', line 3
+
+def doi
+  @doi
+end
+
+
+ + + +
+

+ + - (Object) type + + + + + +

+
+ +

Returns the value of attribute type

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+3
+4
+5
+ 		+ 
# File 'lib/textminer/fetch.rb', line 3
+
+def type
+  @type
+end
+
+
+ +
+ + +
+

Instance Method Details

+ + +
+

+ + - (Object) fetchtext + + + + + +

+ + + + +
+ 
+
+
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+ 		+ 
# File 'lib/textminer/fetch.rb', line 10
+
+def fetchtext
+  lks = Textminer.links(self.doi)
+  lk = pick_link(lks)
+  case self.type
+  when "xml"
+    # HTTParty.get(lk)
+    coll = []
+    Array(lk).each do |x|
+      coll << HTTParty.get(x)
+    end
+    return coll
+  when "pdf"
+    serialize_pdf(lk, self.doi)
+  end
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Textminer/Mined.html b/doc/Textminer/Mined.html new file mode 100644 index 0000000..5f9a0bc --- /dev/null +++ b/doc/Textminer/Mined.html @@ -0,0 +1,509 @@ + + + + + + Class: Textminer::Mined + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Textminer::Mined + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/mined.rb
+ +
+
+ +

Overview

+
+ +

:nodoc:

+ + +
+
+
+ + +
+ + + +

Instance Attribute Summary (collapse)

+ + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + +
+

Constructor Details

+ +
+

+ + - (Mined) initialize(url, path, type) + + + + + +

+
+ +

Returns a new instance of Mined

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+13
+14
+15
+16
+17
+ 		+ 
# File 'lib/textminer/mined.rb', line 13
+
+def initialize(url, path, type)
+  self.url = url
+  self.path = path
+  self.type = type
+end
+
+
+ +
+ +
+

Instance Attribute Details

+ + + +
+

+ + - (Object) path + + + + + +

+
+ +

Returns the value of attribute path

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+10
+11
+12
+ 		+ 
# File 'lib/textminer/mined.rb', line 10
+
+def path
+  @path
+end
+
+
+ + + +
+

+ + - (Object) type + + + + + +

+
+ +

Returns the value of attribute type

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+11
+12
+13
+ 		+ 
# File 'lib/textminer/mined.rb', line 11
+
+def type
+  @type
+end
+
+
+ + + +
+

+ + - (Object) url + + + + + +

+
+ +

Returns the value of attribute url

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+9
+10
+11
+ 		+ 
# File 'lib/textminer/mined.rb', line 9
+
+def url
+  @url
+end
+
+
+ +
+ + +
+

Instance Method Details

+ + +
+

+ + - (Object) parse + + + + + +

+ + + + +
+ 
+
+
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+ 		+ 
# File 'lib/textminer/mined.rb', line 19
+
+def parse
+  case self.type
+  when 'xml'
+    parse_xml(self.path)
+  when 'plain'
+    parse_plain(self.path)
+  when 'pdf'
+    parse_pdf(self.path)
+  end
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Textminer/Miner.html b/doc/Textminer/Miner.html new file mode 100644 index 0000000..6f9f49e --- /dev/null +++ b/doc/Textminer/Miner.html @@ -0,0 +1,385 @@ + + + + + + Class: Textminer::Miner + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Textminer::Miner + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/miner.rb
+ +
+
+ +

Overview

+
+ +

:nodoc:

+ + +
+
+
+ + +
+ + + +

Instance Attribute Summary (collapse)

+ + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + +
+

Constructor Details

+ +
+

+ + - (Miner) initialize(url) + + + + + +

+
+ +

Returns a new instance of Miner

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+16
+17
+18
+ 		+ 
# File 'lib/textminer/miner.rb', line 16
+
+def initialize(url)
+  self.url = url
+end
+
+
+ +
+ +
+

Instance Attribute Details

+ + + +
+

+ + - (Object) url + + + + + +

+
+ +

Returns the value of attribute url

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+14
+15
+16
+ 		+ 
# File 'lib/textminer/miner.rb', line 14
+
+def url
+  @url
+end
+
+
+ +
+ + +
+

Instance Method Details

+ + +
+

+ + - (Object) perform + + + + + +

+ + + + +
+ 
+
+
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+ 		+ 
# File 'lib/textminer/miner.rb', line 20
+
+def perform
+  conn = Faraday.new self.url do |c|
+    c.use FaradayMiddleware::FollowRedirects
+    c.adapter :net_http
+  end
+
+  if is_elsevier_wiley(self.url)
+    res = conn.get do |req|
+      req.headers['CR-Clickthrough-Client-Token'] = Textminer.tdm_key
+    end
+  else
+    res = conn.get
+  end
+
+  type = detect_type(res)
+  path = make_path(type)
+  write_disk(res, path)
+
+  return Mined.new(self.url, path, type)
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Textminer/Request.html b/doc/Textminer/Request.html new file mode 100644 index 0000000..7e682f8 --- /dev/null +++ b/doc/Textminer/Request.html @@ -0,0 +1,669 @@ + + + + + + Class: Textminer::Request + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Textminer::Request + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/request.rb
+ +
+
+ +

Overview

+
+ +

:nodoc:

+ + +
+
+
+ + +
+ + + +

Instance Attribute Summary (collapse)

+ + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + +
+

Constructor Details

+ +
+

+ + - (Request) initialize(doi, member, filter, limit, options) + + + + + +

+
+ +

Returns a new instance of Request

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+9
+10
+11
+12
+13
+14
+15
+ 		+ 
# File 'lib/textminer/request.rb', line 9
+
+def initialize(doi, member, filter, limit, options)
+  self.doi = doi
+  self.member = member
+  self.filter = filter
+  self.limit = limit
+  self.options = options
+end
+
+
+ +
+ +
+

Instance Attribute Details

+ + + +
+

+ + - (Object) doi + + + + + +

+
+ +

Returns the value of attribute doi

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+3
+4
+5
+ 		+ 
# File 'lib/textminer/request.rb', line 3
+
+def doi
+  @doi
+end
+
+
+ + + +
+

+ + - (Object) filter + + + + + +

+
+ +

Returns the value of attribute filter

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+5
+6
+7
+ 		+ 
# File 'lib/textminer/request.rb', line 5
+
+def filter
+  @filter
+end
+
+
+ + + +
+

+ + - (Object) limit + + + + + +

+
+ +

Returns the value of attribute limit

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+6
+7
+8
+ 		+ 
# File 'lib/textminer/request.rb', line 6
+
+def limit
+  @limit
+end
+
+
+ + + +
+

+ + - (Object) member + + + + + +

+
+ +

Returns the value of attribute member

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+4
+5
+6
+ 		+ 
# File 'lib/textminer/request.rb', line 4
+
+def member
+  @member
+end
+
+
+ + + +
+

+ + - (Object) options + + + + + +

+
+ +

Returns the value of attribute options

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+7
+8
+9
+ 		+ 
# File 'lib/textminer/request.rb', line 7
+
+def options
+  @options
+end
+
+
+ +
+ + +
+

Instance Method Details

+ + +
+

+ + - (Object) perform + + + + + +

+ + + + +
+ 
+
+
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+ 		+ 
# File 'lib/textminer/request.rb', line 17
+
+def perform
+  fac = nil
+
+  if member.nil?
+    res = Serrano.works(ids: doi, filter: filter, limit: limit, options: options)
+    if doi.nil?
+      fac = Serrano.works(ids: doi, filter: filter, options: options, facet: 'license:*', limit: 0)
+      fac = fac['message']['facets']['license']['value-count'].to_s
+    end
+  else
+    res = Serrano.members(ids: member, filter: filter, works: true, limit: limit, options: options)
+    if member.nil?
+      fac = Serrano.member(ids: member, filter: filter, options: options, facet: 'license:*', limit: 0)
+      fac = fac['message']['facets']['license']['value-count'].to_s
+    end
+  end
+  Response.new(self.doi, self.member, res, fac)
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/Textminer/Response.html b/doc/Textminer/Response.html new file mode 100644 index 0000000..87ee0a8 --- /dev/null +++ b/doc/Textminer/Response.html @@ -0,0 +1,923 @@ + + + + + + Class: Textminer::Response + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + + + + + +

Class: Textminer::Response + + + +

+ +
+ +
Inherits:
+
+ Object + +
    +
  • Object
    • + + + +
+ show all + +
+ + + + + + + + + +
Defined in:
+
lib/textminer/response.rb
+ +
+
+ +

Overview

+
+ +

:nodoc:

+ + +
+
+
+ + +
+ + + +

Instance Attribute Summary (collapse)

+ + + + + + +

+ Instance Method Summary + (collapse) +

+ + + + +
+

Constructor Details

+ +
+

+ + - (Response) initialize(doi, member, response, facet) + + + + + +

+
+ +

Returns a new instance of Response

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+9
+10
+11
+12
+13
+14
+ 		+ 
# File 'lib/textminer/response.rb', line 9
+
+def initialize(doi, member, response, facet)
+  @doi = doi
+  @member = member
+  @response = response
+  @facet = facet
+end
+
+
+ +
+ +
+

Instance Attribute Details

+ + + +
+

+ + - (Object) doi (readonly) + + + + + +

+
+ +

Returns the value of attribute doi

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+7
+8
+9
+ 		+ 
# File 'lib/textminer/response.rb', line 7
+
+def doi
+  @doi
+end
+
+
+ + + +
+

+ + - (Object) facet (readonly) + + + + + +

+
+ +

Returns the value of attribute facet

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+7
+8
+9
+ 		+ 
# File 'lib/textminer/response.rb', line 7
+
+def facet
+  @facet
+end
+
+
+ + + +
+

+ + - (Object) member (readonly) + + + + + +

+
+ +

Returns the value of attribute member

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+7
+8
+9
+ 		+ 
# File 'lib/textminer/response.rb', line 7
+
+def member
+  @member
+end
+
+
+ + + +
+

+ + - (Object) response (readonly) + + + + + +

+
+ +

Returns the value of attribute response

+ + +
+
+
+ + +
+ + + + +
+ 
+
+
+7
+8
+9
+ 		+ 
# File 'lib/textminer/response.rb', line 7
+
+def response
+  @response
+end
+
+
+ +
+ + +
+

Instance Method Details

+ + +
+

+ + - (Object) body + + + + + +

+ + + + +
+ 
+
+
+38
+39
+40
+ 		+ 
# File 'lib/textminer/response.rb', line 38
+
+def body
+  @response
+end
+
+
+ +
+

+ + - (Object) inspect + + + + + +

+ + + + +
+ 
+
+
+34
+35
+36
+ 		+ 
# File 'lib/textminer/response.rb', line 34
+
+def inspect
+  to_s
+end
+
+
+ +
+

+ + - (Object) links(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+42
+43
+44
+45
+ 		+ 
# File 'lib/textminer/response.rb', line 42
+
+def links(just_urls = true)
+  tmp = @response.links(just_urls)
+  compactif(tmp)
+end
+
+
+ +
+

+ + - (Object) links_pdf(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+52
+53
+54
+55
+ 		+ 
# File 'lib/textminer/response.rb', line 52
+
+def links_pdf(just_urls = true)
+  tmp = @response.links_pdf(just_urls)
+  compactif(tmp)
+end
+
+
+ +
+

+ + - (Object) links_plain(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+57
+58
+59
+60
+ 		+ 
# File 'lib/textminer/response.rb', line 57
+
+def links_plain(just_urls = true)
+  tmp = @response.links_plain(just_urls)
+  compactif(tmp)
+end
+
+
+ +
+

+ + - (Object) links_xml(just_urls = true) + + + + + +

+ + + + +
+ 
+
+
+47
+48
+49
+50
+ 		+ 
# File 'lib/textminer/response.rb', line 47
+
+def links_xml(just_urls = true)
+  tmp = @response.links_xml(just_urls)
+  compactif(tmp)
+end
+
+
+ +
+

+ + - (Object) to_s + + + + + +

+ + + + +
+ 
+
+
+16
+17
+18
+19
+20
+21
+22
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+24
+25
+26
+27
+28
+29
+30
+31
+32
+ 		+ 
# File 'lib/textminer/response.rb', line 16
+
+def to_s
+  if !@doi.nil?
+    if @doi.length > 3
+      ending = '...'
+    else
+      ending = ''
+    end
+    tt = sprintf('dois: %s %s', Array(@doi)[0..2].join(', '), ending)
+  end
+  if !@member.nil?
+    tt = 'member: ' + @member.to_s
+  end
+  if @doi.nil? && @member.nil?
+    tt = ''
+  end
+  sprintf("<textminer>: \n      search: %s\n      no. licenses: %s", tt, @facet)
+end
+
+
+ +
+ +
+ + + + + \ No newline at end of file diff --git a/doc/_index.html b/doc/_index.html new file mode 100644 index 0000000..5e79f2f --- /dev/null +++ b/doc/_index.html @@ -0,0 +1,135 @@ + + + + + + + Documentation by YARD 0.9.24 + + + + + + + + + + + + + + + + + +
+ +
+
+ +
+ + +

Documentation by YARD 0.9.24

+
+

Alphabetic Index

+ +

File Listing

+ + +
+

Namespace Listing A-Z

+ + + + + + + + + + +
+ + +
    +
  • A
    • + +
+ + + + + +
    +
  • S
    • + +
+ +
+ +
+ +
+ + + +
+ + \ No newline at end of file diff --git a/doc/class_list.html b/doc/class_list.html new file mode 100644 index 0000000..090a2c4 --- /dev/null +++ b/doc/class_list.html @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + Class List + + + +
+
+

Class List

+ + + +
+ + +
+ + diff --git a/doc/css/common.css b/doc/css/common.css new file mode 100644 index 0000000..cf25c45 --- /dev/null +++ b/doc/css/common.css @@ -0,0 +1 @@ +/* Override this file with custom rules */ \ No newline at end of file diff --git a/doc/css/full_list.css b/doc/css/full_list.css new file mode 100644 index 0000000..fa35982 --- /dev/null +++ b/doc/css/full_list.css @@ -0,0 +1,58 @@ +body { + margin: 0; + font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; + font-size: 13px; + height: 101%; + overflow-x: hidden; + background: #fafafa; +} + +h1 { padding: 12px 10px; padding-bottom: 0; margin: 0; font-size: 1.4em; } +.clear { clear: both; } +.fixed_header { position: fixed; background: #fff; width: 100%; padding-bottom: 10px; margin-top: 0; top: 0; z-index: 9999; height: 70px; } +#search { position: absolute; right: 5px; top: 9px; padding-left: 24px; } +#content.insearch #search, #content.insearch #noresults { background: url(data:image/gif;base64,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) no-repeat center left; } +#full_list { padding: 0; list-style: none; margin-left: 0; margin-top: 80px; font-size: 1.1em; } +#full_list ul { padding: 0; } +#full_list li { padding: 0; margin: 0; list-style: none; } +#full_list li .item { padding: 5px 5px 5px 12px; } +#noresults { padding: 7px 12px; background: #fff; } +#content.insearch #noresults { margin-left: 7px; } +li.collapsed ul { display: none; } +li a.toggle { cursor: default; position: relative; left: -5px; top: 4px; text-indent: -999px; width: 10px; height: 9px; margin-left: -10px; display: block; float: left; background: url(data:image/png;base64,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) no-repeat bottom left; } +li.collapsed a.toggle { opacity: 0.5; cursor: default; background-position: top left; } +li { color: #888; cursor: pointer; } +li.deprecated { text-decoration: line-through; font-style: italic; } +li.odd { background: #f0f0f0; } +li.even { background: #fafafa; } +.item:hover { background: #ddd; } +li small:before { content: "("; } +li small:after { content: ")"; } +li small.search_info { display: none; } +a, a:visited { text-decoration: none; color: #05a; } +li.clicked > .item { background: #05a; color: #ccc; } +li.clicked > .item a, li.clicked > .item a:visited { color: #eee; } +li.clicked > .item a.toggle { opacity: 0.5; background-position: bottom right; } +li.collapsed.clicked a.toggle { background-position: top right; } +#search input { border: 1px solid #bbb; border-radius: 3px; } +#full_list_nav { margin-left: 10px; font-size: 0.9em; display: block; color: #aaa; } +#full_list_nav a, #nav a:visited { color: #358; } +#full_list_nav a:hover { background: transparent; color: #5af; } +#full_list_nav span:after { content: ' | '; } +#full_list_nav span:last-child:after { content: ''; } + +#content h1 { margin-top: 0; } +li { white-space: nowrap; cursor: normal; } +li small { display: block; font-size: 0.8em; } +li small:before { content: ""; } +li small:after { content: ""; } +li small.search_info { display: none; } +#search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; } +#content.insearch #search { background-position: center right; } +#search input { width: 110px; } + +#full_list.insearch ul { display: block; } +#full_list.insearch .item { display: none; } +#full_list.insearch .found { display: block; padding-left: 11px !important; } +#full_list.insearch li a.toggle { display: none; } +#full_list.insearch li small.search_info { display: block; } diff --git a/doc/css/style.css b/doc/css/style.css new file mode 100644 index 0000000..62f4349 --- /dev/null +++ b/doc/css/style.css @@ -0,0 +1,496 @@ +html { + width: 100%; + height: 100%; +} +body { + font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; + font-size: 13px; + width: 100%; + margin: 0; + padding: 0; + display: flex; + display: -webkit-flex; + display: -ms-flexbox; +} + +#nav { + position: relative; + width: 100%; + height: 100%; + border: 0; + border-right: 1px dotted #eee; + overflow: auto; +} +.nav_wrap { + margin: 0; + padding: 0; + width: 20%; + height: 100%; + position: relative; + display: flex; + display: -webkit-flex; + display: -ms-flexbox; + flex-shrink: 0; + -webkit-flex-shrink: 0; + -ms-flex: 1 0; +} +#resizer { + position: absolute; + right: -5px; + top: 0; + width: 10px; + height: 100%; + cursor: col-resize; + z-index: 9999; +} +#main { + flex: 5 1; + -webkit-flex: 5 1; + -ms-flex: 5 1; + outline: none; + position: relative; + background: #fff; + padding: 1.2em; + padding-top: 0.2em; +} + +@media (max-width: 920px) { + .nav_wrap { width: 100%; top: 0; right: 0; overflow: visible; position: absolute; } + #resizer { display: none; } + #nav { + z-index: 9999; + background: #fff; + display: none; + position: absolute; + top: 40px; + right: 12px; + width: 500px; + max-width: 80%; + height: 80%; + overflow-y: scroll; + border: 1px solid #999; + border-collapse: collapse; + box-shadow: -7px 5px 25px #aaa; + border-radius: 2px; + } +} + +@media (min-width: 920px) { + body { height: 100%; overflow: hidden; } + #main { height: 100%; overflow: auto; } + #search { display: none; } +} + +#main img { max-width: 100%; } +h1 { font-size: 25px; margin: 1em 0 0.5em; padding-top: 4px; border-top: 1px dotted #d5d5d5; } +h1.noborder { border-top: 0px; margin-top: 0; padding-top: 4px; } +h1.title { margin-bottom: 10px; } +h1.alphaindex { margin-top: 0; font-size: 22px; } +h2 { + padding: 0; + padding-bottom: 3px; + border-bottom: 1px #aaa solid; + font-size: 1.4em; + margin: 1.8em 0 0.5em; + position: relative; +} +h2 small { font-weight: normal; font-size: 0.7em; display: inline; position: absolute; right: 0; } +h2 small a { + display: block; + height: 20px; + border: 1px solid #aaa; + border-bottom: 0; + border-top-left-radius: 5px; + background: #f8f8f8; + position: relative; + padding: 2px 7px; +} +.clear { clear: both; } +.inline { display: inline; } +.inline p:first-child { display: inline; } +.docstring, .tags, #filecontents { font-size: 15px; line-height: 1.5145em; } +.docstring p > code, .docstring p > tt, .tags p > code, .tags p > tt { + color: #c7254e; background: #f9f2f4; padding: 2px 4px; font-size: 1em; + border-radius: 4px; +} +.docstring h1, .docstring h2, .docstring h3, .docstring h4 { padding: 0; border: 0; border-bottom: 1px dotted #bbb; } +.docstring h1 { font-size: 1.2em; } +.docstring h2 { font-size: 1.1em; } +.docstring h3, .docstring h4 { font-size: 1em; border-bottom: 0; padding-top: 10px; } +.summary_desc .object_link a, .docstring .object_link a { + font-family: monospace; font-size: 1.05em; + color: #05a; background: #EDF4FA; padding: 2px 4px; font-size: 1em; + border-radius: 4px; +} +.rdoc-term { padding-right: 25px; font-weight: bold; } +.rdoc-list p { margin: 0; padding: 0; margin-bottom: 4px; } +.summary_desc pre.code .object_link a, .docstring pre.code .object_link a { + padding: 0px; background: inherit; color: inherit; border-radius: inherit; +} + +/* style for */ +#filecontents table, .docstring table { border-collapse: collapse; } +#filecontents table th, #filecontents table td, +.docstring table th, .docstring table td { border: 1px solid #ccc; padding: 8px; padding-right: 17px; } +#filecontents table tr:nth-child(odd), +.docstring table tr:nth-child(odd) { background: #eee; } +#filecontents table tr:nth-child(even), +.docstring table tr:nth-child(even) { background: #fff; } +#filecontents table th, .docstring table th { background: #fff; } + +/* style for
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index 0000000..0b3876f --- /dev/null +++ b/doc/method_list.html @@ -0,0 +1,155 @@ + + + + + + + + + + + + + + + + + + Method List + + + +
+
+

Method List

+ + + +
+ + +
+ + diff --git a/doc/top-level-namespace.html b/doc/top-level-namespace.html new file mode 100644 index 0000000..54a07d0 --- /dev/null +++ b/doc/top-level-namespace.html @@ -0,0 +1,397 @@ + + + + + + + Top Level Namespace + + — Documentation by YARD 0.9.24 + + + + + + + + + + + + + + + + + +
+ +
+
+ +
+ + +

Top Level Namespace + + + +

+
+ + + + + + + + + + + +
+ +

Defined Under Namespace

+

+ + + Modules: Extcite + + + + Classes: Array, String + + +

+ + + + + + + + +

+ Instance Method Summary + collapse +

+ + + + + + +
+

Instance Method Details

+ + +
+

+ + #dir_files(x) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+11
+12
+13
+14
+15
+16
+17
+ 		+ 
# File 'lib/extcite/utils.rb', line 11
+
+def dir_files(x)
+	Dir.entries(x).select { |entry|
+		!File.directory? File.join(x, entry) and !(entry =='.' || entry == '..')
+	}.map { |z|
+		x + '/' + z
+	}
+end
+
+ + +
+

+ + #make_paths(x) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+ 		+ 
# File 'lib/extcite/utils.rb', line 19
+
+def make_paths(x)
+	path = Array(x)
+  if path.length == 1    # if a directory
+
+    if File.directory?(path[0])      # keep only files with .pdf extension
+
+      path = dir_files(path[0]).keep_if { |z| !!z.match(/.pdf/) }
+    end
+  end
+
+  # check that files exist
+  path.each do |z|
+    if !File.exist?(z)
+      raise z + ' not found'
+    end
+  end
+
+  return path
+end
+
+
+ +
+

+ + #pdf_doi(x) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+39
+40
+41
+42
+43
+44
+45
+46
+47
+ 		+ 
# File 'lib/extcite/utils.rb', line 39
+
+def pdf_doi(x)
+  xml = Oga.parse_xml(x)
+  begin
+    tt = xml.xpath('//rdf:Description')
+    return tt.attr('dc:identifier')[0].text.sub(/doi:/, '')
+  rescue
+    return nil
+  end
+end
+
+
+ +
+

+ + #singlearray2hash(x) ⇒ Object + + + + + +

+ + + + +
+ 
+
+
+3
+4
+5
+6
+7
+8
+9
+ 		+ 
# File 'lib/extcite/utils.rb', line 3
+
+def singlearray2hash(x)
+  if x.length == 1 && x.class == Array
+    return x[0]
+  else
+    return x
+  end
+end
+
+
+ + + + + + + + + + \ No newline at end of file