rubyscholar 0.0.3 → 0.0.4

data/CHANGELOG.md

@@ -0,0 +1,6 @@
+## Changelog
+
+version 0.0.4
+
+* Support for custom config files and output file in commands.
+* Command for creating a config.yml file using `rubyscholar init`. 

data/README.md

@@ -13,6 +13,13 @@ Some features:
 
 # How to use:
 
+### As a Ruby Gem:
+1. Install the gem using: `[sudo] gem install rubyscholar`
+2. Create and configure a `config.yml` file.
+3. Run as `rubyscholar scrape`.
+4. A `scholar.html` file is created.
+5. Done!
+
 ### As a ruby script:
 1. Configure "config.yml"
    If you want DOI retreival to work (including Altmetrics), you need to be 

data/bin/rubyscholar

@@ -22,10 +22,9 @@ command :scrape do |c|
   c.option '--out [Output File]', 'File to output the scrapes to'
 
   c.action do |args, options|
-   options.default \
-      :config => 'config.yml',
-      :out  => 'scholar.html'
-   config    = YAML.load_file('config.yml')
+   options.default :config => "config.yml", :out  => "scholar.html"
+   configFile= "#{options.config}"
+   config    = YAML.load_file(configFile)
    parsed    = Rubyscholar::Parser.new(config["url"], 
                                 config["email"])
    formatter = Rubyscholar::Formatter.new(parsed, 
@@ -38,10 +37,40 @@ command :scrape do |c|
        config["italicize"].each do |term|
        html.gsub!( term , '<em>' + term + '</em>')
    end
-
-   f= File.open('scholar.html','w')
+   outFile="#{options.out}"
+   f= File.open(outFile,'w')
    f.write html
    f.close()
 end
 end
 
+command :init do |c|
+  c.syntax = 'rubyscholar init'
+  c.description = 'Creates a sample config.yml file for Scraping.'
+  c.action do |args, options|
+    say '# Intialising a configuration file for Rubyscholar.'
+    if File.exist?("config.yml")
+      abort("Initialisation aborted!") if ask("config.yml already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+    end
+    puts "# Creating config.yml."
+    open("config.yml", 'w') do |page|
+      page.puts "# Google Scholar page (you can choose how you sort it)"
+      page.puts "url: "
+      page.puts "\n\n# Name to highlight (withing \" and \")"
+      page.puts "highlight: "
+      page.puts "\n\n# Need an Email address that has been registered with CrossRef to obtain DOIs using their OpenURL service. "
+      page.puts "# e.g. the following should provide an XML file: "
+      page.puts "# http://www.crossref.org/openurl?redirect=false&pid=YOUR@EMAIL>COM&aulast=Wurm&atitle=Behavioral%20Genomics:%20A,%20Bee,%20C,%20G,%20T"
+      page.puts "email: your@email.com"
+      page.puts "\n\n# Show \"[Cited Nx]\" if N > the following number"
+      page.puts "minCitations: 5 "
+      page.puts "\n\n# Words to italicize (emphasize). These will have \"<em>\" around them. "
+      page.puts "italicize: "
+      page.puts "\n\n# DOIs of articles for which we should show altmetric.org badges. "
+      page.puts "altmetricDOIs:  "
+      page.puts "\n\n# Article titles for which we have urls to PDFs in \"name\" : \"url\" format"
+      page.puts "pdfs:"
+    end
+  end
+end
+

data/lib/rubyscholar/version.rb

@@ -1,3 +1,3 @@
 module Rubyscholar
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rubyscholar
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -55,13 +55,13 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- CHANGELOG.md
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
 - bin/rubyscholar
 - bin/scrape.rb
-- config.yml
 - lib/rubyscholar.rb
 - lib/rubyscholar/version.rb
 - rubyscholar.gemspec

data/config.yml

@@ -1,49 +0,0 @@
-# Google Scholar page (you can choose how you sort it)
-url: "http://scholar.google.com/citations?sortby=pubdate&hl=en&user=k6y0EGsAAAAJ&view_op=list_works"
-
-# Name to highlight 
-highlight: "Y Wurm"
-
-
-# Need an Email address that has been registered with CrossRef to obtain DOIs 
-# using their OpenURL service. 
-# e.g. the following should provide an XML file: 
-# http://www.crossref.org/openurl?redirect=false&pid=YOUR@EMAIL>COM&aulast=Wurm&atitle=Behavioral%20Genomics:%20A,%20Bee,%20C,%20G,%20T
-email: your@email.com
-
-
-# Show "[Cited Nx]" if N > the following number
-minCitations: 5
-
-# Words to italicize (emphasize). These will have "<em>" around them. 
-italicize: 
- - Solenopsis invicta
- - Acromyrmex echinatior
- - de novo
-
-# DOIs of articles for which we should show altmetric.org badges. 
-altmetricDOIs: 
- - "10.1038/nature11832"
- - "10.1101/gr.121392.111"
- - "10.1073/pnas.1009690108"
- - "10.1073/pnas.1104825108"
-
-# Article titles for which we have urls to PDFs
-pdfs:
-  "A Y-like social chromosome causes alternative colony organization in fire ants" : "/publications/wangwurm2013socialChromosome.pdf"
-  "Duplication and concerted evolution in a master sex determiner under balancing selection" : "/publications/procb2013.pdf"
-  "Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates" : "/publications/hdy2012122a.pdf"
-  "The Molecular Clockwork of the Fire Ant Solenopsis invicta" : "/publications/ingram2012-fireAntClockGenes.pdf"
-  "Epigenetics: The Making of Ant Castes" : "/publications/2012CurrBiolAntepigenetics.pdf"
-  "Visualization and quality assessment of de novo genome assemblies" : "/publications/Bioinformatics-2011-Riba-Grognuz-3425-6"
-  "The genomic impact of 100 million years of social evolution in seven ant species" : "/publications/TiG2011.pdf"
-  "Relaxed selection is a precursor to the evolution of phenotypic plasticity" : "/publications/hunt2011phenotypicPlasticity.pdf"
-  "The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming" : "/publications/nygaard2011-acromyrmex-genome.pdf"
-  "Behind the Scenes of an Ant Genome Project" : "/publications/wurm2011antGenomeBehindTheScenes.pdf"
-  "The genome of the fire ant Solenopsis invicta" : "/publications/wurm2011fireAntGenome.pdf"
-  "Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins" : "/publications/gotzek2011obps.pdf"
-  "Parasitoid Wasps: From Natural History to Genomic Studies" : "/publications/wurm2010wasps.pdf"
-  "Changes in reproductive roles are associated with changes in gene expression in fire ant queens" : "/publications/wurm2010fireAntQueenDealationExpression.pdf"
-  "Fourmidable: a database for ant genomics" : "/publications/wurm2009antDatabase.pdf"
-  "Behavioral Genomics: A, Bee, C, G, T" : "/publications/wurm2007bees.pdf"
-  "An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta" : "/publications/wang2007fireAntMicroarrays.pdf"