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require 'rubygems'
require 'bio'

module PubMed

  # Download and annotate the given pubmed_id and return a citation in textile format.
  # Example Citation: 
  # Smythe MA, Stephens JL, Koerber JM, Mattson JC: A comparison of lepirudin and argatroban outcomes. 
  # Clin Appl Thromb Hemost. 2005 Oct;11(4):371-4. "Pubmed":http://www.ncbi.nlm.nih.gov/pubmed/16244762
  def PubMed.annotate(pubmed_id)

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require 'zip/zip'

# Interface to the mutfinder library 
class ReadAnalysis  
  
  @@nml_dir = File.join(Rails.root, 'lib', 'mutfinder')
  @@result_dir = File.join(@@nml_dir, '/var/results/')
  
  # Main entry point for analysis. Just pass an analysis ID
  # (An object is not passed because this doesnt work with delayed_job)

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def check_cas_number
  # Check the CAS number for validity (the last number in a CAS number is a checksum)
  if cas_number.present?
    matches = cas_number.scan(/^(\d{1,7})-(\d{1,2})-(\d)$/)
    
    if matches.first.blank? || matches.first.size != 3
      self.errors.add(:cas_number, "format invalid")
    else
      match = matches.first

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require 'zip/zipfilesystem'
require 'builder'
namespace :hmdb do
  namespace :export do
    DOWNLOAD_PATH = 'public/downloads'

    desc "Run all export tasks"
    task :all => [ :xml, :structures, :sequences ]

    # desc 'Export all compounds to json format'

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require 'zip/zipfilesystem'
require 'builder'
namespace :hmdb do
  namespace :export do
    DOWNLOAD_PATH = 'public/downloads'

    desc "Run all export tasks"
    task :all => [ :xml, :structures, :sequences ]

    # desc 'Export all compounds to json format'

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  def concentration_value(c)
        unit = ""
        conc = c.conc_value
        mean = 0
        error = 0
        
        if (conc.nil?)
          return ""
        elsif(conc == "Detected")
          mean = -1

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########################################################################
#
# This class finds properties of a compound, given the SMILES string.
# For required programs, check the comments before each method.
#
# Written by Roman Eisner, 2010
#
# Updated by Yannick Djoumbou
#######################################################################

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class ApplicationController < ActionController::Base
  protect_from_forgery

  rescue_from ActiveRecord::RecordNotFound, :with => :render_404

  # Render 404: Not Found
  def render_404(exception = nil)
    logger.info( clean_backtrace(exception, "Rendering 404 due to exception") )
    if /(jpe?g|png|gif)/i === request.path
      # Images should simply return the error as text

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require 'nokogiri'
require 'open-uri'

module Uniprot
  
  # Download and annotate the given uniprot_id and return an entry as an array
  def Uniprot.annotate_name(uniprot_id)
    doc = Nokogiri::XML( open("http://www.uniprot.org/uniprot/#{uniprot_id}.xml") )
    doc.remove_namespaces!
    name_node = doc.at_xpath("//recommendedName/fullName")

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  def index
    options = params
    options[:page] ||= 1
    options[:limit] ||= 50

    @pathway_visualizations = 
      PathwayVisualization.search(load: true, page: options[:page], 
                                  per_page: options[:limit]) do |search|
        if options[:term].present?
          search.query do |query|