#
# bio/db/medline.rb - NCBI PubMed/MEDLINE database class
#
#   Copyright (C) 2001, 2005 KATAYAMA Toshiaki <k@bioruby.org>
#
#  This library is free software; you can redistribute it and/or
#  modify it under the terms of the GNU Lesser General Public
#  License as published by the Free Software Foundation; either
#  version 2 of the License, or (at your option) any later version.
#
#  This library is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#  Lesser General Public License for more details.
#
#  You should have received a copy of the GNU Lesser General Public
#  License along with this library; if not, write to the Free Software
#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
#
#  $Id: medline.rb,v 1.12 2005/09/08 01:22:11 k Exp $
#

require 'bio/db'

module Bio

  class MEDLINE < NCBIDB

    def initialize(entry)
      @pubmed = Hash.new('')

      tag = ''
      entry.each_line do |line|
        if line =~ /^\w/
          tag = line[0,4].strip
        end
        @pubmed[tag] += line[6..-1] if line.length > 6
      end
    end


    # Reference object
    def reference
      hash = Hash.new('')

      hash['authors']	= authors
      hash['title']	= title
      hash['journal']	= journal
      hash['volume']	= volume
      hash['issue']	= issue
      hash['pages']	= pages
      hash['year']	= year
      hash['pubmed']	= pmid
      hash['medline']  	= ui
      hash['abstract']	= abstract
      hash['mesh']	= mesh
      hash['affiliations'] = affiliations

      hash.delete_if { |k, v| v.nil? or v.empty? }

      return Reference.new(hash)
    end


    ### Common MEDLINE tags

    # PMID - PubMed Unique Identifier
    #   Unique number assigned to each PubMed citation.
    def pmid
      @pubmed['PMID'].strip
    end
    alias entry_id pmid

    # UI   - MEDLINE Unique Identifier
    #   Unique number assigned to each MEDLINE citation.
    def ui
      @pubmed['UI'].strip
    end

    # TA   - Journal Title Abbreviation
    #   Standard journal title abbreviation.
    def ta
      @pubmed['TA'].gsub(/\s+/, ' ').strip
    end
    alias journal ta

    # VI   - Volume
    #   Journal volume.
    def vi
      @pubmed['VI'].strip
    end
    alias volume vi

    # IP   - Issue
    #   The number of the issue, part, or supplement of the journal in which
    #   the article was published.
    def ip
      @pubmed['IP'].strip
    end
    alias issue ip

    # PG   - Page Number
    #   The full pagination of the article.
    def pg
      @pubmed['PG'].strip
    end

    def pages
      pages = pg
      if pages =~ /-/
        from, to = pages.split('-')
        if (len = from.length - to.length) > 0
          to = from[0,len] + to
        end
        pages = "#{from}-#{to}"
      end
      return pages
    end

    # DP   - Publication Date
    #   The date the article was published.
    def dp
      @pubmed['DP'].strip
    end
    alias date dp

    def year
      dp[0,4]
    end

    # TI   - Title Words
    #   The title of the article.
    def ti
      @pubmed['TI'].gsub(/\s+/, ' ').strip
    end
    alias title ti

    # AB   - Abstract
    #   Abstract.
    def ab
      @pubmed['AB'].gsub(/\s+/, ' ').strip
    end
    alias abstract ab

    # AU   - Author Name
    #   Authors' names.
    def au
      @pubmed['AU'].strip
    end

    def authors
      authors = []
      au.split(/\n/).each do |author|
        if author =~ / /
          name = author.split(/\s+/)
          suffix = name[-2] =~ /^[A-Z]+$/ ? name.pop : nil	# Jr etc.
          initial = name.pop.split(//).join('. ')
          author = "#{name.join(' ')}, #{initial}."
        end
        if suffix
          author << " " + suffix
        end
        authors.push(author)
      end
      return authors
    end

    # SO   - Source
    #   Composite field containing bibliographic information.
    def so
      @pubmed['SO'].strip
    end
    alias source so

    # MH   - MeSH Terms
    #   NLM's controlled vocabulary.
    def mh
      @pubmed['MH'].strip.split(/\n/)
    end
    alias mesh mh

    # AD   - Affiliation
    #   Institutional affiliation and address of the first author, and grant
    #   numbers.
    def ad
      @pubmed['AD'].strip.split(/\n/)
    end
    alias affiliations ad


    ### Other MEDLINE tags

    # AID  - Article Identifier
    #   Article ID values may include the pii (controlled publisher identifier)
    #   or doi (Digital Object Identifier).

    # CI   - Copyright Information
    #   Copyright statement.

    # CIN  - Comment In
    #   Reference containing a comment about the article.

    # CN   - Collective Name
    #   Corporate author or group names with authorship responsibility.

    # CON  - Comment On
    #   Reference upon which the article comments.

    # CY   - Country
    #   The place of publication of the journal.

    # DA   - Date Created
    #   Used for internal processing at NLM.

    # DCOM - Date Completed
    #   Used for internal processing at NLM.

    # DEP  - Date of Electronic Publication
    #   Electronic publication date.

    # EDAT - Entrez Date
    #   The date the citation was added to PubMed.

    # EIN  - Erratum In
    #   Reference containing a published erratum to the article.

    # GS   - Gene Symbol
    #   Abbreviated gene names (used 1991 through 1996).

    # ID   - Identification Number 
    #   Research grant numbers, contract numbers, or both that designate
    #   financial support by any agency of the US PHS (Public Health Service).

    # IS   - ISSN
    #   International Standard Serial Number of the journal.

    # JC   - Journal Title Code
    #   MEDLINE unique three-character code for the journal.

    # JID  - NLM Unique ID
    #   Unique journal ID in NLM's catalog of books, journals, and audiovisuals.

    # LA   - Language
    #   The language in which the article was published.

    # LR   - Last Revision Date
    #   The date a change was made to the record during a maintenance procedure.

    # MHDA - MeSH Date
    #   The date MeSH terms were added to the citation. The MeSH date is the
    #   same as the Entrez date until MeSH are added.

    # PHST - Publication History Status Date
    #   History status date.

    # PS   - Personal Name as Subject
    #   Individual is the subject of the article.

    # PST  - Publication Status
    #   Publication status.

    # PT   - Publication Type
    #   The type of material the article represents.
    def pt
      @pubmed['PT'].strip.split(/\n/)   
    end
    alias publication_type pt

    # RF   - Number of References
    #   Number of bibliographic references for Review articles.

    # RIN  - Retraction In
    #   Retraction of the article

    # RN   - EC/RN Number
    #   Number assigned by the Enzyme Commission to designate a particular
    #   enzyme or by the Chemical Abstracts Service for Registry Numbers.

    # ROF  - Retraction Of
    #   Article being retracted.

    # RPF  - Republished From
    #   Original article.

    # SB   - Journal Subset
    #   Code for a specific set of journals.

    # SI   - Secondary Source Identifier
    #   Identifies a secondary source that supplies information, e.g., other
    #   data sources, databanks and accession numbers of molecular sequences
    #   discussed in articles.

    # TT   - Transliterated / Vernacular Title 
    #   Non-Roman alphabet language titles are transliterated.

    # UIN  - Update In
    #   Update to the article.

    # UOF  - Update Of
    #   The article being updated.

    # URLF - URL Full-Text
    #   Link to the full-text of article at provider's website. Links are
    #   incomplete. Use PmLink for the complete set of available links.
    #   [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html

    # URLS - URL Summary
    #   Link to the article summary at provider's website. Links are
    #   incomplete. Use PmLink for the complete set of available links.
    #   [PmLink] http://www.ncbi.nlm.nih.gov/entrez/utils/pmlink_help.html

  end

end