biblio_style_ama.inc in Bibliography Module 5

File

biblio_style_ama.inc

<?php

// Original File:       ./cite/styles/cite_AMA.php
// Original Author(s):  Matthias Steffens <mailto:[e-mail]> and
//                      Richard Karnesky <mailto:[e-mail]>
// This is a citation style file (which must reside within the 'cite/styles/' sub-directory of your refbase root directory). It contains a
// version of the 'citeRecord()' function that outputs a reference list from selected records according to the citation style used by
// the American Medical Association (AMA)
// based on 'cite_Chicago.php'
// TODO: - abstracts, conference proceedings, patents, reports
//       - book/volume/report/etc titles should be formatted in heading caps
//       - don't add a dot if the abbreviated journal (or series title) ends with a dot!
// Modified for use in biblio by Ron Jerome
//

/**
 * Get the style information
 *
 * @return
 *   The name of the style
 */
function biblio_style_ama_info() {
  return array(
    'ama' => 'American Medical Association (AMA)',
  );
}
function biblio_style_ama_author_options() {
  $author_options = array(
    'oldAuthorsInitialsDelim' => ',',
    'BetweenAuthorsDelimStandard' => ', ',
    'BetweenAuthorsDelimLastAuthor' => ', ',
    'AuthorsInitialsDelimFirstAuthor' => ' ',
    'AuthorsInitialsDelimStandard' => ' ',
    'betweenInitialsDelim' => '',
    'initialsBeforeAuthorFirstAuthor' => FALSE,
    'initialsBeforeAuthorStandard' => FALSE,
    'shortenGivenNames' => TRUE,
    'numberOfAuthorsTriggeringEtAl' => 6,
    'includeNumberOfAuthors' => 3,
    'customStringAfterFirstAuthors' => ', et al.',
    'encodeHTML' => true,
  );
  return $author_options;
}
function biblio_style_ama($node, $base = 'biblio', $inline = false) {
  $markupPatternsArray = array(
    "italic-prefix" => '<i>',
    "italic-suffix" => '</i>',
    "endash" => '-',
  );
  $author_options = biblio_style_ama_author_options();
  $authors = theme('biblio_format_authors', $node->biblio_authors, $author_options, $inline);

  //$editors = theme('biblio_format_authors', $node->biblio_contributors[2], $author_options, $inline);

  //if (empty($authors)) $authors = theme('biblio_authors', $node->biblio_contributors[5], 'mla', 5, $inline);  // if no authors substitute corp author if available

  //if (empty($authors)) $authors = '[' . t('Anonymous') . ']';  // use anonymous if we still have nothing.

  //$output .= '<span class="biblio-authors">' . $authors . "</span>.&nbsp; \n";
  if (!empty($node->biblio_citekey) && variable_get('biblio_display_citation_key', 0)) {
    $output .= '[' . check_plain($node->biblio_citekey) . '] ';
  }
  switch ($node->biblio_type) {
    case 102:

    //Journal Article
    case 105:

    //Newspaper Article
    case 106:

      //Magazine Article
      if (!empty($authors)) {
        if (!ereg("\\. *\$", $authors)) {
          $output .= $authors . ".";
        }
        else {
          $output .= $authors;
        }
      }
      if (!empty($node->title)) {

        // title
        if (!empty($authors)) {
          $output .= " ";
        }
        $output .= '"';
        $link = variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? $node->biblio_url : ($inline ? "{$base}/viewinline/{$node->nid}" : "node/{$node->nid}");
        $attrib = variable_get('biblio_links_target_new_window', null) && variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? array(
          'target' => '_blank',
        ) : null;
        $output .= l($node->title, $link, $attrib);

        //$output .= $inline ? l("$node->title", "$base/viewinline/$node->nid") : l("$node->title", "node/$node->nid");
        if (!ereg("[?!.]\$", $node->title)) {
          $output .= ".";
        }
        $output .= '"';
      }

      // From here on we'll assume that at least either the 'author' or the 'title' field did contain some contents
      // if this is not the case, the output string will begin with a space. However, any preceding/trailing whitespace will be removed at the cleanup stage (see below)
      if (!empty($node->biblio_alternate_title)) {

        // abbreviated journal name
        $output .= " " . $markupPatternsArray["italic-prefix"] . $node->biblio_alternate_title . $markupPatternsArray["italic-suffix"];
      }
      elseif (!empty($node->biblio_secondary_title)) {

        // publication (= journal) name
        $output .= " " . $markupPatternsArray["italic-prefix"] . $node->biblio_secondary_title . $markupPatternsArray["italic-suffix"];
      }
      if ($node->biblio_type == 105 || $node->biblio_type == 106 and !preg_match("/^\\d+\$/", $node->biblio_volume)) {

        // for newspaper articles (and magazine articles if w/o volume number), volume (=month) and issue (=day) information is printed before the year
        if (!empty($node->biblio_volume)) {

          // volume (=month)
          $output .= ". " . $node->biblio_volume;
        }
        if (!empty($node->biblio_issue)) {

          // issue (=day)
          $output .= " " . $node->biblio_issue;
        }
        if (!empty($node->biblio_year)) {

          // year
          $output .= ", " . $node->biblio_year;
        }
      }
      else {

        // journal article (or a magazine article with volume numbers)
        if (!empty($node->biblio_year)) {

          // year
          $output .= ". " . $node->biblio_year;
        }
        if (!empty($node->biblio_volume) || !empty($node->biblio_issue)) {
          $output .= ";";
        }
        if (!empty($node->biblio_volume)) {

          // volume
          $output .= $node->biblio_volume;
        }
        if (!empty($node->biblio_issue)) {

          // issue
          $output .= "(" . $node->biblio_issue . ")";
        }
      }
      if (!empty($node->biblio_pages)) {

        // pages
        if (!empty($node->biblio_year) || !empty($node->biblio_volume) || !empty($node->biblio_issue) || !empty($node->biblio_alternate_title) || !empty($node->biblio_secondary_title)) {

          // only add ": " if either year, volume, issue, abbrev_journal or publication isn't empty
          $output .= ":";
        }
        $output .= theme_biblio_page_number($node->biblio_pages, $markupPatternsArray["endash"]);

        // function 'formatPageInfo()' is defined in 'cite.inc.php'
      }
      if ($row['online_publication'] == "yes") {

        // this record refers to an online article
        // append an optional string (given in 'online_citation') plus the current date and the DOI (or URL):
        $today = date("F j, Y");
        if (!empty($row['online_citation'])) {

          // online_citation
          if (!empty($node->biblio_year) || !empty($node->biblio_volume) || !empty($node->biblio_issue) || !empty($node->biblio_alternate_title) || !empty($node->biblio_secondary_title)) {

            // only add ":" or "," if either year, volume, issue, abbrev_journal or publication isn't empty
            if (empty($node->biblio_pages)) {
              $output .= ":";
            }
            else {
              $output .= ",";
            }

            // append to pages
          }
          $output .= $row['online_citation'];
        }
        if (!empty($row['doi'])) {

          // doi
          if (!empty($row['online_citation']) or empty($row['online_citation']) and !empty($node->biblio_year) || !empty($node->biblio_volume) || !empty($node->biblio_issue) || !empty($node->biblio_alternate_title) || !empty($node->biblio_secondary_title)) {

            // only add "." if online_citation isn't empty, or else if either year, volume, issue, abbrev_journal or publication isn't empty
            $output .= ".";
          }
          if ($encodeHTML) {
            $output .= " " . encodeHTML("http://dx.doi.org/" . $row['doi']) . ". Accessed " . $today;
          }
          else {
            $output .= " " . "http://dx.doi.org/" . $row['doi'] . ". Accessed " . $today;
          }
        }
        elseif (!empty($row['url'])) {

          // url
          if (!empty($row['online_citation']) or empty($row['online_citation']) and !empty($node->biblio_year) || !empty($node->biblio_volume) || !empty($node->biblio_issue) || !empty($node->biblio_alternate_title) || !empty($node->biblio_secondary_title)) {

            // only add "." if online_citation isn't empty, or else if either year, volume, issue, abbrev_journal or publication isn't empty
            $output .= ".";
          }
          if ($encodeHTML) {
            $output .= " " . encodeHTML($row['url']) . ". Accessed " . $today;
          }
          else {
            $output .= " " . $row['url'] . ". Accessed " . $today;
          }
        }
      }
      if (!ereg("\\. *\$", $output)) {
        $output .= ".";
      }
      break;
    case 101:

    //Book Chapter
    case 103:

      //Conference Paper
      if (!empty($authors)) {
        if (!ereg("\\. *\$", $authors)) {
          $output .= $authors . ".";
        }
        else {
          $output .= $authors;
        }
      }
      if (!empty($node->title)) {

        // title
        if (!empty($authors)) {
          $output .= " ";
        }
        $output .= '"<i>';
        $link = variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? $node->biblio_url : ($inline ? "{$base}/viewinline/{$node->nid}" : "node/{$node->nid}");
        $attrib = variable_get('biblio_links_target_new_window', null) && variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? array(
          'target' => '_blank',
        ) : null;
        $output .= l($node->title, $link, $attrib);

        //$output .= $inline ? l("$node->title", "$base/viewinline/$node->nid") : l("$node->title", "node/$node->nid");
        $output .= '</i>';
        if (!ereg("[?!.]\$", $node->title)) {
          $output .= ".";
        }
        $output .= '"';
      }
      if (!empty($node->biblio_secondary_authors)) {

        // editor
        $editor_options = array(
          'oldAuthorsInitialsDelim' => ',',
          'BetweenAuthorsDelimStandard' => ', ',
          'BetweenAuthorsDelimLastAuthor' => ', ',
          'AuthorsInitialsDelimFirstAuthor' => ' ',
          'AuthorsInitialsDelimStandard' => ' ',
          'betweenInitialsDelim' => '',
          'initialsBeforeAuthorFirstAuthor' => FALSE,
          'initialsBeforeAuthorStandard' => FALSE,
          'shortenGivenNames' => TRUE,
          'numberOfAuthorsTriggeringEtAl' => 6,
          'includeNumberOfAuthors' => 3,
          'customStringAfterFirstAuthors' => ' et al.',
          'encodeHTML' => true,
        );
        $editor = theme('biblio_format_authors', $node->biblio_secondary_authors, $editor_options, $inline);
        $output .= " In: " . $editor . ", ";
        if (count($node->biblio_secondary_authors) > 1) {

          // there are at least two editors (separated by ';')
          $output .= "eds";
        }
        else {

          // there's only one editor (or the editor field is malformed with multiple editors but missing ';' separator[s])
          $output .= "ed";
        }
      }
      $publication = ereg_replace("[ \r\n]*\\(Eds?:[^\\)\r\n]*\\)", "", $node->biblio_secondary_title);
      if (!empty($publication)) {

        // publication
        if (!ereg("[?!.] *\$", $output)) {
          $output .= ".";
        }
        if (empty($editor)) {
          $output .= " In:";
        }

        // TODO: container titles should be formatted in heading caps, however, this doesn't yet work correctly if the publication title contains HTML entities
        $output .= " " . $markupPatternsArray["italic-prefix"] . $publication . $markupPatternsArray["italic-suffix"];

        //        $output .= " " . $markupPatternsArray["italic-prefix"] . changeCase("heading", $publication) . $markupPatternsArray["italic-suffix"]; // function 'changeCase()' is defined in 'include.inc.php'
      }
      if (!empty($node->biblio_volume)) {

        // volume
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        $output .= " Vol. " . $node->biblio_volume;
      }
      if (!empty($node->biblio_edition) && !preg_match("/^(1|1st|first|one)( ed\\.?| edition)?\$/i", $node->biblio_edition)) {

        // edition
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        if (preg_match("/^\\d{1,3}\$/", $node->biblio_edition)) {

          // if the edition field contains a number of up to three digits, we assume it's an edition number (such as "2nd ed.")
          if ($node->biblio_edition == "2") {
            $editionSuffix = "nd";
          }
          elseif ($node->biblio_edition == "3") {
            $editionSuffix = "rd";
          }
          else {
            $editionSuffix = "th";
          }
        }
        else {
          $editionSuffix = "";
        }
        if (!preg_match("/( ed\\.?| edition)\$/i", $node->biblio_edition)) {
          $editionSuffix .= " ed.";
        }
        $output .= " " . $node->biblio_edition . $editionSuffix;
      }
      if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
        $output .= ".";
      }
      if (!empty($node->biblio_place_published)) {

        // place
        $output .= " " . $node->biblio_place_published;
      }
      if (!empty($node->biblio_publisher)) {

        // publisher
        if (!empty($node->biblio_place_published)) {
          $output .= ":";
        }
        $output .= " " . $node->biblio_publisher;
      }
      if (!empty($node->biblio_year)) {

        // year
        $output .= "; " . $node->biblio_year;
      }
      if (!empty($node->biblio_pages)) {

        // pages
        $output .= ":" . theme('biblio_page_number', $node->biblio_pages, $markupPatternsArray["endash"]);
      }

      // function 'formatPageInfo()' is defined in 'cite.inc.php'
      if (!empty($node->biblio_alternate_title) or !empty($node->biblio_tertiary_title)) {

        // if there's either a full or an abbreviated series title
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        $output .= " ";
        if (!empty($node->biblio_alternate_title)) {
          $output .= $node->biblio_alternate_title;
        }
        elseif (!empty($node->biblio_tertiary_title)) {
          $output .= $node->biblio_tertiary_title;
        }

        // full series title
        if (!empty($node->biblio_volume) || !empty($node->biblio_issue)) {
          $output .= " ";
        }
        if (!empty($node->biblio_volume)) {

          // series volume
          $output .= $node->biblio_volume;
        }
        if (!empty($node->biblio_issue)) {

          // series issue (I'm not really sure if -- for this cite style -- the series issue should be rather omitted here)
          $output .= "(" . $node->biblio_issue . ")";
        }

        // is it correct to format series issues similar to journal article issues?
      }
      if (!ereg("\\. *\$", $output)) {
        $output .= ".";
      }
      break;
    default:

      // all other types

      //TODO

      //        if (ereg("[ \r\n]*\(ed\)", $node->author)) // single editor
      //          $author = $author . ", ed";
      //        elseif (ereg("[ \r\n]*\(eds\)", $node->author)) // multiple editors
      //          $author = $author . ", eds";
      if (!empty($authors)) {

        // author
        if (!ereg("\\. *\$", $authors)) {
          $output .= $authors . ".";
        }
        else {
          $output .= $authors;
        }
      }
      if (!empty($node->title)) {

        // title
        if (!empty($authors)) {
          $output .= " ";
        }
        $output .= '<i>';

        // TODO: book/volume/report/etc titles should be formatted in heading caps, however, this doesn't yet work correctly if the publication title contains HTML entities
        $link = variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? $node->biblio_url : ($inline ? "{$base}/viewinline/{$node->nid}" : "node/{$node->nid}");
        $attrib = variable_get('biblio_links_target_new_window', null) && variable_get('biblio_link_title_url', 0) && !empty($node->biblio_url) ? array(
          'target' => '_blank',
        ) : null;
        $output .= l($node->title, $link, $attrib);

        //$output .= $inline ? l("$node->title", "$base/viewinline/$node->nid") : l("$node->title", "node/$node->nid");
        $output .= '</i>';
      }
      if ($node->biblio_type == "Software") {

        // for software, add software label
        $output .= " [computer program]";
      }
      if (!empty($node->biblio_volume) and $node->biblio_type != "Software") {

        // volume
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        $output .= " Vol. " . $node->biblio_volume;
      }
      if (!empty($node->biblio_edition)) {

        // edition
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        if ($row['type'] == "Software") {

          // software edition (=version)
          $output .= " Version " . $node->biblio_edition;
        }
        elseif (!preg_match("/^(1|1st|first|one)( ed\\.?| edition)?\$/i", $node->biblio_edition)) {

          // edition
          if (preg_match("/^\\d{1,3}\$/", $node->biblio_edition)) {

            // if the edition field contains a number of up to three digits, we assume it's an edition number (such as "2nd ed.")
            if ($node->biblio_edition == "2") {
              $editionSuffix = "nd";
            }
            elseif ($node->biblio_edition == "3") {
              $editionSuffix = "rd";
            }
            else {
              $editionSuffix = "th";
            }
          }
          else {
            $editionSuffix = "";
          }
          if (!preg_match("/( ed\\.?| edition)\$/i", $node->biblio_edition)) {
            $editionSuffix .= " ed.";
          }
          $output .= " " . $node->biblio_edition . $editionSuffix;
        }
      }
      if (!empty($node->biblio_secondary_authors)) {

        // editor (if different from author, see note above regarding the check for ' (ed)' or ' (eds)')
        $editor_options = array(
          'oldAuthorsInitialsDelim' => ',',
          'BetweenAuthorsDelimStandard' => ', ',
          'BetweenAuthorsDelimLastAuthor' => ', ',
          'AuthorsInitialsDelimFirstAuthor' => ' ',
          'AuthorsInitialsDelimStandard' => ' ',
          'betweenInitialsDelim' => '',
          'initialsBeforeAuthorFirstAuthor' => FALSE,
          'initialsBeforeAuthorStandard' => FALSE,
          'shortenGivenNames' => TRUE,
          'numberOfAuthorsTriggeringEtAl' => 6,
          'includeNumberOfAuthors' => 3,
          'customStringAfterFirstAuthors' => ' et al.',
          'encodeHTML' => true,
        );
        $editor = theme('biblio_format_authors', $node->biblio_secondary_authors, $editor_options, $inline);
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        $output .= " " . $editor;
        if (count($node->biblio_secondary_authors) > 1) {

          // there are at least two editors (separated by ';')
          $output .= ", eds";
        }
        else {

          // there's only one editor (or the editor field is malformed with multiple editors but missing ';' separator[s])
          $output .= ", ed";
        }
      }
      if (!empty($row['thesis'])) {

        // thesis
        // TODO: do we need to use the term "[dissertation]" instead of "[Ph.D. thesis]", etc? What about other thesis types then?
        $output .= " [" . $row['thesis'] . "]";
      }
      if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
        $output .= ".";
      }
      if (!empty($node->biblio_place_published)) {

        // place
        $output .= " " . $node->biblio_place_published;
      }
      if (!empty($node->biblio_publisher)) {

        // publisher
        if (!empty($node->biblio_place_published)) {
          $output .= ":";
        }
        $output .= " " . $node->biblio_publisher;
      }
      $output .= ";";
      if ($row['type'] == "Software") {

        // for software, volume (=month) and issue (=day) information is printed before the year (similar to newspaper articles)
        if (!empty($node->biblio_volume)) {

          // volume (=month)
          $output .= " " . $node->biblio_volume;
        }
        if (!empty($node->biblio_issue)) {

          // issue (=day)
          $output .= " " . $node->biblio_issue;
        }
        $output .= ",";
      }
      if (!empty($node->biblio_year)) {

        // year
        $output .= " " . $node->biblio_year;
      }
      if (!empty($node->biblio_alternate_title) or !empty($node->biblio_tertiary_title)) {

        // if there's either a full or an abbreviated series title
        if (!ereg("[?!.][ \"" . $markupPatternsArray["italic-suffix"] . "]*\$", $output)) {
          $output .= ".";
        }
        $output .= " ";
        if (!empty($node->biblio_alternate_title)) {
          $output .= $node->biblio_alternate_title;
        }
        elseif (!empty($node->biblio_tertiary_title)) {
          $output .= $node->biblio_tertiary_title;
        }

        // full series title
        if (!empty($node->biblio_volume) || !empty($node->biblio_issue)) {
          $output .= " ";
        }
        if (!empty($node->biblio_volume)) {

          // series volume
          $output .= $node->biblio_volume;
        }
        if (!empty($node->biblio_issue)) {

          // series issue (I'm not really sure if -- for this cite style -- the series issue should be rather omitted here)
          $output .= "(" . $node->biblio_issue . ")";
        }

        // is it correct to format series issues similar to journal article issues?
      }
      if ($row['online_publication'] == "yes" || $row['type'] == "Software") {

        // this record refers to an online article, or a computer program/software
        // append an optional string (given in 'online_citation') plus the current date and the DOI (or URL):
        $today = date("F j, Y");
        if (!empty($row['online_citation'])) {

          // online_citation
          if (!ereg("\\. *\$", $output)) {
            $output .= ".";
          }
          $output .= $row['online_citation'];
        }
        if (!empty($row['doi'])) {

          // doi
          if (!ereg("\\. *\$", $output)) {
            $output .= ".";
          }
          if ($encodeHTML) {
            $output .= " " . encodeHTML("http://dx.doi.org/" . $row['doi']) . ". Accessed " . $today;
          }
          else {
            $output .= " " . "http://dx.doi.org/" . $row['doi'] . ". Accessed " . $today;
          }
        }
        elseif (!empty($row['url'])) {

          // url
          if (!ereg("\\. *\$", $output)) {
            $output .= ".";
          }
          if ($encodeHTML) {
            $output .= " " . encodeHTML($row['url']) . ". Accessed " . $today;
          }
          else {
            $output .= " " . $row['url'] . ". Accessed " . $today;
          }
        }
      }
      if (!ereg("\\. *\$", $output)) {
        $output .= ".";
      }
      break;
  }
  return filter_xss($output, biblio_get_allowed_tags());
}

Functions

Name	Description
biblio_style_ama
biblio_style_ama_author_options
biblio_style_ama_info	Get the style information