Subversion Repositories eFlore/Applications.cel

<?php

// declare(encoding='UTF-8');

/**

 * Classe permettant de convertir une chaine d'un nom scientifique en un format standard.

 *

 * Source orignale :

 * Taxamatch-Webservice PHP v1.0.0

 * @author Michael Giddens

 * @link http://www.silverbiology.com

 *

 *

 * @internal   Mininum PHP version : 5.2

 * @category   CEL

 * @package    Services

 * @subpackage Bibliothèques

 * @version    0.1

 * @author     Mathias CHOUET <mathias@tela-botanica.org>

 * @author     David DELON <david@clapas.net>

 * @author     Jean-Pascal MILCENT <jpm@tela-botanica.org>

 * @author     Aurelien PERONNET <aurelien@tela-botanica.org>

 * @license    GPL v3 <http://www.gnu.org/licenses/gpl.txt>

 * @license    CECILL v2 <http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt>

 * @copyright  1999-2014 Tela Botanica <accueil@tela-botanica.org>

 */

class NameParser {

	/**

	 * Whether to debug or nor

	 * @var bool|integer

	 */

	public $debug_flag;

	/**

	 * Sets value to the method property

	 * @param mixed $name class property name

	 * @param mixed $value class property value

	 */

	public function set($name, $value) {

		$this->$name = $value;

	}

	/**

	 * Reduce Spaces

	 * This will reduce the string to only allow once space between characters

	 * @param string $str : string to reduce space

	 * @return string : string with only once space between characters

	 */

	private function reduce_spaces($str) {

		$str = preg_replace('/ {2,}/', ' ', $str );

		$str = trim( $str );

		return( $str );

	}

	/**

	 * Function: parse_auth

	 * Purpose: Produce a parsed version of authority of a taxon name

	 * @author Tony Rees (Tony.Rees@csiro.au)

	 * Date created: March 2008

	 * Inputs: authority string as str

	 * Remarks:

	 *  (1) Performs authority expension of known abbreviated authornames using

	 *   table "auth_abbrev_test1" (must be available and populated with relevant content)

	 *  (2) Recognises "and", "et", "&" as equivalents (special case for "et al.") - all parsed to ampersand

	 *  (3) Recognises (e.g.) "Smith 1980" and "Smith, 1980" as equivalents - comma is removed in these cases

	 *  (4) Recognises (e.g.) "F. J. R. Taylor, 1980" and "F.J.R. Taylor, 1980" as equivalents -

	 *      extra space after full stops is ignored in these cases

	 *  (5) Returns uppercase string, diacritical marks intact

	 *

	 * @param string $str : authority string

	 * @param integer $upcase : convert to uppercase if $upcase = 1

	 * @return string : parsed author string

	 */

	public function parse_auth($str, $upcase = 1) {

		$this->debug['parse_auth'][] = "1";

		$temp = $str = trim($str);

  		if ( ($str == NULL) || ($str == '') ) {

				$this->debug['parse_auth'][] = "1a";

		    return '';

		}

		if ( ( $temp == null ) || ( $temp == '') ) {

			$this->debug['parse_auth'][] = "2a";

			return('');

		} else {

			$this->debug['parse_auth'][] = "2b";

			// add space after full stops, except at end (NB, will also add spece before some close brackets)

			$temp = rtrim( str_replace('.', '. ', $temp) );

			$this->debug['parse_auth'][] = "4 (temp:$temp)";

			//normalise "et", "and" to ampersand (et al. is a special case)

			// if ( $temp like '% et al%' ) {

			if ( preg_match('/ et al/', $temp) ) {

				$temp = str_replace(' et al','zzzzz', $temp);

				$this->debug['parse_auth'][] = "4a (temp:$temp)";

			}

			$temp = str_replace(' et ',' & ', $temp );

			$temp = str_replace(' and ',' & ', $temp );

			$temp = str_replace('zzzzz',' et al', $temp);

			$this->debug['parse_auth'][] = "5 (temp:$temp)";

			//remove commas before dates (only)

			//	like '%, 17%'

			if ( preg_match('/, 17/', $temp) ) {

				$temp = str_replace(', 17',' 17', $temp);

				$this->debug['parse_auth'][] = "5a (temp:$temp)";

			}

			//	like '%, 18%'

			if ( preg_match('/, 18/', $temp) ) {

				$temp = str_replace(', 18',' 18', $temp);

				$this->debug['parse_auth'][] = "5b (temp:$temp)";

			}

			//	like '%, 19%'

			if ( preg_match('/, 19/', $temp) ) {

				$temp = str_replace(', 19',' 19', $temp);

				$this->debug['parse_auth'][] = "5c (temp:$temp)";

			}

			//	like '%, 20%'

			if ( preg_match('/, 20/', $temp) ) {

				$temp = str_replace(', 20',' 20', $temp);

				$this->debug['parse_auth'][] = "5d (temp:$temp)";

			}

			// reduce multiple internal spaces to single space

			$temp = $this->reduce_spaces( $temp );

			//	like '% -%'

			$temp = str_replace(' -', '-', $temp);

			$this->debug['parse_auth'][] = "6 (temp:$temp)";

			foreach (explode(' ', $temp) as $this_word) {

				//$this->debug['parse_auth'][] = "7 (this_word:$this_word)";

				$elapsed_chars = '';

				//	like '(%'

				if ( preg_match('/^\(/', $this_word) ) {

					$elapsed_chars .= '(';

					$this_word = substr( $this_word, 1 );

					//$this->debug['parse_auth'][] = "7a (this_word:$this_word) (elapsed_chars:$elapsed_chars)";

				}

				// Add back the word to the final translation

				$elapsed_chars .= $this_word . ' ';

				//$this->debug['parse_auth'][] = "7c (this_word:$this_word) (elapsed_chars:$elapsed_chars)";

			}

			$elapsed_chars = $this->reduce_spaces( str_replace(' )', ')', $elapsed_chars) );

			return trim( $elapsed_chars ) ;

		}

	}

	/**

	 * Function: parse

	 * Purpose: Produces parsed version of an input string (scientific name components)

	 * @author Tony Rees (Tony.Rees@csiro.au)

	 * Date created: June 2007-November 2008

	 * Inputs: input string as str (this version presumes genus, genus+species, or

	 * genus+species+authority)

	 * Outputs: parsed version of input string, for match purposes

	 * Remarks:

	 *    (1) Removes known text elements e.g.

	 *      'aff.', 'cf.', 'subsp.', subgenera if enclosed in brackets, etc. as desired

	 *    (2) Removes accented and non A-Z characters other than full stops

	 *       (in scientific name portions)

	 *    (3) Returns uppercase scientific name (genus + species only)

	 *       plus unaltered (presumed) authority

	 *     examples;

	 *       Anabaena cf. flos-aquae Ralfs ex Born. et Flah. => ANABAENA FLOSAQUAE Ralfs

	 *       ex Born. et Flah.

	 *       Abisara lemÈe-pauli => ABISARA LEMEEPAULI

	 *       Fuc/us Vesiculos2us => FUCUS VESICULOSUS

	 *       Buffo ignicolor LacÈpËde, 1788 => BUFFO IGNICOLOR LacÈpËde, 1788

	 *       Barbatia (Mesocibota) bistrigata (Dunker, 1866) => BARBATIA BISTRIGATA (Dunker, 1866)

	 *    (4) Thus version does not handle genus+author, or genus+species+infraspecies

	 *       (second" good" term is presumed to be species epithet, anything after is

	 *       considered to be start of the authority), however could be adapted further as required

     *         and actually it was done in this version for Tela Botanica

	 *    (5) There is a separate function "parse_auth" for normalizing authorities when required

	 *      (e.g. for authority comparisons)

	 *

	 * @param string $str : input string ( genus, genus+species, or genus+species+authority )

	 * @return string : parsed string

	 */

	public function parse( $str = NULL ) {

		unset($this->debug['parse']);

		$temp = '';

		$first_str_part = NULL;

		$second_str_part = NULL;

		$temp_genus = '';

		$temp_species = '';

		$temp_genus_species = '';

		$temp_authority = '';

		$temp_infra = '';

		//$this->debug['parse'][] = "1";

		if ( ($str == NULL) || ( trim($str) == '') ) {

			//$this->debug[] = "N1a<br>";

			return '';

		} else {

			//	trim any leading, trailing spaces or line feeds

			$temp = trim( $str );

			//$this->debug['parse'][] = "1b";

		}

		if ( $temp == NULL || $temp == '') {

			//$this->debug['parse'][] = "2a";

			return '';

		} else {

			//$this->debug['parse'][] = "2b";

			// replace any HTML ampersands

			$set = array('%', '&', 'amp;%', 'AMP;%');

			$temp = str_replace( $set, '&', $temp );

			//$this->debug['parse'][] = "2b1 (temp:$temp)";

			// remove any content in angle brackets (e.g. html tags - <i>, </i>, etc.)

			$html_pattern = '(\<(/?[^\>]+)\>)';

			//? This should not just handle html tags but all <*>

			$temp = preg_replace( $html_pattern, '', $temp);

			//$this->debug['parse'][] = "2b2 (temp:$temp)";

			// if second term (only) is in round brackets, presume it is a subgenus or a comment and remove it

			// examples: Barbatia (Mesocibota) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)

			// Barbatia (?) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)

			// (obviously this will not suit genus + author alone, where first part of authorname is in brackets,

			// however this is very rare?? and in any case we are not supporting genus+authority in this version)

			//if ( $temp like '% (%)%'

			$temp = preg_replace( '/ \(\w*\W*\)/', '', $temp, 1 );

			//? Not sure if this will catch if

			//$this->debug['parse'][] = "2b3 (temp:$temp)";

			// if second term (only) is in square brackets, presume it is a comment and remove it

			// example: Aphis [?] ficus Theobald, [1918] => Aphis ficus Theobald, [1918]

			//if ( $temp like '% [%]%'

			$temp = preg_replace( '/ \[\w*\W*\]/', '', $temp, 1 );

			//? Not sure if this will catch if

			//$this->debug['parse'][] = "2b4 (temp:$temp)";

			// drop indicators of questionable id's - presume all are lowercase for now (could extend as needed)

			$temp = preg_replace('/ cf /', ' ', $temp );

			$temp = preg_replace('/ cf\. /', ' ', $temp );

			$temp = preg_replace('/ near /', ' ', $temp );

			$temp = preg_replace('/ aff\. /', ' ', $temp );

			$temp = preg_replace('/ sp\. /', ' ', $temp );

			$temp = preg_replace('/ spp\. /', ' ', $temp );

			$temp = preg_replace('/ spp /', ' ', $temp );

			//$this->debug['parse'][] = "2b5 (temp:$temp)";

			// eliminate or close up any stray spaces introduced by the above

			$temp = $this->reduce_spaces( $temp );

			//$this->debug['parse'][] = "2b6 (temp:$temp)";

			// now presume first element is genus, second (if present) is species, remainder

			//   (if present) is authority

			// look for genus name

			$ar = explode(' ', $temp, 2);

			if ( count( $ar ) ) {

				$temp_genus = $ar[0];

				$temp = @$ar[1];

			} else {

				$temp_genus = $temp;

				$temp = '';

			}

			//$this->debug['parse'][] = "2b7 (temp_genus:$temp_genus) (temp:$temp)";

			// look for species epithet and authority

			$ar = explode(' ', $temp, 2);

			if ( count( $ar ) ) {

				$temp_species = $ar[0];

				$temp_authority = @$ar[1];

			} else {

				$temp_species = $temp;

				$temp_authority = '';

			}

			// look for subspecies

			$infras =array('subsp.','var.');

			$temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);

			$temp_authority = preg_replace( "/ssp /", "subsp.", $temp_authority);

			$temp_authority = preg_replace( "/subsp /", "subsp.", $temp_authority);

			$temp_authority = preg_replace( "/var /", "var.", $temp_authority);

			$temp_infra_authority = '';

			$temp_infra_type = '';

			foreach ($infras as $infra) {

				$pos = strpos($temp_authority, $infra);

				if ($pos === false) {

					continue;

				} else {

					$temp_infra=substr($temp_authority,$pos+strlen($infra));

					$temp_authority=substr($temp_authority,0,$pos);

					$temp_infra=trim($temp_infra);

					$temp_infra_type=$infra;

					// look for infra epithet and authority

					$ar = explode(' ', $temp_infra, 2);

					if ( count( $ar ) ) {

						$temp_infra = $ar[0];

						$temp_infra_authority = @$ar[1];

					}

					break; // on s'arrete au premier trouve

				}

			}

			//$this->debug['parse'][] = "2b8 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

			// replace selected ligatures here (Genus names can contain Æ, OE ligature)

			$temp_genus = str_replace( 'Æ', 'AE', $temp_genus);

			$temp_species = str_replace( 'Æ', 'AE', $temp_species);

			$temp_infra = str_replace( 'Æ', 'AE', $temp_infra );

			//$this->debug['parse'][] = "2b9 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

			$temp_genus= trim($temp_genus);

			$temp_species= trim($temp_species);

			$temp_infra= trim($temp_infra );

			// reduce any new multiple internal spaces to single space, if present

			$temp_genus= $this->reduce_spaces( $temp_genus );

			$temp_species= $this->reduce_spaces( $temp_species );

			$temp_infra= $this->reduce_spaces( $temp_infra );

			//$this->debug['parse'][] = "2b10 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

			if (isset($temp_authority) && ($temp_authority!='') ) {

				$temp_authority=$this->parse_auth($temp_authority);

			}

			if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {

				$temp_infra_authority=$this->parse_auth($temp_infra_authority);

			}

			//$this->debug['parse'][] = "2b11 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

			return array("genus"=>$temp_genus, "species"=>$temp_species, "authority"=>$temp_authority, "infra"=>$temp_infra, "infra_authority"=>$temp_infra_authority, "infra_type"=>$temp_infra_type);

		}

	}

}