Subversion Repositories eFlore/Applications.cel

<?php

/**

 * Taxamatch-Webservice PHP v1.0.0

 * @author Michael Giddens

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

 */

 /* Adapation par David Delon Decembre 2010 : gestion sous espece

 */

	/**

	 * Class NameParser

	 * Used to convert a string to a standarized format.

	 */

	class NameParser {

		/**

		 * Whether to debug or nor

		 * @var bool|integer

		 */

		public $debug_flag;

		/**

		 * Constructor

		 */

		public function __construct( ) {

		}

		/**

		 * 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)";

					//	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);

                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);

			}

		} // End NameParser

	} // End Class

?>