WebSVN – eFlore/Applications.cel – Diff – /trunk/jrest/bibliotheque/NameParser.php

 <?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
- */
+ *
+ *
- /* Adapation par David Delon Decembre 2010 : gestion sous espece
+ * @internal   Mininum PHP version : 5.2
- */
+ * @category   CEL
-/**
+ * @package    Services
+ * @subpackage Bibliothèques
- * Class NameParser
+ * @version    0.1
- * Used to convert a string to a standarized format.
+ * @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;
-	/**
-	 * 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,$value) {
+	public function set($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( $str ) {
+	private function reduce_spaces($str) {
-		$str = preg_replace("/ {2,}/", ' ', $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, $upcase=1 ) {
+	public function parse_auth($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 ) {
+			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 = "(\<(/?[^\>]+)\>)";
+			$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 );
+			$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 );
+			$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( "/ cf\. /", " ", $temp );
+			$temp = preg_replace('/ cf\. /', ' ', $temp );
-			$temp = preg_replace( "/ near /", " ", $temp );
+			$temp = preg_replace('/ near /', ' ', $temp );
-			$temp = preg_replace( "/ aff\. /", " ", $temp );
+			$temp = preg_replace('/ aff\. /', ' ', $temp );
-			$temp = preg_replace( "/ sp\. /", " ", $temp );
+			$temp = preg_replace('/ sp\. /', ' ', $temp );
-			$temp = preg_replace( "/ spp\. /", " ", $temp );
+			$temp = preg_replace('/ spp\. /', ' ', $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);
+			$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);
+			$ar = explode(' ', $temp, 2);
 			if ( count( $ar ) ) {
 				$temp_species = $ar[0];
 				$temp_authority = @$ar[1];
 			} else {
 				$temp_species = $temp;
 				$temp_authority = '';
+			}
-            // look for subspecies
+			// look for subspecies
-            $infras =array('subsp.','var.');
+			$infras =array('subsp.','var.');
-            $temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
+			$temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
-            $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( "/subsp /", "subsp.", $temp_authority);
-            $temp_authority = preg_replace( "/var /", "var.", $temp_authority);
+			$temp_authority = preg_replace( "/var /", "var.", $temp_authority);
-            $temp_infra_authority = '';
+			$temp_infra_authority = '';
-            $temp_infra_type = '';
+			$temp_infra_type = '';
-            foreach ($infras as $infra) {
+			foreach ($infras as $infra) {
-            	$pos = strpos($temp_authority, $infra);
+				$pos = strpos($temp_authority, $infra);
-                if ($pos === false) {
+				if ($pos === false) {
-                	continue;
+					continue;
-                } else {
+				} else {
-                	$temp_infra=substr($temp_authority,$pos+strlen($infra));
+					$temp_infra=substr($temp_authority,$pos+strlen($infra));
-                    $temp_authority=substr($temp_authority,0,$pos);
+					$temp_authority=substr($temp_authority,0,$pos);
-                    $temp_infra=trim($temp_infra);
+					$temp_infra=trim($temp_infra);
-                    $temp_infra_type=$infra;
+					$temp_infra_type=$infra;
-                    // look for infra epithet and authority
+					// look for infra epithet and authority
-                    $ar = explode(" ", $temp_infra, 2);
+					$ar = explode(' ', $temp_infra, 2);
-                    if ( count( $ar ) ) {
+					if ( count( $ar ) ) {
-                    	$temp_infra = $ar[0];
+						$temp_infra = $ar[0];
-                        $temp_infra_authority = @$ar[1];
+						$temp_infra_authority = @$ar[1];
-                    }
+					}
-                    break; // on s'arrete au premier trouve
+					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 √Ü, OE ligature)
 			$temp_genus = str_replace( '√Ü', 'AE', $temp_genus);
 			$temp_species = str_replace( '√Ü', 'AE', $temp_species);
 			$temp_infra = str_replace( '√Ü', '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);
+			$temp_genus= trim($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_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!='') ) {
+			if (isset($temp_authority) && ($temp_authority!='') ) {
-            	$temp_authority=$this->parse_auth($temp_authority);
+				$temp_authority=$this->parse_auth($temp_authority);
-            }
+			}
-            if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
+			if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
-            	$temp_infra_authority=$this->parse_auth($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
-?>
+			//$this->debug['parse'][] = "2b11 (temp_genus:$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);
+		}
+	}
+}

Subversion Repositories eFlore/Applications.cel

(root)/trunk/jrest/bibliotheque/NameParser.php @ 3919 – Rev 2459 → 2462