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| 0,0 → 1,358 |
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| <?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)"; |
| $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); |
| } |
| } // End NameParser |
| } // End Class |
| ?> |