public function aggregate($taxamatch = null)
{
$taxamatch_result = $taxamatch->getData();
$parsed = array();
$parsed["family"] = $taxamatch->this_search_family;
$parsed["genus"] = $taxamatch->this_search_genus;
$parsed["species"] = $taxamatch->this_search_species;
$parsed["infra1"] = $taxamatch->this_search_infra1;
$parsed["infra2"] = $taxamatch->this_search_infra2;
$parsed["authority"] = $taxamatch->this_authority;
$parsed["authorities"] = $taxamatch->this_authorities;
$parsed["rank1"] = $taxamatch->this_search_rank1;
$parsed["rank2"] = $taxamatch->this_search_rank2;
$start_string = $taxamatch->this_start_string;
$family_string = $taxamatch->this_family_string;
$family_unmatched = $taxamatch->this_family_unmatched;
$status_string = $taxamatch->this_status_string;
$cleaned_txt = $taxamatch->this_cleaned_txt;
$preprocessed_txt = $taxamatch->this_preprocessed_txt;
$scientificname = $taxamatch->searchtxt;
if ($taxamatch->parse_only) {
$unparsed = $preprocessed_txt;
foreach (array_keys($parsed) as $pk) {
if ($pk == 'authority') {
continue;
} elseif ($pk == 'authorities') {
foreach ($parsed[$pk] as $auth) {
if ($auth) {
$unparsed = str_ireplace_first($auth, '', $unparsed);
}
}
} elseif ($parsed[$pk]) {
$unparsed = str_ireplace_first($parsed[$pk], '', $unparsed);
if ($parsed[$pk] == 'f.' && ($pk == "rank1" || $pk == "rank2")) {
$unparsed = str_ireplace_first(self::$forma, '', $unparsed);
}
}
}
if (isset($start_string)) {
$unparsed = $start_string . $unparsed;
}
$unparsed = trim($unparsed);
$parsed_rank1 = array_key_exists($parsed["rank1"], self::$standard_rank) ? self::$standard_rank[$parsed["rank1"]] : $parsed["rank1"];
$parsed_rank2 = array_key_exists($parsed["rank2"], self::$standard_rank) ? self::$standard_rank[$parsed["rank2"]] : $parsed["rank2"];
$this->data[] = array('Name_submitted' => $scientificname, 'Family' => $parsed["family"], 'Genus' => $parsed["genus"], 'Specific_epithet' => $parsed["species"], 'Infraspecific_rank' => $parsed_rank1, 'Infraspecific_epithet' => $parsed["infra1"], 'Infraspecific_rank_2' => $parsed_rank2, 'Infraspecific_epithet_2' => $parsed["infra2"], 'Author' => $parsed["authority"], 'Annotations' => $status_string, 'Unmatched_terms' => $unparsed);
return true;
}
$lowest_parsed_rank = '';
$lowest_matched_rank = '';
foreach (array_keys(self::$rank) as $rk) {
if ($parsed[$rk]) {
$lowest_parsed_rank = $rk;
}
}
$gni_parser_result = null;
if (isset($taxamatch_result["gni_parser_result"])) {
$gni_parser_result = $taxamatch_result["gni_parser_result"];
}
$all_id = array();
$all_name = array();
$matched = array();
$matched_by_source = array();
$synonym = array();
$name_source_data = array();
$classification_family = array();
$phonetic_id = array();
$alt_accepted_family = array();
$family_matched = array();
$genus_matched = array();
$species_matched = array();
$infra1_matched = array();
$infra2_matched = array();
$all_matched = array();
$best_ed = array();
$higher_taxa_ed = array();
foreach (array_keys(self::$rank) as $rk) {
$all_matched[$rk] = array();
if (isset($taxamatch_result[$rk]) && count($taxamatch_result[$rk])) {
foreach (array_keys(self::$match_type) as $type) {
if (isset($taxamatch_result[$rk][$type])) {
if (!isset($best_ed[$rk]) || $best_ed[$rk] > self::$match_type[$type]) {
$best_ed[$rk] = self::$match_type[$type];
}
foreach ($taxamatch_result[$rk][$type] as &$match) {
$match["match_type"] = $type;
$match["match_score"] = 0;
$match["Lowest_matched_rank"] = $rk;
$match["Name_matched_id"] = $match[$rk . "_id"];
$all_id[] = $match["Name_matched_id"];
if ($type == 'exact' || $type == 'phonetic') {
$phonetic_id[$match["Name_matched_id"]] = 1;
}
}
$all_matched[$rk] = array_merge($all_matched[$rk], $taxamatch_result[$rk][$type]);
}
}
}
}
if (count($all_id)) {
$name_res = $this->db->getScientificName($all_id);
$accepted_name_id = array();
foreach ($name_res as $nm) {
$all_name[$nm->nameID] = $nm;
$name_source_data[$nm->nameID][$nm->sourceID]['url'] = $nm->name_source_url;
$name_source_data[$nm->nameID][$nm->sourceID]['lsid'] = $nm->lsid;
}
$miss_accepted_name_id = array();
$synonym_res = $this->db->getSynonym($all_id);
foreach ($synonym_res as $sn) {
$nid = $sn->nameID;
$sid = $sn->sourceID;
if ($sn->acceptance == 'Accepted') {
$synonym[$nid][$sid]["accepted_name_id"] = $nid;
$synonym[$nid][$sid]["acceptance"] = $sn->acceptance;
//} elseif ($sn->acceptance == 'Synonym' || $sn->acceptance == 'Invalid' || $sn->acceptance == 'Illegitimate') {
} elseif (!is_null($sn->acceptance)) {
if ($sn->accepted_name_id) {
$accepted_name_id[] = $sn->accepted_name_id;
$synonym[$nid][$sid]["accepted_name_id"] = $sn->accepted_name_id;
}
$synonym[$nid][$sid]["acceptance"] = $sn->acceptance;
}
}
//print_r($synonym);
if (count($accepted_name_id)) {
$name_res = $this->db->getScientificName($accepted_name_id);
foreach ($name_res as $nm) {
$all_name[$nm->nameID] = $nm;
$name_source_data[$nm->nameID][$nm->sourceID]['url'] = $nm->name_source_url;
$name_source_data[$nm->nameID][$nm->sourceID]['lsid'] = $nm->lsid;
}
}
//print_r($all_name);
$classificationfamily_res = $this->db->getClassificationFamily(array_keys($all_name));
$cl_fam = array();
foreach ($classificationfamily_res as $cf) {
$cl_fam[$cf->nameID][$cf->sourceID] = $cf->family;
}
$source_id = array();
if (isset($this->db->classification_id)) {
$source_id[] = $this->db->classification_id;
} else {
$source_id = array_keys($this->db->source_name);
}
foreach (array_keys($cl_fam) as $nid) {
foreach ($source_id as $sid) {
if (isset($cl_fam[$nid][$sid])) {
$classification_family[$nid] = $cl_fam[$nid][$sid];
break;
}
}
}
}
//print_r($name_source_data);
//print_r($classification_family);
if (count($all_matched['family'])) {
$fm = array();
foreach ($all_matched['family'] as $fam) {
$fm[] = $fam['family'];
}
$fam_res = $this->db->getFamilyAcceptedFamily($fm);
foreach ($fam_res as $fam) {
$alt_accepted_family[$fam->family] = $fam->accepted_family;
}
}
foreach (array_keys(self::$rank) as $rk) {
foreach ($all_matched[$rk] as &$match) {
if (self::$rank[$rk] > self::$rank['family']) {
$match["Family_matched"] = "";
$match["family_ed"] = 0;
if ($parsed["family"]) {
$match["family_ed"] = strlen($parsed["family"]);
$accepted_family = isset($classification_family[$match["Name_matched_id"]]) ? $classification_family[$match["Name_matched_id"]] : '';
$genus = $all_name[$match["Name_matched_id"]]->genus;
$family_filtered = $this->filterFamily($all_matched["family"], $accepted_family, $genus, $alt_accepted_family);
if (count($family_filtered)) {
$match["family_ed"] = $family_filtered[0]["family_ed"];
$match["Family_matched"] = $family_filtered[0]["family"];
$match["Family_score"] = self::getEDScore($match["family_ed"], $match["Family_matched"], $parsed["family"]);
$match["match_score"] += $match["Family_score"];
}
}
}
}
}
if (count($all_matched["infra2"])) {
foreach ($all_matched["infra2"] as &$match) {
if (isset($higher_taxa_ed["infra2"]) && $higher_taxa_ed["infra2"] <= $match["infra2_ed"]) {
continue;
}
$name = $all_name[$match["Name_matched_id"]];
$match["Genus_matched"] = $name->genus;
$match["Specific_epithet_matched"] = $name->specificEpithet;
$match["Infraspecific_rank"] = $name->rankIndicator;
$match["Infraspecific_epithet_matched"] = $name->infraspecificEpithet;
$match["Infraspecific_rank_2"] = $name->infraspecificRank2;
$match["Infraspecific_epithet_2_matched"] = $name->infraspecificEpithet2;
$match["Genus_score"] = self::getEDScore($match["genus_ed"], $match["Genus_matched"], $parsed["genus"]);
$match["Specific_epithet_score"] = self::getEDScore($match["species_ed"], $match["Specific_epithet_matched"], $parsed["species"]);
$match["Infraspecific_epithet_score"] = self::getEDScore($match["infra1_ed"], $match["Infraspecific_epithet_matched"], $parsed["infra1"]);
$match["Infraspecific_epithet_2_score"] = self::getEDScore($match["infra2_ed"], $match["Infraspecific_epithet_2_matched"], $parsed["infra2"]);
$match["Name_matched"] = $match["genus_species_infra1_infra2"];
if (!isset($higher_taxa_ed["infra1"]) || $higher_taxa_ed["infra1"] > $match["infra1_ed"]) {
$higher_taxa_ed["infra1"] = $match["infra1_ed"];
}
if (!isset($higher_taxa_ed["species"]) || $higher_taxa_ed["species"] > $match["species_ed"]) {
$higher_taxa_ed["species"] = $match["species_ed"];
}
if (!isset($higher_taxa_ed["genus"]) || $higher_taxa_ed["genus"] > $match["genus_ed"]) {
$higher_taxa_ed["genus"] = $match["genus_ed"];
}
if (isset($match["family_ed"]) && (!isset($higher_taxa_ed["family"]) || $higher_taxa_ed["family"] > $match["family_ed"])) {
$higher_taxa_ed["family"] = $match["family_ed"];
}
if (self::cmpRank($match["Infraspecific_rank"], $parsed["rank1"]) !== true) {
$match["Infraspecific_epithet_score"] -= self::$rank_penalty;
}
if (self::cmpRank($match["Infraspecific_rank_2"], $parsed["rank2"]) !== true) {
$match["Infraspecific_epithet_2_score"] -= self::$rank_penalty;
}
$match["match_score"] += $match["Specific_epithet_score"] + $match["Genus_score"] + $match["Infraspecific_epithet_score"] + $match["Infraspecific_epithet_2_score"];
$matched[] = $match;
}
}
if (count($all_matched["infra1"]) && (!isset($higher_taxa_ed["infra1"]) || isset($best_ed["infra1"]) && $higher_taxa_ed["infra1"] > $best_ed["infra1"])) {
foreach ($all_matched["infra1"] as &$match) {
if (isset($higher_taxa_ed["infra1"]) && $higher_taxa_ed["infra1"] <= $match["infra1_ed"]) {
continue;
}
$name = $all_name[$match["Name_matched_id"]];
$match["Genus_matched"] = $name->genus;
$match["Specific_epithet_matched"] = $name->specificEpithet;
$match["Infraspecific_rank"] = $name->rankIndicator;
$match["Infraspecific_epithet_matched"] = $name->infraspecificEpithet;
$match["Genus_score"] = self::getEDScore($match["genus_ed"], $match["Genus_matched"], $parsed["genus"]);
$match["Specific_epithet_score"] = self::getEDScore($match["species_ed"], $match["Specific_epithet_matched"], $parsed["species"]);
$match["Infraspecific_epithet_score"] = self::getEDScore($match["infra1_ed"], $match["Infraspecific_epithet_matched"], $parsed["infra1"]);
$match["Name_matched"] = $match["genus_species_infra1"];
if (!isset($higher_taxa_ed["species"]) || $higher_taxa_ed["species"] > $match["species_ed"]) {
$higher_taxa_ed["species"] = $match["species_ed"];
}
if (!isset($higher_taxa_ed["genus"]) || $higher_taxa_ed["genus"] > $match["genus_ed"]) {
$higher_taxa_ed["genus"] = $match["genus_ed"];
}
if (isset($match["family_ed"]) && (!isset($higher_taxa_ed["family"]) || $higher_taxa_ed["family"] > $match["family_ed"])) {
$higher_taxa_ed["family"] = $match["family_ed"];
}
if (self::cmpRank($match["Infraspecific_rank"], $parsed["rank1"]) !== true) {
$match["Infraspecific_epithet_score"] -= self::$rank_penalty;
}
$match["match_score"] += $match["Specific_epithet_score"] + $match["Genus_score"] + $match["Infraspecific_epithet_score"];
$matched[] = $match;
}
}
if (count($all_matched["species"]) && (!isset($higher_taxa_ed["species"]) || isset($best_ed["species"]) && $higher_taxa_ed["species"] > $best_ed["species"])) {
foreach ($all_matched["species"] as &$match) {
if (isset($higher_taxa_ed["species"]) && $higher_taxa_ed["species"] <= $match["species_ed"]) {
continue;
}
$name = $all_name[$match["Name_matched_id"]];
$match["Genus_matched"] = $name->genus;
$match["Specific_epithet_matched"] = $name->specificEpithet;
$match["Genus_score"] = self::getEDScore($match["genus_ed"], $match["Genus_matched"], $parsed["genus"]);
$match["Specific_epithet_score"] = self::getEDScore($match["species_ed"], $match["Specific_epithet_matched"], $parsed["species"]);
$match["Name_matched"] = $match["genus_species"];
if (!isset($higher_taxa_ed["genus"]) || $higher_taxa_ed["genus"] > $match["genus_ed"]) {
$higher_taxa_ed["genus"] = $match["genus_ed"];
}
if (isset($match["family_ed"]) && (!isset($higher_taxa_ed["family"]) || $higher_taxa_ed["family"] > $match["family_ed"])) {
$higher_taxa_ed["family"] = $match["family_ed"];
}
$match["match_score"] += $match["Genus_score"] + $match["Specific_epithet_score"];
$matched[] = $match;
}
}
if (count($all_matched["genus"]) && (!isset($higher_taxa_ed["genus"]) || isset($best_ed["genus"]) && $higher_taxa_ed["genus"] > $best_ed["genus"])) {
foreach ($all_matched["genus"] as &$match) {
if (isset($higher_taxa_ed["genus"]) && $higher_taxa_ed["genus"] <= $match["genus_ed"]) {
continue;
}
$name = $all_name[$match["Name_matched_id"]];
$match["Genus_matched"] = $name->genus;
$match["Specific_epithet_matched"] = '';
$match["Genus_score"] = self::getEDScore($match["genus_ed"], $match["Genus_matched"], $parsed["genus"]);
$match["Specific_epithet_score"] = '';
$match["Name_matched"] = $match["Genus_matched"];
if (isset($match["family_ed"]) && (!isset($higher_taxa_ed["family"]) || $higher_taxa_ed["family"] > $match["family_ed"])) {
$higher_taxa_ed["family"] = $match["family_ed"];
}
$match["match_score"] += $match["Genus_score"];
$matched[] = $match;
}
}
if (count($all_matched["family"]) && (!isset($higher_taxa_ed["family"]) || isset($best_ed["family"]) && $higher_taxa_ed["family"] > $best_ed["family"])) {
foreach ($all_matched["family"] as &$match) {
if (isset($higher_taxa_ed["family"]) && $higher_taxa_ed["family"] <= $match["family_ed"]) {
continue;
}
$match["Family_matched"] = $match["family"];
$match["Specific_epithet_matched"] = '';
$match["Genus_matched"] = '';
$match["Family_score"] = self::getEDScore($match["family_ed"], $match["Family_matched"], $parsed["family"]);
$match["Genus_score"] = '';
$match["Specific_epithet_score"] = '';
$match["Name_matched"] = $match["Family_matched"];
$match["match_score"] += $match["Family_score"];
$matched[] = $match;
}
}
if (!count($matched)) {
$matched[] = array("Lowest_matched_rank" => "", "Name_score" => "", "Family_matched" => "", "Author_score" => "", "Name_matched_accepted_family" => "", "Warnings" => 0);
}
$status = $status_string;
if ($status) {
if (preg_match("/vel\\.? sp\\.? aff\\.?/i", $status)) {
$status = "vel. sp. aff.";
} elseif (preg_match("/\\-?aff?\\.?/i", $status)) {
$status = "aff.";
} elseif (preg_match("/\\-?cf\\.?/i", $status) || $status == '?') {
$status = "cf.";
}
}
$unmatched = array();
foreach ($matched as &$match) {
$match["Name_submitted"] = $scientificname;
$match["Family_submitted"] = $parsed["family"];
$match["Genus_submitted"] = $parsed["genus"];
$match["Specific_epithet_submitted"] = $parsed["species"];
$match["Author_submitted"] = $parsed["authority"];
$match["Annotations"] = $status;
$rk = $match["Lowest_matched_rank"];
$parsed_part = 0;
$matched_part = 0;
if ($rk) {
$matched_part = self::$rank[$rk];
if ($match["Family_matched"]) {
$matched_part++;
}
}
if ($lowest_parsed_rank) {
$parsed_part = self::$rank[$lowest_parsed_rank];
}
if ($parsed["family"]) {
$parsed_part++;
}
$unmatched = '';
$unmatched_part = 0;
$extra_part = 0;
if (!$rk || self::$rank[$rk] < self::$rank['genus'] || $gni_parser_result && $gni_parser_result->scientificName->parsed) {
$unmatched = $preprocessed_txt;
} elseif ($preprocessed_txt != $cleaned_txt) {
$unmatched = str_ireplace_first($cleaned_txt, '', $preprocessed_txt);
}
if ($match["Family_matched"]) {
$unmatched = str_ireplace_first($parsed['family'], '', $unmatched);
}
if ($rk && $gni_parser_result && $gni_parser_result->scientificName->parsed) {
foreach (array_keys(self::$rank) as $rki) {
if (self::$rank[$rki] >= self::$rank['genus'] && self::$rank[$rki] <= self::$rank[$rk]) {
$unmatched = str_ireplace_first($parsed[$rki], '', $unmatched);
}
}
foreach ($parsed["authorities"] as $auth) {
if ($auth) {
$unmatched = str_ireplace_first($auth, '', $unmatched);
}
}
if (($rk == 'infra1' || $rk == 'infra2') && $parsed["rank1"]) {
$unmatched = str_ireplace_first($parsed["rank1"], '', $unmatched);
$matched_part++;
if ($parsed["rank1"] == 'f.') {
$unmatched = str_ireplace_first(self::$forma, '', $unmatched);
}
}
if ($rk == 'infra2' && $parsed["rank2"]) {
$unmatched = str_ireplace_first($parsed["rank2"], '', $unmatched);
$matched_part++;
if ($parsed["rank2"] == 'f.') {
$unmatched = str_ireplace_first(self::$forma, '', $unmatched);
}
}
if ($all_name[$match["Name_matched_id"]]->isHybrid) {
$unmatched = str_ireplace_first(' x', ' ', $unmatched);
$unmatched = str_ireplace_first(' ×', ' ', $unmatched);
}
}
//print_r($matched);
if (strlen($unmatched)) {
$unmatched = trim(preg_replace("/ {2,}/", ' ', $unmatched));
}
if (strlen($unmatched)) {
$unmatched_part = count(explode(" ", $unmatched));
$extra_part = $unmatched_part + $matched_part - $parsed_part;
if ($parsed["rank1"]) {
$extra_part--;
}
if ($parsed["rank2"]) {
$extra_part--;
}
if ($extra_part > 1) {
$unmatched_part -= $extra_part - 1;
}
}
if (isset($start_string)) {
$unmatched = $start_string . $unmatched;
}
$match["Unmatched_terms"] = trim($unmatched);
if ($rk) {
$matched_id[] = $match["Name_matched_id"];
$match["Canonical_author"] = $match["temp_authority"];
if (array_key_exists($match[$rk . "_id"], $phonetic_id)) {
$match["Phonetic"] = 'Y';
} else {
$match["Phonetic"] = "";
}
if (!isset($match["Warnings"])) {
$match["Warnings"] = 0;
}
if (isset($gni_parser_result) && $lowest_parsed_rank != $match["Lowest_matched_rank"]) {
$match["Warnings"] |= self::$flag_def['Partial'];
}
if (!$lowest_matched_rank || self::$rank[$match["Lowest_matched_rank"]] > self::$rank[$lowest_matched_rank]) {
$lowest_matched_rank = $match["Lowest_matched_rank"];
}
if ($parsed["authority"] && !($match["Warnings"] & self::$flag_def['Partial'])) {
$match["Author_matched"] = $match["temp_authority"];
$match["Author_score"] = $match["auth_similarity"];
} else {
$match["Author_matched"] = '';
$match["Author_score"] = '';
}
#$match["Name_score"]=$match["match_score"]/$parsed_part;
$match["Name_score"] = self::num_to_score($match["match_score"], $parsed_part, 2, 1);
#$match["Overall_score"]=self::getOverallScore($match["match_score"], $match["Author_score"], $matched_part+$unmatched_part);
$match["Overall_score"] = self::getOverallScore($match["Name_score"], $match["Author_score"], $extra_part);
}
}
$source_order = 0;
foreach ($this->db->source as $so) {
$source_order++;
$matched_by_source[$so] = array();
$sid = $this->db->source_id[$so];
foreach ($matched as &$match) {
if (isset($match["Name_matched_id"])) {
$nid = $match["Name_matched_id"];
if (array_key_exists($sid, $name_source_data[$nid])) {
$match["Source"] = $so;
$match["Source_order"] = $source_order;
$match["Name_matched_rank"] = $all_name[$nid]->nameRank;
$match["Name_matched_accepted_family"] = isset($classification_family[$nid]) ? $classification_family[$nid] : '';
$match["Name_matched_url"] = $name_source_data[$nid][$sid]['url'];
$match["Name_matched_lsid"] = $name_source_data[$nid][$sid]['lsid'];
$match["Taxonomic_status"] = isset($synonym[$nid][$sid]["acceptance"]) ? $synonym[$nid][$sid]["acceptance"] : 'No opinion';
$match["Accepted_name"] = '';
if (isset($synonym[$nid][$sid]["accepted_name_id"])) {
$match["Accepted_name_id"] = $synonym[$nid][$sid]["accepted_name_id"];
$accepted_name = $all_name[$match["Accepted_name_id"]];
$match["Accepted_name"] = $accepted_name->scientific_name;
$match["Accepted_name_author"] = $accepted_name->author;
$match["Accepted_name_url"] = $name_source_data[$match["Accepted_name_id"]][$sid]['url'];
$match["Accepted_name_lsid"] = $name_source_data[$match["Accepted_name_id"]][$sid]['lsid'];
$match["Accepted_name_rank"] = $accepted_name->nameRank;
$match["Accepted_family"] = isset($classification_family[$match["Accepted_name_id"]]) ? $classification_family[$match["Accepted_name_id"]] : "";
}
$match["Accepted_species"] = "";
if ($match["Accepted_name"] && self::$rank[$match["Lowest_matched_rank"]] >= self::$rank["species"]) {
if ($all_name[$match["Accepted_name_id"]]->isHybrid) {
$match["Accepted_species"] = $all_name[$match["Accepted_name_id"]]->scientific_name;
} else {
$match["Accepted_species"] = $all_name[$match["Accepted_name_id"]]->genus . ' ' . $all_name[$match["Accepted_name_id"]]->specificEpithet;
}
}
$matched_by_source[$so][] = $match;
}
} else {
$matched_by_source[""] = $match;
}
}
}
$matched = array();
if (isset($matched_by_source[""])) {
$matched[] = $matched_by_source[""];
} else {
foreach ($this->db->source as $so) {
foreach ($matched_by_source[$so] as &$match) {
$matched[] = $match;
}
}
}
self::$sort_scheme = 'overall';
usort($matched, array($this, "cmpMatched"));
$order = 1;
foreach ($matched as &$match) {
$match["Overall_score_order"] = $order++;
}
self::$sort_scheme = 'highertaxa';
usort($matched, array($this, "cmpMatched"));
$order = 1;
foreach ($matched as &$match) {
$match["Highertaxa_score_order"] = $order++;
}
foreach ($matched as &$match) {
if (isset($match['Name_matched_id']) && isset(self::$ambiguous[$match['Name_matched_id']])) {
$match['Warnings'] |= self::$flag_def['Ambiguous'];
}
if ($match["Highertaxa_score_order"] > $match["Overall_score_order"]) {
$match['Warnings'] |= self::$flag_def['HigherTaxa'];
} elseif ($match["Highertaxa_score_order"] < $match["Overall_score_order"]) {
$match['Warnings'] |= self::$flag_def['Overall'];
}
}
foreach ($matched as &$match) {
$result = array();
foreach (self::$field as $fd) {
if (array_key_exists($fd, $match) && !is_null($match[$fd])) {
$result[$fd] = $match[$fd];
} else {
$result[$fd] = '';
}
}
$this->data[] = $result;
}
}
$outfile = isset($options["o"]) ? $options["o"] : "";
$cache = false;
$source = explode(",", $source);
$db = select_source($source, $classification);
$header = TnrsAggregator::$field;
if (isset($count)) {
array_unshift($header, "ID");
}
$outfh = fopen($outfile, 'w') or die("can't open outputfile");
fputcsv($outfh, $header);
$handle = fopen($file, "r");
while (($field = fgetcsv($handle, 1000, ",")) !== FALSE) {
if (!isset($field[0]) || $field[0] == '') {
continue;
}
$ta = new TnrsAggregator($db);
$tm = new Taxamatch($db);
$tm->set('debug_flag', '');
$tm->set('output_type', '');
$tm->set('cache_flag', false);
$tm->set('cache_path', CACHE_PATH);
$tm->set('name_parser', NAME_PARSER);
$tm->set('chop_overload', CHOP_OVERLOAD);
$tm->set('parse_only', $parse_only);
$name = escapeshellarg($field[0]);
if ($tm->process($name, $search_mode, $cache) && !$parse_only) {
$tm->generateResponse($cache);
}
$ta->aggregate($tm);
$result = $ta->getData();
foreach ($result as $re) {
$data = array();
$names = preg_split("/[\r\n;]+/u", $str);
if (is_array($names)) {
foreach ($names as $name) {
$tm = new Taxamatch($db);
$tm->set('debug_flag', $debug);
$tm->set('output_type', strtolower($output));
$tm->set('cache_flag', $authorities[$source]['cache_flag']);
$tm->set('cache_path', CACHE_PATH);
$tm->set('name_parser', NAME_PARSER);
$tm->set('chop_overload', CHOP_OVERLOAD);
$tm->set('parse_only', $parse_only);
if ($tm->process($name, $search_mode, $cache)) {
$tm->generateResponse($cache);
}
$ta = new TnrsAggregator($db);
$ta->aggregate($tm);
$data[] = $ta->getData();
}
}
//$debug = $tm->debug;
//if($output == 'xml') {
// $data = $tm->getXML();
//}
break;
case 'sources':
$db = select_source($source, $classification);
$data = $db->getSources();
break;
//case 'sources':
// $sources = getSources();
