private function create_synonym($rec)
{
$exclude = array('"species"');
foreach ($rec["synonyms"] as $syn) {
if (in_array($syn["synonym"], $exclude)) {
continue;
}
$synonym = new \eol_schema\Taxon();
if (!Functions::is_utf8($syn["synonym"]) || !Functions::is_utf8($syn["syn_author"])) {
continue;
}
$synonym->taxonID = (string) $syn["syn_id"];
if (self::starts_with_small_letter($syn["synonym"])) {
$parts = explode(" ", $rec["sciname"]);
$syn["synonym"] = $parts[0] . " " . $syn["synonym"];
}
$synonym->scientificName = (string) $syn["synonym"];
$synonym->scientificNameAuthorship = (string) $syn["syn_author"];
$synonym->acceptedNameUsageID = (string) $rec["taxon_id"];
$synonym->taxonomicStatus = "synonym";
$synonym->taxonRemarks = (string) $syn["syn_remark"];
$synonym->furtherInformationURL = (string) $syn["syn_url"];
// special case e.g. http://turbellaria.umaine.edu/turb3.php?action=6&code=1412
if (@$rec["parent_id"] == 10408) {
$rec["parent_id"] = "";
}
$synonym->parentNameUsageID = (string) $rec["parent_id"];
if (!$synonym->scientificName) {
continue;
}
if ($synonym->scientificName == $rec["sciname"]) {
echo "\n alert: synonym == valid name \n";
print_r($rec);
self::save_to_dump($synonym->taxonID, $this->dump_file_synonyms);
continue;
}
if (!isset($this->taxon_ids[$synonym->taxonID])) {
$this->archive_builder->write_object_to_file($synonym);
$this->taxon_ids[$synonym->taxonID] = 1;
self::save_to_dump($synonym->taxonID, $this->dump_file_synonyms);
}
}
}
private function write_archive($taxon)
{
$t = new \eol_schema\Taxon();
$t->taxonID = $taxon['avibaseid'];
$t->scientificName = $taxon['sciname'];
$t->scientificNameAuthorship = $taxon['authorship'];
$t->order = ucfirst(strtolower($taxon['order']));
$t->family = $taxon['family'];
$t->genus = self::get_genus($taxon['sciname']);
$t->furtherInformationURL = self::AVIBASE_SOURCE_URL . $taxon['avibaseid'];
if (!isset($this->taxon_ids[$t->taxonID])) {
$this->taxon_ids[$t->taxonID] = '';
$this->archive_builder->write_object_to_file($t);
}
//write comnames and synonyms
$language_iso_codes = self::language_iso_codes();
foreach ($taxon['comnames'] as $name) {
if (!@$name['comnames']) {
continue;
}
// e.g. http://avibase.bsc-eoc.org/species.jsp?avibaseid=483A2A51F4A5E37E -- see Malayalam
foreach (@$name['comnames'] as $comname) {
if (!($comname = trim($comname))) {
continue;
}
if (!Functions::is_utf8($comname)) {
$comname = utf8_encode($comname);
}
if ($name['lang'] == "Latin") {
if ($t->scientificName == $comname) {
continue;
}
$synonym = new \eol_schema\Taxon();
$synonym->taxonID = strtolower(str_ireplace(" ", "_", $comname));
$synonym->scientificName = $comname;
$synonym->acceptedNameUsageID = $taxon['avibaseid'];
$synonym->taxonomicStatus = "synonym";
if (!isset($this->taxon_ids[$synonym->taxonID])) {
$this->taxon_ids[$synonym->taxonID] = '';
$this->archive_builder->write_object_to_file($synonym);
}
} else {
$v = new \eol_schema\VernacularName();
$v->taxonID = $taxon['avibaseid'];
$v->vernacularName = $comname;
$v->language = $language_iso_codes[$name['lang']];
$id = md5($v->vernacularName);
if (!isset($unique_id[$id])) {
$unique_id[$id] = '';
$this->archive_builder->write_object_to_file($v);
}
}
}
}
}
function get_common_names($names)
{
// might need or not need this...
$common = utf8_encode($name['commonName']);
if (Functions::is_utf8($common)) {
$arr_names[] = array("name" => Functions::import_decode($common), "language" => $name['xml_lang']);
}
}
private function get_texts($description, $taxon_id, $title, $subject, $code, $reference_ids = null, $agent_ids = null)
{
$description = utf8_encode($description);
if (!Functions::is_utf8($description)) {
return;
}
$mr = new \eol_schema\MediaResource();
if ($reference_ids) {
$mr->referenceID = implode("; ", $reference_ids);
}
if ($agent_ids) {
$mr->agentID = implode("; ", $agent_ids);
}
$mr->taxonID = $taxon_id;
$mr->identifier = $mr->taxonID . "_" . $code;
$mr->type = 'http://purl.org/dc/dcmitype/Text';
$mr->language = 'en';
$mr->format = 'text/html';
$mr->furtherInformationURL = $this->taxon_link["species"] . str_replace("s_", "", $taxon_id);
$mr->description = $description;
$mr->CVterm = $subject;
$mr->title = $title;
$mr->creator = '';
$mr->CreateDate = '';
$mr->modified = '';
$mr->UsageTerms = 'http://creativecommons.org/licenses/by-nc/3.0/';
$mr->Owner = '';
$mr->publisher = '';
$mr->audience = 'Everyone';
$mr->bibliographicCitation = $this->bibliographic_citation;
$this->archive_builder->write_object_to_file($mr);
}
private function process_fields($records, $class, $allowed_fields)
{
foreach ($records as $rec) {
if ($class == "VernacularName") {
$c = new \eol_schema\VernacularName();
} elseif ($class == "Agent") {
$c = new \eol_schema\Agent();
} elseif ($class == "Reference") {
$c = new \eol_schema\Reference();
} elseif ($class == "Taxon") {
$c = new \eol_schema\Taxon();
} elseif ($class == "MeasurementOrFact") {
$c = new \eol_schema\MeasurementOrFact();
} elseif ($class == "Occurrence") {
$c = new \eol_schema\Occurrence();
} elseif ($class == "Distribution") {
$c = new \eol_schema\MediaResource();
} elseif ($class == "Image") {
$c = new \eol_schema\MediaResource();
}
$keys = array_keys($rec);
$save = true;
foreach ($keys as $key) {
$temp = pathinfo($key);
$field = $temp["basename"];
/* resource specifications */
// if($this->resource_id == "345") //3I Interactive resource
// if(true)
// {
// if($class == "Image" && $field == "license") $field = "UsageTerms";
// if($class == "Distribution" && $field == "locality") $field = "Description";
// }
/* end specifications */
// manual adjustment bec. of a typo in meta.xml, without "s"
if ($field == "measurementRemark") {
$field = "measurementRemarks";
}
/*
// sample way to exclude if field is to be excluded
if($field == "attribution") continue; //not recognized in eol: http://indiabiodiversity.org/terms/attribution
*/
if (!in_array($field, $allowed_fields)) {
$this->debug["undefined"][$class][$field] = '';
continue;
}
// some fields have '#', e.g. "http://schemas.talis.com/2005/address/schema#localityName"
$parts = explode("#", $field);
if ($parts[0]) {
$field = $parts[0];
}
if (@$parts[1]) {
$field = $parts[1];
}
$value = trim((string) $rec[$key]);
$value = trim(Functions::import_decode($value));
if (!Functions::is_utf8($value)) {
$save = false;
}
//special arrangement
if ($class == "Reference") {
if ($field == "identifier") {
$this->reference_ids[$value] = '';
}
if ($field == "full_reference") {
if (!$value) {
$full_ref = "";
if ($val = (string) @$rec["http://eol.org/schema/reference/primaryTitle"]) {
$full_ref .= $val;
} elseif ($val = (string) @$rec["http://purl.org/dc/terms/title"]) {
$full_ref .= $val;
}
if ($val = (string) @$rec["http://purl.org/ontology/bibo/pageStart"]) {
$full_ref .= ". Page(s) " . $val;
}
if ($val = (string) @$rec["http://purl.org/ontology/bibo/pageEnd"]) {
$full_ref .= " - " . $val;
}
if ($val = (string) @$rec["http://purl.org/ontology/bibo/volume"]) {
$full_ref .= ". Vol. " . $val;
}
if ($val = (string) @$rec["http://purl.org/dc/terms/publisher"]) {
$full_ref .= ". Publisher: " . $val;
}
if ($val = (string) @$rec["http://purl.org/ontology/bibo/authorList"]) {
$full_ref .= ". Author: " . $val;
}
if ($val = (string) @$rec["http://purl.org/ontology/bibo/editorList"]) {
$full_ref .= ". Editor: " . $val;
}
if ($val = (string) @$rec["http://purl.org/dc/terms/created"]) {
$full_ref .= ". " . $val;
}
if ($val = $full_ref) {
$value = $full_ref;
} else {
echo " -- still blank";
}
}
}
}
// if($class == "MeasurementOrFact" && $field == "referenceID")
// {
// if($value)
// {
// if(!isset($this->reference_ids[$value])) echo " -- undefined refid:[$value]";
// }
// }
if ($value) {
$c->{$field} = $value;
}
}
/* if($class == "objects") {} // sample way to filter */
if ($save) {
$this->archive_builder->write_object_to_file($c);
}
}
}
private function get_names()
{
//0 tsn serial not null
//1 unit_ind1 char(1)
//2 unit_name1 char(35) not null
//3 unit_ind2 char(1)
//4 unit_name2 varchar(35)
//5 unit_ind3 varchar(7)
//6 unit_name3 varchar(35)
//7 unit_ind4 varchar(7)
//8 unit_name4 varchar(35)
//9 unnamed_taxon_ind char(1)
//10 usage varchar(12,5) not null
//11 unaccept_reason varchar(50,9)
//12 credibility_rtng varchar(40,17) not null
//13 completeness_rtng char(10)
//14 currency_rating char(7)
//15 phylo_sort_seq smallint
//16 initial_time_stamp datetime year to second not null
//17 parent_tsn integer
//18 taxon_author_id integer
//19 hybrid_author_id integer
//20 kingdom_id smallint not null
//21 rank_id smallint not null
//22 update_date date not null
//23 uncertain_prnt_ind char(3)
$written_publication_ids = array();
$path = $this->download_directory . "/" . $this->filenames['taxonomic_units'];
$i = 0;
foreach (new FileIterator($path) as $line) {
if (!$line) {
continue;
}
$line_data = explode("|", $line);
$name_tsn = trim($line_data[0]);
$x1 = trim($line_data[1]);
$name_part_1 = trim($line_data[2]);
$x2 = trim($line_data[3]);
$name_part_2 = trim($line_data[4]);
$sp_marker_1 = trim($line_data[5]);
$name_part_3 = trim($line_data[6]);
$sp_marker_2 = trim($line_data[7]);
$name_part_4 = trim($line_data[8]);
$validity = trim($line_data[10]);
$reason = trim($line_data[11]);
$comp_rating = trim($line_data[12]);
$cred_rating = trim($line_data[13]);
$curr_rating = trim($line_data[14]);
$parent_tsn = trim($line_data[17]);
$author_id = trim($line_data[18]);
$rank_id = trim($line_data[21]);
if (!$parent_tsn) {
$parent_tsn = 0;
}
$name_string = $name_part_1;
if (preg_match("/^[a-z]/", $name_part_1)) {
echo "???????? {$name_tsn}) {$name_part_1}\n";
}
if ($x1) {
$name_string = $x1 . " " . $name_string;
}
if ($x2) {
$name_string .= " " . $x2;
}
if ($name_part_2) {
$name_string .= " " . $name_part_2;
}
if ($sp_marker_1) {
$name_string .= " " . $sp_marker_1;
}
if ($name_part_3) {
$name_string .= " " . $name_part_3;
}
if ($sp_marker_2) {
$name_string .= " " . $sp_marker_2;
}
if ($name_part_4) {
$name_string .= " " . $name_part_4;
}
if ($a = @$this->authors[$author_id]) {
$name_string = utf8_encode($name_string) . " " . $a;
}
$name_string = trim($name_string);
$remarks = "";
if ($comp_rating && $comp_rating != "unknown") {
$remarks .= "Completeness: {$comp_rating}. ";
}
if ($cred_rating && $cred_rating != "unknown") {
$remarks .= "Credibility: {$cred_rating}. ";
}
// if($curr_rating && $curr_rating != "unknown") $remarks .= "Currency: $curr_rating. ";
if (isset($this->comment_links[$name_tsn])) {
foreach ($this->comment_links[$name_tsn] as $comment_id) {
if ($c = @$this->comments[$comment_id]) {
$remarks .= $c . ". ";
}
}
}
$remarks = str_replace("..", ".", $remarks);
$remarks = trim($remarks);
if (isset($this->synonym_of[$name_tsn])) {
static $unavailable_reasons = array('database artifact', 'unavailable, database artifact', 'unavailable, incorrect orig. spelling', 'unavailable, literature misspelling', 'unavailable, suppressed by ruling', 'unavailable, other', 'unjustified emendation', 'nomen dubium', 'homonym (illegitimate)', 'superfluous renaming (illegitimate)');
if (in_array($reason, $unavailable_reasons)) {
continue;
}
$taxon = new \eol_schema\Taxon();
$taxon->taxonID = $name_tsn;
$taxon->scientificName = $name_string;
$taxon->parentNameUsageID = $this->synonym_of[$name_tsn];
$taxon->taxonRank = $this->ranks[$rank_id];
$taxon->taxonRemarks = $remarks;
// $taxon->namePublishedIn = $publications;
$taxon->taxonomicStatus = $reason;
// if(isset($this->locations[$name_tsn])) $taxon->spatial = $this->locations[$name_tsn];
if ($val = @$this->locations[$name_tsn]) {
self::add_string_types($taxon->taxonID, md5($val), $val, "http://eol.org/schema/terms/Present", true);
}
// http://rs.tdwg.org/ontology/voc/SPMInfoItems#Distribution - possible value for ITIS geographic division
if (!Functions::is_utf8($taxon->scientificName)) {
echo "NOT UTF8 SYN: {$name_tsn} : {$taxon->scientificName}\n";
}
$this->archive_builder->write_object_to_file($taxon);
@($this->all_statuses['synonyms'][$validity] += 1);
@($this->all_statuses['synonym_reasons'][$reason] += 1);
} else {
// first loop and find all vernacular names
$vernacular_names = array();
if (isset($this->vernaculars[$name_tsn])) {
foreach ($this->vernaculars[$name_tsn] as $name_hash) {
$vernacular = new \eol_schema\VernacularName();
$vernacular->taxonID = $name_tsn;
$vernacular->vernacularName = $name_hash['name'];
$vernacular->language = self::get_iso_code_for_language($name_hash['language']);
if (!Functions::is_utf8($vernacular->vernacularName)) {
echo "NOT UTF8 VERN: {$name_tsn} : {$vernacular->vernacularName}\n";
}
$this->archive_builder->write_object_to_file($vernacular);
@($this->all_statuses['languages'][$name_hash['language']] += 1);
}
}
$publication_ids = array();
if (isset($this->publication_links[$name_tsn])) {
foreach ($this->publication_links[$name_tsn] as $pub_id) {
if ($p = @$this->publications[$pub_id]) {
if (!isset($written_publication_ids[$pub_id])) {
$reference = new \eol_schema\Reference();
$reference->identifier = $pub_id;
$reference->full_reference = $p;
if (!Functions::is_utf8($reference->full_reference)) {
echo "NOT UTF8 REF: {$name_tsn} : {$reference->full_reference}\n";
}
$this->archive_builder->write_object_to_file($reference);
$written_publication_ids[$pub_id] = 1;
}
$publication_ids[] = $pub_id;
}
}
}
if ($i % 5000 == 0) {
echo "{$i} : {$name_tsn} : {$name_string} : " . time_elapsed() . " : " . memory_get_usage() . "\n";
}
$i++;
$taxon = new \eol_schema\Taxon();
$taxon->taxonID = $name_tsn;
$taxon->scientificName = $name_string;
$taxon->parentNameUsageID = $parent_tsn;
$taxon->taxonRank = $this->ranks[$rank_id];
$taxon->taxonRemarks = $remarks;
$taxon->referenceID = implode(";", $publication_ids);
$taxon->taxonomicStatus = $validity;
// if(isset($this->locations[$name_tsn])) $taxon->spatial = $this->locations[$name_tsn];
if ($val = @$this->locations[$name_tsn]) {
self::add_string_types($taxon->taxonID, md5($val), $val, "http://eol.org/schema/terms/Present", true);
}
if (!Functions::is_utf8($taxon->scientificName)) {
echo "NOT UTF8: {$name_tsn} : {$taxon->scientificName}\n";
}
$this->archive_builder->write_object_to_file($taxon);
@($this->all_statuses['valids'][$validity] += 1);
}
}
}
private function format_utf8($string)
{
$string = Functions::import_decode($string);
if (!Functions::is_utf8($string)) {
return utf8_encode($string);
}
return $string;
}
private function clean_string($str)
{
$str = trim($str);
if (substr($str, 0, 1) == '"' && substr($str, -1) == '"') {
$str = substr($str, 1, strlen($str) - 2);
}
if (!Functions::is_utf8($str)) {
$str = utf8_encode($str);
}
return trim($str);
}
function format_utf8($str)
{
if (Functions::is_utf8($str)) {
return $str;
} else {
return utf8_encode($str);
}
}
private function format_utf8($str)
{
if (!Functions::is_utf8($str)) {
return utf8_encode($str);
}
return $str;
}
private static function lookup_with_cache_vimeo_call($vimeo, $command, $param, $options = array())
{
// default expire time is 15 days
if (!isset($options['expire_seconds'])) {
$options['expire_seconds'] = 1296000;
}
//debug orig value = 1296000
if (!isset($options['timeout'])) {
$options['timeout'] = 240;
}
if (!isset($options['cache_path'])) {
$options['cache_path'] = DOC_ROOT . "tmp/cache/";
}
// if(!isset($options['cache_path'])) $options['cache_path'] = "/Volumes/Eli black/eol_cache/"; //debug - only during development
$url = $command . implode("_", $param);
$md5 = md5($url);
$cache1 = substr($md5, 0, 2);
$cache2 = substr($md5, 2, 2);
$options['cache_path'] .= "vimeo/";
if (!file_exists($options['cache_path'])) {
mkdir($options['cache_path']);
}
if (!file_exists($options['cache_path'] . $cache1)) {
mkdir($options['cache_path'] . $cache1);
}
if (!file_exists($options['cache_path'] . "{$cache1}/{$cache2}")) {
mkdir($options['cache_path'] . "{$cache1}/{$cache2}");
}
$cache_path = $options['cache_path'] . "{$cache1}/{$cache2}/{$md5}.cache";
if (file_exists($cache_path)) {
$file_contents = file_get_contents($cache_path);
if (!Functions::is_utf8($file_contents)) {
$file_contents = utf8_encode($file_contents);
}
$obj = json_decode($file_contents);
if ($file_contents || strval($file_contents) == "0") {
$file_age_in_seconds = time() - filemtime($cache_path);
if ($file_age_in_seconds < $options['expire_seconds']) {
return $obj;
}
if ($options['expire_seconds'] === false) {
return $obj;
}
}
@unlink($cache_path);
}
if ($obj = $vimeo->call($command, $param)) {
$file_contents = json_encode($obj);
if ($FILE = Functions::file_open($cache_path, 'w+')) {
fwrite($FILE, $file_contents);
fclose($FILE);
} else {
if (!($h = Functions::file_open(DOC_ROOT . "/public/tmp/cant_delete.txt", 'a'))) {
return;
}
fwrite($h, $cache_path . "\n");
fclose($h);
}
return $obj;
}
return false;
}
private function get_texts($description, $taxon_id, $title, $subject, $code, $reference_ids = null, $agent_ids = null)
{
$description = utf8_encode(self::remove_quotes($description));
$description = str_ireplace("<br>", "xxxyyy", $description);
$description = strip_tags($description);
$description = str_ireplace("xxxyyy", "<br>", $description);
if (in_array($code, $this->media_ids)) {
return;
}
if (!Functions::is_utf8($description)) {
return;
}
$this->media_ids[] = $code;
if (in_array($subject, array("#TypeInformation"))) {
$subject = $this->EOL . $subject;
} else {
$subject = $this->SPM . $subject;
}
$mr = new \eol_schema\MediaResource();
if ($reference_ids) {
$mr->referenceID = implode("; ", $reference_ids);
}
if ($agent_ids) {
$mr->agentID = implode("; ", $agent_ids);
}
$mr->taxonID = $taxon_id;
$mr->identifier = $code;
$mr->type = "http://purl.org/dc/dcmitype/Text";
$mr->language = "en";
$mr->format = "text/html";
$mr->furtherInformationURL = $this->taxon_url . $taxon_id;
$mr->description = (string) $description;
$mr->CVterm = $subject;
$mr->title = $title;
$mr->creator = "";
$mr->CreateDate = "";
$mr->modified = "";
$mr->UsageTerms = "http://creativecommons.org/licenses/by-nc/3.0/";
$mr->Owner = "";
$mr->publisher = "";
$mr->audience = "Everyone";
$mr->bibliographicCitation = "";
$this->archive_builder->write_object_to_file($mr);
}
function get_common_names($names)
{
$arr_names = array();
if ($names) {
foreach ($names as $name) {
$common = utf8_encode($name['commonName']);
if (Functions::is_utf8($common)) {
$arr_names[] = array("name" => Functions::import_decode($common), "language" => $name['xml_lang']);
} else {
echo "\n not utf8 common name: [" . $common . "]\n";
}
}
}
return $arr_names;
}
private function get_contributor_name($url)
{
$options = array('resource_id' => 'gbif', 'expire_seconds' => false, 'download_wait_time' => 1000000, 'timeout' => 900, 'download_attempts' => 2, 'delay_in_minutes' => 2);
// 15mins timeout
$options = array('resource_id' => 'gbif', 'expire_seconds' => false, 'download_wait_time' => 1000000, 'timeout' => 900);
// 15mins timeout
if ($html = Functions::lookup_with_cache($url, $options)) {
// <title property="dc:title">Herbarium Berolinense - Dataset detail</title>
if (preg_match("/\"dc:title\">(.*?)\\- Dataset detail/ims", $html, $arr)) {
if (!Functions::is_utf8($arr[1])) {
exit("\n culprit is contributor name \n");
}
return Functions::import_decode(trim($arr[1]));
}
}
}
function fix_latin1_mangled_with_utf8_maybe_hopefully_most_of_the_time($str)
{
return preg_replace_callback('#[\\xA1-\\xFF](?![\\x80-\\xBF]{2,})#', function ($m) {
// utf8_encode($m[0]);
if (Functions::is_utf8($m[0])) {
$str = utf8_decode($m[0]);
$str = utf8_encode($str);
return $str;
} else {
return utf8_encode($m[0]);
}
}, $str);
}
private function get_descriptions_from_html($html, $rec)
{
$descriptions = array();
if (preg_match("/AUTHORSHIP AND CITATION\\:(.*?)Available\\:/ims", $html, $arr)) {
$authorship_citation = self::clean_str(strip_tags($arr[1]), true);
$authorship_citation = self::get_authorship_citation($authorship_citation);
$descriptions["AUTHORSHIP AND CITATION"] = $authorship_citation;
} else {
echo "\n ALERT: no authorship and citation: " . $rec['url'];
}
if ($rec["kingdom"] == "Animalia") {
$html = str_ireplace("ORDER :", "ORDER:", $html);
$html = str_ireplace("CLASS :", "CLASS:", $html);
if (preg_match("/ORDER\\:(.*?)<a name\\=\"CLASS\"/ims", $html, $arr) || preg_match("/ORDER\\:(.*?)<b>CLASS\\:/ims", $html, $arr)) {
$order = trim(strip_tags($arr[1]));
}
if (isset($order)) {
if (preg_match("/(.*?)\\(/ims", $order, $arr)) {
$order = trim($arr[1]);
}
//remove parenthesis
echo "\n order:[{$order}]\n";
$rec["order"] = $order;
}
if (isset($rec["order"])) {
if ($rec["order"] == "Caudata") {
$rec["class"] = "Amphibian";
} elseif (in_array($rec["order"], array("Passeriformes", "Piciformes", "Ciconiiformes", "Galliformes"))) {
$rec["class"] = "Bird";
} elseif (in_array($rec["order"], array("Artiodactyla", "Carnivora"))) {
$rec["class"] = "Mammal";
}
} else {
if (preg_match("/CLASS\\:(.*?)<a name\\=\"FEDERAL LEGAL STATUS\"/ims", $html, $arr) || preg_match("/CLASS\\:(.*?)<a name\\=\"FederalLegalStatus\"/ims", $html, $arr) || preg_match("/CLASS\\:(.*?)<b>FEDERAL LEGAL STATUS/ims", $html, $arr) || preg_match("/CLASS\\:(.*?)<a name\\=\"DistributionAndOccurrence\"/ims", $html, $arr) || preg_match("/CLASS\\:(.*?)<a name\\=\"DISTRIBUTION AND OCCURRENCE\"/ims", $html, $arr)) {
$class = trim(strip_tags($arr[1]));
}
if (isset($class)) {
if (preg_match("/(.*?)\\(/ims", $class, $arr)) {
$class = trim($arr[1]);
}
//remove parenthesis
$rec["class"] = $class;
}
}
if (isset($rec["class"])) {
echo "\n class:" . $rec["class"];
}
}
// taxonomy
if (preg_match("/TAXONOMY \\:(.*?)<b>/ims", $html, $arr)) {
$taxonomy = $arr[1];
} else {
if (preg_match("/TAXONOMY\\:(.*?)<span/ims", $html, $arr)) {
$taxonomy = $arr[1];
} elseif (preg_match("/TAXONOMY\\:(.*?)<em/ims", $html, $arr)) {
$taxonomy = $arr[1];
} elseif (preg_match("/TAXONOMY\\:(.*?)<br><br>/ims", $html, $arr)) {
$taxonomy = $arr[1];
} elseif (preg_match("/TAXONOMY\\:(.*?)<b>/ims", $html, $arr)) {
$taxonomy = $arr[1];
}
}
if (isset($taxonomy)) {
$taxonomy = utf8_encode($taxonomy);
if (Functions::is_utf8($taxonomy)) {
$descriptions["TAXONOMY"] = $taxonomy;
}
}
// SYNONYMS
if (preg_match("/SYNONYMS \\:(.*?)<b>/ims", $html, $arr)) {
$synonyms = self::clean_str(strip_tags($arr[1], "<br><a>"));
} elseif (preg_match("/SYNONYMS\\:(.*?)<br><br>/ims", $html, $arr)) {
$synonyms = self::clean_str(strip_tags($arr[1], "<br><a>"));
}
if (isset($synonyms)) {
$synonyms = self::further_clean($synonyms, "SYNONYMS", $html);
}
if (isset($synonyms)) {
$descriptions["SYNONYMS"] = $synonyms;
} else {
echo "\n -no synonyms- \n";
}
//debug
// COMMON NAMES
if (preg_match("/COMMON NAMES \\:(.*?)<b>/ims", $html, $arr)) {
$comnames = self::clean_str(strip_tags($arr[1], "<br><a>"));
} elseif (preg_match("/COMMON NAMES\\:(.*?)<br><br>/ims", $html, $arr)) {
$comnames = self::clean_str(strip_tags($arr[1], "<br><a>"));
} elseif (preg_match("/COMMON NAMES\\:(.*?)<\\/td/ims", $html, $arr)) {
$comnames = self::clean_str(strip_tags($arr[1], "<br><a>"));
}
if (isset($comnames)) {
$comnames = self::further_clean($comnames, "COMMON NAMES", $html);
$descriptions["COMMON NAMES"] = $comnames;
} else {
echo "\n -no comnames- \n";
}
//debug
if (in_array($rec["url"], array("http://www.fs.fed.us/database/feis/plants/shrub/ceaoph/all.html", "http://www.fs.fed.us/database/feis/plants/shrub/bernev/all.html"))) {
if (preg_match("/LIFE FORM\\:(.*?)<hr/ims", $html, $arr)) {
$lifeform = $arr[1];
if (!(stripos($lifeform, "federal legal status") != "" || stripos($lifeform, "other status") != "")) {
$descriptions["LIFE FORM"] = $lifeform;
}
}
} else {
$html = str_ireplace("<b>LIFE FORM :", "LIFE FORM:", $html);
if (preg_match("/LIFE FORM\\:(.*?)<br><br>/ims", $html, $arr)) {
$lifeform = $arr[1];
} elseif (preg_match("/LIFE FORM\\:(.*?)<b>/ims", $html, $arr)) {
$lifeform = $arr[1];
}
if (isset($lifeform)) {
$descriptions["LIFE FORM"] = $lifeform;
if (stripos($lifeform, "federal legal status") != "" || stripos($lifeform, "other status") != "") {
$descriptions["LIFE FORM"] = "";
if (preg_match("/(.*?)<a name\\=/ims", $lifeform, $arr)) {
$lifeform = $arr[1];
$descriptions["LIFE FORM"] = $lifeform;
if (stripos($lifeform, "federal legal status") != "" || stripos($lifeform, "other status") != "") {
$descriptions["LIFE FORM"] = "";
if (preg_match("/(.*?)<b>/ims", $lifeform, $arr)) {
$lifeform = $arr[1];
if (!(stripos($lifeform, "federal legal status") != "" || stripos($lifeform, "other status") != "")) {
$descriptions["LIFE FORM"] = $lifeform;
}
}
}
}
}
}
}
$html = str_ireplace("FEDERAL LEGAL STATUS :", "FEDERAL LEGAL STATUS:", $html);
if ($rec["kingdom"] == "Plantae") {
if (preg_match("/FEDERAL LEGAL STATUS\\:(.*?)<br><br>/ims", $html, $arr)) {
$federal_stat = $arr[1];
} elseif (preg_match("/FEDERAL LEGAL STATUS\\:(.*?)<b>/ims", $html, $arr)) {
$federal_stat = $arr[1];
}
if (isset($federal_stat)) {
$descriptions["FEDERAL LEGAL STATUS"] = $federal_stat;
if (stripos($federal_stat, "other status") != "") {
$descriptions["FEDERAL LEGAL STATUS"] = "";
if (preg_match("/(.*?)<a name\\=/ims", $federal_stat, $arr)) {
$federal_stat = $arr[1];
$descriptions["FEDERAL LEGAL STATUS"] = $federal_stat;
if (stripos($federal_stat, "other status") != "") {
$descriptions["FEDERAL LEGAL STATUS"] = "";
if (preg_match("/(.*?)<b>/ims", $federal_stat, $arr)) {
$federal_stat = $arr[1];
if (stripos($federal_stat, "other status") == "") {
$descriptions["FEDERAL LEGAL STATUS"] = $federal_stat;
}
}
}
}
}
}
if (isset($descriptions["FEDERAL LEGAL STATUS"])) {
if (stripos($descriptions["FEDERAL LEGAL STATUS"], "No special status") != "") {
$descriptions["FEDERAL LEGAL STATUS"] = "";
}
if (stripos($descriptions["FEDERAL LEGAL STATUS"], "No legal status") != "") {
$descriptions["FEDERAL LEGAL STATUS"] = "";
}
}
}
// kingdom = Plantae
$html = str_ireplace("OTHER STATUS :", "OTHER STATUS:", $html);
if (preg_match("/OTHER STATUS\\:(.*?)<a name\\=/ims", $html, $arr)) {
$other_stat = $arr[1];
}
if (isset($other_stat)) {
$descriptions["OTHER STATUS"] = $other_stat;
if (stripos($other_stat, "Management considerations") != "") {
$descriptions["OTHER STATUS"] = "";
if (preg_match("/(.*?)Management considerations\\:/ims", $other_stat, $arr)) {
$descriptions["OTHER STATUS"] = $arr[1];
}
}
}
/* DISTRIBUTION AND OCCURRENCE */
$html = str_ireplace("GENERAL DISTRIBUTION :", "GENERAL DISTRIBUTION:", $html);
if (in_array($rec["url"], array("http://www.fs.fed.us/database/feis/plants/shrub/ceaoph/all.html", "http://www.fs.fed.us/database/feis/plants/shrub/bernev/all.html"))) {
if (preg_match("/GENERAL DISTRIBUTION\\:(.*?)United States\\:/ims", $html, $arr)) {
$general_dist = $arr[1];
} elseif (preg_match("/GENERAL DISTRIBUTION\\:(.*?)States\\:/ims", $html, $arr)) {
$general_dist = $arr[1];
}
} else {
if (preg_match("/GENERAL DISTRIBUTION\\:(.*?)<b>ECOSYSTEMS/ims", $html, $arr)) {
$general_dist = $arr[1];
} elseif (preg_match("/GENERAL DISTRIBUTION\\:(.*?)<span/ims", $html, $arr)) {
$general_dist = $arr[1];
}
}
if (isset($general_dist)) {
$descriptions["GENERAL DISTRIBUTION"] = $general_dist;
}
if (preg_match("/ECOSYSTEMS \\:(.*?)<b>STATES/ims", $html, $arr) || preg_match("/ECOSYSTEMS\\:(.*?)<a name\\=\"STATES\"/ims", $html, $arr) || preg_match("/<a name\\=\"ECOSYSTEMS\">(.*?)<a name\\=\"STATES/ims", $html, $arr)) {
$ecosystems = $arr[1];
$descriptions["ECOSYSTEMS"] = $ecosystems;
}
if (in_array($rec["url"], array("http://www.fs.fed.us/database/feis/plants/shrub/ceaoph/all.html", "http://www.fs.fed.us/database/feis/plants/shrub/bernev/all.html"))) {
if (preg_match("/states\\:(.*?)Site Characteristics\\:/ims", $html, $arr)) {
$states = $arr[1];
}
} else {
if (preg_match("/STATES \\:(.*?)<b>BLM/ims", $html, $arr) || preg_match("/STATES\\:(.*?)<a name\\=\"BLM PHYSIOGRAPHIC REGIONS\"/ims", $html, $arr) || preg_match("/<a name\\=\"STATES\\/PROVINCES\">(.*?)<a name\\=\"BLM PHYSIOGRAPHIC REGIONS\"/ims", $html, $arr)) {
$states = $arr[1];
}
}
if (isset($states)) {
$states = str_ireplace("(key to state/province abbreviations)", "", $states);
$descriptions["STATES"] = $states;
}
if (preg_match("/BLM PHYSIOGRAPHIC REGIONS \\:(.*?)<b>KUCHLER/ims", $html, $arr) || preg_match("/BLM PHYSIOGRAPHIC REGIONS\\:(.*?)<a name\\=\"KUCHLER PLANT ASSOCIATIONS\"/ims", $html, $arr) || preg_match("/<a name\\=\"BLM PHYSIOGRAPHIC REGIONS\">(.*?)<a name\\=\"KUCHLER PLANT ASSOCIATIONS\"/ims", $html, $arr)) {
$blm_regions = $arr[1];
$descriptions["BLM PHYSIOGRAPHIC REGIONS"] = $blm_regions;
}
if (preg_match("/KUCHLER PLANT ASSOCIATIONS \\:(.*?)<b>SAF/ims", $html, $arr) || preg_match("/KUCHLER PLANT ASSOCIATIONS\\:(.*?)<a name\\=\"SAF COVER TYPES\"/ims", $html, $arr) || preg_match("/<a name\\=\"KUCHLER PLANT ASSOCIATIONS\">(.*?)<a name\\=\"SAF COVER TYPES\"/ims", $html, $arr)) {
$kuchler_assoc = $arr[1];
$descriptions["KUCHLER PLANT ASSOCIATIONS"] = $kuchler_assoc;
}
if (preg_match("/SAF COVER TYPES \\:(.*?)<b>SRM/ims", $html, $arr) || preg_match("/SAF COVER TYPES\\:(.*?)<a name\\=\"SRM \\(RANGELAND\\) COVER TYPES\"/ims", $html, $arr) || preg_match("/<a name\\=\"SAF COVER TYPES\">(.*?)<a name\\=\"SRM \\(RANGELAND\\) COVER TYPES\"/ims", $html, $arr)) {
$saf_types = $arr[1];
$descriptions["SAF COVER TYPES"] = $saf_types;
}
if (preg_match("/SRM \\(RANGELAND\\) COVER TYPES \\:(.*?)<b>HABITAT TYPES AND PLANT COMMUNITIES/ims", $html, $arr)) {
$srm_types = $arr[1];
} elseif (preg_match("/SRM \\(RANGELAND\\) COVER TYPES \\:(.*?)<b>PLANT COMMUNITIES/ims", $html, $arr)) {
$srm_types = $arr[1];
} elseif (preg_match("/SRM \\(RANGELAND\\) COVER TYPES\\:(.*?)<a name\\=\"PLANT COMMUNITIES\"/ims", $html, $arr)) {
$srm_types = $arr[1];
} elseif (preg_match("/<a name\\=\"SRM \\(RANGELAND\\) COVER TYPES\">(.*?)<a name\\=\"HABITAT TYPES/ims", $html, $arr)) {
$srm_types = $arr[1];
}
if (isset($srm_types)) {
$descriptions["SRM (RANGELAND) COVER TYPES"] = $srm_types;
}
if (in_array($rec["url"], array("http://www.fs.fed.us/database/feis/plants/shrub/ceaoph/all.html", "http://www.fs.fed.us/database/feis/plants/shrub/bernev/all.html"))) {
if (preg_match("/plant communities\\:(.*?)<a name\\=/ims", $html, $arr)) {
$habitat_types = $arr[1];
}
} else {
if (preg_match("/HABITAT TYPES AND PLANT COMMUNITIES\\:(.*?)<a name\\=\"BOTANICAL AND ECOLOGICAL CHARACTERISTICS/ims", $html, $arr)) {
$habitat_types = $arr[1];
} elseif (preg_match("/HABITAT TYPES AND PLANT COMMUNITIES\\:(.*?)<a name\\=\"BotanicalAndEcologicalCharacteristics/ims", $html, $arr)) {
$habitat_types = $arr[1];
} elseif (preg_match("/HABITAT TYPES AND PLANT COMMUNITIES \\:(.*?)<a name\\=\"MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$habitat_types = $arr[1];
}
}
if (isset($habitat_types)) {
if (is_numeric(stripos($habitat_types, '<a name="MANAGEMENT CONSIDERATIONS"></a>'))) {
if (preg_match("/HABITAT TYPES AND PLANT COMMUNITIES\\:(.*?)<a name\\=\"MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$habitat_types = $arr[1];
}
}
$descriptions["HABITAT TYPES AND PLANT COMMUNITIES"] = $habitat_types;
}
if ($rec["kingdom"] == "Animalia") {
//animals
$html = str_ireplace("<b>PLANT COMMUNITIES :", "<b>PLANT COMMUNITIES:", $html);
if (preg_match("/PLANT COMMUNITIES\\:(.*?)<a name\\=\"BIOLOGICAL DATA AND HABITAT REQUIREMENTS\"/ims", $html, $arr) || preg_match("/PLANT COMMUNITIES\\:(.*?)<a name\\=\"BiologicalDataAndHabitatRequirements\"/ims", $html, $arr) || preg_match("/PLANT COMMUNITIES\\:(.*?)<a name\\=\"BIOLOGICAL DATA AND HABITAT\"/ims", $html, $arr)) {
$plant_comm = $arr[1];
$descriptions["PLANT COMMUNITIES"] = $plant_comm;
}
/* BIOLOGICAL DATA AND HABITAT REQUIREMENTS */
//animals
// LIFE HISTORY subtopics
$html_utf8 = utf8_encode($html);
$html_utf8 = str_ireplace("Phenology</font>", "Phenology", $html_utf8);
if (preg_match("/Ontogeny<\\/b>(.*?)Phenology<\\/b>/ims", $html_utf8, $arr)) {
$ontogeny = $arr[1] . "xxx";
if (preg_match("/Mating:(.*?)Reproductive rates:/ims", $ontogeny, $arr)) {
$descriptions["Mating"] = $arr[1];
}
if (preg_match("/Reproductive rates:(.*?)Gestation and litter size:/ims", $ontogeny, $arr)) {
$descriptions["Reproductive rates"] = $arr[1];
}
if (preg_match("/Gestation and litter size:(.*?)Development:/ims", $ontogeny, $arr)) {
$descriptions["Gestation and litter size"] = $arr[1];
}
if (preg_match("/Development:(.*?)Survival rates and mortality:/ms", $ontogeny, $arr)) {
$descriptions["Development"] = $arr[1];
}
if (preg_match("/Survival rates and mortality:(.*?)xxx/ims", $ontogeny, $arr)) {
$descriptions["Survival rates and mortality"] = $arr[1];
}
}
if (preg_match("/Phenology<\\/b>(.*?)Home range\\:/ims", $html_utf8, $arr)) {
$descriptions["Phenology"] = $arr[1];
}
if (preg_match("/Home range\\:(.*?)<a name\\=\"PREFERRED HABITAT\"/ims", $html_utf8, $arr)) {
$descriptions["Home range"] = $arr[1];
}
if (preg_match("/Physical description\\:(.*?)<a name\\=\"Physiology\">/ims", $html, $arr)) {
$descriptions["Physical description"] = $arr[1];
} elseif (preg_match("/Physical description\\:(.*?)<a name\\=\"CourtshipAndMating\">/ims", $html, $arr)) {
$descriptions["Physical description"] = $arr[1];
}
if (preg_match("/Physiology\\:(.*?)<a name\\=\"CourtshipAndMating\">/ims", $html, $arr)) {
$descriptions["Physiology"] = $arr[1];
}
if (preg_match("/Courtship and mating\\:(.*?)<a name\\=\"ReproductionAndDevelopment\">/ims", $html, $arr)) {
$descriptions["Courtship and mating"] = $arr[1];
}
if (preg_match("/Reproduction and development\\:(.*?)<a name\\=\"SocialBehavior\">/ims", $html, $arr)) {
$descriptions["Reproduction and development"] = $arr[1];
} elseif (preg_match("/Reproduction and development\\:(.*?)<a name\\=\"Growth\">/ims", $html, $arr)) {
$descriptions["Reproduction and development"] = $arr[1];
}
if (preg_match("/Social behavior\\:(.*?)<a name\\=\"HomeRangeAndMovements\">/ims", $html, $arr)) {
$descriptions["Social behavior"] = $arr[1];
} elseif (preg_match("/Social behavior\\:(.*?)<a name\\=\"MovementsAndHomeRange\">/ims", $html, $arr)) {
$descriptions["Social behavior"] = $arr[1];
}
if (preg_match("/Home range and movements\\:(.*?)<a name\\=\"PopulationDensity\">/ims", $html, $arr)) {
$descriptions["Home range and movements"] = $arr[1];
} elseif (preg_match("/Movements and home range\\:(.*?)<a name\\=\"PopulationDensity\">/ims", $html, $arr)) {
$descriptions["Home range and movements"] = $arr[1];
} elseif (preg_match("/Home range and movement\\:(.*?)<a name\\=\"PREFERRED HABITAT\">/ims", $html, $arr)) {
$descriptions["Home range and movements"] = $arr[1];
}
if (preg_match("/Population density\\:(.*?)<a name\\=\"Survival\">/ims", $html, $arr)) {
$descriptions["Population density"] = $arr[1];
} elseif (preg_match("/Population density\\:(.*?)<a name\\=\"LifeSpanAndSurvival\">/ims", $html, $arr)) {
$descriptions["Population density"] = $arr[1];
} elseif (preg_match("/Population density\\:(.*?)<a name\\=\"Home Range and Movements\">/ims", $html, $arr)) {
$descriptions["Population density"] = $arr[1];
}
if (preg_match("/Survival\\:(.*?)<a name\\=\"LifeSpan\">/ims", $html, $arr)) {
$descriptions["Survival"] = $arr[1];
} elseif (preg_match("/Survival\\:(.*?)<a name\\=\"Population Density\">/ims", $html, $arr)) {
$descriptions["Survival"] = $arr[1];
}
if (preg_match("/Life span\\:(.*?)<a name\\=\"DiseasesAndSourcesOfMortality\">/ims", $html, $arr)) {
$descriptions["Life span"] = $arr[1];
}
if (preg_match("/Life span and survival\\:(.*?)<a name\\=\"Diet\">/ims", $html, $arr)) {
$descriptions["Life span and survival"] = $arr[1];
}
/* other life history subtopics e.g http://www.fs.fed.us/database/feis/animals/reptile/gopo/all.html - Daily activity, Annual activity, Social interactions, Growth, Longevity */
if (preg_match("/Daily activity\\:(.*?)<a name\\=\"Annual Activity\">/ims", $html, $arr)) {
$descriptions["Daily activity"] = $arr[1];
}
if (preg_match("/Annual activity\\:(.*?)<a name\\=\"Social Interactions\">/ims", $html, $arr)) {
$descriptions["Annual activity"] = $arr[1];
}
if (preg_match("/Social interactions\\:(.*?)<a name\\=\"Reproduction and Development\">/ims", $html, $arr)) {
$descriptions["Social interactions"] = $arr[1];
}
if (preg_match("/Growth\\:(.*?)<a name\\=\"Longevity\">/ims", $html, $arr)) {
$descriptions["Growth"] = $arr[1];
}
if (preg_match("/Longevity\\:(.*?)<a name\\=\"Survival\">/ims", $html, $arr)) {
$descriptions["Longevity"] = $arr[1];
}
/* other life history subtopics e.g http://www.fs.fed.us/database/feis/animals/reptile/goag/all.html - Longevity and survivorship, Maturation, Reproduction, Annual cycle, Activity and movement, Density and home range */
if (preg_match("/Longevity and survivorship<\\/a><\\/font>(.*?)<a name\\=\"Maturation\">/ims", $html, $arr)) {
$descriptions["Longevity and survivorship"] = $arr[1];
}
if (preg_match("/Maturation<\\/a><\\/font>(.*?)<a name\\=\"Reproduction\">/ims", $html, $arr)) {
$descriptions["Maturation"] = $arr[1];
}
if (preg_match("/Reproduction<\\/a><\\/font>(.*?)<a name\\=\"Annual Cycle\">/ims", $html, $arr)) {
$descriptions["Reproduction"] = $arr[1];
}
if (preg_match("/Annual cycle<\\/a><\\/font>(.*?)<a name\\=\"Activity and movement\">/ims", $html, $arr)) {
$descriptions["Annual cycle"] = $arr[1];
} elseif (preg_match("/Annual cycle<\\/a>\\:(.*?)<a name\\=\"Activity and movement\">/ims", $html, $arr)) {
$descriptions["Annual cycle"] = $arr[1];
}
if (preg_match("/Activity and movement<\\/a><\\/font>(.*?)<a name\\=\"Density and home range\">/ims", $html, $arr)) {
$descriptions["Activity and movement"] = $arr[1];
}
if (preg_match("/Density and home range<\\/a><\\/font>(.*?)<a name\\=\"PREFERRED HABITAT\">/ims", $html, $arr)) {
$descriptions["Density and home range"] = $arr[1];
}
//animals
if (!(@$descriptions["Mating"] || @$descriptions["Reproductive rates"] || @$descriptions["Gestation and litter size"] || @$descriptions["Development"] || @$descriptions["Survival rates and mortality"] || @$descriptions["Ontogeny"] || @$descriptions["Phenology"] || @$descriptions["Home range"] || @$descriptions["Physical description"] || @$descriptions["Physiology"] || @$descriptions["Courtship and mating"] || @$descriptions["Reproduction and development"] || @$descriptions["Social behavior"] || @$descriptions["Home range and movements"] || @$descriptions["Population density"] || @$descriptions["Survival"] || @$descriptions["Life span"] || @$descriptions["Life span and survival"] || @$descriptions["Daily activity"] || @$descriptions["Annual activity"] || @$descriptions["Social interactions"] || @$descriptions["Growth"] || @$descriptions["Longevity"] || @$descriptions["Longevity and survivorship"] || @$descriptions["Maturation"] || @$descriptions["Reproduction"] || @$descriptions["Annual cycle"] || @$descriptions["Activity and movement"] || @$descriptions["Density and home range"])) {
if (preg_match("/LIFE HISTORY\\:(.*?)<a name\\=\"DiseasesAndSourcesOfMortality\"/ims", $html, $arr)) {
$life_history = $arr[1];
} elseif (preg_match("/LIFE HISTORY\\:(.*?)<a name\\=\"Diseases And Sources Of Mortality\"/ims", $html, $arr)) {
$life_history = $arr[1];
} elseif (preg_match("/LIFE HISTORY\\:(.*?)<a name\\=\"Diet\"/ims", $html, $arr)) {
$life_history = $arr[1];
} elseif (preg_match("/LIFE HISTORY\\:(.*?)<a name\\=\"PREFERRED HABITAT\"/ims", $html, $arr)) {
$life_history = $arr[1];
}
//http://www.fs.fed.us/database/feis/animals/mammal/neal/all.html
if (isset($life_history)) {
$descriptions["LIFE HISTORY"] = $life_history;
} else {
//animals
if (preg_match("/BIOLOGICAL DATA\\:(.*?)<a name\\=\"PreferredHabitat\"/ims", $html, $arr)) {
$biological_data = $arr[1];
$descriptions["BIOLOGICAL DATA"] = $biological_data;
}
}
}
if (preg_match("/DIET\\:(.*?)<a name\\=\"PreferredHabitat\"/ims", $html, $arr)) {
$descriptions["DIET"] = $arr[1];
}
// http://www.fs.fed.us/database/feis/animals/bird/apco/all.html
//animals
if (preg_match("/DISEASES AND SOURCES OF MORTALITY\\:(.*?)<a name\\=\"PreferredHabitat\"/ims", $html, $arr) || preg_match("/DISEASES AND SOURCES OF MORTALITY\\:(.*?)<a name\\=\"Preferred Habitat\"/ims", $html, $arr)) {
$diseases = $arr[1];
$descriptions["DISEASES AND SOURCES OF MORTALITY"] = $diseases;
}
//animals
$html = str_ireplace("<b>TIMING OF MAJOR LIFE HISTORY EVENTS :", "<b>TIMING OF MAJOR LIFE HISTORY EVENTS:", $html);
if (preg_match("/TIMING OF MAJOR LIFE HISTORY EVENTS\\:(.*?)<a name\\=\"PREFERRED HABITAT\"/ims", $html, $arr) || preg_match("/TIMING OF MAJOR LIFE HISTORY EVENTS\\:(.*?)<b>PREFERRED HABITAT/ims", $html, $arr)) {
$major_life_history = $arr[1];
$descriptions["TIMING OF MAJOR LIFE HISTORY EVENTS"] = $major_life_history;
}
//animals
$html = str_ireplace("<b>PREFERRED HABITAT :", "<b>PREFERRED HABITAT:", $html);
if (preg_match("/PREFERRED HABITAT\\:(.*?)<a name\\=\"COVER REQUIREMENTS\"/ims", $html, $arr) || preg_match("/PREFERRED HABITAT\\:(.*?)<a name\\=\"COVERREQUIREMENTS\"/ims", $html, $arr) || preg_match("/PREFERRED HABITAT\\:(.*?)<a name\\=\"FoodHabits\"/ims", $html, $arr) || preg_match("/PREFERRED HABITAT\\:(.*?)<a name\\=\"Food Habits\"/ims", $html, $arr) || preg_match("/PREFERRED HABITAT\\:(.*?)<b>COVER REQUIREMENTS/ims", $html, $arr) || preg_match("/PREFERRED HABITAT\\:(.*?)<a name\\=\"ManagementConsiderations\"/ims", $html, $arr)) {
$pref_habitat = $arr[1];
}
if (isset($pref_habitat)) {
$descriptions["PREFERRED HABITAT"] = $pref_habitat;
}
if (!is_numeric(stripos(@$descriptions["PREFERRED HABITAT"], "Cover requirements:"))) {
//animals
$html = str_ireplace("<b>COVER REQUIREMENTS :", "<b>COVER REQUIREMENTS:", $html);
if (preg_match("/COVER REQUIREMENTS\\:(.*?)<a name\\=\"FOOD HABITS\"/ims", $html, $arr) || preg_match("/COVER REQUIREMENTS\\:(.*?)<b>FOOD HABITS/ims", $html, $arr) || preg_match("/<a name\\=\"CoverRequirements\">(.*?)<a name\\=\"FOODHABITS\"/ims", $html, $arr)) {
$cover_req = $arr[1];
$descriptions["COVER REQUIREMENTS"] = $cover_req;
}
}
//animals
$html = str_ireplace("<b>FOOD HABITS :", "<b>FOOD HABITS:", $html);
// 1 of 2
if (preg_match("/FOOD HABITS\\:(.*?)<a name\\=\"PREDATORS\"/ims", $html, $arr) || preg_match("/FOOD HABITS\\:(.*?)<a name\\=\"FederalLegalStatus\"/ims", $html, $arr) || preg_match("/FOOD HABITS\\:(.*?)<a name\\=\"Federal Legal Status\"/ims", $html, $arr) || preg_match("/FOOD HABITS\\:(.*?)<a name\\=\"Management Considerations\"/ims", $html, $arr) || preg_match("/FOOD HABITS\\:(.*?)<b>PREDATORS/ims", $html, $arr)) {
$food_habits = $arr[1];
$descriptions["FOOD HABITS"] = $food_habits;
}
//animals
if (preg_match("/FEDERAL LEGAL STATUS\\:(.*?)<a name\\=\"OtherStatus\"/ims", $html, $arr)) {
$federal_legal_stat = $arr[1];
} elseif (preg_match("/FEDERAL LEGAL STATUS\\:(.*?)<a name\\=\"Other Status\"/ims", $html, $arr)) {
$federal_legal_stat = $arr[1];
} elseif (preg_match("/FEDERAL LEGAL STATUS\\:(.*?)<b>OTHER STATUS:/ims", $html, $arr)) {
$federal_legal_stat = $arr[1];
}
if (isset($federal_legal_stat)) {
$descriptions["FEDERAL LEGAL STATUS"] = $federal_legal_stat;
}
//animals
if (preg_match("/OTHER STATUS\\:(.*?)<a name\\=\"ManagementConsiderations\"/ims", $html, $arr)) {
$descriptions["OTHER STATUS"] = $arr[1];
}
if (!is_numeric(stripos(@$descriptions["DISEASES AND SOURCES OF MORTALITY"], "Predators:")) && !is_numeric(stripos(@$descriptions["Life span and survival"], "Predators:"))) {
//animals
$html = str_ireplace("<b>PREDATORS :", "<b>PREDATORS:", $html);
if (preg_match("/PREDATORS\\:(.*?)<a name\\=\"MANAGEMENT CONSIDERATIONS\"/ims", $html, $arr) || preg_match("/PREDATORS\\:(.*?)<b>MANAGEMENT CONSIDERATIONS/ims", $html, $arr) || preg_match("/PREDATORS\\:(.*?)<a name\\=\"federallegalstatus\"/ims", $html, $arr)) {
$predators = $arr[1];
}
if (isset($predators)) {
$descriptions["PREDATORS"] = $predators;
}
}
//animals
$html = str_ireplace("MANAGEMENT CONSIDERATIONS :", "MANAGEMENT CONSIDERATIONS:", $html);
if (preg_match("/MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"FIRE EFFECTS AND USE\"/ims", $html, $arr) || preg_match("/MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"FIRE EFFECTS\"/ims", $html, $arr) || preg_match("/MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"FireEffectsAndManagement\"/ims", $html, $arr) || preg_match("/MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"Fire Effects And Management\"/ims", $html, $arr) || preg_match("/<b>MANAGEMENT CONSIDERATIONS\\:(.*?)<b>REFERENCES/ims", $html, $arr)) {
$descriptions["MANAGEMENT CONSIDERATIONS"] = $arr[1];
}
//animals
$html = str_ireplace("<b>DIRECT FIRE EFFECTS ON ANIMALS :", "<b>DIRECT FIRE EFFECTS ON ANIMALS:", $html);
if (preg_match("/DIRECT FIRE EFFECTS ON ANIMAL\\:(.*?)<a name\\=\"HABITAT RELATED FIRE EFFECTS\"/ims", $html, $arr) || preg_match("/DIRECT FIRE EFFECTS ON ANIMALS\\:(.*?)<b>HABITAT RELATED FIRE EFFECTS/ims", $html, $arr) || preg_match("/DIRECT FIRE EFFECTS\\:(.*?)<a name\\=\"IndirectFireEffects\"/ims", $html, $arr) || preg_match("/DIRECT FIRE EFFECTS\\:(.*?)<a name\\=\"Indirect Fire Effects\"/ims", $html, $arr) || preg_match("/DIRECT FIRE EFFECTS ON ANIMALS\\:(.*?)<a name\\=\"HABITAT-RELATED FIRE EFFECTS\"/ims", $html, $arr)) {
$descriptions["DIRECT FIRE EFFECTS ON ANIMAL"] = $arr[1];
}
if (preg_match("/INDIRECT FIRE EFFECTS\\:(.*?)<a name\\=\"FireRegimes\"/ims", $html, $arr) || preg_match("/INDIRECT FIRE EFFECTS\\:(.*?)<a name\\=\"Fire Regimes\"/ims", $html, $arr)) {
$descriptions["INDIRECT FIRE EFFECTS"] = $arr[1];
}
if (preg_match("/FUELS AND FIRE REGIMES\\:(.*?)<a name\\=\"FIRE MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$fuels_and_fire_regimes = $arr[1];
} elseif (preg_match("/FUELS AND FIRE REGIMES\\:(.*?)<a name\\=\"FireManagementConsiderations\"/ims", $html, $arr)) {
$fuels_and_fire_regimes = $arr[1];
}
if (isset($fuels_and_fire_regimes)) {
$descriptions["FUELS AND FIRE REGIMES"] = $fuels_and_fire_regimes;
}
//animals
$html = str_ireplace("<b>HABITAT RELATED FIRE EFFECTS :", "<b>HABITAT RELATED FIRE EFFECTS:", $html);
if (preg_match("/HABITAT RELATED FIRE EFFECTS\\:(.*?)<a name\\=\"FIRE USE\"/ims", $html, $arr) || preg_match("/HABITAT RELATED FIRE EFFECTS\\:(.*?)<b>FIRE USE/ims", $html, $arr) || preg_match("/Habitat-related Fire Effects\\:(.*?)<a name\\=\"FIRE USE\"/ims", $html, $arr) || preg_match("/Habitat-related Fire Effects\\:(.*?)<b>FIRE USE/ims", $html, $arr)) {
$habitat_related = $arr[1];
} elseif (preg_match("/HABITAT-RELATED FIRE EFFECTS\\:(.*?)<a name\\=\"FIRE MANAGEMENT CONSIDERATIONS\"/ims", $html, $arr) || preg_match("/HABITAT RELATED FIRE EFFECTS\\:(.*?)<a name\\=\"FIRE MANAGEMENT CONSIDERATIONS\"/ims", $html, $arr)) {
$habitat_related = $arr[1];
}
if (isset($habitat_related)) {
$descriptions["HABITAT RELATED FIRE EFFECTS"] = $habitat_related;
}
//animals
$html = str_ireplace("<b>FIRE USE :", "<b>FIRE USE:", $html);
if (preg_match("/FIRE USE\\:(.*?)<b>REFERENCES/ims", $html, $arr)) {
$fire_use1 = trim($arr[1]);
}
if (preg_match("/FIRE USE\\:(.*?)<a name\\=\"REFERENCES\"/ims", $html, $arr)) {
$fire_use2 = trim($arr[1]);
}
if (isset($fire_use1) && isset($fire_use2)) {
$fire_use = $fire_use1;
if (strlen($fire_use2) < strlen($fire_use)) {
$fire_use = $fire_use2;
}
$descriptions["FIRE USE"] = $fire_use;
} elseif (isset($fire_use1)) {
$descriptions["FIRE USE"] = $fire_use1;
} elseif (isset($fire_use2)) {
$descriptions["FIRE USE"] = $fire_use2;
}
}
//if($rec["kingdom"] == "Animalia")
/* MANAGEMENT CONSIDERATIONS */
if (preg_match("/WOOD PRODUCTS VALUE \\:(.*?)<b>IMPORTANCE TO LIVESTOCK/ims", $html, $arr) || preg_match("/WOOD PRODUCTS VALUE \\:(.*?)<b>IMPORTANCE TO WILDLIFE/ims", $html, $arr)) {
$descriptions["WOOD PRODUCTS VALUE"] = $arr[1];
}
if (preg_match("/IMPORTANCE TO LIVESTOCK AND WILDLIFE \\:(.*?)<b>PALATABILITY/ims", $html, $arr) || preg_match("/IMPORTANCE TO WILDLIFE AND LIVESTOCK\\:(.*?)<a name\\=\"Palatability/ims", $html, $arr) || preg_match("/IMPORTANCE TO WILDLIFE AND LIVESTOCK\\:(.*?)<a name\\=\"VALUE FOR REHABILITATION OF DISTURBED SITES/ims", $html, $arr) || preg_match("/IMPORTANCE TO LIVESTOCK AND WILDLIFE\\:(.*?)<a name\\=\"VALUE FOR REHABILITATION OF DISTURBED SITES/ims", $html, $arr) || preg_match("/IMPORTANCE TO LIVESTOCK AND WILDLIFE\\:(.*?)<a name\\=\"OTHER USES/ims", $html, $arr)) {
$impt_livestock = $arr[1];
$descriptions["IMPORTANCE TO LIVESTOCK AND WILDLIFE"] = $impt_livestock;
}
if (preg_match("/PALATABILITY \\:(.*?)<b>NUTRITIONAL VALUE/ims", $html, $arr)) {
$palatability = $arr[1];
$descriptions["PALATABILITY"] = $palatability;
}
if (preg_match("/PALATABILITY\\/NUTRITIONAL VALUE \\:(.*?)<b>COVER VALUE/ims", $html, $arr)) {
$palatability_and_nutritional = $arr[1];
} elseif (preg_match("/PALATABILITY AND NUTRITIONAL VALUE \\:(.*?)<b>COVER VALUE/ims", $html, $arr)) {
$palatability_and_nutritional = $arr[1];
} elseif (preg_match("/PALATABILITY AND NUTRITIONAL VALUE\\:(.*?)<a name\\=\"CoverValue\"/ims", $html, $arr)) {
$palatability_and_nutritional = $arr[1];
}
if (isset($palatability_and_nutritional)) {
$descriptions["PALATABILITY AND NUTRITIONAL VALUE"] = $palatability_and_nutritional;
}
if (preg_match("/NUTRITIONAL VALUE \\:(.*?)<b>COVER VALUE/ims", $html, $arr)) {
$nutritional_value = $arr[1];
$descriptions["NUTRITIONAL VALUE"] = $nutritional_value;
}
if (preg_match("/COVER VALUE \\:(.*?)<b>VALUE FOR REHABILITATION/ims", $html, $arr)) {
$cover_value = $arr[1];
} elseif (preg_match("/Cover Value for Wildlife \\:(.*?)<b>VALUE FOR REHABILITATION/ims", $html, $arr)) {
$cover_value = $arr[1];
}
if (isset($cover_value)) {
$descriptions["COVER VALUE"] = $cover_value;
}
if (preg_match("/VALUE FOR REHABILITATION OF DISTURBED SITES \\:(.*?)<b>OTHER USES/ims", $html, $arr)) {
$rehabilitation_value = $arr[1];
} elseif (preg_match("/VALUE FOR REHABILITATION OF DISTURBED SITES\\:(.*?)<a name\\=\"OTHER USES/ims", $html, $arr)) {
$rehabilitation_value = $arr[1];
}
if (isset($rehabilitation_value)) {
$descriptions["VALUE FOR REHABILITATION OF DISTURBED SITES"] = $rehabilitation_value;
}
if (preg_match("/OTHER USES AND VALUES \\:(.*?)<b>OTHER MANAGEMENT/ims", $html, $arr)) {
$other_uses = $arr[1];
} elseif (preg_match("/OTHER USES\\:(.*?)<a name\\=\"OTHER MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$other_uses = $arr[1];
} elseif (preg_match("/OTHER USES\\:(.*?)<a name\\=\"Impacts\"/ims", $html, $arr)) {
$other_uses = $arr[1];
} elseif (preg_match("/OTHER USES\\:(.*?)<a name\\=\"IMPACTS AND CONTROL\"/ims", $html, $arr)) {
$other_uses = $arr[1];
}
if (isset($other_uses)) {
$descriptions["OTHER USES AND VALUES"] = $other_uses;
}
if (preg_match("/IMPACTS\\:(.*?)<a name\\=\"Control\"/ims", $html, $arr)) {
$impacts = $arr[1];
}
if (isset($impacts)) {
$descriptions["IMPACTS"] = $impacts;
}
if (preg_match("/CONTROL\\:(.*?)<a name\\=\"AppendixFireRegimeTable\"/ims", $html, $arr)) {
$control = $arr[1];
}
if (isset($control)) {
$descriptions["CONTROL"] = $control;
}
if (preg_match("/IMPACTS AND CONTROL\\:(.*?)<a name\\=\"REFERENCES\"/ims", $html, $arr)) {
$impacts_and_control = $arr[1];
}
if (isset($impacts_and_control)) {
$descriptions["IMPACTS AND CONTROL"] = $impacts_and_control;
}
if (preg_match("/OTHER MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"BOTANICAL AND ECOLOGICAL/ims", $html, $arr)) {
$other_management = $arr[1];
} elseif (preg_match("/OTHER MANAGEMENT CONSIDERATIONS \\:(.*?)<a name\\=\"BOTANICAL AND ECOLOGICAL/ims", $html, $arr)) {
$other_management = $arr[1];
} elseif (preg_match("/OTHER MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"APPENDIX: FIRE REGIME TABLE/ims", $html, $arr)) {
$other_management = $arr[1];
} elseif (preg_match("/OTHER MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"REFERENCES\"/ims", $html, $arr)) {
$other_management = $arr[1];
}
if (isset($other_management)) {
$descriptions["OTHER MANAGEMENT CONSIDERATIONS"] = $other_management;
}
/* BOTANICAL AND ECOLOGICAL CHARACTERISTICS */
if (preg_match("/GENERAL BOTANICAL CHARACTERISTICS \\:(.*?)<b>RAUNKIAER/ims", $html, $arr)) {
$gen_botanical = $arr[1];
} elseif (preg_match("/GENERAL BOTANICAL CHARACTERISTICS\\:(.*?)<a name\\=\"RAUNKIAER LIFE FORM/ims", $html, $arr)) {
$gen_botanical = $arr[1];
} elseif (preg_match("/GENERAL BOTANICAL CHARACTERISTICS\\:(.*?)<a name\\=\"SeasonalDevelopment\"/ims", $html, $arr)) {
$gen_botanical = $arr[1];
}
if (isset($gen_botanical)) {
$descriptions["GENERAL BOTANICAL CHARACTERISTICS"] = $gen_botanical;
}
if (!is_numeric(stripos(@$descriptions["GENERAL BOTANICAL CHARACTERISTICS"], "Raunkiaer"))) {
if (preg_match("/RAUNKIAER LIFE FORM \\:(.*?)<b>REGENERATION/ims", $html, $arr)) {
$raunkiaer_lifeform = $arr[1];
} elseif (preg_match("/<a name\\=\"RAUNKIAER LIFE FORM\">(.*?)<a name\\=\"REGENERATION PROCESSES\"/ims", $html, $arr)) {
$raunkiaer_lifeform = $arr[1];
}
if (isset($raunkiaer_lifeform)) {
$descriptions["RAUNKIAER LIFE FORM"] = $raunkiaer_lifeform;
}
}
if (preg_match("/REGENERATION PROCESSES \\:(.*?)<b>SITE CHARACTERISTICS/ims", $html, $arr)) {
$regene_proc = $arr[1];
} elseif (preg_match("/REGENERATION PROCESSES\\:(.*?)<a name\\=\"SITE CHARACTERISTICS/ims", $html, $arr)) {
$regene_proc = $arr[1];
} elseif (preg_match("/REGENERATION PROCESSES\\:(.*?)<a name\\=\"SiteCharacteristics\"/ims", $html, $arr)) {
$regene_proc = $arr[1];
}
if (isset($regene_proc)) {
$descriptions["REGENERATION PROCESSES"] = $regene_proc;
}
if (preg_match("/SITE CHARACTERISTICS \\:(.*?)<b>SUCCESSIONAL STATUS/ims", $html, $arr)) {
$site_char = $arr[1];
} elseif (preg_match("/SITE CHARACTERISTICS\\:(.*?)<a name\\=\"SUCCESSIONAL STATUS/ims", $html, $arr)) {
$site_char = $arr[1];
} elseif (preg_match("/SITE CHARACTERISTICS\\:(.*?)<a name\\=\"SuccessionalStatus\"/ims", $html, $arr)) {
$site_char = $arr[1];
}
if (isset($site_char)) {
$descriptions["SITE CHARACTERISTICS"] = $site_char;
}
if (preg_match("/SUCCESSIONAL STATUS \\:(.*?)<b>SEASONAL DEVELOPMENT/ims", $html, $arr)) {
$successional_stat = $arr[1];
} elseif (preg_match("/SUCCESSIONAL STATUS\\:(.*?)<a name\\=\"SEASONAL DEVELOPMENT/ims", $html, $arr)) {
$successional_stat = $arr[1];
} elseif (preg_match("/SUCCESSIONAL STATUS\\:(.*?)<a name\\=\"SeasonalDevelopment\"/ims", $html, $arr)) {
$successional_stat = $arr[1];
} elseif (preg_match("/SUCCESSIONAL STATUS\\:(.*?)<a name\\=\"FireEffectsAndManagement\"/ims", $html, $arr)) {
$successional_stat = $arr[1];
}
if (isset($successional_stat)) {
$descriptions["SUCCESSIONAL STATUS"] = $successional_stat;
}
$html = str_ireplace("SEASONAL DEVELOPMENT :", "SEASONAL DEVELOPMENT:", $html);
if (preg_match("/SEASONAL DEVELOPMENT\\:(.*?)<a name\\=\"FIRE ECOLOGY/ims", $html, $arr)) {
$seasonal_dev = $arr[1];
} elseif (preg_match("/SEASONAL DEVELOPMENT\\:(.*?)<a name\\=\\'FIRE EFFECTS AND MANAGEMENT/ims", $html, $arr)) {
$seasonal_dev = $arr[1];
} elseif (preg_match("/SEASONAL DEVELOPMENT\\:(.*?)<a name\\=\"RegenerationProcesses\"/ims", $html, $arr)) {
$seasonal_dev = $arr[1];
}
if (isset($seasonal_dev)) {
$descriptions["SEASONAL DEVELOPMENT"] = $seasonal_dev;
}
/* FIRE EFFECTS AND MANAGEMENT */
if (preg_match("/FIRE EFFECTS\\:(.*?)<a name\\=\"FUELS AND FIRE REGIMES/ims", $html, $arr)) {
$fire_effects = $arr[1];
} elseif (preg_match("/FIRE EFFECTS\\:(.*?)<a name\\=\"FuelsAndFireRegimes\"/ims", $html, $arr)) {
$fire_effects = $arr[1];
}
if (isset($fire_effects)) {
$descriptions["FIRE EFFECTS"] = $fire_effects;
}
/* FIRE ECOLOGY */
if (preg_match("/FIRE ECOLOGY OR ADAPTATIONS \\:(.*?)<b>POSTFIRE REGENERATION/ims", $html, $arr)) {
$fire_ecology = $arr[1];
} elseif (preg_match("/FIRE ECOLOGY OR ADAPTATIONS\\:(.*?)<a name\\=\"POSTFIRE REGENERATION/ims", $html, $arr)) {
$fire_ecology = $arr[1];
} elseif (preg_match("/FIRE ECOLOGY OR ADAPTATIONS\\:(.*?)<a name\\=\"PostfireRegeneration/ims", $html, $arr)) {
$fire_ecology = $arr[1];
}
if (isset($fire_ecology)) {
$descriptions["FIRE ECOLOGY OR ADAPTATIONS"] = $fire_ecology;
}
$html = str_ireplace("POSTFIRE REGENERATION STRATEGY :", "POSTFIRE REGENERATION STRATEGY:", $html);
if (preg_match("/POSTFIRE REGENERATION STRATEGY\\:(.*?)<a name\\=\"FIRE EFFECTS/ims", $html, $arr)) {
$postfire_rege = $arr[1];
} elseif (preg_match("/<a name\\=\"POSTFIRE REGENERATION STRATEGY\">(.*?)<a name\\=\"FIRE EFFECTS/ims", $html, $arr)) {
$postfire_rege = $arr[1];
} elseif (preg_match("/<a name\\=\"POSTFIRE REGENERATION STRATEGY\">(.*?)<a name\\=\"FIREEFFECTS/ims", $html, $arr)) {
$postfire_rege = $arr[1];
}
if (isset($postfire_rege)) {
$descriptions["POSTFIRE REGENERATION STRATEGY"] = $postfire_rege;
}
if (!is_numeric(stripos(@$descriptions["FUELS AND FIRE REGIMES"], "Fire regimes:")) && !is_numeric(stripos(@$descriptions["FIRE ECOLOGY OR ADAPTATIONS"], "Fire regimes:"))) {
if (preg_match("/FIRE REGIMES\\:(.*?)<a name\\=\"FireManagementConsiderations\"/ims", $html, $arr) || preg_match("/FIRE REGIMES\\:(.*?)<a name\\=\"Fire Management Considerations\"/ims", $html, $arr)) {
$descriptions["FIRE REGIMES"] = $arr[1];
}
}
/* FIRE EFFECTS */
if (preg_match("/IMMEDIATE FIRE EFFECT ON LICHEN\\:(.*?)<a name\\=\"DISCUSSION AND QUALIFICATION OF FIRE EFFECT/ims", $html, $arr)) {
$imm_fire_effect_lichen = $arr[1];
}
if (isset($imm_fire_effect_lichen)) {
$descriptions["IMMEDIATE FIRE EFFECT ON LICHEN"] = $imm_fire_effect_lichen;
}
if (preg_match("/LICHEN RESPONSE TO FIRE\\:(.*?)<a name\\=\"DISCUSSION AND QUALIFICATION OF LICHEN RESPONSE/ims", $html, $arr)) {
$lichen_response_2fire = $arr[1];
}
if (isset($lichen_response_2fire)) {
$descriptions["LICHEN RESPONSE TO FIRE"] = $lichen_response_2fire;
}
if (preg_match("/DISCUSSION AND QUALIFICATION OF LICHEN RESPONSE\\:(.*?)<a name\\=\"FIRE MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$d_and_q_of_lichen_response = $arr[1];
}
if (isset($d_and_q_of_lichen_response)) {
$descriptions["DISCUSSION AND QUALIFICATION OF LICHEN RESPONSE"] = $d_and_q_of_lichen_response;
}
if (preg_match("/IMMEDIATE FIRE EFFECT ON PLANT \\:(.*?)<b>DISCUSSION AND QUALIFICATION OF FIRE EFFECT/ims", $html, $arr)) {
$immediate_fire_effect = $arr[1];
} elseif (preg_match("/IMMEDIATE FIRE EFFECT ON PLANT\\:(.*?)<a name\\=\"DISCUSSION AND QUALIFICATION OF FIRE EFFECT/ims", $html, $arr)) {
$immediate_fire_effect = $arr[1];
}
if (isset($immediate_fire_effect)) {
$descriptions["IMMEDIATE FIRE EFFECT ON PLANT"] = $immediate_fire_effect;
}
if (preg_match("/DISCUSSION AND QUALIFICATION OF FIRE EFFECT \\:(.*?)<b>PLANT RESPONSE TO FIRE/ims", $html, $arr)) {
$discussion_fire_effect = $arr[1];
} elseif (preg_match("/DISCUSSION AND QUALIFICATION OF FIRE EFFECT\\:(.*?)<a name\\=\"PLANT RESPONSE TO FIRE/ims", $html, $arr)) {
$discussion_fire_effect = $arr[1];
} elseif (preg_match("/DISCUSSION AND QUALIFICATION OF FIRE EFFECT\\:(.*?)<a name\\=\"LICHEN RESPONSE TO FIRE/ims", $html, $arr)) {
$discussion_fire_effect = $arr[1];
}
if (isset($discussion_fire_effect)) {
$descriptions["DISCUSSION AND QUALIFICATION OF FIRE EFFECT"] = $discussion_fire_effect;
}
if (preg_match("/PLANT RESPONSE TO FIRE \\:(.*?)<b>DISCUSSION AND QUALIFICATION OF PLANT RESPONSE/ims", $html, $arr)) {
$plant_response_2fire = $arr[1];
} elseif (preg_match("/PLANT RESPONSE TO FIRE\\:(.*?)<a name\\=\"DISCUSSION AND QUALIFICATION OF PLANT RESPONSE/ims", $html, $arr)) {
$plant_response_2fire = $arr[1];
}
if (isset($plant_response_2fire)) {
$descriptions["PLANT RESPONSE TO FIRE"] = $plant_response_2fire;
}
if (preg_match("/DISCUSSION AND QUALIFICATION OF PLANT RESPONSE \\:(.*?)<b>FIRE MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$discussion_plant_response = $arr[1];
} elseif (preg_match("/DISCUSSION AND QUALIFICATION OF PLANT RESPONSE\\:(.*?)<a name\\=\"FIRE MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$discussion_plant_response = $arr[1];
}
if (isset($discussion_plant_response)) {
if (in_array($rec['url'], array("http://www.fs.fed.us/database/feis/plants/vine/smirot/all.html", "http://www.fs.fed.us/database/feis/plants/tree/tsucan/all.html", "http://www.fs.fed.us/database/feis/plants/tree/quevel/all.html", "http://www.fs.fed.us/database/feis/plants/tree/querub/all.html", "http://www.fs.fed.us/database/feis/plants/tree/quemar/all.html", "http://www.fs.fed.us/database/feis/plants/tree/quealb/all.html", "http://www.fs.fed.us/database/feis/plants/tree/pinvir/all.html", "http://www.fs.fed.us/database/feis/plants/tree/pinstr/all.html")) || is_numeric(stripos($html, "<!DOCTYPE html PUBLIC"))) {
$discussion_plant_response = str_ireplace(array("<br>", "\n"), " ", $discussion_plant_response);
}
$descriptions["DISCUSSION AND QUALIFICATION OF PLANT RESPONSE"] = $discussion_plant_response;
}
if (preg_match("/FIRE MANAGEMENT CONSIDERATIONS \\:(.*?)<a name\\=\"FIRE CASE STUDIES/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"AppendixFireRegimeTable/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"Appendix: Fire Regime Table/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE MANAGEMENT CONSIDERATIONS \\:(.*?)<a name\\=\"REFERENCES/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"REFERENCES/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE MANAGEMENT CONSIDERATIONS\\:(.*?)<a name\\=\"MANAGEMENT CONSIDERATIONS/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE CONSIDERATIONS\\:(.*?)<a name\\=\"AppendixFireRegimeTable/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
} elseif (preg_match("/FIRE CONSIDERATIONS\\:(.*?)<a name\\=\"Appendix: Fire Regime Table/ims", $html, $arr)) {
$fire_mgnt_considerations = $arr[1];
}
if (isset($fire_mgnt_considerations)) {
$descriptions["FIRE MANAGEMENT CONSIDERATIONS"] = $fire_mgnt_considerations;
}
$link_text = "Follow this link to the U.S. Forest Service Fire Effects Information Service to see a table with fire regime information that may be relevant to habitats in which this species occurs";
$link = false;
if (preg_match("/<a name\\=\"APPENDIX: FIRE REGIME TABLE\">(.*?)/ims", $html, $arr)) {
$link = $rec['url'] . "#APPENDIX: FIRE REGIME TABLE";
} elseif (preg_match("/<a name\\=\"AppendixFireRegimeTable\">(.*?)/ims", $html, $arr)) {
$link = $rec['url'] . "#AppendixFireRegimeTable";
}
if ($link) {
$descriptions["APPENDIX: FIRE REGIME TABLE"] = "<a href='" . $link . "'>{$link_text}</a>";
}
/* FIRE CASE STUDIES */
$html = str_ireplace("FIRE CASE STUDY CITATION :", "FIRE CASE STUDY CITATION:", $html);
$html = str_ireplace("SEASON/SEVERITY CLASSIFICATION :", "SEASON/SEVERITY CLASSIFICATION:", $html);
$html = str_ireplace("STUDY LOCATION :", "STUDY LOCATION:", $html);
$html = str_ireplace("PREFIRE HABITAT :", "PREFIRE HABITAT:", $html);
$html = str_ireplace("SITE DESCRIPTION :", "SITE DESCRIPTION:", $html);
$html = str_ireplace("FIRE DESCRIPTION :", "FIRE DESCRIPTION:", $html);
$html = str_ireplace("FIRE EFFECTS ON ANIMAL SPECIES AND HABITAT :", "FIRE EFFECTS ON ANIMAL SPECIES AND HABITAT:", $html);
$html = str_ireplace("FIRE MANAGEMENT IMPLICATIONS :", "FIRE MANAGEMENT IMPLICATIONS:", $html);
if (preg_match("/<b>FIRE CASE STUDY CITATION\\:(.*?)<b>FIRE CASE STUDY REFERENCE\\:/ims", $html, $arr)) {
$descriptions["FIRE CASE STUDY CITATION"] = self::clean_str(strip_tags($arr[1]), true);
}
if (preg_match("/<b>FIRE CASE STUDY REFERENCE\\:(.*?)<b>SEASON\\/SEVERITY CLASSIFICATION\\:/ims", $html, $arr)) {
$descriptions["FIRE CASE STUDY REFERENCE"] = self::clean_str(strip_tags($arr[1]), true);
}
if (preg_match("/<b>SEASON\\/SEVERITY CLASSIFICATION\\:(.*?)<b>STUDY LOCATION\\:/ims", $html, $arr)) {
$descriptions["SEASON/SEVERITY CLASSIFICATION"] = $arr[1];
}
if (preg_match("/<b>STUDY LOCATION\\:(.*?)<b>PREFIRE HABITAT\\:/ims", $html, $arr)) {
$descriptions["STUDY LOCATION"] = $arr[1];
}
if (preg_match("/<b>PREFIRE HABITAT\\:(.*?)<b>SITE DESCRIPTION\\:/ims", $html, $arr)) {
$descriptions["PREFIRE HABITAT"] = $arr[1];
}
if (preg_match("/<b>SITE DESCRIPTION\\:(.*?)<b>FIRE DESCRIPTION\\:/ims", $html, $arr)) {
$descriptions["SITE DESCRIPTION"] = $arr[1];
}
if (preg_match("/<b>FIRE DESCRIPTION\\:(.*?)<b>FIRE EFFECTS ON ANIMAL SPECIES AND HABITAT\\:/ims", $html, $arr)) {
$descriptions["FIRE DESCRIPTION"] = $arr[1];
}
if (preg_match("/<b>FIRE EFFECTS ON ANIMAL SPECIES AND HABITAT\\:(.*?)<b>FIRE MANAGEMENT IMPLICATIONS\\:/ims", $html, $arr)) {
$descriptions["FIRE EFFECTS ON ANIMAL SPECIES AND HABITAT"] = $arr[1];
}
if (preg_match("/<b>FIRE MANAGEMENT IMPLICATIONS\\:(.*?)<a name\\=\"REFERENCES\"/ims", $html, $arr)) {
$descriptions["FIRE MANAGEMENT IMPLICATIONS"] = $arr[1];
}
$rec['texts'] = $descriptions;
return $rec;
}
public function check_if_with_content($phylum, $taxid, $dc_source, $barcode_image_url = false, $with_stats, $public_barcodes)
{
$src = self::BOLDS_DOMAIN_NEW . "/connect/REST/getBarcodeRepForSpecies.php?taxid=" . $taxid . "&iwidth=400";
if ($barcode_image_url || self::barcode_image_available($src)) {
$description = "The following is a representative barcode sequence, the centroid of all available sequences for this species.<br><a target='barcode' href='{$src}'><img src='{$src}' height=''></a>";
} else {
$description = "Barcode image not yet available.";
}
$description .= "<br><br>";
if (!in_array($phylum, $this->phylum_without_sequence)) {
//start get text dna sequece
/* replaced
$url = self::BOLDS_DOMAIN . "/pcontr.php?action=doPublicSequenceDownload&taxids=$taxid";
$arr = self::get_text_dna_sequence($url);
*/
$arr = $this->get_text_dna_sequence_v2($taxid);
$count_sequence = $arr["count_sequence"];
$text_dna_sequence = $arr["best_sequence"];
// $url_fasta_file = $arr["url_fasta_file"]; this will point to the fasta.fas file from BOLDS temp folder
echo "\n[{$public_barcodes}]=[{$count_sequence}]\n";
$str = "";
if ($count_sequence > 0) {
if ($count_sequence == 1) {
$str = "There is 1 barcode sequence available from BOLD and GenBank. \n Below is the sequence of the barcode region Cytochrome oxidase subunit 1 (COI or COX1) from a member of the species.\n See the <a target='BOLDSys' href='{$dc_source}'>BOLD taxonomy browser</a> for more complete information about this specimen.\n Other sequences that do not yet meet barcode criteria may also be available.";
} else {
$str = "There are {$count_sequence} barcode sequences available from BOLD and GenBank.\n Below is a sequence of the barcode region Cytochrome oxidase subunit 1 (COI or COX1) from a member of the species.\n See the <a target='BOLDSys' href='{$dc_source}'>BOLD taxonomy browser</a> for more complete information about this specimen and other sequences.";
}
$str .= "<br><br>";
$text_dna_sequence .= "<br>-- end --<br>";
}
if (trim($text_dna_sequence) != "") {
$temp = "{$str} ";
$temp .= "<div style='font-size : x-small;overflow : scroll;'> {$text_dna_sequence} </div>";
} else {
$temp = "No available public DNA sequences. <br>";
}
if ($count_sequence > 0 || $with_stats) {
/* one-click
$url_fasta_file = "http://services.eol.org/eol_php_code/applications/barcode/get_text_dna_sequence.php?taxid=$taxid";
*/
/* 2-click per PL advice */
$url_fasta_file = self::BOLDS_DOMAIN . "/pcontr.php?action=doPublicSequenceDownload&taxids={$taxid}";
$temp .= "<br><a target='fasta' href='{$url_fasta_file}'>Download FASTA File</a>";
}
$description .= $temp;
//end get text dna sequence
} else {
echo "\n this phylum is non-animal: [{$phylum}]";
}
if (is_numeric(stripos("Barcode image not yet available.", $description)) && is_numeric(stripos("No available public DNA sequences.", $description)) && !is_numeric(stripos("Download FASTA File", $description))) {
return false;
}
if (Functions::is_utf8($description)) {
return $description;
} else {
return false;
}
}
public static function is_utf8($v)
{
$v = trim($v);
if (!$v) {
return true;
}
$return = Functions::is_utf8($v);
return $return;
}
