$dataObjects[] = get_data_object($amphibID . "_trends_threats", "Life History, Abundance, Activity, and Special Behaviors", $trends_and_threats, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Threats", $refs, $agents, $pageURL);
}
if ($relation_to_humans) {
$dataObjects[] = get_data_object($amphibID . "_relation_to_humans", "Relation to Humans", $relation_to_humans, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#RiskStatement", $refs, $agents, $pageURL);
}
if ($description != "") {
if ($comments != "") {
$description .= $comments;
} else {
if ($comments != "") {
$description = $comments;
}
}
}
if ($description) {
$dataObjects[] = get_data_object($amphibID . "_description", "Description", $description, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription", $refs, $agents, $pageURL);
}
/* we didn't get <comments>
if($comments) $dataObjects[] = get_data_object("Comments", $comments, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription", $refs, $agents, $pageURL);
*/
foreach ($dataObjects as $k => $v) {
$taxonParameters["dataObjects"][] = new \SchemaDataObject($v);
unset($v);
}
$taxa[] = new \SchemaTaxon($taxonParameters);
//if($i >= 5) break; //debug
}
$new_resource_xml = \SchemaDocument::get_taxon_xml($taxa);
$old_resource_path = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . ".xml";
if (!($OUT = Functions::file_open($old_resource_path, "w+"))) {
return;
$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Associations";
$data_object_parameters = get_data_object("text", $taxon, "bio_association", $dc_source, $agent_name, $agent_role, $html_biological_associations, $copyright, $image_url, $title, $subject);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
}
//end biological_associations
//start nematocysts
if ($html_nematocysts != "") {
$do_count++;
$agent_name = "";
$agent_role = "";
$image_url = "";
$copyright = "";
$title = "Biology: Nematocysts";
$dc_source = $url_for_nematocysts;
$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Biology";
$data_object_parameters = get_data_object("text", $taxon, "nematocyst", $dc_source, $agent_name, $agent_role, $html_nematocysts, $copyright, $image_url, $title, $subject);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
}
//end
$used_taxa[$taxon] = $taxon_parameters;
}
//with photos
//end main loop
}
foreach ($used_taxa as $taxon_parameters) {
$schema_taxa[] = new \SchemaTaxon($taxon_parameters);
}
////////////////////// ---
$new_resource_xml = SchemaDocument::get_taxon_xml($schema_taxa);
$old_resource_path = CONTENT_RESOURCE_LOCAL_PATH . $resource->id . ".xml";
if (!($OUT = fopen($old_resource_path, "w+"))) {
if ($object->specimenPart) {
$desc .= "<br>Specimen part: " . $object->specimenPart;
}
if ($object->developmentalStage) {
$desc .= "<br>Developmental stage: " . $object->developmentalStage;
}
if ($object->sex) {
$desc .= "<br>Sex: " . $object->sex;
}
if ($object->form) {
$desc .= "<br>Form: " . $object->form;
}
if ($desc) {
$desc = substr($desc, 4, strlen($desc));
}
$data_object_parameters = get_data_object($dc_identifier, $dcterms_created, $dcterms_modified, $copyright_text, $license, $agent, $desc, "image");
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
}
$used_taxa[$taxon_identifier] = $taxon_parameters;
}
}
foreach ($used_taxa as $taxon_parameters) {
$schema_taxa[] = new \SchemaTaxon($taxon_parameters);
}
$new_resource_xml = \SchemaDocument::get_taxon_xml($schema_taxa);
$old_resource_path = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . ".xml";
if (!($OUT = fopen($old_resource_path, "w+"))) {
debug(__CLASS__ . ":" . __LINE__ . ": Couldn't open file: " . $old_resource_path);
return;
}
fwrite($OUT, $new_resource_xml);
function get_GeneralDescription($legend, $adaptation, $links, $reference, $language, $taxon_identifier, $dc_source)
{
$dc_identifier = $taxon_identifier . "_GenDesc";
$title = "Description";
if ($language == "es") {
$dc_identifier .= "_es";
$title = "Descripción";
}
$description = $legend;
if ($adaptation != "") {
if ($language == "en") {
$description .= "<br><br>Adaptation: {$adaptation}";
} elseif ($language == "es") {
$description .= "<br><br>Adaptación: {$adaptation}";
}
}
if ($links != "") {
// remove the double qoutes around 'links'
$links = str_replace('""', '"', trim($links));
$links = substr($links, 1, strlen($links) - 2);
if ($language == "en") {
$links = "<br><br>Links:<br>" . str_ireplace("<br><br>", "<br>", $links);
} elseif ($language == "es") {
$links = "<br><br>Enlaces:<br>" . str_ireplace("<br><br>", "<br>", $links);
}
$description .= $links;
}
//$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription";
$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#TaxonBiology";
// re-mapped so it will show in Brief Summary and not in Comprehensive Description
return get_data_object($dc_identifier, $dc_source, $description, $reference, $subject, $title, $language);
}
function start($resource_id)
{
$new_resource_path = DOC_ROOT . "temp/" . $resource_id . ".xml";
// $file = 'http://localhost/cp/Amphibiaweb/amphib_dump.xml';
$file = 'http://amphibiaweb.org/amphib_dump.xml';
if (!($new_resource_xml = Functions::lookup_with_cache($file, array('timeout' => 1200, 'download_attempts' => 5, 'expire_seconds' => 86400)))) {
echo "\n\n Content partner's server is down, connector will now terminate.\n";
} else {
// These may look like the same wrong characters - but they are several different wrong characters
$new_resource_xml = str_replace("", "\"", $new_resource_xml);
$new_resource_xml = str_replace("", "\"", $new_resource_xml);
$new_resource_xml = str_replace("", "-", $new_resource_xml);
if (!($OUT = Functions::file_open($new_resource_path, "w+"))) {
return;
}
fwrite($OUT, $new_resource_xml);
fclose($OUT);
unset($new_resource_xml);
$taxa = array();
$xml = simplexml_load_file($new_resource_path);
$total = count($xml->species);
$i = 0;
foreach (@$xml->species as $species) {
$i++;
if ($i % 1000 == 0) {
echo "\n {$i} of {$total} ";
}
$amphibID = (int) trim($species->amphib_id);
$genus = format_utf8((string) trim($species->genus));
$speciesName = format_utf8((string) trim($species->species));
$order = format_utf8((string) trim($species->ordr));
$family = format_utf8((string) trim($species->family));
$commonNames = format_utf8((string) trim($species->common_name));
$commonNames = explode(",", $commonNames);
$submittedBy = format_utf8((string) trim($species->submittedby));
$editedBy = format_utf8((string) trim($species->editedby));
$description = format_utf8((string) trim($species->description));
$distribution = format_utf8((string) trim($species->distribution));
$life_history = format_utf8((string) trim($species->life_history));
$trends_and_threats = format_utf8((string) trim($species->trends_and_threats));
$relation_to_humans = format_utf8((string) trim($species->relation_to_humans));
$comments = format_utf8((string) trim($species->comments));
$ref = format_utf8((string) trim($species->refs));
$separator = "<p>";
$separator = "<p>";
$ref = explode($separator, $ref);
$refs = array();
foreach ($ref as $r) {
$refs[] = array("fullReference" => trim($r));
}
$description = fix_article($description);
$distribution = fix_article($distribution);
$life_history = fix_article($life_history);
$trends_and_threats = fix_article($trends_and_threats);
$relation_to_humans = fix_article($relation_to_humans);
$comments = fix_article($comments);
$pageURL = "http://amphibiaweb.org/cgi/amphib_query?where-genus=" . $genus . "&where-species=" . $speciesName . "&account=amphibiaweb";
if (!$submittedBy) {
continue;
}
$agents = array();
if ($submittedBy) {
$parts = preg_split("/(,| and )/", $submittedBy);
while (list($key, $val) = each($parts)) {
$val = trim($val);
if (!$val) {
continue;
}
$agentParameters = array();
$agentParameters["role"] = "author";
$agentParameters["fullName"] = $val;
$agents[] = new \SchemaAgent($agentParameters);
}
}
$nameString = trim($genus . " " . $speciesName);
$taxonParameters = array();
$taxonParameters["identifier"] = $amphibID;
$taxonParameters["source"] = $pageURL;
$taxonParameters["kingdom"] = "Animalia";
$taxonParameters["phylum"] = "Chordata";
$taxonParameters["class"] = "Amphibia";
$taxonParameters["order"] = $order;
$taxonParameters["family"] = $family;
$taxonParameters["scientificName"] = $nameString;
foreach ($commonNames as $common_name) {
$taxonParameters['commonNames'][] = new \SchemaCommonName(array("name" => $common_name, "language" => "en"));
}
$taxonParameters["dataObjects"] = array();
$dataObjects = array();
if ($distribution) {
$dataObjects[] = get_data_object($amphibID . "_distribution", "Distribution and Habitat", $distribution, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Distribution", $refs, $agents, $pageURL);
}
if ($life_history) {
$dataObjects[] = get_data_object($amphibID . "_life_history", "Life History, Abundance, Activity, and Special Behaviors", $life_history, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Trends", $refs, $agents, $pageURL);
}
if ($trends_and_threats) {
$dataObjects[] = get_data_object($amphibID . "_trends_threats", "Life History, Abundance, Activity, and Special Behaviors", $trends_and_threats, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Threats", $refs, $agents, $pageURL);
}
if ($relation_to_humans) {
$dataObjects[] = get_data_object($amphibID . "_relation_to_humans", "Relation to Humans", $relation_to_humans, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#RiskStatement", $refs, $agents, $pageURL);
}
if ($description != "") {
if ($comments != "") {
$description .= $comments;
} else {
if ($comments != "") {
$description = $comments;
}
}
}
if ($description) {
$dataObjects[] = get_data_object($amphibID . "_description", "Description", $description, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription", $refs, $agents, $pageURL);
}
/* we didn't get <comments>
if($comments) $dataObjects[] = get_data_object("Comments", $comments, "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription", $refs, $agents, $pageURL);
*/
foreach ($dataObjects as $k => $v) {
$taxonParameters["dataObjects"][] = new \SchemaDataObject($v);
unset($v);
}
$taxa[] = new \SchemaTaxon($taxonParameters);
//if($i >= 5) break; //debug
}
$new_resource_xml = \SchemaDocument::get_taxon_xml($taxa);
$old_resource_path = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . ".xml";
if (!($OUT = Functions::file_open($old_resource_path, "w+"))) {
return;
}
fwrite($OUT, $new_resource_xml);
fclose($OUT);
// Functions::set_resource_status_to_force_harvest($resource_id);
shell_exec("rm " . $new_resource_path);
// Functions::gzip_resource_xml($resource_id);
// $elapsed_time_sec = microtime(1)-$timestart;
// echo "\n";
// echo "elapsed time = $elapsed_time_sec sec \n";
// echo "elapsed time = " . $elapsed_time_sec/60 . " minutes \n";
// echo "elapsed time = " . $elapsed_time_sec/60/60 . " hours \n";
// echo "\n\n Done processing.";
}
}
$taxon_parameters["scientificName"] = $taxa;
$taxon_parameters["source"] = $home_url;
$used_taxa[$taxon] = $taxon_parameters;
}
if (1 == 1) {
//if($do_count == 0)//echo "$wrap$wrap phylum = " . $taxa . "$wrap";
$dc_source = $home_url;
$do_count++;
$agent_name = $photo_credit;
$agent_role = "photographer";
/* for debugging
$image_url = "http://127.0.0.1/test.tif";
$image_url = "http://www.findingspecies.org/indu/images/YIH_13569_MED_EOL.TIFF";
*/
// /* just debug; no images for now
$data_object_parameters = get_data_object("image", $taxon, $do_count, $dc_source, $agent_name, $agent_role, $desc_pic, $copyright, $image_url, "");
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
// */
/* no text descriptions per Katja
if($desc_taxa != "")
{
$temp = trim(strip_tags($desc_taxa));
if(substr($temp,0,9) != "Outlinks:")
{
if(substr($temp,0,11) == "Categories:") $title="Categories";
//$desc_taxa="<b>Discussion on disease(s) caused by this organism:</b>" . $desc_taxa;
$do_count++;
$agent_name = $providers;
$agent_role = "source";
$data_object_parameters = get_data_object("text",$taxon,$do_count,$dc_source,$agent_name,$agent_role,$desc_taxa,$copyright,$image_url,$title);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
function assign_variables($sciname, $desc, $arr_agents, $dc_rights, $dc_source, $do_count)
{
global $species_list;
global $used_taxa;
global $keys_url;
global $wrap;
global $not_found;
//$genus = substr($sciname,0,stripos($sciname," "));
//if(isset(@$species_list["$sciname"]["symbol"]))
if (@$species_list["{$sciname}"]["symbol"] != "") {
$taxon_identifier = @$species_list[$sciname]["symbol"] . "_" . str_ireplace(" ", "_", $sciname);
$source_url = $dc_source . @$species_list[$sciname]["symbol"];
$do_identifier = $taxon_identifier . "_USDA_keys_object";
} else {
$taxon_identifier = str_ireplace(" ", "_", $sciname) . "_USDA_keys";
$source_url = $keys_url;
$do_identifier = str_ireplace(" ", "_", $sciname) . "_USDA_keys_object";
/*
$not_found++;
print("<hr> $not_found not found in USDA list xxxyyy $sciname <hr>");//debug
*/
}
if (@$used_taxa[$taxon_identifier]) {
$taxon_parameters = $used_taxa[$taxon_identifier];
} else {
$taxon_parameters = array();
$taxon_parameters["identifier"] = $taxon_identifier;
$taxon_parameters["kingdom"] = trim(@$species_list["{$sciname}"]["Kingdom"]);
$taxon_parameters["class"] = trim(@$species_list["{$sciname}"]["Class"]);
$taxon_parameters["order"] = trim(@$species_list["{$sciname}"]["Order"]);
$taxon_parameters["family"] = trim(@$species_list["{$sciname}"]["Family"]);
$taxon_parameters["genus"] = trim(@$species_list["{$sciname}"]["Genus"]);
$taxon_parameters["scientificName"] = $sciname;
$taxon_parameters["source"] = $source_url;
/*
$taxon_parameters["commonNames"] = array();
$arr_comname=conv_2array($comname);
foreach ($arr_comname as $commonname)
{
$commonname = str_ireplace(';' , '', $commonname);
$taxon_parameters["commonNames"][] = new \SchemaCommonName(array("name" => $commonname, "language" => "en"));
}
*/
/////////////////////////////////////////////////////////////
/*
$taxon_params["synonyms"] = array();
$arr_synonym=conv_2array($synonymy);
foreach ($arr_synonym as $synonym)
{
$taxon_parameters["synonyms"][] = new \SchemaSynonym(array("synonym" => $synonym, "relationship" => "synonym"));
}
*/
/////////////////////////////////////////////////////////////
$taxon_parameters["dataObjects"] = array();
$used_taxa[$taxon_identifier] = $taxon_parameters;
}
//start text dataobject
$dc_identifier = $do_identifier;
//$dc_identifier = "";
$desc = $desc;
$title = "Physical Description";
$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#Description";
$type = "text";
$reference = "";
$data_object_parameters = get_data_object($dc_identifier, $desc, $dc_rights, $title, $source_url, $subject, $type, $reference, $arr_agents);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
//end text dataobject
//start text dataobject
//end text dataobject
//start img dataobject
//end img dataobject
$used_taxa[$taxon_identifier] = $taxon_parameters;
return "";
}
$taxonParameters["genus"] = $genus;
$taxonParameters["scientificName"] = $sciname;
$taxonParameters["created"] = $created;
$taxonParameters["modified"] = $modified;
$taxonParameters["synonyms"] = array();
foreach ($t->synonym as $syn) {
$taxonParameters["synonyms"][] = new \SchemaSynonym(array("synonym" => $syn, "relationship" => $url = $syn["relationship"]));
}
//start process dataObjects =====================================================================
$taxonParameters["dataObjects"] = array();
$dataObjects = array();
$arr = $t->dataObject;
foreach ($arr as $do) {
$t_dc2 = $do->children("http://purl.org/dc/elements/1.1/");
$t_dcterms = $do->children("http://purl.org/dc/terms/");
$dataObjects[] = get_data_object($do, $t_dc2, $t_dcterms);
}
foreach ($dataObjects as $k => $v) {
$taxonParameters["dataObjects"][] = new \SchemaDataObject($v);
unset($v);
}
//end process dataObjects =====================================================================
///////////////////////////////////////////////////////////////////////////////////
$taxa = array();
$taxa[] = new \SchemaTaxon($taxonParameters);
//$new_resource_xml = SchemaDocument::get_taxon_xml($taxa);
$str = '';
foreach ($taxa as $tax) {
$str .= $tax->__toXML();
}
fwrite($OUT, $str);
$taxon_parameters["source"] = $source_url;
$taxon_parameters["dataObjects"] = array();
$used_taxa[$taxon_identifier] = $taxon_parameters;
if (isset($rec->original_description)) {
$dcterms_created = "";
$dcterms_modified = "";
$copyright_text = "";
$dc_identifier = $taxon_identifier . "_GenDesc";
$dc_source = $source_url;
$agent_name = $agent;
$license = "http://creativecommons.org/licenses/by-nc/3.0/";
$desc = $rec->original_description;
$taxon_id = $rec["ID"];
$taxon_ref = @$arr_taxon_ref["{$taxon_id}"];
print " taxon_id = {$taxon_id} ";
$data_object_parameters = get_data_object($dc_identifier, $dcterms_created, $dcterms_modified, $copyright_text, $license, $agent_name, $desc, "text", $source_url, $taxon_ref, $arr_ref);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
}
}
/* start 2nd dataobject - image */
/* end second dataobject - image */
$used_taxa[$taxon_identifier] = $taxon_parameters;
$k++;
//if($k == 3)break; //debug - to limit no. of records
}
foreach ($used_taxa as $taxon_parameters) {
$schema_taxa[] = new \SchemaTaxon($taxon_parameters);
}
////////////////////// ---
$new_resource_xml = SchemaDocument::get_taxon_xml($schema_taxa);
$old_resource_path = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . ".xml";
//start get rights and publisher from page
$arr = parse_image_page($source);
$rightsHolder = trim($arr[0]);
$publisher = trim($arr[1]);
//end get rights and publisher from page
$id = parse_url($mediaURL, PHP_URL_QUERY);
$id = trim(substr($id, stripos($id, "=") + 1, strlen($id)));
$mediaURL = $image_url . $id;
$desc = Functions::import_decode($t->{$cap_str});
$mimeType = Functions::import_decode($t->{$mim_str});
$do_count++;
//$do_identifier = $identifier . "_" . $do_count;
$do_identifier = $mediaURL;
$do_agents = array();
$do_agents[] = array("name" => $publisher, "role" => "publisher");
$dataObjects[] = get_data_object($desc, $do_identifier, $subject, $dataType, $mimeType, $title, $source, $do_agents, $rightsHolder, $mediaURL);
}
}
//print"<hr>";
//print"<pre>";print_r($img);print"</pre>";
//end images =================================================================================================
foreach ($dataObjects as $k => $v) {
$taxonParameters["dataObjects"][] = new \SchemaDataObject($v);
unset($v);
}
//end process dataObjects =====================================================================
///////////////////////////////////////////////////////////////////////////////////
$taxa = array();
$taxa[] = new \SchemaTaxon($taxonParameters);
//$new_resource_xml = SchemaDocument::get_taxon_xml($taxa);
$str = '';
function process_dataobjects($item, $type, $object_id)
{
global $taxon_identifier;
global $taxon_parameters;
global $used_taxa;
global $taxon;
global $species_url;
global $main;
$dc_source = $species_url . $taxon_identifier;
$dcterms_created = "";
$ref = "";
if ($type == 1) {
$dc_identifier = "";
$description = trim($item->de_description);
$description = str_ireplace("Dimensions.", "Dimensions. ", $description);
$description = str_ireplace("Habitat.", "Habitat. ", $description);
$title = "Description";
$subject = "http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription";
$mediaURL = "";
$dataType = "http://purl.org/dc/dcmitype/Text";
$mimeType = "text/html";
$agentParameters = array();
$agentParameters["role"] = "author";
$agentParameters["fullName"] = $item->de_author . " " . $item->de_year;
$agents[] = new \SchemaAgent($agentParameters);
$license = "http://creativecommons.org/licenses/" . $item->de_license;
$dcterms_modified = $item->de_date;
} else {
$dc_identifier = $item->url;
$description = trim($item->im_description);
$title = "";
$subject = "";
$mediaURL = $item->url;
$dataType = "http://purl.org/dc/dcmitype/StillImage";
$mimeType = "image/jpeg";
if ($item->photo_by != "") {
$agentParameters = array();
$agentParameters["role"] = "author";
$agentParameters["fullName"] = $item->photo_by;
$agents[] = new \SchemaAgent($agentParameters);
}
$license = "http://creativecommons.org/licenses/" . $item->im_license;
$dcterms_modified = $item->im_date;
}
if (isset($main->contributed_by)) {
$agentParameters["role"] = "source";
$agentParameters["fullName"] = $main->contributed_by;
$agents[] = new \SchemaAgent($agentParameters);
}
$agentParameters["role"] = "project";
$agentParameters["fullName"] = "Radiolaria.org";
$agentParameters["homepage"] = "http://www.radiolaria.org/index.htm";
$agents[] = new \SchemaAgent($agentParameters);
$data_object_parameters = get_data_object($dc_identifier, $dcterms_created, $dcterms_modified, $license, $description, $subject, $title, $dc_source, $mediaURL, $dataType, $mimeType, $ref, $agents);
$taxon_parameters["dataObjects"][] = new \SchemaDataObject($data_object_parameters);
$used_taxa[$taxon] = $taxon_parameters;
}
