private function get_uris($params)
{
$fields = array();
if (in_array($params["dataset"], array("NMNH", "NHM"))) {
$fields["institutionCode"] = "institutionCode_uri";
$fields["sex"] = "sex_uri";
$fields["typeStatus"] = "typeStatus_uri";
$fields["lifeStage"] = "lifeStage_uri";
$fields["collectionCode"] = "collectionCode_uri";
}
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
$spreadsheet_options = array("cache" => 1, "timeout" => 3600, "file_extension" => "xlsx", 'download_attempts' => 2, 'delay_in_minutes' => 2);
$spreadsheet_options["expire_seconds"] = 0;
// false => won't expire; 0 => expires now
$uris = array();
if ($spreadsheet = @$params["uri_file"]) {
if ($arr = $func->convert_spreadsheet($spreadsheet, 0, $spreadsheet_options)) {
foreach ($fields as $key => $value) {
$i = 0;
foreach ($arr[$key] as $item) {
$item = trim($item);
if ($item) {
$uris[$item] = $arr[$value][$i];
}
$i++;
}
}
}
}
return $uris;
}
function export_lifedesk_to_eol($params)
{
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
if ($this->text_path = $func->load_zip_contents($params["lifedesk"])) {
self::update_eol_xml("LD_" . $params["name"]);
}
// remove temp dir
$parts = pathinfo($this->text_path["eol_xml"]);
recursive_rmdir($parts["dirname"]);
debug("\n temporary directory removed: " . $parts["dirname"]);
}
private function get_institution_uris()
{
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
$arr = $func->convert_spreadsheet($this->institutions_xls, 0);
$institutions = array();
$k = 0;
foreach ($arr["Code"] as $code) {
$institutions[$code] = $arr["URI"][$k];
$k++;
}
echo "\nInstitutions from spreadsheet [{$this->institutions_xls}]:" . count($institutions) . "\n";
return $institutions;
}
private function get_uris()
{
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
$spreadsheet_options = array("cache" => 1, "timeout" => 3600, "file_extension" => "xlsx", 'download_attempts' => 2, 'delay_in_minutes' => 2);
// $spreadsheet_options["expire_seconds"] = 0; // false => won't expire; 0 => expires now
$temp = $func->convert_spreadsheet($this->triple_uris_spreadsheet, 0, $spreadsheet_options);
/* spreadsheet headers: Wikipedia triple - Measurement Type - Measurement Value1 - Measurement Value2 */
$uris = array();
$i = -1;
foreach ($temp["Wikipedia triple"] as $triple) {
$i++;
if ($temp["Measurement Type"][$i] == "EXCLUDE") {
continue;
}
$uris[$triple]["mtype"] = $temp["Measurement Type"][$i];
$uris[$triple]["v1"] = @$temp["Measurement Value1"][$i];
$uris[$triple]["v2"] = @$temp["Measurement Value2"][$i];
}
return $uris;
}
public function get_array_from_spreadsheet($options)
{
$records = array();
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
if ($spreadsheet = @$options["spreadsheet_file"]) {
if ($arr = $func->convert_spreadsheet($spreadsheet, 0, $options)) {
$fields = array_keys($arr);
$fields[] = "record_id";
$i = 0;
foreach ($arr[$fields[0]] as $val) {
$rec = array();
foreach ($fields as $field) {
if ($field == "record_id") {
$rec[$field] = $i + 1;
} else {
$rec[$field] = $arr[$field][$i];
}
}
if ($rec) {
$records[] = $rec;
}
$i++;
}
}
}
return $records;
}
private function access_spreadsheet($params, $sheet_no)
{
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
if ($val = @$params["spreadsheet_options"]) {
$spreadsheet_options = $val;
} else {
$spreadsheet_options = $this->spreadsheet_options;
}
if ($arr = $func->convert_spreadsheet($params['spreadsheet'], $sheet_no, $spreadsheet_options)) {
return $arr;
}
}
$params[$desk]["remote"]["name"] = $desk;
//Dropbox
$params[$desk]["dropbox"]["lifedesk"] = "";
$params[$desk]["dropbox"]["bibtex_file"] = "";
$params[$desk]["dropbox"]["scratchpad_images"] = "";
$params[$desk]["dropbox"]["name"] = $desk;
//local
$params[$desk]["local"]["lifedesk"] = "http://localhost/cp/LD2Scratchpad/" . $desk . "/eol-partnership.xml.gz";
$params[$desk]["local"]["bibtex_file"] = "";
$params[$desk]["local"]["scratchpad_images"] = "http://localhost/cp/LD2Scratchpad/" . $desk . "/file_importer_image_xls.xls";
$params[$desk]["local"]["name"] = $desk;
$params[$desk]["local"]["scratchpad_biblio"] = "http://localhost/cp/LD2Scratchpad/" . $desk . "/node_importer_biblio_xls.xls";
if ($desk == "africanamphibians") {
$params[$desk]["local"]["scratchpad_taxonomy"] = "http://localhost/cp/LD2Scratchpad/" . $desk . "/taxonomy_importer_xls.xls";
}
$func = new LifeDeskToScratchpadAPI();
$func->export_lifedesk_to_scratchpad($params[$desk]["local"]);
}
// */
/* start: Generate taxonomy of a LifeDesk
// neotropicalfishes local
$lifedesk = 'neotropicalfishes';
$lifedesk = 'echinoderms';
$params = array();
$params[$lifedesk]["local"]["lifedesk"] = "http://localhost/cp/LD2Scratchpad/" . $lifedesk . "/eol-partnership.xml.gz";
$params[$lifedesk]["local"]["name"] = $lifedesk;
$parameters = $params[$lifedesk]["local"];
$func = new LifeDeskToScratchpadAPI();
$func->export_lifedesk_taxonomy($parameters);
*/
private function get_spreadsheet($spreadsheet)
{
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
$final = array();
$habitats = array();
$spreadsheet_options = array("cache" => 0, "timeout" => 3600, "file_extension" => "xlsx", 'download_attempts' => 2, 'delay_in_minutes' => 1);
//we don't want to cache spreadsheet
if ($filename = Functions::save_remote_file_to_local($spreadsheet, $spreadsheet_options)) {
if ($arr = $func->convert_spreadsheet($filename, 0, $spreadsheet_options)) {
$i = 0;
foreach ($arr['subsection'] as $subsection) {
if ($subsection) {
$final[$subsection]['section'] = $arr['section'][$i];
$final[$subsection]['habitats'][] = $arr['source text'][$i];
}
$habitats[$arr['source text'][$i]] = $arr['term'][$i];
$i++;
}
}
unlink($filename);
}
$final = array_filter($final);
//remove null arrays
$habitats = array_filter($habitats);
//remove null arrays
return array('subsections' => $final, 'habitats' => $habitats);
}
function get_uris($params, $spreadsheet)
{
$fields = array();
if ($params["dataset"] == "GBIF") {
$fields["sex"] = "sex_uri";
$fields["typeStatus"] = "typeStatus_uri";
if (@$params["country"] == "Sweden") {
$fields["datasetKey"] = "Type Specimen Repository URI";
} else {
$fields["institutionCode"] = "institutionCode_uri";
}
//rule case
if (@$params["uri_type"] == "citation") {
$fields["datasetKey France"] = "BibliographicCitation";
//886
$fields["datasetKey UK"] = "BibliographicCitation";
//894
$fields["datasetKey Germany"] = "BibliographicCitation";
//872
$fields["datasetKey Brazil"] = "BibliographicCitation";
//892
$fields["datasetKey"] = "BibliographicCitation";
//from Netherlands (887), Sweden (893) spreadsheet
}
} else {
$fields = $params["fields"];
}
require_library('connectors/LifeDeskToScratchpadAPI');
$func = new LifeDeskToScratchpadAPI();
if ($val = @$params["spreadsheet_options"]) {
$spreadsheet_options = $val;
} else {
$spreadsheet_options = $this->spreadsheet_options;
}
$uris = array();
if ($spreadsheet) {
if ($arr = $func->convert_spreadsheet($spreadsheet, 0, $spreadsheet_options)) {
foreach ($fields as $key => $value) {
$i = 0;
if (@$arr[$key]) {
foreach ($arr[$key] as $item) {
$item = trim($item);
if ($item) {
$temp = $arr[$value][$i];
$temp = trim(str_replace(array("\n"), "", $temp));
$uris[$item] = $temp;
if (!Functions::is_utf8($temp)) {
echo "\nnot utf8: [{$temp}]\n";
}
}
$i++;
}
}
}
}
}
return $uris;
}
