$emode = array_key_exists("emode", $_REQUEST) ? $_REQUEST["emode"] : 0;
$action = array_key_exists("formsubmit", $_REQUEST) ? $_REQUEST["formsubmit"] : '';
$cSet = array_key_exists("cset", $_REQUEST) ? $_REQUEST["cset"] : '';
$schema = array_key_exists("schema", $_REQUEST) ? $_REQUEST["schema"] : 1;
$dwcaManager = new DwcArchiverOccurrence();
$includeDets = 1;
$includeImgs = 1;
$redactLocalities = 1;
if ($action) {
if (!array_key_exists('dets', $_POST)) {
$includeDets = 0;
$dwcaManager->setIncludeDets(0);
}
if (!array_key_exists('imgs', $_POST)) {
$includeImgs = 0;
$dwcaManager->setIncludeImgs(0);
}
if (!array_key_exists('redact', $_POST)) {
$redactLocalities = 0;
$dwcaManager->setRedactLocalities(0);
}
$dwcaManager->setTargetPath($serverRoot . (substr($serverRoot, -1) == '/' ? '' : '/') . 'collections/datasets/dwc/');
}
$isEditor = 0;
if ($isAdmin || array_key_exists("CollAdmin", $userRights) && in_array($collId, $userRights["CollAdmin"])) {
$isEditor = 1;
}
$collArr = array();
if ($collId) {
$dwcaManager->setCollArr($collId);
$collArr = $dwcaManager->getCollArr();
public function exportDataset($dsid)
{
//Get occurrence records
$zip = array_key_exists('zip', $_POST) ? $_POST['zip'] : 0;
$format = $_POST['format'];
$extended = array_key_exists('extended', $_POST) ? $_POST['extended'] : 0;
$redactLocalities = 1;
$rareReaderArr = array();
if ($IS_ADMIN || array_key_exists("CollAdmin", $userRights)) {
$redactLocalities = 0;
} elseif (array_key_exists("RareSppAdmin", $userRights) || array_key_exists("RareSppReadAll", $userRights)) {
$redactLocalities = 0;
} else {
if (array_key_exists('CollEditor', $userRights)) {
$rareReaderArr = $userRights['CollEditor'];
}
if (array_key_exists('RareSppReader', $userRights)) {
$rareReaderArr = array_unique(array_merge($rareReaderArr, $userRights['RareSppReader']));
}
}
$dwcaHandler = new DwcArchiverOccurrence();
$dwcaHandler->setCharSetOut($cSet);
$dwcaHandler->setSchemaType($schema);
$dwcaHandler->setExtended($extended);
$dwcaHandler->setDelimiter($format);
$dwcaHandler->setVerbose(0);
$dwcaHandler->setRedactLocalities($redactLocalities);
if ($rareReaderArr) {
$dwcaHandler->setRareReaderArr($rareReaderArr);
}
$occurManager = new OccurrenceManager();
$dwcaHandler->setCustomWhereSql($occurManager->getSqlWhere());
$outputFile = null;
if ($zip) {
//Ouput file is a zip file
$includeIdent = array_key_exists('identifications', $_POST) ? 1 : 0;
$dwcaHandler->setIncludeDets($includeIdent);
$images = array_key_exists('images', $_POST) ? 1 : 0;
$dwcaHandler->setIncludeImgs($images);
$outputFile = $dwcaHandler->createDwcArchive('webreq');
} else {
//Output file is a flat occurrence file (not a zip file)
$outputFile = $dwcaHandler->getOccurrenceFile();
}
//ob_start();
$contentDesc = '';
if ($schema == 'dwc') {
$contentDesc = 'Darwin Core ';
} else {
$contentDesc = 'Symbiota ';
}
$contentDesc .= 'Occurrence ';
if ($zip) {
$contentDesc .= 'Archive ';
}
$contentDesc .= 'File';
header('Content-Description: ' . $contentDesc);
if ($zip) {
header('Content-Type: application/zip');
} elseif ($format == 'csv') {
header('Content-Type: text/csv; charset=' . $charset);
} else {
header('Content-Type: text/html; charset=' . $charset);
}
header('Content-Disposition: attachment; filename=' . basename($outputFile));
header('Content-Transfer-Encoding: binary');
header('Expires: 0');
header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
header('Pragma: public');
header('Content-Length: ' . filesize($outputFile));
ob_clean();
flush();
//od_end_clean();
readfile($outputFile);
unlink($outputFile);
}
$isEditor = true;
}
if ($isEditor) {
$processingStatus = array_key_exists('ps', $_REQUEST) ? $_REQUEST['ps'] : '';
$customField1 = array_key_exists('cf1', $_POST) ? $_POST['cf1'] : '';
$customField2 = array_key_exists('cf2', $_POST) ? $_POST['cf2'] : '';
$dwcaHandler = new DwcArchiverOccurrence();
$dwcaHandler->setCollArr($collid);
$dwcaHandler->setCharSetOut('UTF-8');
$dwcaHandler->setSchemaType('coge');
$dwcaHandler->setExtended(false);
$dwcaHandler->setDelimiter('csv');
$dwcaHandler->setVerbose(0);
$dwcaHandler->setRedactLocalities(0);
$dwcaHandler->setIncludeDets(0);
$dwcaHandler->setIncludeImgs(0);
$dwcaHandler->addCondition('decimallatitude', 'NULL');
$dwcaHandler->addCondition('decimallongitude', 'NULL');
$dwcaHandler->addCondition('catalognumber', 'NOTNULL');
$dwcaHandler->addCondition('locality', 'NOTNULL');
if ($processingStatus) {
$dwcaHandler->addCondition('processingstatus', 'EQUALS', $processingStatus);
}
if ($customField1) {
$dwcaHandler->addCondition($customField1, $_POST['ct1'], $_POST['cv1']);
}
if ($customField2) {
$dwcaHandler->addCondition($customField2, $_POST['ct2'], $_POST['cv2']);
}
//Set GeoLocate CoGe variables
$dwcaHandler->setGeolocateVariables(array('cogecomm' => $_POST['cogecomm'], 'cogename' => $_POST['cogename'], 'cogedescr' => $_POST['cogedescr']));
$stArrSearchJson = str_replace("%apos;", "'", $stArrSearchJson);
$collStArr = json_decode($stArrCollJson, true);
$searchStArr = json_decode($stArrSearchJson, true);
$stArr = array_merge($searchStArr, $collStArr);
$occurManager->setSearchTermsArr($stArr);
}
if ($schema == "backup") {
$collid = $_POST["collid"];
if ($collid && is_numeric($collid)) {
//check permissions due to sensitive localities not being redacted
if ($isAdmin || array_key_exists("CollAdmin", $userRights) && in_array($collid, $userRights["CollAdmin"])) {
$dwcaHandler->setSchemaType('backup');
$dwcaHandler->setCharSetOut($cSet);
$dwcaHandler->setVerbose(0);
$dwcaHandler->setIncludeDets(1);
$dwcaHandler->setIncludeImgs(1);
$dwcaHandler->setRedactLocalities(0);
$dwcaHandler->setCollArr($collid);
$archiveFile = $dwcaHandler->createDwcArchive();
if ($archiveFile) {
//ob_start();
header('Content-Description: Symbiota Occurrence Backup File (DwC-Archive data package)');
header('Content-Type: application/zip');
header('Content-Disposition: attachment; filename=' . basename($archiveFile));
header('Content-Transfer-Encoding: binary');
header('Expires: 0');
header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
header('Pragma: public');
header('Content-Length: ' . filesize($archiveFile));
//od_end_clean();
readfile($archiveFile);
}
if (isset($tok[1]) && $tok[1]) {
$valueArr = explode(',', $tok[1]);
}
if ($valueArr) {
foreach ($valueArr as $v) {
$dwcaHandler->addCondition($field, $cond, $v);
}
} else {
$dwcaHandler->addCondition($field, $cond);
}
}
}
}
$dwcaHandler->setIncludeDets($includeDets);
$dwcaHandler->setIncludeImgs($includeImgs);
$archiveFile = $dwcaHandler->createDwcArchive('webreq');
if ($archiveFile) {
//ob_start();
header('Content-Description: DwC-A File Transfer');
header('Content-Type: application/zip');
header('Content-Disposition: attachment; filename=' . basename($archiveFile));
header('Content-Transfer-Encoding: binary');
header('Expires: 0');
header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
header('Pragma: public');
header('Content-Length: ' . filesize($archiveFile));
ob_clean();
flush();
//od_end_clean();
readfile($archiveFile);
<?php
include_once '../../config/symbini.php';
include_once $serverRoot . '/classes/DwcArchiverOccurrence.php';
$collStr = $argv[1];
$serverDomain = $argv[2];
$includeDets = 1;
$includeImgs = 1;
$redactLocalities = 1;
if ($argc > 3 && is_numeric($argv[3])) {
$includeDets = $argv[3];
if ($argc > 4 && is_numeric($argv[4])) {
$includeImgs = $argv[4];
if ($argc > 5 && is_numeric($argv[5])) {
$redactLocalities = $argv[5];
}
}
}
if ($collStr) {
$dwcaManager = new DwcArchiverOccurrence();
$dwcaManager->setIncludeDets($includeDets);
$dwcaManager->setIncludeImgs($includeImgs);
$dwcaManager->setRedactLocalities($redactLocalities);
$dwcaManager->setServerDomain($serverDomain);
$dwcaManager->setTargetPath($serverRoot . (substr($serverRoot, -1) == '/' ? '' : '/') . 'collections/datasets/dwc/');
$dwcaManager->setVerbose(0);
$collArr = explode(',', $collStr);
$dwcaManager->batchCreateDwca($collArr);
}
