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);
}
<?php
include_once '../../config/symbini.php';
include_once $serverRoot . '/classes/DwcArchiverOccurrence.php';
header("Content-Type: text/html; charset=" . $charset);
$collId = array_key_exists("collid", $_REQUEST) ? $_REQUEST["collid"] : 0;
$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"])) {
public function writeEmlFile()
{
global $clientRoot, $defaultTitle, $adminEmail;
$this->logOrEcho("Creating eml.xml (" . date('h:i:s A') . ")... ");
$urlPathPrefix = 'http://' . $_SERVER["SERVER_NAME"] . $clientRoot . (substr($clientRoot, -1) == '/' ? '' : '/');
$emlArr = array();
$emlArr['alternateIdentifier'][] = UuidFactory::getUuidV4();
$emlArr['title'] = $this->title;
$emlArr['creator'][0]['organizationName'] = $defaultTitle;
$emlArr['creator'][0]['electronicMailAddress'] = $adminEmail;
$emlArr['creator'][0]['onlineUrl'] = $urlPathPrefix . 'index.php';
$emlArr['metadataProvider'][0]['organizationName'] = $defaultTitle;
$emlArr['metadataProvider'][0]['electronicMailAddress'] = $adminEmail;
$emlArr['metadataProvider'][0]['onlineUrl'] = $urlPathPrefix . 'index.php';
$emlArr['pubDate'] = date("Y-m-d");
$emlArr['language'] = 'eng';
$emlArr['description'] = $this->description;
//Get EML string
$dwcaHandler = new DwcArchiverOccurrence();
$emlDoc = $dwcaHandler->getEmlDom($emlArr);
$tempFileName = $this->targetPath . $this->ts . '-eml.xml';
$emlDoc->save($tempFileName);
$this->zipArchive->addFile($tempFileName);
$this->zipArchive->renameName($tempFileName, 'eml.xml');
$this->logOrEcho("Done!! (" . date('h:i:s A') . ")\n");
}
include_once $SERVER_ROOT . '/classes/DwcArchiverOccurrence.php';
header("Cache-Control: no-cache, must-revalidate");
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
header("Content-Type: text/html; charset=" . $charset);
$collid = $_REQUEST["collid"];
$cntStr = '';
if ($collid && is_numeric($collid)) {
$isEditor = false;
if ($IS_ADMIN || array_key_exists("CollAdmin", $USER_RIGHTS) && in_array($collid, $USER_RIGHTS["CollAdmin"])) {
$isEditor = true;
}
if ($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->setVerbose(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']);
}
header("Cache-Control: no-cache, must-revalidate");
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
header("Content-Type: text/html; charset=" . $charset);
$collid = $_REQUEST["collid"];
$archiveFile = '';
$retArr = array();
if ($collid && is_numeric($collid)) {
$isEditor = false;
if ($IS_ADMIN || array_key_exists("CollAdmin", $USER_RIGHTS) && in_array($collid, $USER_RIGHTS["CollAdmin"])) {
$isEditor = true;
}
if ($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);
<?php
include_once '../../config/symbini.php';
include_once $serverRoot . '/classes/DwcArchiverOccurrence.php';
$collId = $_REQUEST["collid"];
if ($collId && is_numeric($collId)) {
$dwcaManager = new DwcArchiverOccurrence();
$dwcaManager->setCollArr($collId);
$collArr = $dwcaManager->getCollArr();
header('Content-Description: ' . $collArr[$collId]['collname'] . ' EML');
header('Content-Type: text/xml');
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
header("Cache-Control: no-cache");
header("Pragma: no-cache");
$xmlDom = $dwcaManager->getEmlDom();
echo $xmlDom->saveXML();
}
$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']));
}
}
//Is an occurrence download
$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);
}
$mapManager = new MapInterfaceManager();
if ($type == 'selection' || $type == 'dsselectionquery') {
$selections = preg_match('#\\[(.*?)\\]#', $selections, $match);
$selections = $match[1];
$mapWhere = 'WHERE o.occid IN(' . $selections . ') ';
}
<?php
include_once '../../config/symbini.php';
include_once $serverRoot . '/classes/OccurrenceDownload.php';
include_once $serverRoot . '/classes/OccurrenceManager.php';
include_once $serverRoot . '/classes/DwcArchiverOccurrence.php';
header("Cache-Control: no-cache, must-revalidate");
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
$schema = array_key_exists("schema", $_POST) ? $_POST["schema"] : "symbiota";
$cSet = array_key_exists("cset", $_POST) ? $_POST["cset"] : '';
$stArrCollJson = array_key_exists("jsoncollstarr", $_REQUEST) ? $_REQUEST["jsoncollstarr"] : '';
$stArrSearchJson = array_key_exists("starr", $_REQUEST) ? $_REQUEST["starr"] : '';
$dlManager = new OccurrenceDownload();
$dwcaHandler = new DwcArchiverOccurrence();
$occurManager = new OccurrenceManager();
if ($stArrCollJson && $stArrSearchJson) {
$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);
Header("Content-Type: text/turtle; charset=" . $CHARSET);
$dwcManager = new DwcArchiverOccurrence();
$dwcManager->setCustomWhereSql(" o.occid = {$occid} ");
echo $dwcManager->getAsTurtle();
$done = TRUE;
}
if ($mediarange == 'application/rdf+xml' || $format == 'rdf') {
Header("Content-Type: application/rdf+xml; charset=" . $CHARSET);
$dwcManager = new DwcArchiverOccurrence();
$dwcManager->setCustomWhereSql(" o.occid = {$occid} ");
echo $dwcManager->getAsRdfXml();
$done = TRUE;
}
if ($mediarange == 'application/json' || $format == 'json') {
Header("Content-Type: application/json; charset=" . $CHARSET);
$dwcManager = new DwcArchiverOccurrence();
$dwcManager->setCustomWhereSql(" o.occid = {$occid} ");
echo $dwcManager->getAsJson();
$done = TRUE;
}
}
if ($done) {
die;
}
if ($SYMB_UID) {
//Check editing status
if ($IS_ADMIN || array_key_exists('CollAdmin', $USER_RIGHTS) && in_array($collId, $USER_RIGHTS['CollAdmin'])) {
$isEditor = true;
} elseif (array_key_exists('CollEditor', $USER_RIGHTS) && in_array($collId, $USER_RIGHTS['CollEditor'])) {
$isEditor = true;
} elseif ($occArr['observeruid'] == $SYMB_UID) {
header("Cache-Control: no-cache, must-revalidate");
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
header("Content-Type: text/html; charset=" . $charset);
$collid = $_REQUEST["collid"];
$archiveFile = '';
$retArr = array();
if ($collid && is_numeric($collid)) {
$isEditor = false;
if ($IS_ADMIN || array_key_exists("CollAdmin", $USER_RIGHTS) && in_array($collid, $USER_RIGHTS["CollAdmin"])) {
$isEditor = true;
}
if ($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');
$dwcaHandler->addCondition('locality', 'NOTNULL');
if ($processingStatus) {
$dwcaHandler->addCondition('processingstatus', 'EQUALS', $processingStatus);
}
<?php
include_once '../../config/symbini.php';
include_once $serverRoot . '/classes/DwcArchiverOccurrence.php';
$action = array_key_exists("action", $_REQUEST) ? $_REQUEST["action"] : '';
$collid = array_key_exists("collid", $_REQUEST) ? $_REQUEST["collid"] : 0;
$cond = array_key_exists("cond", $_REQUEST) ? $_REQUEST["cond"] : '';
$collType = array_key_exists("colltype", $_REQUEST) ? $_REQUEST["colltype"] : 'specimens';
$includeDets = array_key_exists("dets", $_REQUEST) ? $_REQUEST["dets"] : 1;
$includeImgs = array_key_exists("imgs", $_REQUEST) ? $_REQUEST["imgs"] : 1;
if ($collid) {
$dwcaHandler = new DwcArchiverOccurrence();
$dwcaHandler->setVerbose(0);
$dwcaHandler->setCollArr($collid, $collType);
if ($cond) {
//String of cond-key/value pairs (e.g. country:USA,United States;stateprovince:Arizona,New Mexico;county-start:Pima,Eddy
$cArr = explode(';', $cond);
foreach ($cArr as $rawV) {
$tok = explode(':', $rawV);
if ($tok) {
$field = $tok[0];
$cond = 'EQUALS';
$valueArr = array();
if ($p = strpos($tok[0], '-')) {
$field = substr($tok[0], 0, $p);
$cond = strtoupper(substr($tok[0], $p + 1));
}
if (isset($tok[1]) && $tok[1]) {
$valueArr = explode(',', $tok[1]);
}
if ($valueArr) {
</select>
<input name="customvalue2" type="text" value="<?php
echo $customValue2;
?>
" style="width:200px;" onchange="cogeUpdateCount(this)" />
</div>
</td>
</tr>
<tr>
<td colspan="2">
<fieldset style="margin:10px;padding:20px;">
<legend><b>CoGe Status</b></legend>
<div>
<b>Match Count:</b>
<?php
$dwcaHandler = new DwcArchiverOccurrence();
$dwcaHandler->setCollArr($collid);
$dwcaHandler->setVerbose(0);
$dwcaHandler->addCondition('decimallatitude', 'NULL');
$dwcaHandler->addCondition('decimallongitude', 'NULL');
$dwcaHandler->addCondition('locality', 'NOTNULL');
$dwcaHandler->addCondition('catalognumber', 'NOTNULL');
echo '<span id="countdiv">' . $dwcaHandler->getOccurrenceCnt() . '</span> records';
?>
<span id="recalspan" style="color:orange;display:none;">recalculating... <img src="../../images/workingcircle.gif" style="width:13px;" /></span>
</div>
<div>
<b>CoGe Authentication:</b>
<span id="coge-status" style="width:150px;color:red;">Disconnected</span>
<span style="margin-left:40px"><input type="button" name="cogeCheckStatusButton" value="Check Status" onclick="cogeCheckAuthentication()" /></span>
<span style="margin-left:40px"><a href="https://www.museum.tulane.edu/coge/" target="_blank" onclick="startAuthMonitoring()">Login to CoGe</a></span>
<?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);
}
