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); }