*
* Author: David B. Lowery
*/
include_once '../../../config/symbini.php';
include_once 'fp/FPNetworkFactory.php';
include_once 'fp/common/AnnotationGenerator.php';
// check that the client helper has been installed
$file = 'fp/FPNetworkFactory.php';
$includePaths = explode(PATH_SEPARATOR, get_include_path());
$fileExists = false;
foreach ($includePaths as $p) {
$fullname = $p . DIRECTORY_SEPARATOR . $file;
if (is_file($fullname)) {
$fileExists = true;
break;
}
}
if (!$fileExists) {
echo "FilteredPush Support has been enabled in this Symbiota installation, but FilteredPush helper code is not installed.<BR>";
echo "<strong>{$file} not found.</strong>";
} else {
// Check for required query params
if (array_key_exists('catalognumber', $_GET) && (array_key_exists('collectioncode', $_GET) || array_key_exists('institutioncode', $_GET))) {
$endpoint = FPNetworkFactory::getSparqlEndpoint();
// returns query result formatted as html
$results = $endpoint->getAnnotations($_GET);
echo $results;
} else {
throw new Exception("catalognumber and either collectioncode or institutioncode required for \"Annotations\" tab view.");
}
}
public function addDetermination($detArr, $isEditor)
{
$status = "Determination submitted successfully!";
if (!$this->occid) {
return 'ERROR: occid is null';
}
$isCurrent = 0;
if (!array_key_exists('makecurrent', $detArr)) {
$detArr['makecurrent'] = 0;
}
if (!array_key_exists('printqueue', $detArr)) {
$detArr['printqueue'] = 0;
}
if ($detArr['makecurrent'] == 1 && $isEditor < 3) {
$isCurrent = 1;
}
if ($isEditor == 3) {
$status = "Determination has been added successfully, but is pending approval before being activated";
}
$sortSeq = 1;
if (preg_match('/([1,2]{1}\\d{3})/', $detArr['dateidentified'], $matches)) {
$sortSeq = 2100 - $matches[1];
}
if ($isCurrent) {
//Set all dets for this specimen to not current
$sqlSetCur1 = 'UPDATE omoccurdeterminations SET iscurrent = 0 WHERE appliedstatus = 1 AND occid = ' . $this->occid;
if (!$this->conn->query($sqlSetCur1)) {
$status = 'ERROR resetting dets to not current: ' . $this->conn->error;
//$status .= '; '.$sqlSetCur1;
}
}
//Load new determination into omoccurdeterminations
$sciname = $this->cleanInStr($detArr['sciname']);
$notes = $this->cleanInStr($detArr['identificationremarks']);
if ($isEditor == 3 && is_numeric($detArr['confidenceranking'])) {
$notes .= ($notes ? '; ' : '') . 'ConfidenceRanking: ' . $detArr['confidenceranking'];
}
$sql = 'INSERT INTO omoccurdeterminations(occid, identifiedBy, dateIdentified, sciname, scientificNameAuthorship, ' . 'identificationQualifier, iscurrent, printqueue, appliedStatus, identificationReferences, identificationRemarks, sortsequence) ' . 'VALUES (' . $this->occid . ',"' . $this->cleanInStr($detArr['identifiedby']) . '","' . $this->cleanInStr($detArr['dateidentified']) . '","' . $sciname . '",' . ($detArr['scientificnameauthorship'] ? '"' . $this->cleanInStr($detArr['scientificnameauthorship']) . '"' : 'NULL') . ',' . ($detArr['identificationqualifier'] ? '"' . $this->cleanInStr($detArr['identificationqualifier']) . '"' : 'NULL') . ',' . $detArr['makecurrent'] . ',' . $detArr['printqueue'] . ',' . ($isEditor == 3 ? 0 : 1) . ',' . ($detArr['identificationreferences'] ? '"' . $this->cleanInStr($detArr['identificationreferences']) . '"' : 'NULL') . ',' . ($notes ? '"' . $notes . '"' : 'NULL') . ',' . $sortSeq . ')';
//echo "<div>".$sql."</div>";
if ($this->conn->query($sql)) {
//Create and insert Symbiota GUID for determination(UUID)
$guid = UuidFactory::getUuidV4();
$detId = $this->conn->insert_id;
if (!$this->conn->query('INSERT INTO guidoccurdeterminations(guid,detid) VALUES("' . $guid . '",' . $detId . ')')) {
$status .= ' (Warning: Symbiota GUID mapping #1 failed)';
}
//If is current, move old determination from omoccurrences to omoccurdeterminations and then load new record into omoccurrences
if ($isCurrent) {
//If determination is already in omoccurdeterminations, INSERT will fail move omoccurrences determination to table
$sqlInsert = 'INSERT INTO omoccurdeterminations(occid, identifiedBy, dateIdentified, sciname, scientificNameAuthorship, ' . 'identificationQualifier, identificationReferences, identificationRemarks, sortsequence) ' . 'SELECT occid, IFNULL(identifiedby,"unknown") AS idby, IFNULL(dateidentified,"unknown") AS di, ' . 'sciname, scientificnameauthorship, identificationqualifier, identificationreferences, identificationremarks, 10 AS sortseq ' . 'FROM omoccurrences WHERE (occid = ' . $this->occid . ')';
//echo "<div>".$sqlInsert."</div>";
if ($this->conn->query($sqlInsert)) {
//Create and insert Symbiota GUID for determination(UUID)
$guid = UuidFactory::getUuidV4();
$detId = $this->conn->insert_id;
if (!$this->conn->query('INSERT INTO guidoccurdeterminations(guid,detid) VALUES("' . $guid . '",' . $detId . ')')) {
$status .= ' (Warning: Symbiota GUID mapping #2 failed)';
}
}
$tidToAdd = $detArr['tidtoadd'];
if ($tidToAdd && !is_numeric($tidToAdd)) {
$tidToAdd = 0;
}
//Check to see if taxon has a locality security protection (rare, threatened, or sensitive species)
$sStatus = 0;
if ($tidToAdd) {
$sqlSs = 'SELECT securitystatus FROM taxa WHERE (tid = ' . $tidToAdd . ')';
$rsSs = $this->conn->query($sqlSs);
if ($rSs = $rsSs->fetch_object()) {
if ($rSs->securitystatus == 1) {
$sStatus = 1;
}
}
$rsSs->free();
if (!$sStatus) {
$sql2 = 'SELECT c.clid ' . 'FROM fmchecklists c INNER JOIN fmchklsttaxalink cl ON c.clid = cl.clid ' . 'INNER JOIN taxstatus ts1 ON cl.tid = ts1.tid ' . 'INNER JOIN taxstatus ts2 ON ts1.tidaccepted = ts2.tidaccepted ' . 'INNER JOIN omoccurrences o ON c.locality = o.stateprovince ' . 'WHERE c.type = "rarespp" AND ts1.taxauthid = 1 AND ts2.taxauthid = 1 ' . 'AND (ts2.tid = ' . $tidToAdd . ') AND (o.occid = ' . $this->occid . ')';
//echo $sql; exit;
$rsSs2 = $this->conn->query($sql2);
if ($rsSs2->num_rows) {
$sStatus = 1;
}
$rsSs2->free();
}
}
//Load new determination into omoccurrences table
$sqlNewDet = 'UPDATE omoccurrences ' . 'SET identifiedBy = "' . $this->cleanInStr($detArr['identifiedby']) . '", dateIdentified = "' . $this->cleanInStr($detArr['dateidentified']) . '",' . 'family = ' . ($detArr['family'] ? '"' . $this->cleanInStr($detArr['family']) . '"' : 'NULL') . ',' . 'sciname = "' . $sciname . '",genus = NULL, specificEpithet = NULL, taxonRank = NULL, infraspecificepithet = NULL,' . 'scientificNameAuthorship = ' . ($detArr['scientificnameauthorship'] ? '"' . $this->cleanInStr($detArr['scientificnameauthorship']) . '"' : 'NULL') . ',' . 'identificationQualifier = ' . ($detArr['identificationqualifier'] ? '"' . $this->cleanInStr($detArr['identificationqualifier']) . '"' : 'NULL') . ',' . 'identificationReferences = ' . ($detArr['identificationreferences'] ? '"' . $this->cleanInStr($detArr['identificationreferences']) . '"' : 'NULL') . ',' . 'identificationRemarks = ' . ($detArr['identificationremarks'] ? '"' . $this->cleanInStr($detArr['identificationremarks']) . '"' : 'NULL') . ', ' . 'tidinterpreted = ' . ($tidToAdd ? $tidToAdd : 'NULL') . ', localitysecurity = ' . $sStatus . ' WHERE (occid = ' . $this->occid . ')';
//echo "<div>".$sqlNewDet."</div>";
$this->conn->query($sqlNewDet);
//Add identification confidence
if (isset($detArr['confidenceranking'])) {
$idStatus = $this->editIdentificationRanking($detArr['confidenceranking'], '');
if ($idStatus) {
$status .= '; ' . $idStatus;
}
}
//Remap images
$sql = 'UPDATE images SET tid = ' . ($tidToAdd ? $tidToAdd : 'NULL') . ' WHERE (occid = ' . $this->occid . ')';
//echo $sql;
if (!$this->conn->query($sql)) {
$status = 'ERROR: Annotation added but failed to remap images to new name';
$status .= ': ' . $this->conn->error;
}
}
//FP code
global $fpEnabled;
if (isset($fpEnabled) && $fpEnabled && isset($detArr['fpsubmit']) && $detArr['fpsubmit']) {
$status = "Determination added successfully and submitted to Filtered Push!";
try {
// create an array that the annotation generator can understand from $detArr
$annotation = fpNewDetArr($detArr);
// generate rdf/xml
$generator = FPNetworkFactory::getAnnotationGenerator();
$rdf = $generator->generateRdfXml($annotation);
// inject annotation into fp
$network = FPNetworkFactory::getNetworkFacade();
$response = $network->injectIntoFP($rdf);
} catch (Exception $e) {
error_log($e->getFile() . '(' . $e->getLine() . '): ' . $e->getMessage());
$status = "Determination added successfully but there was an error during submission to Filtered Push!";
}
}
} else {
$status = 'ERROR - failed to add determination: ' . $this->conn->error;
}
return $status;
}
Annotator Name: <input type="text" size="20" name="annotator_name"/><br/>
Annotator Email: <input type="text" size="20" name="annotator_email"/><br/>
<input type="radio" name="polarity" value="positive"/> Agree <input type="radio" name="polarity"
value="neutral"/> Neutral <input
type="radio" name="polarity" value="negative"/> Disagree<br/>
Opinion Text: <input type="text" size="40" name="opinionText"/><br/>
Evidence: <br/>
<textarea name="evidence" rows="10" cols="35"></textarea><br/>
<input type="hidden" name="annotationURI" value="<?php
echo $_GET['uri'];
?>
"/>
<input type="submit" value="Respond"/>
</form>
<?php
} else {
if ($_SERVER['REQUEST_METHOD'] == "POST") {
$fp = FPNetworkFactory::getNetworkFacade();
$annotation = array();
$annotation['target'] = array("annotationUri" => $_POST['annotationURI']);
$annotation['body'] = array("polarity" => array("name" => $_POST['polarity']), "describesObject" => array("annotationUri" => $_POST['annotationURI']), "opinionText" => $_POST['opinionText']);
$annotation['annotator_name'] = $_POST['annotator_name'];
$annotation['annotator_email'] = $_POST['annotator_email'];
$annotation['evidence'] = array("chars" => $_POST['evidence']);
echo $fp->respond(AnnotationGenerator::responseAnnotation($annotation));
echo "<script type='text/javascript'>";
echo "window.close();";
echo "</script>";
}
}
}
