function setIdentifier($form_values)
{
require_once drupal_get_path('module', 'Fedora_Repository') . '/ObjectHelper.php';
require_once drupal_get_path('module', 'Fedora_Repository') . '/CollectionClass.php';
$collectionHelper = new CollectionClass();
$ppid = $_SESSION['pid'];
$itqlquery = 'select $object from <#ri> where $object <fedora-rels-ext:isPartOf><info:fedora/' . $ppid . '> and $object <fedora-rels-ext:isMemberOfCollection><info:fedora/vre:mnpl-compounds>and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active>';
$relatedItems = $collectionHelper->getRelatedItems($this->pid, $itqlquery);
$sxe = new SimpleXMLElement($relatedItems);
$nmspace = $sxe->getNamespaces(true);
$regspace = $sxe->registerXPathNamespace('ri', implode($nmspace));
$link = $sxe->xpath('//@uri');
$labid = $_SESSION['labid'];
if (empty($link)) {
$ident = $labid . '-C-0';
} else {
//loop through returns , trim to create identifier and increment highest value
$xia = array();
foreach ($link as $path) {
$path1 = substr($path, '30');
$path2 = strrchr($path1, "-");
$path = str_replace($path2, '', $path1);
$xi = ltrim($path2, "-");
$xnew = array_push($xia, $xi);
}
$num = max($xia);
$numinc = $num + 1;
$ident = $labid . '-C-' . $numinc;
}
return $ident;
}
function get_RIQueryResults($pid, $query)
{
module_load_include('php', 'Fedora_Repository', 'CollectionClass');
$collectionClass = new CollectionClass();
$results = $collectionClass->getRelatedItems($pid, $query);
return $results;
}
function handleSpecimenEditForm($form_id, $form_values, $soap_client)
{
// ======================================
// = begin creation of foxml dom object for critter/specimen stream=
// ======================================
module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
$objectHelper = new ObjectHelper();
$critterStream = $objectHelper->getStream($form_values['pid'], 'CRITTER', true);
$sxec = new SimpleXMLElement($critterStream);
$dom = new DomDocument("1.0", "UTF-8");
$dom->formatOutput = true;
///begin writing critter datastream
$spec = $dom->createElement("critters:sample");
$spec->setAttribute('xmlns:critters', "http://vre.upei.ca/critters/");
$spec->setAttribute('name', implode($sxec->xpath('//@name')));
// critter sample (root) elements
$date = $dom->createElement("critters:date_collected", $form_values['date']);
$size = $dom->createElement("critters:samplesize", implode($sxec->xpath('//critters:samplesize')));
$lab_id = $dom->createElement("critters:lab_id", implode($sxec->xpath('//critters:lab_id')));
$type = $dom->createElement("critters:type", $form_values['type']);
$desc = $dom->createElement("critters:description", implode($sxec->xpath('//critters:description')));
$spec->appendChild($lab_id);
$spec->appendChild($type);
$spec->appendChild($date);
$spec->appendChild($size);
$spec->appendChild($desc);
//critter taxonomy elements
$taxon = $dom->createElement("critters:taxonomy");
$phylum = $dom->createElement("critters:phylum", $form_values['phylum']);
$subphylum = $dom->createElement("critters:subPhylum", $form_values['subphylum']);
$class = $dom->createElement("critters:class", $form_values['class']);
$order = $dom->createElement("critters:order", $form_values['order']);
$family = $dom->createElement("critters:family", $form_values['family']);
$genus = $dom->createElement("critters:genus", $form_values['genus']);
$species = $dom->createElement("critters:species", $form_values['species']);
$taxon->appendChild($phylum);
$taxon->appendChild($subphylum);
$taxon->appendChild($class);
$taxon->appendChild($order);
$taxon->appendChild($family);
$taxon->appendChild($genus);
$taxon->appendChild($species);
// critter photos
$photos = $dom->createElement("critters:photos");
$photos->setAttribute('quantity', implode($sxec->xpath('//@quantity')));
foreach ($sxec->xpath('//@id') as $idkey => $photo) {
$image = $dom->createElement("critters:photo");
$image->setAttribute('id', $photo);
foreach ($sxec->xpath('//critters:location') as $key => $value) {
if ($key == $idkey) {
$location = $dom->createElement("critters:location", $value);
$image->appendChild($location);
}
}
$photos->appendChild($image);
}
// critter site elements
$site = $dom->createElement("critters:site");
$sitename = $dom->createElement("critters:sitename", $form_values['sitename']);
$country = $dom->createElement("critters:country", $form_values['country']);
$region = $dom->createElement("critters:region", $form_values['region']);
$latitude = $dom->createElement("critters:latitude", $form_values['latitude']);
$longitude = $dom->createElement("critters:longitude", $form_values['longitude']);
$depth = $dom->createElement("critters:depth", $form_values['depth']);
$site->appendChild($sitename);
$site->appendChild($country);
$site->appendChild($region);
$site->appendChild($latitude);
$site->appendChild($longitude);
$site->appendChild($depth);
// critter collectors
$collectors = $dom->createElement("critters:collectors");
foreach ($sxec->xpath('//critters:collector') as $individual) {
$collector = $dom->createElement("critters:collector", $individual);
$collectors->appendChild($collector);
}
// append nested elements
$spec->appendChild($taxon);
$spec->appendChild($photos);
$spec->appendChild($site);
$spec->appendChild($collectors);
$dom->appendChild($spec);
$newxml = $dom->saveXML();
// map critter form elements to DC stream
// loop through taxonomy to create label pulled from dctitle
if ($form_values['species'] != '' and $form_values['genus'] != '') {
$label = " <i>" . $form_values['genus'] . " " . $form_values['species'] . "</i>";
} elseif ($form_values['species'] != '' and $form_values['genus'] == '') {
$label = " <i>" . $form_values['species'] . "</i>";
} elseif ($form_values['species'] == '' and $form_values['genus'] != '') {
$label = " <i>" . $form_values['genus'] . "</i>";
} elseif ($form_values['species'] == '' and $form_values['genus'] == '' and $form_values['family'] != '') {
$label = " " . $form_values['family'];
} elseif ($form_values['species'] == '' and $form_values['genus'] == '' and $form_values['family'] == '' and $form_values['order'] != '') {
$label = " " . $form_values['order'];
} elseif ($form_values['species'] == '' and $form_values['genus'] == '' and $form_values['family'] == '' and $form_values['order'] == '' and $form_values['class'] != '') {
$label = " " . $form_values['class'];
} elseif ($form_values['species'] == '' and $form_values['genus'] == '' and $form_values['family'] == '' and $form_values['order'] == '' and $form_values['class'] == '' and $form_values['subphylum'] != '') {
$label = " " . $form_values['subphylum'];
} elseif ($form_values['species'] == '' and $form_values['genus'] == '' and $form_values['family'] == '' and $form_values['order'] == '' and $form_values['class'] == '' and $form_values['subphylum'] == '' and $form_values['phylum'] != '') {
$label = " " . $form_values['phylum'];
}
$dom2 = new DomDocument("1.0", "UTF-8");
$dom2->formatOutput = true;
///begin writing dc datastream
$oai = $dom2->createElement("oai_dc:dc");
$oai->setAttribute('xmlns:oai_dc', "http://www.openarchives.org/OAI/2.0/oai_dc/");
$oai->setAttribute('xmlns:dc', "http://purl.org/dc/elements/1.1/");
$oai->setAttribute('xmlns:dcterms', "http://purl.org/dc/terms/");
$oai->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
$dctitle = $dom2->createElement("dc:title", implode($sxec->xpath('//critters:lab_id')) . $label);
$dccreator = $dom2->createElement("dc:creator", 'Marine Natural Products Lab, University of Prince Edward Island');
// list specimen taxonomy as dc:subject
$dcphylum = $dom2->createElement("dc:subject", $form_values['phylum']);
$dcsubphylum = $dom2->createElement("dc:subject", $form_values['subphylum']);
$dcclass = $dom2->createElement("dc:subject", $form_values['class']);
$dcorder = $dom2->createElement("dc:subject", $form_values['order']);
$dcfamily = $dom2->createElement("dc:subject", $form_values['family']);
$dcgenus = $dom2->createElement("dc:subject", $form_values['genus']);
$dcspecies = $dom2->createElement("dc:subject", $form_values['species']);
// end taxonomy
$dcdesc = $dom2->createElement("dc:description", implode($sxec->xpath('//critters:description')));
$dcpublisher = $dom2->createElement("dc:publisher", 'Marine Natural Products Lab, University of Prince Edward Island');
$dcpid = $dom2->createElement("dc:identifier", $form_values['pid']);
$dcident = $dom2->createElement("dc:identifier", implode($sxec->xpath('//critters:lab_id')));
$dcid = $dom2->createElement("dc:identifier", implode($sxec->xpath('//@name')));
$dcdate = $dom2->createElement("dc:date", implode($sxec->xpath('//critters:date_collected')));
$dctype = $dom2->createElement("dc:type", implode($sxec->xpath('//critters:type')));
$dcformat = $dom2->createElement("dc:format", 'text/html');
$dclang = $dom2->createElement("dc:language", 'eng');
$dcsource = $dom2->createElement("dc:source", '');
$dcrelation = $dom2->createElement("dc:relation", 'vre:mnpl-specimens');
$dcrights = $dom2->createElement("dc:rights", 'All Rights Reserved - Marine Natural Products Lab. For permission to use this material please contact MNPL at rkerr@upei.ca.');
// append elements
$oai->appendChild($dctitle);
$oai->appendChild($dccreator);
$oai->appendChild($dcphylum);
$oai->appendChild($dcsubphylum);
$oai->appendChild($dcclass);
$oai->appendChild($dcorder);
$oai->appendChild($dcfamily);
$oai->appendChild($dcgenus);
$oai->appendChild($dcspecies);
$oai->appendChild($dcdesc);
$oai->appendChild($dcpublisher);
//loop for contributors
foreach ($sxec->xpath('//critters:collector') as $individual) {
$dccontrib = $dom2->createElement("dc:contributor", $individual);
$oai->appendChild($dccontrib);
}
$oai->appendChild($dcdate);
$oai->appendChild($dctype);
$oai->appendChild($dcformat);
$oai->appendChild($dcpid);
$oai->appendChild($dcident);
$oai->appendChild($dcid);
$oai->appendChild($dcsource);
$oai->appendChild($dcrelation);
$oai->appendChild($dcrights);
$dom2->appendChild($oai);
$dcxml = $dom2->saveXML();
$params = array("pid" => $form_values['pid'], "dsID" => 'DC', "altIDs" => "", "dsLabel" => "Dublin Core Record", "MIMEType" => "text/xml", "formatURI" => "URL", "dsContent" => $dcxml, "checksumType" => "DISABLED", "checksum" => "none", "logMessage" => "datastream_modified", "force" => "true");
$soapHelper = new ConnectionHelper();
$client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://*****:*****@uri') as $link) {
$partpid = ltrim($link, 'info:fedora/');
$params = array("pid" => $partpid, "dsID" => $dsId, "altIDs" => "", "dsLabel" => "Parent Critter Record", "MIMEType" => "text/xml", "formatURI" => "URL", "dsContent" => $newxml, "checksumType" => "DISABLED", "checksum" => "none", "logMessage" => "datastream_modified", "force" => "true");
$soapHelper = new ConnectionHelper();
$client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
$object = $client->__soapCall('ModifyDatastreamByValue', array($params));
}
// end of update other datastreams - begin soap call for main critter record
$params = array("pid" => $pid, "dsID" => $dsId, "altIDs" => "", "dsLabel" => "CRITTER", "MIMEType" => "text/xml", "formatURI" => "URL", "dsContent" => $newxml, "checksumType" => "DISABLED", "checksum" => "none", "logMessage" => "datastream_modified", "force" => "true");
try {
$soapHelper = new ConnectionHelper();
$client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
if ($client == null) {
drupal_set_message(t('Error Getting Soap Client.'), 'error');
return;
}
$object = $client->__soapCall('ModifyDatastreamByValue', array($params));
return true;
} catch (exception $e) {
drupal_set_message(t('Error Editing Specimen! ') . $e->getMessage(), 'error');
watchdog(t("Fedora_Repository"), t("Error Editing Specimen!") . $e->getMessage(), WATCHDOG_ERROR);
return;
}
}
function handleForm(&$form_values)
{
$errorMessage = NULL;
module_load_include('php', 'Fedora_Repository', 'CollectionClass');
module_load_include('php', 'Fedora_Repository', 'ContentModel');
module_load_include('php', 'fedora_repository', 'api/fedora_item');
$content_model_pid = ContentModel::getPidFromIdentifier($form_values['models']);
$content_model_dsid = ContentModel::getDSIDFromIdentifier($form_values['models']);
$collectionHelper = new CollectionClass();
$startTime = time();
$collection_pid = $form_values['collection_pid'];
$this->parse_refworks_item($form_values);
$this->security_helper = new SecurityClass();
$collection_item = new Fedora_Item($collection_pid);
$this->collection_policy_stream = $collection_item->get_datastream_dissemination('CHILD_SECURITY');
if (empty($this->collection_policy_stream)) {
$this->collection_policy_stream = file_get_contents(drupal_get_path('module', 'fedora_repository') . '/policies/noObjectEditPolicy.xml');
}
$success = 0;
$errors = 0;
foreach ($this->referencelist as $reference) {
$dom = new DomDocument("1.0", "UTF-8");
$dom->substituteEntities = FALSE;
$dom->formatOutput = true;
$pid = $collectionHelper->getNextPid($collection_pid, $content_model_dsid);
$rootElement = $dom->createElement("foxml:digitalObject");
$rootElement->setAttribute('VERSION', '1.1');
$rootElement->setAttribute('PID', "{$pid}");
$rootElement->setAttribute('xmlns:foxml', "info:fedora/fedora-system:def/foxml#");
$rootElement->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
$rootElement->setAttribute('xsi:schemaLocation', "info:fedora/fedora-system:def/foxml# http://www.fedora.info/definitions/1/0/foxml1-1.xsd");
$dom->appendChild($rootElement);
//create standard fedora stuff
$qdc_element = $this->createQDCStream($dom, $rootElement, $reference);
if (!$qdc_element) {
drupal_set_message(t('Error Create DC for Refworks'), 'error');
continue;
}
$item_title = '';
foreach ($reference->t1 as $value) {
$item_title .= ' --- ' . $value;
}
$this->createStandardFedoraStuff($form_values, $dom, $rootElement, $reference);
$rootElement->appendChild($qdc_element);
//create relationships
$this->createRelationShips($form_values, $dom, $rootElement, $pid);
//create dublin core
$this->createFedoraDataStreams($form_values, $dom, $rootElement, $reference);
if (!empty($this->collection_policy_stream)) {
$this->create_security_policies($dom, $rootElement, $reference);
}
$params = array('objectXML' => $dom->saveXML(), 'format' => 'info:fedora/fedora-system:FOXML-1.1', 'logMessage' => "Fedora Object Ingested");
try {
$soapHelper = new ConnectionHelper();
$client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
if ($client == null) {
drupal_set_message(t('Error Getting Soap Client.'), 'error');
watchdog(t("FEDORA_REPOSITORY"), t("Error Getting SOAP client") . $e, null, WATCHDOG_ERROR);
return;
}
$object = $client->__soapCall('ingest', array($params));
watchdog(t("FEDORA_REPOSITORY"), t("Successfully added repository item ") . $pid . ' - ' . $item_title, null, WATCHDOG_INFO);
$deleteFiles = $form_values['delete_file'];
//remove files from drupal file system
if ($deleteFiles > 0) {
unlink($form_values['fullpath']);
}
} catch (exception $e) {
$errors++;
$errorMessage = 'yes';
//drupal_set_message(t('Error Ingesting Object! Check Drupal watchdog logs for more info' . $e->getMessage()), 'error');
watchdog(t("FEDORA_REPOSITORY"), t("Error during ingest") . $item_title . ' ' . $e, null, WATCHDOG_ERROR);
//return ' ';
}
$success++;
}
if (isset($errorMessage)) {
drupal_set_message(t('Error Ingesting one or more records! Check Drupal watchdog logs for more info'), 'error');
}
$endTime = time();
drupal_set_message(t('Successfull ingest of %success records. %errors records failed. Ingest took %seconds seconds', array('%success' => $success - $errors, '%errors' => $errors, '%seconds' => $endTime - $startTime)), 'info');
//drupal_set_message(t('ingest took %seconds ',array('%seconds'=>$endTime-$startTime)),'info');
}
function showCompound()
{
$dsid = 'COMPOUND';
$path = drupal_get_path('module', 'Fedora_Repository');
require_once drupal_get_path('module', 'Fedora_Repository') . '/ObjectHelper.php';
require_once drupal_get_path('module', 'Fedora_Repository') . '/CollectionClass.php';
$collectionHelper = new CollectionClass();
$xmlstr = $collectionHelper->getStream($this->pid, "COMPOUND");
html_entity_decode($xmlstr);
if ($xmlstr == null || strlen($xmlstr) < 5) {
return " ";
}
try {
$proc = new XsltProcessor();
} catch (Exception $e) {
drupal_set_message(t($e->getMessage()), 'error');
return " ";
}
$xsl = new DomDocument();
$xsl->load($path . '/mnpl/xsl/compound.xsl');
$input = new DomDocument();
$input->loadXML(trim($xmlstr));
$xsl = $proc->importStylesheet($xsl);
$newdom = $proc->transformToDoc($input);
$content = $newdom->saveXML();
// get parent pid and build link
$pid = $this->pid;
$itqlquery = 'select $object from <#ri> where <info:fedora/' . $pid . '><fedora-rels-ext:isPartOf> $object ';
$relatedItems = $collectionHelper->getRelatedItems($this->pid, $itqlquery);
$sxe = new SimpleXMLElement($relatedItems);
$nmspace = $sxe->getNamespaces(true);
$regspace = $sxe->registerXPathNamespace('ri', implode($nmspace));
// begin fractions
$flabel = '<h4>Parent Specimen Record for This Compound</h4><p>';
$link = implode($sxe->xpath('//@uri'));
$link = substr($link, 12);
global $base_url;
$plink .= '<a href =' . $base_url . '/fedora/repository/' . $link . '>Parent Specimen</a><br>';
if (user_access('edit fedora meta data')) {
$editcomp = '<a href =' . $base_url . '/fedora/repository/editmetadata/' . $pid . '/' . $dsid . '>Edit This Compound</a><br>';
} else {
$editcomp = '';
}
// display other compounds for this parent
$itqlQuery = 'select $object $title from <#ri> where $object <fedora-model:label> $title and $object <fedora-rels-ext:isPartOf> <info:fedora/' . $link . '> and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active> order by $title';
$relatedItems = $collectionHelper->getRelatedItems($this->pid, $itqlQuery);
$sxe = new SimpleXMLElement($relatedItems);
$nmspace = $sxe->getNamespaces(true);
$regspace = $sxe->registerXPathNamespace('ri', implode($nmspace));
// begin display compounds
global $base_url;
$altcomp = '<h4> Other Compounds For Parent Sepcimen</h4><div>';
if (stristr(implode($sxe->xpath('//ri:title')), 'compound')) {
foreach ($sxe->xpath('//@uri') as $link2) {
if (strstr($link2, 'compound')) {
$pidlink = substr($link2, 12);
if ($pidlink != $pid) {
$compound .= '<a href = "' . $base_url . '/fedora/repository/' . $pidlink . '">' . substr($link2, 30) . '</a><br>';
}
}
}
}
if ($compound == NULL) {
$compound = "<div>No other Compounds present for this Specimen</div>";
}
$collection_fieldset = array('#title' => t('MNPL Compound Record'), '#collapsible' => TRUE, '#collapsed' => FALSE, '#value' => $content . $editcomp . $flabel . $plink . $altcomp . $compound);
return theme('fieldset', $collection_fieldset);
}
function showRomeo($collapsed = false)
{
$path = drupal_get_path('module', 'Fedora_Repository');
module_load_include('php', 'Fedora_Repository', 'CollectionClass');
$collectionHelper = new CollectionClass();
//$returnValue['title']="Description";
$xmlstr = $collectionHelper->getStream($this->pid, "ROMEO", 0);
if ($xmlstr == null || strlen($xmlstr) < 5) {
return " ";
}
try {
$proc = new XsltProcessor();
} catch (Exception $e) {
drupal_set_message(t($e->getMessage()), 'error');
return;
}
$xsl = new DomDocument();
$xsl->load($path . '/xsl/romeo.xsl');
$input = new DomDocument();
$input->loadXML(trim($xmlstr));
$xsl = $proc->importStylesheet($xsl);
$newdom = $proc->transformToDoc($input);
$content = $newdom->saveXML();
$collection_fieldset = array('#title' => t('Romeo'), '#collapsible' => TRUE, '#collapsed' => $collapsed, '#value' => $content);
return theme('fieldset', $collection_fieldset);
}
/**
* Look in the content model for rules to run on the specified datastream.
*
* @param string $pid
* @param string $dsid
* @return boolean
*/
function get_and_do_datastream_rules($pid, $dsid, $file = '')
{
if (!user_access('ingest new fedora objects')) {
drupal_set_message(t('You do not have permission to add datastreams.'));
return FALSE;
}
$collection_object = new CollectionClass();
$content_model_list = $this->get_content_models_list($pid);
foreach ($content_model_list as $content_model) {
$content_model_xml = $this->getStream($content_model, variable_get('Islandora_Content_Model_DSID', 'ISLANDORACM'), 1);
if (!empty($content_model_xml->display_in_fieldset->datastream)) {
foreach ($content_model_xml->display_in_fieldset->datastream as $datastream) {
if ($datastream['id'] == $dsid) {
$collection_object->callMethods($file, $datastream->add_datastream_method);
break;
}
}
}
if (!empty($_SESSION['fedora_ingest_files'])) {
foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
$file_obj = new stdClass();
// $file->uid = $user->uid;
$file_obj->status = 0;
$file_obj->filename = substr($createdFile, strrpos($createdFile, '/'));
$file_obj->filepath = $createdFile;
$file_obj->filemime = file_get_mimetype($createdFile);
$this->addStream($pid, $dsid, $file_obj);
file_delete($createdFile);
}
$_SESSION['fedora_ingest_files'] = '';
}
}
}
