Beispiel #1
0
 function canIngestHere($collection_pid)
 {
     global $user;
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     $objectHelper = new ObjectHelper();
     //get the childsecurity policy from the collection.
     $policyStream = $objectHelper->getStream($collection_pid, SECURITYCLASS::$SECURITYSTREAM, false);
     if ($policyStream == null) {
         //no child policy stream so collection is wide open to anyone to ingest, that has the permission ingest in Drupal.
         //maybe we should return false here?? would be more secure.
         return true;
     }
     $allowedUsersAndRoles = $this->getAllowedUsersAndRoles($policyStream);
     if (!$allowedUsersAndRoles) {
         //error processing stream so don't let them ingest here.
         return false;
     }
     $allowedUsers = $allowedUsersAndRoles["users"];
     $allowedRoles = $allowedUsersAndRoles["roles"];
     foreach ($user->roles as $role) {
         if (in_array($role, $allowedRoles)) {
             return true;
         }
     }
     if (in_array($user->name, $allowedUsers)) {
         return true;
     }
     return false;
 }
Beispiel #2
0
 private function getNid($pid)
 {
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     //get Nid from Pid
     $object = new ObjectHelper($pid);
     $spec = $object->getStream($pid, 'MAG', 0);
     $xml = new SimpleXMLElement($spec);
     $nid = implode($xml->xpath('//nid'));
     //		$urlNid = implode($xml->xpath('//nurl'));
     //		$strNid = explode('node/', $urlNid);
     //		$nid = $strNid[1];
     return $nid;
 }
Beispiel #3
0
 function createPolicy($collectionPid, &$dom, &$rootElement)
 {
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     $objectHelper = new ObjectHelper();
     $dsid = 'CHILD_SECURITY';
     $policyStreamDoc = $objectHelper->getStream($collectionPid, $dsid, false);
     if (!isset($policyStreamDoc)) {
         return null;
         //there is no policy stream so object will not have a policy stream
     }
     try {
         $xml = new SimpleXMLElement($policyStreamDoc);
     } catch (Exception $e) {
         watchdog(t("Fedora_Repository"), t("Problem getting Security Policy!"), NULL, WATCHDOG_ERROR);
         drupal_set_message(t('Problem getting Security Policy! ') . $e->getMessage(), 'error');
         return false;
     }
     $policyElement = $dom->createDocumentFragment();
     if (!$policyElement) {
         drupal_set_message(t('error parsing security policy stream!'));
         watchdog(t("Fedora_Repository"), t("Error parsing security policy stream, could not parse policy stream!"), NULL, WATCHDOG_NOTICE);
         return false;
     }
     $dom->importNode($policyElement, true);
     $value = $policyElement->appendXML($policyStreamDoc);
     if (!$value) {
         drupal_set_message(t('error creating security policy stream!'));
         watchdog(t("Fedora_Repository"), t("Error creating security policy stream, could not parse collection policy template file!"), NULL, WATCHDOG_NOTICE);
         return false;
     }
     $ds1 = $dom->createElement("foxml:datastream");
     $rootElement->appendChild($ds1);
     $ds1->setAttribute("ID", "POLICY");
     $ds1->setAttribute("STATE", "A");
     $ds1->setAttribute("CONTROL_GROUP", "X");
     $ds1v = $dom->createElement("foxml:datastreamVersion");
     $ds1->appendChild($ds1v);
     $ds1v->setAttribute("ID", "POLICY.0");
     $ds1v->setAttribute("MIMETYPE", "text/xml");
     $ds1v->setAttribute("LABEL", "POLICY");
     //$ds1v->setAttribute("FORMAT_URI","info:fedora/fedora-system:format/xml.fedora.audit");
     $content = $dom->createElement("foxml:xmlContent");
     $ds1v->appendChild($content);
     $content->appendChild($policyElement);
     return true;
 }
 function show_compound_details($compound_pid)
 {
     module_load_include('php', 'fedora_repository', 'ObjectHelper');
     $object_helper = new ObjectHelper();
     $compound_stream = new SimpleXMLElement($object_helper->getStream($compound_pid, 'COMPOUND'));
     $fields = array('weight', 'ptp1b', 'hct116', 'hela', 'pc3', 'are', 'antiproliferative');
     foreach ($fields as $field) {
         if (implode($compound_stream->xpath("//compounds:{$field}")) == 'Hit') {
             $td = '<td bgcolor="red">';
         } elseif (implode($compound_stream->xpath("//compounds:{$field}")) == 'Strong') {
             $td = '<td bgcolor = "yellow">';
         } elseif (implode($compound_stream->xpath("//compounds:{$field}")) == 'Medium') {
             $td = '<td bgcolor = "orange">';
         } elseif (implode($compound_stream->xpath("//compounds:{$field}")) == 'Low') {
             $td = '<td bgcolor = "grey">';
         } else {
             $td = '<td>';
         }
         $row_html .= $td . implode($compound_stream->xpath("//compounds:{$field}")) . '</td>';
     }
     return $row_html;
 }
Beispiel #5
0
 function buildFractionEditForm()
 {
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     $object = new ObjectHelper();
     $frac = $object->getStream($this->pid, 'FRACTION', 0);
     $doc = new DomDocument();
     if (!isset($frac)) {
         drupal_set_message(t('Error getting fraction metadata stream'), 'error');
         return null;
     }
     $xml = new SimpleXMLElement($frac);
     $radioValues = array();
     $radioValues['No_Assay'] = 'No_Assay';
     $radioValues['Hit'] = 'Hit';
     $radioValues['Strong'] = 'Strong';
     $radioValues['Medium'] = 'Medium';
     $radioValues['Low'] = 'Low';
     $radioValues['Inactive'] = 'Inactive';
     $form = array();
     $identifier = $xml->xpath('//fractions:identifier');
     $form['identifier'] = array('#type' => 'hidden', '#title' => t('<strong>Identifier</strong>'), '#value' => implode($identifier));
     $form['ident'] = array('#type' => 'item', '#title' => t('<strong>Identifier</strong>'), '#value' => implode($identifier));
     $plate = $xml->xpath('//fractions:plate');
     $form['plate'] = array('#type' => 'textfield', '#default_value' => implode($plate), '#title' => t('<strong>Plate</strong>'));
     $weight = $xml->xpath('//fractions:weight');
     $form['weight'] = array('#type' => 'textfield', '#default_value' => implode($weight), '#title' => t('<strong>Weight</strong>'));
     $pt = $xml->xpath('//fractions:ptp1b');
     $form['pt'] = array('#type' => 'radios', '#default_value' => implode($pt), '#options' => $radioValues, '#title' => t('<strong>PTP1B</strong>'));
     $pt_com = $xml->xpath('//fractions:ptp1b_com');
     $form['pt_com'] = array('#type' => 'textfield', '#default_value' => implode($pt_com), '#title' => t('<strong>PTP1B Comments</strong>'));
     $hct = $xml->xpath('//fractions:hct116');
     $form['hct'] = array('#type' => 'radios', '#default_value' => implode($hct), '#options' => $radioValues, '#title' => t('<strong>HCT116</strong>'));
     $hct_com = $xml->xpath('//fractions:hct116_com');
     $form['hct_com'] = array('#type' => 'textfield', '#default_value' => implode($hct_com), '#title' => t('<strong>HCT116 Comments</strong>'));
     $hela = $xml->xpath('//fractions:hela');
     $form['hela'] = array('#type' => 'radios', '#default_value' => implode($hela), '#options' => $radioValues, '#title' => t('<strong>HELA</strong>'));
     $hela_com = $xml->xpath('//fractions:hela_com');
     $form['hela_com'] = array('#type' => 'textfield', '#default_value' => implode($hela_com), '#title' => t('<strong>HELA Comments</strong>'));
     $pc3 = $xml->xpath('//fractions:pc3');
     $form['pc3'] = array('#type' => 'radios', '#default_value' => implode($pc3), '#options' => $radioValues, '#title' => t('<strong>PC3</strong>'));
     $pc3_com = $xml->xpath('//fractions:pc3_com');
     $form['pc3_com'] = array('#type' => 'textfield', '#default_value' => implode($pc3_com), '#title' => t('<strong>PC3 Comments</strong>'));
     $are = $xml->xpath('//fractions:are');
     $form['are'] = array('#type' => 'radios', '#default_value' => implode($are), '#options' => $radioValues, '#title' => t('<strong>ARE</strong>'));
     $are_com = $xml->xpath('//fractions:are_com');
     $form['are_com'] = array('#type' => 'textfield', '#default_value' => implode($are_com), '#title' => t('<strong>ARE Comments</strong>'));
     $antiproliferative = $xml->xpath('//fractions:antiproliferative');
     $form['antiproliferative'] = array('#type' => 'radios', '#default_value' => implode($antiproliferative), '#options' => $radioValues, '#title' => t('<strong>Antiproliferative</strong>'));
     $antiproliferative_com = $xml->xpath('//fractions:antiproliferative_com');
     $form['antiproliferative_com'] = array('#type' => 'textfield', '#default_value' => implode($antiproliferative_com), '#title' => t('<strong>Antiproliferative Comments</strong>'));
     $location = $xml->xpath('//fractions:location');
     $form['location'] = array('#type' => 'textfield', '#default_value' => implode($location), '#title' => t('<strong>Location</strong>'));
     $notes = $xml->xpath('//fractions:notes');
     $form['notes'] = array('#type' => 'textarea', '#default_value' => implode($notes), '#title' => t('<strong>Notes</strong>'));
     $form['#redirect'] = 'fedora/repository/' . $this->pid;
     $form['pid'] = array('#type' => 'hidden', '#value' => $this->pid);
     $form['dsid'] = array('#type' => 'hidden', '#value' => 'FRACTION');
     $form['submit'] = array('#type' => 'submit', '#value' => 'Update');
     return $form;
 }
Beispiel #6
0
 function getStream($pid, $dsid, $showError = 1)
 {
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     $objectHelper = new ObjectHelper();
     return $objectHelper->getStream($pid, $dsid, $showError);
 }
Beispiel #7
0
 function handleVideoEditForm($form_id, $form_values, $soap_client)
 {
     //echo "FORM_ID: ".$form_id;
     $pid = $form_values['pid'];
     module_load_include('php', 'Fedora_Repository', 'ObjectHelper');
     $object = new ObjectHelper($pid);
     $spec = $object->getStream($pid, 'MAG', TRUE);
     $xml = new SimpleXMLElement($spec);
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = true;
     $mag = $dom->createElement("mag");
     //		$dom->appendChild($mag);
     $vid = $dom->createElement("video");
     $proxies = $dom->createElement("proxies");
     $metrics = $dom->createElement("video_metrics");
     $dimensions = $dom->createElement("video_dimensions");
     $format = $dom->createElement("format");
     $dis = $dom->createElement("dis");
     $gen = $dom->createElement("gen");
     $bib = $dom->createElement("bib");
     $drup = $dom->createElement("dru");
     $vid->appendChild($dom->createElement('sequence_number', implode($xml->xpath('//sequence_number'))));
     $proxies->appendChild($dom->createElement('size', implode($xml->xpath('//size'))));
     $proxies->appendChild($dom->createElement('md5', implode($xml->xpath('//md5'))));
     $proxies->appendChild($dom->createElement('file', implode($xml->xpath('//file'))));
     $metrics->appendChild($dom->createElement('framerate', implode($xml->xpath('//framerate'))));
     $dimensions->appendChild($dom->createElement('framewidth', implode($xml->xpath('//framewidth'))));
     $dimensions->appendChild($dom->createElement('frameheight', implode($xml->xpath('//frameheight'))));
     $metrics->appendChild($dom->createElement('bitrate', implode($xml->xpath('//bitrate'))));
     $format->appendChild($dom->createElement('mime', implode($xml->xpath('//mime'))));
     //		$vid->appendChild($dom->createElement('samplingfrequencyunit', implode($xml->xpath('//samplingfrequencyunit'))));
     //		$vid->appendChild($dom->createElement('samplingfrequencyplane', implode($xml->xpath('//samplingfrequencyplane'))));
     $dis->appendChild($dom->createElement('item', implode($xml->xpath('//item'))));
     $drup->appendChild($dom->createElement('nid', implode($xml->xpath('//nid'))));
     $drup->appendChild($dom->createElement('nurl', implode($xml->xpath('//nurl'))));
     $previousElement = null;
     //used in case we have to nest elements for qualified dublin core
     foreach ($form_values as $key => $value) {
         $index = strrpos($key, '-');
         if ($index > 01) {
             $key = substr($key, 0, $index);
         }
         $value = trim($value);
         $test = substr($key, 0, 3);
         $element = substr($key, 4);
         if ($test == 'vid') {
             //don't try to process other form values
             try {
                 $previousElement = $dom->createElement($element, $value);
                 if (in_array($element, array('file', 'md5', 'size', 'note'))) {
                     $proxies->appendChild($previousElement);
                 } elseif (in_array($element, array('bitrate', 'framerate'))) {
                     $metrics->appendChild($previousElement);
                 } elseif (in_array($element, array('framewidth', 'frameheight'))) {
                     $dimensions->appendChild($previousElement);
                 } elseif (in_array($element, array('mime'))) {
                     $format->appendChild($previousElement);
                 } else {
                     $vid->appendChild($previousElement);
                 }
             } catch (exception $e) {
                 drupal_set_message(t($e->getMessage()), 'error');
                 continue;
             }
         }
         if ($test == 'dis') {
             //don't try to process other form values
             try {
                 $previousElement = $dom->createElement(substr($key, 4), $value);
                 $dis->appendChild($previousElement);
             } catch (exception $e) {
                 drupal_set_message(t($e->getMessage()), 'error');
                 continue;
             }
         }
         if ($test == 'gen') {
             //don't try to process other form values
             try {
                 $previousElement = $dom->createElement(substr($key, 4), $value);
                 $gen->appendChild($previousElement);
             } catch (exception $e) {
                 drupal_set_message(t($e->getMessage()), 'error');
                 continue;
             }
         }
         if ($test == 'bib') {
             //don't try to process other form values
             try {
                 $previousElement = $dom->createElement(substr($key, 4), $value);
                 $bib->appendChild($previousElement);
             } catch (exception $e) {
                 drupal_set_message(t($e->getMessage()), 'error');
                 continue;
             }
         }
         if ($test == 'dru') {
             //don't try to process other form values
             try {
                 $previousElement = $dom->createElement(substr($key, 4), $value);
                 $drup->appendChild($previousElement);
             } catch (exception $e) {
                 drupal_set_message(t($e->getMessage()), 'error');
                 continue;
             }
         }
         //$rootElement->appendChild($datastream);
     }
     $proxies->appendChild($metrics);
     $proxies->appendChild($dimensions);
     $proxies->appendChild($format);
     $vid->appendChild($proxies);
     $mag->appendChild($vid);
     $mag->appendChild($gen);
     $mag->appendChild($bib);
     $mag->appendChild($dis);
     $mag->appendChild($drup);
     $dom->appendChild($mag);
     $params = array("pid" => "{$pid}", "dsID" => "MAG", "altIDs" => "", "dsLabel" => "Mag Metadata", "MIMEType" => "text/xml", "formatURI" => "", "dsContent" => $dom->saveXML(), "checksumType" => "DISABLED", "checksum" => "none", "logMessage" => "datastream_modified", "force" => "true");
     //drupal_set_message($mag);
     $ccks = array();
     module_load_include('php', 'Fedora_Repository', 'epistemetec/plugins/Node');
     $node = new EpistemetecNode();
     $ccks = $node->hashCCK($form_values);
     try {
         //$soapHelper = new ConnectionHelper();
         //$client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
         $object = $soap_client->__soapCall('ModifyDatastreamByValue', array($params));
         $node->editNode($ccks);
         return $form_id;
     } catch (exception $e) {
         drupal_set_message(t("Error updating  MAG metadata ") . $e->getMessage(), 'error');
     }
 }