public function save(Default_Model_Dataset $value)
{
global $application;
$data = array();
if (!isnull($value->getId())) {
$data['id'] = $value->getId();
}
if (!isnull($value->getName())) {
$data['name'] = $value->getName();
}
if (!isnull($value->getCategory())) {
$data['category'] = $value->getCategory();
}
if (!isnull($value->getDescription())) {
$data['description'] = $value->getDescription();
}
if (!isnull($value->getHomepage())) {
$data['homepage'] = $value->getHomepage();
}
if (!isnull($value->getElixirURL())) {
$data['elixir_url'] = $value->getElixirURL();
}
if (!isnull($value->getDisciplineID())) {
$data['disciplineid'] = $value->getDisciplineID();
}
if (!isnull($value->getAddedByID())) {
$data['addedby'] = $value->getAddedByID();
}
if (!isnull($value->getAddedon())) {
$data['addedon'] = $value->getAddedon();
}
if (!isnull($value->getTags())) {
$data['tags'] = $value->getTags();
}
if (!isnull($value->getGuID())) {
$data['guid'] = $value->getGuID();
}
$q1 = 'id = ?';
$q2 = $value->id;
if (null === ($id = $value->id)) {
unset($data['id']);
$value->id = $this->getDbTable()->insert($data);
} else {
$s = $this->getDbTable()->getAdapter()->quoteInto($q1, $q2);
$this->getDbTable()->update($data, $s);
}
}
public function save(Default_Model_Dataset $value)
{
$oldTags = $value->tags;
if (!is_array($value->tags) || count($value->tags) == 0 || trim($value->tags[0]) == "") {
$value->setTags("NULL");
} else {
$value->setTags(php_to_pg_array($value->tags));
}
// parent::save($value);
global $application;
$data = array();
if (!isnull($value->getId())) {
$data['id'] = $value->getId();
}
if (!isnull($value->getName())) {
$data['name'] = $value->getName();
}
if (!isnull($value->getCategory())) {
$data['category'] = $value->getCategory();
}
if (!isnull($value->getDescription())) {
$data['description'] = $value->getDescription();
}
if (!isnull($value->getHomepage())) {
$data['homepage'] = $value->getHomepage();
}
if (!isnull($value->getElixirURL())) {
$data['elixir_url'] = $value->getElixirURL();
}
if (!isnull($value->getDisciplineID())) {
$data['disciplineid'] = $value->getDisciplineID();
}
if (!isnull($value->getAddedByID())) {
$data['addedby'] = $value->getAddedByID();
}
if (!isnull($value->getAddedon())) {
$data['addedon'] = $value->getAddedon();
}
if (!isnull($value->getTags())) {
$data['tags'] = $value->getTags();
}
if (!isnull($value->getGuID())) {
$data['guid'] = $value->getGuID();
}
if (!isnull($value->getParentID())) {
$data['parentid'] = $value->getParentID();
}
if ($value->getParentID() == "0") {
$data['parentid'] = null;
}
if (trim($value->getHomepage()) === "") {
$data['homepage'] = null;
}
if (trim($value->getElixirURL()) === "") {
$data['elixir_url'] = null;
}
if (trim($value->getDescription()) === "") {
$data['description'] = null;
}
if ($value->getTags() === "NULL") {
$data['tags'] = null;
}
$q1 = 'id = ?';
$q2 = $value->id;
if (null === ($id = $value->id)) {
unset($data['id']);
$value->id = $this->getDbTable()->insert($data);
} else {
$s = $this->getDbTable()->getAdapter()->quoteInto($q1, $q2);
$this->getDbTable()->update($data, $s);
}
$value->setTags($oldTags);
}
/**
* implementation of abstract parse() operation from RestXMLParser.
* @xml SimpleXMLElement the root element of the dataset XML representation
*
* @return Default_Model_Dataset
* @access public
*/
public function parse($xml)
{
global $application;
if (!is_null($this->_user)) {
$ds = new Default_Model_Dataset();
try {
$xml = new SimpleXMLElement($xml);
} catch (Exception $e) {
$this->_error = RestErrorEnum::RE_INVALID_REPRESENTATION;
return $ds;
}
$this->_xml = $xml;
// basic properties
$xmli = $xml->xpath('//dataset:dataset');
if (count($xmli) === 0) {
$this->_error = RestErrorEnum::RE_INVALID_REPRESENTATION;
return $ds;
}
$xml = $xmli[0];
if ($this->_parent->getMethod() === RestMethodEnum::RM_PUT && (count($xml->xpath("//dataset:name")) == 0 || strval($xml->attributes()->category) == "")) {
$this->_error = RestErrorEnum::RE_INVALID_REPRESENTATION;
$this->_extError = "One ore more required entities are missing or contain no data.";
return $ds;
}
if ($this->_parent->getMethod() === RestMethodEnum::RM_POST) {
if ($xml->attributes()->id) {
$ds->id = intval(strval($xml->attributes()->id));
$db = $application->getBootstrap()->getResource('db');
$db->setFetchMode(Zend_Db::FETCH_OBJ);
$r = $db->query('SELECT guid FROM datasets WHERE id = ' . $ds->id)->fetchAll();
if (count($r) > 0) {
$ds->guid = $r[0]->guid;
}
} else {
$this->_error = RestErrorEnum::RE_INVALID_REPRESENTATION;
return $ds;
}
}
if ($this->_parent->getMethod() === RestMethodEnum::RM_PUT) {
$ds->addedByID = $this->_parent->getUser()->id;
}
$newParentID = null;
if (!is_null($this->el($xml, 'dataset:parent[@xsi:nil="true"]'))) {
$newParentID = 0;
} elseif (!is_null($this->el($xml, "dataset:parent"))) {
$newParentID = $this->el($xml, "dataset:parent")->attributes()->id;
if ($newParentID == "") {
$this->_error = RestErrorEnum::RE_INVALID_REPRESENTATION;
return $ds;
} else {
$datasets = new Default_Model_Datasets();
$datasets->filter->id->numequals($newParentID);
if (count($datasets->items) == 0 || count($datasets->items) > 0 && $datasets->items[0]->parentID !== null) {
if (count($datasets->items) == 0) {
$this->_error = RestErrorEnum::RE_ITEM_NOT_FOUND;
$this->_extError = "Parent dataset not found";
} else {
$this->_error = RestErrorEnum::RE_BACKEND_ERROR;
$this->_extError = "Parent dataset must be a primary dataset";
}
return $ds;
}
}
}
if (!is_null($newParentID)) {
// a parentid has been supplied in the XML representation; act upon it
if ($this->_parent->getMethod() === RestMethodEnum::RM_PUT) {
$ds->parentID = $newParentID;
} elseif ($this->_parent->getMethod() === RestMethodEnum::RM_POST) {
// only allow setting parent on update if parent was NULL
$datasets = new Default_Model_Datasets();
$datasets->filter->id->numequals($ds->id);
if ($datasets->items[0]->parentID === null) {
$ds->parentID = $newParentID;
} elseif ($datasets->items[0]->parentID == $newParentID) {
$no_operation = "";
// do nothing
} else {
$this->_error = RestErrorEnum::RE_BACKEND_ERROR;
$this->_extError = "Cannot modify existing parent dataset";
return $ds;
}
}
}
if ($newParentID === null) {
// no parent id has been provided in the XML; look up database if this is an update
if ($this->_parent->getMethod() == RestMethodEnum::RM_POST) {
$datasets = new Default_Model_Datasets();
$datasets->filter->id->numequals($ds->id);
$effectiveParentID = $datasets->items[0]->parentID;
} else {
$effectiveParentID = null;
}
} else {
$effectiveParentID = $newParentID === 0 ? null : $newParentID;
}
if (!is_null($this->el($xml, "dataset:name"))) {
$ds->name = strval($this->el($xml, "dataset:name"));
}
if (!is_null($this->el($xml, "dataset:description"))) {
$ds->description = strval($this->el($xml, "dataset:description"));
}
if (!is_null($this->el($xml, 'dataset:url[@type="homepage"]'))) {
$ds->homepage = strval($this->el($xml, 'dataset:url[@type="homepage"]'));
}
if (!is_null($this->el($xml, 'dataset:url[@type="elixir"]'))) {
$ds->elixirURL = strval($this->el($xml, 'dataset:url[@type="elixir"]'));
}
if (isset($xml->attributes()->tags)) {
$ds->tags = explode(" ", strval($xml->attributes()->tags));
}
if (isset($xml->attributes()->category)) {
$ds->category = strval($xml->attributes()->category);
}
$ds->save();
// Discipline collection
// only sync disciplines for primary datasets, assuming disciplines have been provided
if (count($xml->xpath("//discipline:discipline")) > 0) {
if ($effectiveParentID === null) {
$data = $this->buildCollection($xml, "//discipline:discipline", "disciplineID");
if (is_null($data)) {
$data = array();
}
$this->syncDBCollection("datasetid", $ds->id, "disciplineid", "DatasetDisciplines", "DatasetDiscipline", $data);
} else {
$this->_error = RestErrorEnum::RE_BACKEND_ERROR;
$this->_extError = "Cannot explicitly modify disciplines of derived dataset; disciplines are inherited by the parent dataset";
return $ds;
}
}
// License collection
$data = $this->buildCollection($xml, "//dataset:license", "license");
if (is_null($data)) {
$data = array();
}
$this->syncDBCollection("datasetid", $ds->id, "licenseid", "DatasetLicenses", "DatasetLicense", $data, "license");
// Also save versions if they exist
if (count($xml->xpath('//dataset:version[@xsi:nil="true"]')) > 0) {
db()->exec("SELECT delete_dataset_version(id) FROM datasets WHERE datasetid = " . $ds->id);
} else {
$xmlver = $xml->xpath("//dataset:version");
if (count($xmlver) > 0) {
foreach ($xmlver as $x) {
$data = RestAPIHelper::responseHead("dataset") . $x->asXML() . RestAPIHelper::responseTail();
$verres = new RestDatasetVersionList(array_merge($this->_parent->getParams(), array('data' => $data, 'id' => $ds->id)));
if ($this->_parent->getMethod() === RestMethodEnum::RM_PUT) {
$verres->put();
} else {
if (isset($x->attributes()->id)) {
$verres->post();
} else {
$verres->put();
}
}
$this->_error = $verres->getError();
$this->_extError = $verres->getExtError();
if ($this->_error != RestErrorEnum::RE_OK) {
break;
}
}
}
}
}
return $ds;
}
