public function getToDate()
{
$time = null;
if ($this->GTUdate['time']) {
$time = $this->GTUdate['time'];
}
return $this->GTUdate['to'] ? FuzzyDateTime::getValidDate($this->GTUdate['to']) : $time;
}
private function endElement($parser, $name)
{
$this->cdata = trim($this->cdata);
$this->inside_data = false;
if (in_array($this->getPreviousTag(), array('Bacterial', 'Zoological', 'Botanical', 'Viral'))) {
$this->object->handleKeyword($this->tag, $this->cdata, $this->staging);
} elseif ($this->getPreviousTag() == "efg:LithostratigraphicAttribution" && $name != "efg:InformalLithostratigraphicName") {
$this->object->handleParent($name, strtolower($this->cdata), $this->staging);
} else {
switch ($name) {
case "AccessionCatalogue":
$this->object->addAccession($this->cdata);
break;
case "AccessionDate":
if (date('Y-m-d H:i:s', strtotime($this->cdata)) == $this->cdata) {
$this->object->InitAccessionVar($this->cdata);
}
break;
case "AccessionNumber":
$this->object->accession_num = $this->cdata;
$this->object->HandleAccession($this->staging, $this->object_to_save);
break;
case "Accuracy":
$this->getPreviousTag() == 'Altitude' ? $this->staging['gtu_elevation_accuracy'] = $this->cdata : ($this->property->property->property_accuracy = $this->cdata);
break;
case "AcquisitionDate":
$dt = FuzzyDateTime::getValidDate($this->cdata);
if (!is_null($dt)) {
$this->staging['acquisition_date'] = $dt->getDateTime();
$this->staging['acquisition_date_mask'] = $dt->getMask();
}
break;
case "AcquisitionType":
$this->staging['acquisition_category'] = in_array($this->cdata, SpecimensTable::$acquisition_category) ? array_search($this->cdata, SpecimensTable::$acquisition_category) : 'undefined';
break;
case "AppliesTo":
$this->property->setAppliesTo($this->cdata);
break;
case "AreaClass":
$this->object->tag_group_name = $this->cdata;
break;
case "AreaName":
$this->object->tag_value = $this->cdata;
break;
case "AssociatedUnitID":
if (in_array($this->cdata, array_keys($this->unit_id_ref))) {
$this->object->setStagingRelatedRef($this->unit_id_ref[$this->cdata]);
} else {
$this->object->setSourceId($this->cdata);
$this->object->setUnitType('external');
}
break;
case "AssociatedUnitSourceInstitutionCode":
$this->object->setInstitutionName($this->cdata);
break;
case "AssociatedUnitSourceName":
$this->object->setSourceName($this->cdata);
break;
case "AssociationType":
$this->object->setRelationshipType($this->cdata);
break;
case "efg:ChronostratigraphicAttribution":
$this->cdata = $this->object->setChronoParent();
if ($this->cdata) {
$this->property = new ParsingProperties("Local stage", "chronostratigraphy");
$this->property->property->setLowerValue($this->cdata['name']);
$this->addProperty(true);
}
break;
case "efg:ChronoStratigraphicDivision":
$this->object->getChronoLevel(strtolower($this->cdata));
break;
case "efg:ChronostratigraphicAttributions":
$this->object->saveChrono($this->staging);
break;
case "efg:ChronostratigraphicName":
$this->object->name = $this->cdata;
break;
case "Code":
$this->staging['gtu_code'] = (string) $this->cdata;
break;
case "CoordinateErrorDistanceInMeters":
$this->staging['gtu_lat_long_accuracy'] = $this->cdata;
break;
case "Context":
$this->object->multimedia_data['sub_type'] = $this->cdata;
break;
case "CreatedDate":
$this->object->multimedia_data['creation_date'] = $this->cdata;
break;
case "Country":
$this->staging_tags[] = $this->object->addTagGroups();
break;
case "Database":
$this->object->desc .= "Database ref :" . $this->cdata . ";";
break;
case "DateText":
$this->object->getDateText($this->cdata);
break;
case "DateTime":
if ($this->getPreviousTag() == "Gathering") {
if ($this->object->getFromDate()) {
$this->staging["gtu_from_date"] = $this->object->getFromDate()->getDateTime();
}
if ($this->object->getToDate()) {
$this->staging["gtu_to_date"] = $this->object->getToDate()->getDateTime();
}
if ($this->object->getFromDate()) {
$this->staging["gtu_from_date_mask"] = $this->object->getFromDate()->getMask();
}
if ($this->object->getToDate()) {
$this->staging["gtu_to_date_mask"] = $this->object->getToDate()->getMask();
}
}
break;
case "TimeOfDayBegin":
if ($this->getPreviousTag() == "DateTime") {
$this->object->GTUdate['from'] .= " " . $this->cdata;
}
break;
case "TimeOfDayEnd":
if ($this->getPreviousTag() == "DateTime") {
$this->object->GTUdate['to'] .= " " . $this->cdata;
}
break;
case "dna:Concentration":
$this->property = new ParsingProperties("Concentration", "DNA");
$this->property->property->setLowerValue($this->cdata);
$this->property->property->setPropertyUnit("ng/µl");
$this->addProperty(true);
break;
case "dna:DNASample":
$this->object->addMaintenance($this->staging);
break;
case "dna:ExtractionDate":
$dt = FuzzyDateTime::getValidDate($this->cdata);
if (!is_null($dt)) {
$this->object->maintenance->setModificationDateTime($dt->getDateTime());
$this->object->maintenance->setModificationDateMask($dt->getMask());
}
break;
case "dna:ExtractionMethod":
$this->object->maintenance->setDescription($this->cdata);
break;
case "dna:ExtractionStaff":
$this->handlePeople($this->object->people_type, $this->cdata);
break;
case "dna:GenBankNumber":
$this->handleGenbankNumber($this->cdata);
break;
case "dna:RatioOfAbsorbance260_280":
$this->property = new ParsingProperties("Ratio of absorbance 260/280", "DNA");
$this->property->property->setLowerValue($this->cdata);
$this->addProperty(true);
break;
case "dna:Tissue":
$this->property = new ParsingProperties("Tissue", "DNA");
$this->property->property->setLowerValue($this->cdata);
$this->addProperty(true);
break;
case "dna:Preservation":
$this->addComment(false, "conservation_mean");
break;
case "Duration":
$this->property->setDateTo($this->cdata);
break;
case "FileURI":
$this->handleFileURI($this->cdata);
break;
case "Format":
$this->object->multimedia_data['type'] = $this->cdata;
break;
case "FullName":
$this->people_name = $this->cdata;
break;
case "efg:ScientificNameString":
$this->object->fullname = $this->cdata;
break;
case "FullScientificNameString":
$this->object->fullname = $this->cdata;
break;
case "InformalNameString":
$this->object->fullname = $this->cdata;
$this->object->setInformal(true);
$this->staging["taxon_name"] = $this->object->getLastParentName();
$this->staging["taxon_level_name"] = $this->object->getLastParentLevel();
break;
case "MarkText":
$this->staging->setObjectName($this->cdata);
break;
case "efg:InformalLithostratigraphicName":
$this->addComment(true, "lithostratigraphy");
break;
case "Gathering":
if ($this->object->staging_info !== null) {
$this->object_to_save[] = $this->object->staging_info;
}
break;
case "HigherTaxa":
$this->object->getCatalogueParent($this->staging);
break;
case "HigherTaxon":
$this->object->handleParent();
break;
case "HigherTaxonName":
$this->object->higher_name = $this->cdata;
break;
case "HigherTaxonRank":
$this->object->higher_level = strtolower($this->cdata);
break;
case "TaxonIdentified":
$this->object->checkNoSelfInParents($this->staging);
break;
case "efg:LithostratigraphicAttribution":
$this->staging["litho_parents"] = $this->object->getParent();
break;
case "Identification":
$this->object->save($this->staging);
break;
case "IdentificationHistory":
$this->addComment(true, 'taxonomy');
break;
case "ID-in-Database":
$this->object->desc .= "id in database :" . $this->cdata . " ;";
break;
case "ISODateTimeBegin":
if ($this->getPreviousTag() == "DateTime") {
$this->object->GTUdate['from'] = $this->cdata;
} elseif ($this->getPreviousTag() == "Date") {
$this->object->identification->setNotionDate(FuzzyDateTime::getValidDate($this->cdata));
}
break;
case "ISODateTimeEnd":
if ($this->getPreviousTag() == "DateTime") {
$this->object->GTUdate['to'] = $this->cdata;
}
break;
case "IsQuantitative":
$this->property->property->setIsQuantitative($this->cdata);
break;
case "KindOfUnit":
$this->staging['part'] = $this->cdata;
break;
case "RecordBasis":
if ($this->cdata == "PreservedSpecimen") {
$this->staging->setCategory('specimen');
} else {
$this->staging->setCategory('observation');
}
break;
case "LatitudeDecimal":
$this->staging['gtu_latitude'] = $this->cdata;
break;
case "Length":
$this->object->desc .= "Length : " . $this->cdata . " ;";
break;
case "efg:LithostratigraphicAttributions":
$this->object->setAttribution($this->staging);
break;
case "LocalityText":
(string) $this->addComment(false, "exact_site");
break;
case "LongitudeDecimal":
$this->staging['gtu_longitude'] = $this->cdata;
break;
case "LowerValue":
$this->property->property->setLowerValue($this->cdata);
break;
case "MeasurementDateTime":
$this->property->getDateFrom($this->cdata, $this->getPreviousTag(), $this->staging);
break;
case "Method":
if ($this->getPreviousTag() == "Identification") {
$this->addComment(false, "identifications");
} else {
$this->object_to_save[] = $this->object->addMethod($this->cdata, $this->staging->getId());
}
break;
case "efg:Petrology":
break;
case "MeasurementsOrFacts":
if ($this->object && property_exists($this->object, 'staging_info') && $this->getPreviousTag() != "Unit" && $this->object->staging_info) {
$this->object_to_save[] = $this->object->staging_info;
}
break;
case "MeasurementOrFactAtomised":
if ($this->getPreviousTag() == "Altitude") {
//Set Altitude in meters in GTU
$altitude = str_replace('.', ',', $this->property->property->getLowerValue());
$comma_count = mb_substr_count($altitude, ',');
if ($comma_count > 1) {
$altitude = preg_replace('/\\,/', '', $altitude, $comma_count - 1);
}
$altitude = str_replace(',', '.', $altitude);
$this->staging['gtu_elevation'] = $altitude;
} else {
$this->addProperty();
}
break;
case "MeasurementOrFactText":
$this->addComment();
break;
case "MineralColour":
$this->staging->setMineralColour($this->cdata);
break;
case "efg:MineralRockClassification":
if ($this->getPreviousTag() == "efg:MineralRockGroup") {
$this->object->higher_level = strtolower($this->cdata);
} elseif ($this->getPreviousTag() == "efg:MineralRockNameAtomised") {
$this->object->classification = strtolower($this->cdata);
}
break;
case "efg:MineralRockGroup":
$this->object->handleRockParent();
break;
case "efg:MineralRockGroupName":
$this->object->higher_name = $this->cdata;
break;
case "efg:MineralRockIdentified":
$this->object->getCatalogueParent($this->staging);
if ($this->object->notion !== 'mineralogy') {
$this->object->checkNoSelfInParents($this->staging);
}
break;
case "Name":
if ($this->getPreviousTag() == "Country") {
$this->object->tag_value = $this->cdata;
}
break;
case "efg:NameComments":
$this->object->setNotion(strtolower($this->cdata));
break;
case "NameAddendum":
if (stripos($this->cdata, 'Variety') !== false) {
$this->object->level_name = 'variety';
$this->object->catalogue_parent['variety'] = $this->object->getCatalogueName();
}
break;
case "NamedArea":
$this->staging_tags[] = $this->object->addTagGroups();
break;
case "Notes":
if ($this->getPreviousTag() == "Identification") {
$this->addComment(true, "identifications");
} else {
$this->addComment();
}
break;
case "Parameter":
$this->property->property->setPropertyType($this->cdata);
if ($this->cdata == 'DNA size') {
$this->property->property->setAppliesTo('DNA');
}
break;
case "PersonName":
$this->handlePeople($this->object->people_type, $this->people_name);
break;
case "Person":
$this->handlePeople($this->object->people_type, $this->people_name);
break;
case "efg:MineralDescriptionText":
$this->addComment(true, 'mineralogy');
break;
case "PetrologyDescriptiveText":
//SAME AS BELOW
//SAME AS BELOW
case "efg:PetrologyDescriptiveText":
$this->addComment(true, 'description');
break;
case "PhaseOrStage":
$this->staging->setIndividualStage($this->cdata);
break;
case "Preparation":
$this->addPreparation();
break;
case "PreparationType":
$this->preparation_type = $this->cdata;
break;
case "PreparationMaterials":
$this->preparation_mat = $this->cdata;
break;
case "ProjectTitle":
$this->staging['expedition_name'] = $this->cdata;
break;
case "RecordURI":
$this->addExternalLink($this->cdata);
break;
case "ScientificName":
$this->staging["taxon_name"] = $this->object->getCatalogueName();
$this->staging["taxon_level_name"] = strtolower($this->object->level_name);
break;
case "Sequence":
$this->object->addMaintenance($this->staging, true);
break;
case "Sex":
if (strtolower($this->cdata) == 'm') {
$this->staging->setIndividualSex('male');
} elseif (strtolower($this->cdata) == 'f') {
$this->staging->setIndividualSex('female');
} elseif (strtolower($this->cdata) == 'u') {
$this->staging->setIndividualSex('unknown');
} elseif (strtolower($this->cdata) == 'n') {
$this->staging->setIndividualSex('not applicable');
} elseif (strtolower($this->cdata) == 'x') {
$this->staging->setIndividualSex('mixed');
}
break;
case "storage:Barcode":
$this->addCode("barcode");
break;
// c'est un code avec "2dbarcode" dans le main
// c'est un code avec "2dbarcode" dans le main
case "storage:Institution":
$this->staging->setInstitutionName($this->cdata);
break;
case "storage:Building":
$this->staging->setBuilding($this->cdata);
break;
case "storage:Floor":
$this->staging->setFloor($this->cdata);
break;
case "storage:Room":
$this->staging->setRoom($this->cdata);
break;
case "storage:Column":
$this->staging->setCol($this->cdata);
break;
case "storage:Row":
$this->staging->setRow($this->cdata);
break;
case "storage:Shelf":
$this->staging->setShelf($this->cdata);
break;
case "storage:Rack":
$this->staging->setShelf($this->cdata);
break;
case "storage:Box":
$this->staging->setContainerType('box');
$this->staging->setContainer($this->cdata);
break;
case "storage:Tube":
$this->staging->setSubContainerType('tube');
$this->staging->setSubContainer($this->cdata);
break;
case "storage:ContainerName":
$this->staging->setContainer($this->cdata);
break;
case "storage:ContainerType":
$this->staging->setContainerType($this->cdata);
break;
case "storage:ContainerStorage":
$this->staging->setContainerStorage($this->cdata);
break;
case "storage:SubcontainerName":
$this->staging->setSubContainer($this->cdata);
break;
case "storage:SubcontainerType":
$this->staging->setSubContainerType($this->cdata);
break;
case "storage:SubcontainerStorage":
$this->staging->setSubContainerStorage($this->cdata);
break;
case "storage:Position":
$this->staging->setSubContainerType('position');
$this->staging->setSubContainer($this->cdata);
break;
case "Text":
if ($this->getPreviousTag() == "Biotope") {
$this->object->tag_group_name = 'ecology';
$this->object->tag_value = $this->cdata;
$this->staging_tags[] = $this->object->addTagGroups();
}
break;
case "TitleCitation":
if (substr($this->cdata, 0, 7) == 'http://') {
$this->addExternalLink($this->cdata);
}
if ($this->getPreviousTag() == "UnitReference") {
$this->addComment(true, 'publication');
} else {
$this->addComment(true, "identifications");
}
break;
case "TypeStatus":
$this->staging->setIndividualType($this->cdata);
break;
case "Unit":
$this->saveUnit();
break;
case "UnitAssociation":
$this->staging->addRelated($this->object);
$this->object = null;
break;
case "UnitID":
$this->addCode();
$this->name = $this->cdata;
break;
case "SourceID":
if ($this->cdata != 'Not defined') {
$this->addCode('secondary');
}
break;
case "UnitOfMeasurement":
$this->property->property->setPropertyUnit($this->cdata);
break;
case "Accuracy":
$this->property->property->setPropertyAccuracy($this->cdata);
break;
case "UpperValue":
$this->property->property->setUpperValue($this->cdata);
break;
case "efg:InformalNameString":
$this->addComment(true, "identifications");
break;
case "VerificationLevel":
$this->object->determination_status = $this->cdata;
break;
case "storage:Type":
$this->code_type = $this->cdata;
break;
case "storage:Value":
$this->addCode($this->code_type);
break;
case "Major":
$this->version = $this->cdata;
break;
case "Minor":
$this->version .= !empty($this->cdata) ? '.' . $this->cdata : '';
break;
case "Version":
$this->version_defined = true;
$authorized = sfConfig::get('tpl_authorizedversion');
Doctrine::getTable('Imports')->find($this->import_id)->setTemplateVersion(trim($this->version))->save();
if (!isset($authorized['specimens']) || empty($authorized['specimens']) || isset($authorized['specimens']) && !empty($authorized['specimens']) && !in_array(trim($this->version), $authorized['specimens'])) {
$this->errors_reported .= $this->version_error_msg;
}
break;
}
}
$this->tag = "";
$this->path = substr($this->path, 0, strrpos($this->path, "/{$name}"));
}
public function getDateText($date)
{
$this->identification->setNotionDate(FuzzyDateTime::getValidDate($date));
}
