public function write()
{
global $createNewRec, $result, $debug;
// set up writer class instances
$occ = new OmOccurrences();
// Note: We may create a new instance below.
$det = new OmOccurDeterminations();
$imageHandler = new ImageShared();
$imageHandler->documentGuid = $this->containingDocument->guid;
$imageHandler->documentDate = $this->containingDocument->date;
// Special case handling of HUH double barcode errors
$cc = $this->collectioncode;
if ($cc == 'A' || $cc == 'GH' || $cc == 'FH' || $cc == 'AMES' || $cc == 'ECON' || $cc == 'NEVP') {
// Known cases of sheets where a new barcode number was added in addition to an existing number for the sheet.
// original existing number is the correct number.
if ($this->catalognumber == '00447650') {
$this->catalognumber = '00354371';
$this->occurrenceid = '4b11b05c-03f3-4f72-a917-a4a48fc2fb33';
}
if ($this->catalognumber == '00447657') {
$this->catalognumber = '00354391';
$this->occurrenceid = '96dc15ca-6224-4d63-9039-9633cafca7be';
}
if ($this->catalognumber == '00448806') {
$this->catalognumber = '00348333';
$this->occurrenceid = '1c2e1397-614a-44c0-bfa4-1edc1d4bb455';
}
if ($this->catalognumber == '00448807') {
$this->catalognumber = '00348334';
$this->occurrenceid = 'b5551dfc-53b4-4792-96bc-d66d748f2de2';
}
if ($this->catalognumber == '00448821') {
$this->catalognumber = '00348335';
$this->occurrenceid = '251eb221-b8f8-4d30-a3b7-fafb067262e5';
}
if ($this->catalognumber == '00448775') {
$this->catalognumber = '00348331';
$this->occurrenceid = '032c0d22-78b2-4c8e-88f6-9ef6638fb707';
}
if ($this->catalognumber == '00448797') {
$this->catalognumber = '00348332';
$this->occurrenceid = 'ba20e76f-4d97-4943-b150-b7141b9b24e3';
}
if ($this->catalognumber == '00448506') {
$this->catalognumber = '00415842';
$this->occurrenceid = '1688968c-dd07-4483-b20c-6137d465443a';
}
if ($this->catalognumber == '00448485') {
$this->catalognumber = '00415838';
$this->occurrenceid = '591ddf2e-b92a-46a7-85de-63f628688598';
}
}
// End Special case
if ($debug) {
echo "Preparing to save [{$cc}][{$this->catalognumber}]";
}
$collid = $occ->lookupCollId($this->institutioncode, $this->collectioncode);
$collreportmatch = "collid=[{$collid}], institutionCode=[{$this->institutioncode}], collectionCode=[{$this->collectioncode}]\n";
// Record exists if there is a matching DarwinCore triplet.
$exists = $occ->loadByDWCTriplet($this->institutioncode, $this->collectioncode, $this->catalognumber);
if ($debug) {
echo "Exists=[{$exists}]";
}
if (!$exists) {
// Image upload process in TcnImageTools creates omoccurrences records where
// collectioncode is not populated, but collid is. Need to handle both cases.
$exists = $occ->loadByCollidCatalog($collid, $this->catalognumber);
// Guidance from Ed: omoccurrences.institutioncode and omoccurrences.collectioncode should only
// be populated if different from the values in omcollections for the omoccurrences.collid.
}
if (!$exists) {
$occ = new OmOccurrences();
$occ->setcollid($collid);
$occ->setcollectionCode($this->collectioncode);
$occ->setcollectionID($this->collectionid);
$occ->setinstitutionCode($this->institutioncode);
$occ->setcatalogNumber($this->catalognumber);
$occ->setprocessingStatus("unprocessed");
// Provide for link to authoritative database record (which doesn't yet exist).
// extract just the uuid from the urn:uuid:{uuid} string.
$matches = explode(':', $this->occurrenceid);
if (count($matches) == 3) {
$uuid = $matches[2];
if ($debug) {
echo "extracted uuid=[{$uuid}]";
}
$occ->setdbpk($uuid);
} else {
// if the expected uuid wasn't found, use the catalog number as the best available proxy for dbbk
$occ->setdbpk($this->catalognumber);
}
// if creating a new occurrence record, assume it was created by the annotator on the dc:created date.
$occ->setrecordenteredby($this->recordenteredby);
$occ->setdateentered($this->datemodified);
$occ->setstorageLocation($this->storagelocation);
// NEVP ingest
$occ->setfundingSource($this->fundingsource);
// NEVP ingest
$occ->setdocumentGuid($this->containingDocument->guid);
$occ->setdocumentDate($this->containingDocument->date);
}
$occ->setoccurrenceId($this->occurrenceid);
$occ->setbasisOfRecord($this->basisofrecord);
// Separators in name strings may be amperstand (HUH standard for name pairs), semicolon, or pipe (AppleCore).
// convert all to semicolon and split on that.
$this->recordedby = str_replace("|", ";", $this->recordedby);
$this->recordedby = str_replace("&", ";", $this->recordedby);
if (strpos($this->recordedby, ";") > 0) {
// split on first semicolon.
$occ->setrecordedBy(trim(substr($this->recordedby, 0, strpos($this->recordedby, ";"))));
$occ->setassociatedCollectors(trim(substr($this->recordedby, strpos($this->recordedby, ";") + 1, strlen($this->recordedby))));
} else {
$occ->setrecordedBy(trim($this->recordedby));
$occ->setassociatedCollectors("");
}
$occ->setcollectorid($this->collectorid);
if ($this->recordnumber != null) {
$occ->setrecordNumber($this->recordnumber);
}
$occ->settypeStatus($this->getTypeStatusList());
if ($this->country == null) {
$occ->setcountry(DEFAULT_NEVP_COUNTRY);
} else {
$occ->setcountry($this->country);
}
if ($this->stateprovince != null) {
$occ->setstateProvince($this->stateprovince);
}
if ($this->county != null) {
$occ->setcounty($this->county);
}
$occ->setmunicipality($this->municipality);
if ($this->locality != null) {
$occ->setlocality($this->locality);
}
if ($this->collectingevent != null) {
// Symbiota event date is a mysql date field, thus less
// expressive than an ISO date field, but also has
// startdayofyear and enddayofyear fields for handling ranges within a year.
//
// Pass off responsibility for parsing range to OmOccurrences implementation.
$occ->seteventDate($this->collectingevent->eventdate);
$occ->setyear($this->collectingevent->startyear);
$occ->setmonth($this->collectingevent->startmonth);
$occ->setday($this->collectingevent->startday);
$occ->setverbatimEventDate($this->collectingevent->verbatimeventdate);
}
if (class_exists('Gazeteer')) {
$gazeteer = new Gazeteer();
// For NEVP, lookup georeference from state+municipality
$georef = $gazeteer->lookup($this->stateprovince, $this->municipality, $occ->getyear());
if ($georeference->foundMatch === true) {
$occ->setdecimalLatitude($georef->latitude);
$occ->setdecimalLongitude($georef->longitude);
$occ->setcoordinateUncertaintyInMeters($georef->errorRadius);
$occ->setgeodeticDatum($georef->geodeticDatum);
$occ->setgeoreferencedBy($georef->georeferencedBy);
$occ->setgeoreferenceProtocol($georef->georeferenceProtocol);
$occ->setgeoreferenceSources($georef->georeferenceSources);
}
}
if ($this->minimumelevationinmeters != null) {
$occ->setminimumElevationInMeters($this->minimumelevationinmeters);
}
if ($this->maximumelevationinmeters != null) {
$occ->setmaximumElevationInMeters($this->maximumelevationinmeters);
}
$filedUnder = $this->getFiledUnderID();
if ($filedUnder != null) {
$occ->setsciname($filedUnder->getNameWithoutAuthor());
// without author
$occ->setscientificName($filedUnder->getNameWithAuthor());
// with author
// Set locality security based on TID of accepted name of filed under name
$sectid = $det->lookupAcceptedTID($filedUnder->scientificname);
if ($sectid == null) {
$sectid = $det->lookupTID($filedUnder->scientificname);
}
if ($sectid == null) {
$occ->setlocalitySecurity(0);
} else {
$occ->setlocalitySecurity($det->checkSecurityStatus($sectid));
}
if ($det->lookupAcceptedTID($filedUnder->scientificname) > 0) {
$occ->settidinterpreted($det->lookupAcceptedTID($filedUnder->scientificname));
}
$occ->setfamily($filedUnder->family);
if (strlen($occ->getfamily()) == 0) {
$occ->setfamily($det->lookupFamilyForTID($det->lookupTID($filedUnder->scientificname)));
}
$occ->setgenus($filedUnder->genus);
$occ->setspecificEpithet($filedUnder->specificepithet);
$occ->setinfraSpecificEpithet($filedUnder->infraspecificepithet);
$occ->setidentificationQualifier($filedUnder->identificationqualifier);
$occ->setscientificNameAuthorship($filedUnder->scientificnameauthorship);
$occ->settaxonGuid($filedUnder->taxonguid);
// work out value for taxon rank.
$occ->settaxonRank($filedUnder->infraspecificrank);
if (strlen($filedUnder->infraspecificepithet) > 0 && strlen($filedUnder->infraspecificrank) == 0) {
$occ->settaxonRank("subspecies");
}
if (strlen($filedUnder->infraspecificepithet) == 0 && strlen($filedUnder->specificepithet) > 0) {
$occ->settaxonRank("species");
}
if (strlen($filedUnder->infraspecificepithet) == 0 && strlen($filedUnder->specificepithet) == 0 && strlen($filedUnder->genus) > 0) {
$occ->settaxonRank("genus");
}
if ($filedUnder->dateidentified != NULL) {
$occ->setdateIdentified($filedUnder->identificationdate->writeAll());
}
}
// TODO: Handle motivations (transcribing and NSF abstract numbers).
// NSF abstract number handled here with fundingsource (but not
// implemented in symbiota).
// motivations extracted, but nothing done with here.
if ($debug) {
echo ",createnew=[{$createNewRec}]\n";
}
if (!$exists || $createNewRec == 1) {
// if record exists, then TcnImageConf variable createNewRec specifies policy for update.
$saveresult = $occ->save();
$occid = $occ->getoccid();
if ($debug) {
echo "occid=[{$occid}],saveresult=[{$saveresult}]\n";
}
if ($saveresult === TRUE) {
if (preg_match('/Barcode .* exists\\./', $occ->errorMessage())) {
$result->updatecount++;
} else {
if ($exists) {
if ($debug) {
echo "Updated occid: [" . $occ->getoccid() . "]\n";
}
$result->updatecount++;
} else {
if ($debug) {
echo "Added occid: [" . $occ->getoccid() . "]\n";
}
$result->insertcount++;
}
foreach ($this->identifications as $id) {
$id->occid = $occ->getoccid();
$id->write();
}
}
// Create image records from associatedmedia array.
foreach ($this->associatedmedia as $media) {
$sourceUrl = null;
$imgWebUrl = null;
$sourceID = null;
$imgWebID = null;
$mediaguid = $media->guid;
if (is_array($media->accesspoints)) {
foreach ($media->accesspoints as $accesspoint) {
if (strlen($accesspoint->accessURI) > 0) {
$irodsPath = str_replace('/', '\\/', $accesspoint->accessURI);
$irodsPath = preg_replace('/^file:/', 'irods:', $irodsPath);
$imageresult = getiPlantID($accesspoint->accessURI, $irodsPath);
if ($imageresult->statusok === FALSE) {
echo "Error: " . $imageresult->error . "\n";
$result->imagefailurecount++;
} else {
if ($debug) {
echo "[{$accesspoint->format}]";
}
$iPlantID = $imageresult->resource_uniq;
if ($accesspoint->format == "dng") {
// Original dng file
$sourceUrl = "http://bisque.iplantcollaborative.org/image_service/image/{$iPlantID}";
$sourceID = $iPlantID;
}
if ($accesspoint->format == "jpg") {
// Preconstructed derivative JPG file
$imgWebUrl = "http://bisque.iplantcollaborative.org/image_service/image/{$iPlantID}?resize=1250&format=jpeg";
$imgWebID = $iPlantID;
$imgTnUrl = "http://bisque.iplantcollaborative.org/image_service/image/{$iPlantID}?thumbnail=225,225";
// Because this is a JPEG, no need to request ?rotate=guess&format=jpeg,quality,100
// and the folks at iPlant are requesting that this request be made without the
// un-needed transformation parameters.
$imgLgUrl = "http://bisque.iplantcollaborative.org/image_service/image/{$iPlantID}";
}
}
}
// end if accesspoint has accessURL
}
// end for each accesspoint
}
// end isarray
// Workaround to handle new case of only a JPEG being provided by some insitutions
if ($sourceUrl == null && $imgLgUrl != null) {
// a jpeg was provided, but not a DNG, use the large version of the jpeg as the source.
$sourceUrl = $imgLgUrl;
}
if ($sourceUrl != null && $imgWebUrl != null) {
// found something to save.
$result->imagecount++;
$tid = $det->lookupTID($filedUnder->scientificname);
$caption = "{$this->collectioncode} {$this->catalognumber} {$filedUnder->scientificname}";
$locality = $occ->getcountry() . " {$this->stateprovince} {$this->county} {$this->municipality} {$this->locality}";
$sortsequence = 50;
// default number
$copyright = $media->rights;
$owner = $media->owner;
$notes = $media->usageterms;
$imgid = $imageHandler->getImgIDForSourceURL($sourceUrl);
if ($imgid == "") {
// add this image record
$isaveresult = $imageHandler->databaseImageRecord($imgWebUrl, $imgTnUrl, $imgLgUrl, $tid, $caption, $this->recordenteredby, null, $sourceUrl, $copyright, $owner, $locality, $occid, $notes, $sortsequence, "specimen", "", $sourceID, $copyright, "");
if ($isaveresult == "") {
$result->imageinsertcount++;
} else {
$result->imagefailurecount++;
}
} else {
$isaveresult = $imageHandler->updateImageRecord($imgid, $imgWebUrl, $imgTnUrl, $imgLgUrl, $tid, $caption, $this->recordenteredby, null, $sourceUrl, $copyright, $owner, $locality, $occid, $notes, $sortsequence, "specimen", "", $sourceID, $copyright, "");
if ($isaveresult == "") {
$result->imageupdatecount++;
} else {
$result->imagefailurecount++;
}
}
if ($debug) {
echo "imagesaveresult=[{$isaveresult}]\n";
}
}
}
$result->successcount++;
} else {
$result->errors .= "Error in " . $this->collectioncode . "-" . $this->catalognumber . ": [" . $occ->errorMessage() . "]\n";
if ($occ->errorMessage() == "Cannot add or update a child row: a foreign key constraint fails (`symbiota`.`omoccurrences`, CONSTRAINT `FK_omoccurrences_collid` FOREIGN KEY (`collid`) REFERENCES `omcollections` (`CollID`) ON DELETE CASCADE ON UPDATE CASCADE)") {
$result->errors .= "Interpretation: Record contains a collectionCode and institutionCode combination which was not found in omcollections (or only a collectionCode that was not found in omcollections or omoccurrences). \n";
$result->errors .= $collreportmatch;
}
$result->failurecount++;
}
} else {
echo "Skipping, record exists and specified policy is to not update. [" . $occ->getoccid() . "]\n";
}
}
public function write()
{
global $createNewRec, $result;
$occ = new OmOccurrences();
$det = new OmOccurDeterminations();
$collid = $occ->lookupCollId(null, $this->collectioncode);
// Record exists if there is a matching DarwinCore triplet.
$exists = $occ->loadByDWCTriplet($occ->lookupInstitutionCode($collid), $this->collectioncode, $this->unitid);
if (!$exists) {
// Image upload process in TcnImageTools creates omoccurrences records where
// collectioncode is not populated, but collid is. Need to handle both cases.
$exists = $occ->loadByCollidCatalog($collid, $this->unitid);
// TODO: Question for Ed: Find out if institutioncode and collectioncode should be populated if we
// end up here.
}
if (!$exists) {
// create new record
$occ = new OmOccurrences();
$occ->setcollid($collid);
$occ->setcollectionCode($this->collectioncode);
$occ->setinstitutionCode($occ->lookupInstitutionCode($collid));
$occ->setcatalogNumber($this->unitid);
$occ->setbasisOfRecord("PreservedSpecimen");
$occ->setprocessingStatus("unprocessed");
if (strpos($this->getTypeStatusList(), "Photograph") !== false || strpos($this->getTypeStatusList(), "Drawing") !== false) {
// Handle case of Iconotypes.
// Note: GPI/LAPI schema doesn't have a standard means of identifying non-type drawings.
$occ->setbasisOfRecord("StillImage");
}
}
// Schema documentation suggests, but does not enforce, semicolon as separator for list of collectors.
if (strpos(";", $this->collectors) > 0) {
// split on first semicolon.
$occ->setrecordedBy(substr($this->collectors, 0, strpos(";", $this->collectors)));
$occ->setassociatedCollectors(substr($this->collectors, strpos(";", $this->collectors), strlen($this->collectors)));
} else {
$occ->setrecordedBy($this->collectors);
$occ->setassociatedCollectors("");
}
if ($this->collectornumber != null) {
$occ->setrecordNumber($this->collectornumber);
}
$occ->settypeStatus($this->getTypeStatusList());
if ($this->countryname != null) {
$occ->setcountry($this->countryname);
}
if (substr($this->locality, 0, 1) == "{") {
// Depreciated, but there may be FH documents in the wild that put this into
// Locality rather than Notes.
$locbits = json_decode($this->locality);
$occ->setstateProvince($locbits->{'stateProvince'});
$occ->setcounty($locbits->{'county'});
$occ->setlocality($locbits->{'locality'});
} else {
if ($this->locality != null) {
$occ->setlocality($this->locality);
}
}
if ($this->collectiondate != NULL) {
$occ->seteventDate($this->collectiondate->writeStart());
$occ->setyear($this->collectiondate->startyear);
$occ->setmonth($this->collectiondate->startday);
$occ->setday($this->collectiondate->startday);
$occ->setverbatimEventDate($this->collectiondate->writeAll());
} else {
$occ->setverbatimEventDate("[No Data]");
}
$filedUnder = $this->getFiledUnderID();
if ($filedUnder != null) {
$occ->setsciname($filedUnder->getSciName());
// Set locality security based on TID of accepted name of filed under name
$sectid = $det->lookupAcceptedTID($filedUnder->getSciName());
if ($sectid == null) {
$sectid = $det->lookupTID($filedUnder->getSciName());
}
if ($sectid == null) {
$occ->setlocalitySecurity(0);
} else {
$occ->setlocalitySecurity($det->checkSecurityStatus($sectid));
}
if ($det->lookupAcceptedTID($filedUnder->getSciName()) > 0) {
$occ->settidinterpreted($det->lookupAcceptedTID($filedUnder->getSciName()));
}
if ($filedUnder->family != "NoData") {
$occ->setfamily($filedUnder->family);
}
if (strlen($occ->getfamily()) == 0) {
$occ->setfamily($det->lookupFamilyForTID($det->lookupTID($filedUnder->getSciName())));
}
$occ->setgenus($filedUnder->genus);
$occ->setspecificEpithet($filedUnder->species);
$occ->setinfraSpecificEpithet($filedUnder->infraspecificepithet);
$occ->setscientificNameAuthorship($filedUnder->author);
// work out value for taxon rank.
$occ->settaxonRank($filedUnder->infraspecificrank);
if (strlen($filedUnder->infraspecificepithet) > 0 && strlen($filedUnder->infraspecificrank) == 0) {
$occ->settaxonRank("subspecies");
}
if (strlen($filedUnder->infraspecificepithet) == 0 && strlen($filedUnder->species) > 0) {
$occ->settaxonRank("species");
}
if (strlen($filedUnder->infraspecificepithet) == 0 && strlen($filedUnder->species) == 0 && strlen($filedUnder->genus) > 0) {
$occ->settaxonRank("genus");
}
if ($filedUnder->identificationdate != NULL) {
$occ->setdateIdentified($filedUnder->identificationdate->writeAll());
}
}
if (preg_match("/^[0-9.]+\$/", $this->altitude)) {
$occ->setminimumElevationInMeters($this->altitude);
} else {
if ($this->altitude != null) {
$occ->setverbatimElevation($this->altitude);
}
}
if (substr($this->notes, 0, 1) == "{") {
$bits = json_decode($this->notes);
// Extended higher geography information
if (array_key_exists('stateProvince', $bits)) {
$occ->setstateProvince($bits->{'stateProvince'});
}
if (array_key_exists('county', $bits)) {
$occ->setcounty($bits->{'county'});
}
if (array_key_exists('municipality', $bits)) {
$occ->setmunicipality($bits->{'municipality'});
}
// Exsicatti
$extitle = "";
$exvolume = "";
$exfasicle = "";
$exnumber = "";
$exauthor = "";
if (array_key_exists('extitle', $bits)) {
$extitle = $bits->{'extitle'};
}
if (array_key_exists('exvolume', $bits)) {
$exvolume = $bits->{'exvolume'};
}
if (array_key_exists('fasicle', $bits)) {
$exfasicle = $bits->{'fasicle'};
}
if (array_key_exists('exnumber', $bits)) {
$exnumber = $bits->{'exnumber'};
}
if (array_key_exists('exauthor', $bits)) {
$exauthor = $bits->{'exauthor'};
}
// TODO: Take Exsiccati data and link(/create?) records in Symbiota
} else {
$occ->setoccurrenceRemarks($this->notes);
}
if (!$exists || $createNewRec == 1) {
// if record exists, then TcnImageConf variable createNewRec specifies policy for update.
if ($occ->save()) {
if ($exists) {
//echo "Updated occid: [".$occ->getoccid()."]\n";
$result->successcount++;
$result->updatecount++;
} else {
//echo "Added occid: [".$occ->getoccid()."]\n";
$result->successcount++;
$result->insertcount++;
}
foreach ($this->identifications as $id) {
$id->occid = $occ->getoccid();
$id->write();
}
} else {
$result->errors .= "Error: [" . $occ->errorMessage() . "]\n";
$result->failurecount++;
}
} else {
echo "Skipping, record exists and specified policy is to not update. [" . $occ->getoccid() . "]\n";
}
}