示例#1
0
 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";
     }
 }
示例#2
0
 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";
     }
 }