$v ) // Yii::info ( "KEY: " . $k . " -- " . $v ); if (isset ( $_REQUEST ['name'] )) {throw new NotFoundHttpException('You try to access a page not available for your user group. Go back to search.'); /*return $this->render ( '/site/error', [ "name" => "Oooops", "message" => "Something went wrong.", "exception" => $e ] ); */} else { $filters = array (); $filters ['unitID'] = $_REQUEST ['unitID']; if (isset ( $_REQUEST ['collectioncode'] )) $filters ['collectioncode'] = $_REQUEST ['collectioncode']; else $filters ['collectioncode'] = NULL; if (isset ( $_REQUEST ['institutioncode'] )) $filters ['institutioncode'] = $_REQUEST ['institutioncode']; else $filters ['institutioncode'] = NULL; if (isset ( $_REQUEST ['guid'] )) $filters ['guid'] = $_REQUEST ['guid']; $gbifIDs = [ ]; $colID = ""; $ncbiID = ""; $config = SOLRQueryManager::getConfigSearch (); $query = SOLRQueryManager::createSearchQuery ( $config ); $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", null, $filters, True ); $response = $raw_response; // Yii::info ( "nb res: " . $response->getNumFound () ); if ($response->getNumFound () == 0) { return [ ]; } $tripleidstoreid = ""; foreach ( $response as $doc ) { $tripleidstoreid = $doc->tripleidstoreid; // echo $tripleidstoreid; } $config = SOLRQueryManager::getConfigDetails (); $query = SOLRQueryManager::createSearchQuery ( $config ); $response = SOLRQueryManager::fillAndExecuteQuery ( $query, "tripleidstoreid:" . $tripleidstoreid, null, [ ], True ); if ($response->getNumFound () == 0) { return [ ]; } $multimedia = ""; $loan = [ ]; foreach ( $response as $doc ) { $upperTripleidstoreids = [ ]; $accesspoint = $doc->accesspoint; $guid = $doc->guid; $unitID = $doc->unitID; $collectioncode = $doc->collectioncode; $institutioncode = $doc->institutioncode; $schemaurl = $doc->schemaurl; $digirresourcename = $doc->digirresourcename; $schemaname = $doc->schemaname; $basedirectory = $doc->basedirectory; $sampletype = $doc->sampletype; $tripleidstoreid = $doc->tripleidstoreid; $fullScientificName = $doc->originalName; $occurrenceFile = $doc->filename; $elementtype = $doc->elementtype; $collectors = $doc->collectors; $collectornb = $doc->collectornumbers_nc; try { $guid = $doc->guid; } catch ( Exception $e ) { $guid = null; } try { $indexHerbarorium = $doc->indexHerbarorium; } catch ( Exception $e ) { $indexHerbarorium = null; } try { $fullScientificName = $doc->originalName; } catch ( Exception $e ) { $fullScientificName = null; } try { $preparationtype = $doc->preparationType; } catch ( Exception $e ) { $preparationtype = null; } try { $citesStatus = $doc->citesStatus; } catch ( Exception $e ) { $citesStatus = NULL; } if (! empty ( $collectornb )) { $collectornb = array_unique ( $collectornb ); if (($key = array_search ( 's.n.', $collectornb )) !== false) { unset ( $collectornb [$key] ); } } try { $latitude = $doc->latitude; //Yii::info($latitude); } catch ( Exception $e ) { $latitude [] = NULL; } try { $longitude = $doc->longitude; } catch ( Exception $e ) { $longitude [] = NULL; } try { $canonicalName = $doc->canonicalName; } catch ( Exception $e ) { $canonicalName = NULL; } try { $citesStatus = $doc->citesStatus; } catch ( Exception $e ) { $citesStatus = NULL; } try { $gbifIDs [] = $doc->gbifKey; } catch ( Exception $e ) { } try { $colID = $doc->taxonIDcol; } catch ( Exception $e ) { } try { $ncbiID = $doc->taxonIDncbi; } catch ( Exception $e ) { } try { $upperTripleidstoreids = $doc->upperTripleidstoreids; } catch ( Exception $e ) { $upperTripleidstoreids = [ ]; } if ($upperTripleidstoreids == "") $upperTripleidstoreids = [ ]; try { $tmpids = $doc->lowerTripleidstoreids; if (isset ( $tmpids )) array_merge ( $upperTripleidstoreids, $tmpids ); } catch ( Exception $e ) { } try { // if(isset($doc->multimediaurl) || !empty($doc->multimediaurl) ) { if (is_array ( $doc->multimediaurl ) && $doc->multimediaurl[0] != "N/A") { $multimedia = ''; $multimedia .= '
'; foreach ( $doc->multimediaurl as $index => $murl) { if ($murl != "N/A" && strpos($murl, 'SpecimenPK') == "") { if (! (strpos ( $multimedia, $murl ) === FALSE)) continue; else { if (strpos ( $murl, "http" ) === FALSE) { $murl = "http://" . $murl; } $License = ""; $Copyright = ""; $TermsOfUse = ""; $CreatedWhen = ""; $CreatedBy = ""; if(isset($doc->licenses[$index]) && $doc->licenses[$index] != "N/A") { $License = "License: ". $doc->licenses[$index]."
";} if(isset($doc->copyrights[$index]) && $doc->copyrights[$index] != "N/A") { $Copyright = "Copyright: ". $doc->copyrights[$index]."
";} if(isset($doc->termsofuse[$index]) && $doc->termsofuse[$index] != "N/A") { $TermsOfUse = "Terms of Use: ". $doc->termsofuse[$index]."
";} if(isset($doc->createdwhen[$index]) && $doc->createdwhen[$index] != "N/A" ) { $CreatedWhen = "Created: ". $doc->createdwhen[$index]."
";} if(isset($doc->createdby[$index]) && $doc->createdby[$index] != "N/A") { $CreatedBy = "Photographer: ". $doc->createdby[$index]."
";} $multimedia = $multimedia . "
".$CreatedWhen.$CreatedBy.$Copyright.$TermsOfUse.$License."
"; } } } $multimedia .= "
"; } } catch ( Exception $e ) { } $blocked = $doc->blocked; $blockedUntil = $doc->blockedUntil; $disposition = $doc->disposition; $disposition_clean = $doc->disposition_clean; $condition = $doc->condition; $DNALabel = ""; if (empty ( $blockedUntil ) and $blocked != 'yes' and $blocked != 'Yes' and $blocked != '1') { if ($sampletype == "tissue") $loan [$unitID] = [ " Tissue available ", "OK", "not blocked", $condition, $disposition_clean ]; if ($sampletype == "specimen") $loan [$unitID] = [ " Specimen available ", "OK", "not blocked", $condition, $disposition_clean ]; if ($sampletype == "culture") $loan [$unitID] = [ " Culture available ", "OK", "not blocked", $condition, $disposition_clean ]; if ($sampletype == "DNA") { if($preparationtype == "eDNA") { $DNALabel = "environmental"; } else if($preparationtype == "aDNA") { $DNALabel = "ancient"; } $loan [$unitID] = [ $DNALabel." DNA available ", "OK", "not blocked", $condition, $disposition_clean ];} } else { if (new \DateTime () > new \DateTime ( $blockedUntil )) { // $loan [] = "The unitID " . $unitID . " was blocked until " . $blockedUntil . " under the condition " . $condition . ". There is still " . $disposition_clean . " available."; if ($sampletype == "tissue") $loan [$unitID] = [ " Tissue available ", "OK", "was blocked until " . $blockedUntil, $condition, $disposition_clean ]; if ($sampletype == "DNA") if($preparationtype == "eDNA") { $DNALabel = "environmental"; } else if($preparationtype == "aDNA") { $DNALabel = "ancient"; } $loan [$unitID] = [ $DNALabel." DNA available ", "OK", "was blocked until " . $blockedUntil, $condition, $disposition_clean ]; } if ( $blocked == 'yes' or $blocked == 'Yes' or $blocked == '1') { if ($sampletype == "tissue") $loan [$unitID] = [ " Tissue available ", "BLOCKED", "Blocked for loaning", $condition, $disposition_clean ]; if ($sampletype == "DNA") if($preparationtype == "eDNA") { $DNALabel .= "environmental"; } else if($preparationtype == "aDNA") { $DNALabel .= "ancient"; } $loan [$unitID] = [ $DNALabel." DNA available ", "BLOCKED", "Blocked for loaning", $condition, $disposition_clean ]; } } } if (isset ( $upperTripleidstoreids [0] )) { $tripleidstoreids = SingleRecordManager::getListOfTripleids ( $upperTripleidstoreids, $model ); // remove the tripleidstoreid from the unit already searched unset ( $tripleidstoreids [array_search ( $tripleidstoreid, $tripleidstoreids )] ); $tripleidstoreids = array_values ( $tripleidstoreids ); $SumSize = count ( $tripleidstoreids ); $config = SOLRQueryManager::getConfigDetails (); $query = SOLRQueryManager::createSearchQuery ( $config ); $fq = ""; for($i = 0; $i < $SumSize; $i ++) { $fq .= "tripleidstoreid:" . $tripleidstoreids [$i]; if (isset ( $tripleidstoreids [$i + 1] )) { $fq .= " OR "; } } // Yii::info ( "fq: " . $fq ); if ($fq == "") { $index = 0; $accesspoint2 [$index] = NULL; $unitID2 [$index] = NULL; $tripleid2 [$index] = NULL; $collectioncode2 [$index] = NULL; $institutioncode2 [$index] = NULL; $guid2 [$index] = NULL; $schemaurl2 [$index] = NULL; $schemaname2 [$index] = NULL; $basedirectory2 [$index] = NULL; $sampletype2 [$index] = NULL; $preparationtype2 [$index] = NULL; $recordBasis2 [$index] = NULL; $digirresourcename2 [$index] = NULL; $latitude2 [$index] = NULL; $longitude2 [$index] = NULL; $occurrenceFile2 [$index] = NULL; $elementtype2 [$index] = NULL; $filters ['unitID2'] [$index] = NULL; $filters ['collectioncode2'] [$index] = NULL; $filters ['institutioncode2'] [$index] = NULL; $filters ['guid2'] [$index] = NULL; $citesStatus2 [$index] = NULL; $multimedia2 [$index] = ""; $output = array ( 'response' => $response, 'filters' => $filters, 'accesspoint' => $accesspoint, 'unitID' => $unitID, 'citesStatus' => $citesStatus, 'collectioncode' => $collectioncode, 'institutioncode' => $institutioncode, 'guid' => $guid, 'schemaurl' => $schemaurl, 'digirresourcename' => $digirresourcename, 'schemaname' => $schemaname, 'basedirectory' => $basedirectory, 'sampletype' => $sampletype, 'preparationtype' => $preparationtype, 'fullScientificName' => $fullScientificName, 'multimedia' => $multimedia, 'canonicalName' => $canonicalName, 'tripleid' => $tripleidstoreid, 'latitude' => $latitude, 'longitude' => $longitude, 'loan' => $loan, 'collectors' => $collectors, 'collectornb' => $collectornb, 'indexHerbarorium' => $indexHerbarorium, 'occurrenceFile' => $occurrenceFile, 'elementtype' => $elementtype ); } else { $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True ); $response = $raw_response; foreach ( $response as $index => $doc ) { $occurrenceFile2 [$index] = $doc->filename; try { $accesspoint2 [$index] = $doc->accesspoint; } catch ( Exception $e ) { $accesspoint2 [$index] = ""; } try { $unitID2 [$index] = $doc->unitID; } catch ( Exception $e ) { $unitID2 [$index] = ""; } try { $collectioncode2 [$index] = $doc->collectioncode; } catch ( Exception $e ) { $collectioncode2 [$index] = ""; } try { $tripleid2 [$index] = $doc->tripleidstoreid; } catch ( Exception $e ) { $tripleid2 [$index] = ""; } try { $institutioncode2 [$index] = $doc->institutioncode; } catch ( Exception $e ) { $institutioncode2 [$index] = ""; } try { $guid2 [$index] = $doc->guid; } catch ( Exception $e ) { $guid2 [$index] = ""; } try { $schemaurl2 [$index] = $doc->schemaurl; } catch ( Exception $e ) { $schemaurl2 [$index] = ""; } try { $ocurrenceFile2 [$index] = $doc->filename; } catch ( Exception $e ) { $ocurrenceFile2 [$index] = ""; } try { $schemaname2 [$index] = $doc->schemaname; } catch ( Exception $e ) { $schemaname2 [$index] = ""; } try { $basedirectory2 [$index] = $doc->basedirectory; } catch ( Exception $e ) { $basedirectory2 [$index] = ""; } try { $elementtype2 [$index] = $doc->elementtype; } catch ( Exception $e ) { $elementtype2 [$index] = ""; } try { $sampletype2 [$index] = $doc->sampletype; if (! isset ( $sampletype2 [$index] ) || $sampletype2 [$index] == "unknown") { try { $rb = $doc->recordbasis; // echo "recordbasis: " . $rb . "
"; if (stristr ( $rb, "specimen" ) != FALSE || stristr ( $rb, "occurrence" )) $sampletype2 [$index] = 'specimen'; } catch ( Exception $e ) { } } } catch ( Exception $e ) { $sampletype2 [$index] = "unknown"; try { $rb = $doc->recordbasis; // echo "recordbasis!"; if (stristr ( $rb, "specimen" ) != FALSE || stristr ( $rb, "occurrence" )) $sampletype2 [$index] = 'specimen'; } catch ( Exception $e ) { } } try { $preparationtype2 [$index] = $doc->preparationType; } catch ( Exception $e ) { $preparationtype2 [$index] = ""; } try { $digirresourcename2 [$index] = $doc->digirresourcename; } catch ( Exception $e ) { $digirresourcename2 [$index] = ""; } try { $latitude2 [$index] = $doc->latitude; } catch ( Exception $e ) { $latitude2 [$index] = NULL; } try { $longitude2 [$index] = $doc->longitude; } catch ( Exception $e ) { $longitude2 [$index] = NULL; } try { $citesStatus2 [$index] = $doc->citesStatus; } catch ( Exception $e ) { $citesStatus2 [$index] = NULL; } try { $gbifIDs [] = $doc->gbifKey; } catch ( Exception $e ) { } try { $colID = $doc->taxonIDcol; } catch ( Exception $e ) { } try { $ncbiID = $doc->taxonIDncbi; } catch ( Exception $e ) { } $filters ['unitID2'] [$index] = $doc->unitID; $filters ['collectioncode2'] [$index] = $doc->collectioncode; $filters ['institutioncode2'] [$index] = $doc->institutioncode; $filters ['guid2'] [$index] = $doc->institutioncode; try { $multimedia2 [$index] = ""; try { if (is_array ( $doc->multimediaurl ) && $doc->multimediaurl[0] != "N/A") { $multimedia2 [$index] = '
'; foreach ( $doc->multimediaurl as $ind => $murl ) if ($murl != "N/A" && strpos($murl, 'manifest.json') == "") if (! strpos ( $multimedia2 [$index], $murl )){ $License = ""; $Copyright = ""; $TermsOfUse = ""; $CreatedWhen = ""; $CreatedBy = ""; if (isset($doc->licenses[$ind]) && $doc->licenses[$ind] != "N/A") { $License = "License: " . $doc->licenses[$ind] . "
"; } if (isset($doc->copyrights[$ind]) && $doc->copyrights[$ind] != "N/A") { $Copyright = "Copyright: " . $doc->copyrights[$ind] . "
"; } if (isset($doc->termsofuse[$ind]) && $doc->termsofuse[$ind] != "N/A") { $TermsOfUse = "Terms of Use: " . $doc->termsofuse[$ind] . "
"; } if (isset($doc->createdwhen[$ind]) && $doc->createdwhen[$ind] != "N/A") { $CreatedWhen = "Created: " . $doc->createdwhen[$ind] . "
"; } if (isset($doc->createdby[$ind]) && $doc->createdby[$ind] != "N/A") { $CreatedBy = "Photographer: " . $doc->createdby[$ind] . "
"; } $multimedia2 [$index] = $multimedia2 [$index] . "
" . $CreatedWhen . $CreatedBy . $Copyright . $TermsOfUse . $License . "
"; //$multimedia2 [$index] = $multimedia2 [$index] . ""; }else { $multimedia2 [$index] == ""; } $multimedia2 [$index] .= "
"; } } catch ( Exception $e ) { $multimedia2 [$index] == ""; } } catch ( Exception $e ) { $multimedia2 [$index] = ""; } $blocked = $doc->blocked; $blockedUntil = $doc->blockedUntil; $disposition = $doc->disposition; $disposition_clean = $doc->disposition_clean; $condition = $doc->condition; $DNALabel = ""; if ($sampletype != "tissue") { if (empty ( $blockedUntil )) { if ($sampletype2 [$index] == "tissue") $loan [$filters ['unitID2'] [$index]] = [ " Tissue available ", "OK", "not blocked", $condition, $disposition_clean ]; if ($sampletype2 [$index] == "environmental sample") $loan [$filters ['unitID2'] [$index]] = [ " from ".$preparationtype2 [$index], "OK", "not blocked", $condition, $disposition_clean ]; } else { if (new \DateTime () > new \DateTime ( $blockedUntil )) { // $loan [] = "The unitID " . $filters ['unitID2'] [$index] . " was blocked until " . $blockedUntil . " under the condition " . $condition . ". There is still " . $disposition_clean . " available."; if ($sampletype2 [$index] == "tissue") $loan [$filters ['unitID2'] [$index]] = [ " Tissue available ", "OK", "was blocked until " . $blockedUntil, $condition, $disposition_clean ]; if ($sampletype2 [$index] == "environmental sample") $loan [$filters ['unitID2'] [$index]] = [ " from ".$preparationtype2 [$index], "OK", "was blocked until " . $blockedUntil, $condition, $disposition_clean ]; } else { if ($sampletype2 [$index] == "tissue") $loan [$filters ['unitID2'] [$index]] = [ " Tissue available ", "BLOCKED", "is blocked until " . $blockedUntil, $condition, $disposition_clean ]; if ($sampletype2 [$index] == "environmental sample") $loan [$filters ['unitID2'] [$index]] = [ " from ".$preparationtype2 [$index], "BLOCKED", "is blocked until " . $blockedUntil, $condition, $disposition_clean ]; } } } } $output = array ( 'response' => $response, 'filters' => $filters, 'accesspoint' => $accesspoint, 'unitID' => $unitID, 'collectioncode' => $collectioncode, 'institutioncode' => $institutioncode, 'guid' => $guid, 'schemaurl' => $schemaurl, 'digirresourcename' => $digirresourcename, 'schemaname' => $schemaname, 'basedirectory' => $basedirectory, 'sampletype' => $sampletype, 'preparationtype' => $preparationtype, 'multimedia' => $multimedia, 'canonicalName' => $canonicalName, 'tripleid' => $tripleidstoreid, 'latitude' => $latitude, 'longitude' => $longitude, 'occurrenceFile' => $occurrenceFile, 'elementtype' => $elementtype, 'accesspoint2' => $accesspoint2, 'unitID2' => $unitID2, 'collectioncode2' => $collectioncode2, 'tripleid2' => $tripleid2, 'institutioncode2' => $institutioncode2, 'guid2' => $guid2, 'schemaurl2' => $schemaurl2, 'occurrenceFile2' => $occurrenceFile2, 'elementtype2' => $elementtype2, 'schemaname2' => $schemaname2, 'basedirectory2' => $basedirectory2, 'digirresourcename2' => $digirresourcename2, 'sampletype2' => $sampletype2, 'preparationtype2' => $preparationtype2, 'longitude2' => $longitude2, 'latitude2' => $latitude2, 'multimedia2' => $multimedia2, 'citesStatus2' => $citesStatus2, 'loan' => $loan, 'fullScientificName' => $fullScientificName, 'collectors' => $collectors, 'collectornb' => $collectornb, 'indexHerbarorium' => $indexHerbarorium ); } if (sizeof ( $gbifIDs ) > 0) { $output ['GBIFs'] = array_unique ( $gbifIDs ); // $GBIFs = ExploreManager::getGBIFRecords ( $gbifIDs ); // if (sizeof ( $GBIFs ) > 0) // $output ['GBIFs'] = $GBIFs; } else $output ['GBIFs'] = [ ]; if ($ncbiID != "") { $output ['NCBI'] = $ncbiID; // $NCBI = ExploreManager::getNCBIRecord ( $ncbiID ); // if (! empty ( $NCBI )) // $output ['NCBI'] = $NCBI; } else $output ['NCBI'] = [ ]; $GGBNs = ExploreManager::getGGBNRecords ( $canonicalName, $tripleidstoreid ); if (! empty ( $GGBNs )) { $output ['GGBNs'] = $GGBNs; } else { $output ['GGBNs'] = [ ]; } return $output; } // if($upperTripleidstoreids != "") else { $output = array ( 'response' => $response, 'filters' => $filters, 'accesspoint' => $accesspoint, 'citesStatus' => $citesStatus, 'unitID' => $unitID, 'collectioncode' => $collectioncode, 'institutioncode' => $institutioncode, 'guid' => $guid, 'schemaurl' => $schemaurl, 'digirresourcename' => $digirresourcename, 'schemaname' => $schemaname, 'basedirectory' => $basedirectory, 'sampletype' => $sampletype, 'preparationtype' => $preparationtype, 'multimedia' => $multimedia, 'canonicalName' => $canonicalName, 'tripleid' => $tripleidstoreid, 'latitude' => $latitude, 'longitude' => $longitude, 'loan' => $loan, 'occurrenceFile' => $occurrenceFile, 'fullScientificName' => $fullScientificName, 'collectors' => $collectors, 'collectornb' => $collectornb, 'indexHerbarorium' => $indexHerbarorium, 'elementtype' => $elementtype ); if (sizeof ( $gbifIDs ) > 0) { $output ['GBIFs'] = array_unique ( $gbifIDs ); // $GBIFs = ExploreManager::getGBIFRecords ( $gbifIDs ); // if (sizeof ( $GBIFs ) > 0) // $output ['GBIFs'] = $GBIFs; } else $output ['GBIFs'] = [ ]; if ($ncbiID != "") { $output ['NCBI'] = $ncbiID; // $NCBI = ExploreManager::getNCBIRecord ( $ncbiID ); // if (! empty ( $NCBI )) // $output ['NCBI'] = $NCBI; } else $output ['NCBI'] = [ ]; /* $GGBNs = ExploreManager::getGGBNRecords ( $canonicalName, $tripleidstoreid ); if (! empty ( $GGBNs )) { $output ['GGBNs'] = $GGBNs; } else { $output ['GGBNs'] = [ ]; } */ return $output; } } } public static function createOutputTaxonBased($name) { /* $config = SOLRQueryManager::getConfigDetails (); $query = SOLRQueryManager::createSearchQuery ( $config ); $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, 'fullScientificName:"'. $name . '"', "", [], true );*/ $config = SOLRQueryManager::getConfigSearch (); $query = SOLRQueryManager::createSearchQuery ( $config ); $q = [ 'originalCanonicalName:"'.$name.'" AND accessionStatus:C' ]; $CustomizedFacets = SOLRQueryManager::CustomizedFacetsListView($query, $config, $q, ""); $multimedia = ""; $longitude = []; $latitude = []; //var_dump ($raw_response); /* foreach ( $raw_response as $doc ) { if (is_array ( $doc->multimediaurl ) && $doc->multimediaurl[0] != "N/A") { $multimedia = '
'; foreach ( $doc->multimediaurl as $index => $murl) { if ($murl != "N/A") { if (! (strpos ( $multimedia, $murl ) === FALSE)) continue; else { if (strpos ( $murl, "http" ) === FALSE) { $murl = "http://" . $murl; } $License = ""; $Copyright = ""; $TermsOfUse = ""; $CreatedWhen = ""; $CreatedBy = ""; if($doc->licenses[$index] != "N/A" && isset($doc->licenses[$index])) { $License = "License: ". $doc->licenses[$index]."
";} if($doc->copyrights[$index] != "N/A" && isset($doc->copyrights[$index])) { $Copyright = "Copyright: ". $doc->copyrights[$index]."
";} if($doc->termsofuse[$index] != "N/A" && isset($doc->termsofuse[$index])) { $TermsOfUse = "Terms of Use: ". $doc->termsofuse[$index]."
";} if($doc->createdwhen[$index] != "N/A" && isset($doc->createdwhen[$index])) { $CreatedWhen = "Created: ". $doc->createdwhen[$index]."
";} if($doc->createdby[$index] != "N/A" && isset($doc->createdby[$index])) { $CreatedBy = "Photographer: ". $doc->createdby[$index]."
";} $multimedia = $multimedia . "
".$CreatedWhen.$CreatedBy.$Copyright.$TermsOfUse.$License."
"; } } } $multimedia .= "
"; } if(isset($doc->longitude) or $doc->longitude != "") $longitude = array_merge($longitude, $doc->longitude); if(isset($doc->latitude) or $doc->latitude != "") $latitude = array_merge($latitude, $doc->latitude); } */ $output = array ('fullScientificName' => $name, 'multimedia' => $multimedia, 'longitude' => $longitude, 'latitude' => $latitude, 'facetNumbers' => $CustomizedFacets ); return $output; } public static function getListOfTripleids($baseIds, $model) { static $cnt = 0; static $lowerAndUppers = [ ]; if (sizeof ( $lowerAndUppers ) == 0) { $lowerAndUppers = $baseIds; } $cnt ++; $sizeBefore = sizeof ( $lowerAndUppers ); if ($sizeBefore == 0) $sizeBefore = sizeof ( $baseIds ); foreach ( $baseIds as $id ) { $config = SOLRQueryManager::getConfigDetails (); $query = SOLRQueryManager::createSearchQuery ( $config ); $fq = "tripleidstoreid:" . $id; $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True ); $response = $raw_response; foreach ( $response as $doc ) { $upperTripleidstoreids2 = $doc ['upperTripleidstoreids']; $lowerIDs = $doc ['lowerTripleidstoreids']; if (isset ( $upperTripleidstoreids2 )) { $lowerAndUppers = array_unique ( array_merge ( $lowerAndUppers, $upperTripleidstoreids2 ) ); } if (isset ( $lowerIDs )) { $lowerAndUppers = array_unique ( array_merge ( $lowerAndUppers, $lowerIDs ) ); } } } if (sizeof ( $lowerAndUppers ) > $sizeBefore) { if ($cnt < 5) return self::getListOfTripleids ( $lowerAndUppers, $model ); } return $lowerAndUppers; } public static function createRecordQuery($filters, $schemaurl) { if ($schemaurl == "http://www.tdwg.org/schemas/abcd/2.06") { $query = urlencode ( '
search
http://www.tdwg.org/schemas/abcd/2.06 http://www.tdwg.org/schemas/abcd/2.06 ' . $filters ['unitID'] . ' ' . $filters ['institutioncode'] . ' ' . $filters ['collectioncode'] . ' false' ); } if ($schemaurl == "http://www.tdwg.org/schemas/abcd/2.1") { $query = urlencode ( '
search
http://www.tdwg.org/schemas/abcd/2.1 http://www.tdwg.org/schemas/abcd/2.1 ' . $filters ['unitID'] . ' ' . $filters ['institutioncode'] . ' ' . $filters ['collectioncode'] . ' false' ); } if ($schemaurl == "http://rs.tdwg.org/dwc/") { $query = ""; } return $query; } public static function createAssociatedRecordQuery($associatedUnitID, $associatedCollectionCode, $associatedInstitutionCode, $associatedSchemaUrl, $associatedDigirResourcename, $associatedAccessPoint, $associatedGuid) { // echo ( "createAssociatedRecordQuery " . $associatedUnitID . " " . $associatedSchemaUrl ); $query2 = ""; // TODO // add guid to ABCD Queries if ($associatedSchemaUrl == "http://www.tdwg.org/schemas/abcd/2.06") { $query2 = urlencode ( '
search
http://www.tdwg.org/schemas/abcd/2.06 http://www.tdwg.org/schemas/abcd/2.06 ' . $associatedUnitID . ' ' . $associatedInstitutionCode . ' ' . $associatedCollectionCode . ' false' ); } if ($associatedSchemaUrl == "http://www.tdwg.org/schemas/abcd/2.1") { $query2 = urlencode ( '
search
http://www.tdwg.org/schemas/abcd/2.1 http://www.tdwg.org/schemas/abcd/2.1 ' . $associatedUnitID . ' ' . $associatedInstitutionCode . ' ' . $associatedCollectionCode . ' false' ); } if ($associatedSchemaUrl == "http://rs.tdwg.org/dwc/") { $query2 = ""; } if ($associatedSchemaUrl == "http://bnhm.berkeley.edu/DwC/bnhm_dc2_schema.xsd") { $q = '
1.0.02009-11-13 14:40:56.000 ' . $associatedAccessPoint . ' search
' . $associatedUnitID . ' ' . $associatedInstitutionCode . ' ' . $associatedCollectionCode . ' false'; $query2 = urlencode ( $q ); } return $query2; } public static function getABCD($accesspoint, $query, $unitID, $guid) { // TODO test if url has parameter and set ? or &!!! $fullURL = $accesspoint . "&query=" . $query; // echo $fullURL; $options = [ 'http' => [ 'timeout' => '10' ] ]; $context = stream_context_create ( $options ); libxml_set_streams_context ( $context ); $xml = new DOMDocument ( '1.0', 'UTF-8' ); try { $xml->load ( $fullURL ); $handle = fopen ( Yii::$app->params ['tmpFolder'] . $unitID . '.xml', 'w' ); fwrite ( $handle, $xml->saveXML () ); fclose ( $handle ); } catch ( yii\base\ErrorException $e ) { $xml = NULL; } // Yii::info ( $xml->saveXML () ); return $xml; } public static function parseABCD($xsl, $xml, $tripleid) { $processor = new XSLTProcessor (); $processor->registerPHPFunctions (); $processor->importStyleSheet ( $xsl ); try { $html = $processor->transformToXML ( $xml ); } catch ( yii\base\ErrorException $e ) { Yii::error ( $e ); $html = SingleRecordManager::getFromCache ( $tripleid ); return [ $html, False ]; } // Yii::info("parse ABCD: ".$html); // echo $html; if (strpos ( $html, "hits found for" ) > 0 && $tripleid != NULL) { $out = SingleRecordManager::getFromCache ( $tripleid ); return [ $out, False ]; } else return [ $html, True ]; } public static function readDwC($xsl, $accesspoint, $digirresourcename, $query, $tripleid, $guid) { $processor = new XSLTProcessor (); $processor->importStyleSheet ( $xsl ); $fullURL = $accesspoint . "?request=" . $query; // echo $fullURL; $xml = new DOMDocument ( '1.0', 'UTF-8' ); $xml->load ( $fullURL ); $html = $processor->transformToXML ( $xml ); if (strpos ( $html, "hits found for" ) > 0) { $out = SingleRecordManager::getFromCache ( $tripleid ); return $out; } else return $html; } public static function getFromCache($tripleidstoreid) { Yii::info ( "getFromCache " . $tripleidstoreid ); $config = SOLRQueryManager::getConfigDetails (); $query = SOLRQueryManager::createSearchQuery ( $config ); $fq = "tripleidstoreid:" . $tripleidstoreid; $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True ); $response = $raw_response; $out = ""; foreach ( $response as $doc ) { $out .= "The original unit could not be found - info displayed from the cache"; $out .= "

Identification(s):

"; $out .= $doc->fullScientificName . "
"; if (Yii::$app->params ['siteName'] != 'ggbn_portal') $out .= "

Gathering Event

"; else $out .= "

Collection Info:

"; $out .= "Collector(s): " . $doc->collectors . "
"; if ($doc->fieldnumber != "s.n.") $out .= "Field number: " . $doc->fieldnumber . "
"; $out .= "Locality: " . $doc->locality . "
" . "
"; // $out .= "Other info " . "
"; $out .= "Country: " . $doc->country . "
"; if (! empty ( $doc->continent )) $out .= "Continent: " . implode ( ", ", $doc->continent ) . "
"; if (! empty ( $doc->latitude )) $out .= "Coordinates (Lat|Lon): " . strval(round(floatval($doc->latitude[0]), 1)) . "|" . $doc->longitude [0] . "
"; } return $out; } // type = specimen or tissue or dna public static function readDwCA($unitToFind, $folder, $basedirectory, $dom, $sampleType, $occurrenceFile, $guidToFind) { //Yii::info ( "READ " . $unitToFind . " in file " . $occurrenceFile ); echo ""; $Cores = $dom->getElementsByTagName ( 'core' ); $Extensions = $dom->getElementsByTagName ( 'extension' ); $xml = simplexml_load_file ( $folder . "meta.xml" ); // $xml = simplexml_load_file ("http://bgbm-import/ggbntestunits/8937452-fishes__associated_only_/nmnh_occurrence_archive/associated/smallArchive/" . "meta.xml" ); foreach ( $xml->attributes () as $a => $b ) { if ($a === 'metadata') { $EML = $b; } } foreach ($Cores as $Core) { $encoding = $Core->getAttribute ( 'encoding' ); $fieldTerminatedBy = $Core->getAttribute ( 'fieldsTerminatedBy' ); if($fieldTerminatedBy == ","){ $fieldsTerminatedBy = $fieldTerminatedBy; } else { $fieldsTerminatedBy = "%09"; } $linesTerminatedBy = $Core->getAttribute ( 'linesTerminatedBy' ); $fieldsEnclosedBy = $Core->getAttribute ( 'fieldsEnclosedBy' ); $ignoreHeaderLines = $Core->getAttribute ( 'ignoreHeaderLines' ); $fields = $Core->getElementsByTagName ( 'field'); foreach ($fields as $index => $field) { if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/catalogNumber') { $CatalogNoID = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/occurrenceID') { $OccurrenceID = $field->getAttribute('index'); } } } $output = ''; $relation = ''; $sample = ''; $preservation = ''; $preparation = ''; $sequences = ''; $gelimage = ''; $permit = ''; $prepSex = ''; $locality = ""; $identification = ""; $gathering = ""; $ID_Record = null; $material = ""; $taxonlist = ""; $taxonomySet = false; $latitude = [ ]; $longitude = [ ]; $multimedia = ""; $preparationType = ""; // extract data from EML file $xml = simplexml_load_file ( $folder . $EML );# $datasetxml = $xml->dataset; $creator = $datasetxml->creator; try { $orga = $creator->organizationName; //Yii::info ( "ORGA " . $orga ); } catch ( yii\base\ErrorException $e ) { } try { $creatorxml = $creator->individualName; } catch ( yii\base\ErrorException $e ) { } try { $addressxml = $creator->address; } catch ( yii\base\ErrorException $e ) { } $addressT = [ ]; try { $addressT [] = $creatorxml->surName; $addressT [] .= $creatorxml->givenName; $addressT [] .= $creator->electronicMailAddress; $addressT [] .= $orga; $addressT [] .= $addressxml->deliveryPoint; $addressT [] .= $addressxml->city; $addressT [] .= $addressxml->administrativeArea; $addressT [] .= $addressxml->postalCode; $addressT [] .= $addressxml->country; } catch ( yii\base\ErrorException $e ) { } try { $addressT = array_filter ( $addressT ); } catch ( yii\base\ErrorException $e ) { } $metaprovider = $datasetxml->metadataProvider; try { $orgameta = $metaprovider->organizationName; //Yii::info ( "ORGA Metada " . $orgameta ); } catch ( yii\base\ErrorException $e ) { } try { $metaproviderxml = $metaprovider->individualName; } catch ( yii\base\ErrorException $e ) { } try { $addressmetaxml = $metaprovider->address; } catch ( yii\base\ErrorException $e ) { } $addressMP = [ ]; try { $addressMP [] = $metaproviderxml->surName; $addressMP [] .= $metaproviderxml->givenName; $addressMP [] .= $metaprovider->electronicMailAddress; $addressMP [] .= "(".$metaprovider->positionName.")"; $addressMP [] .= $orgameta; $addressMP [] .= $addressmetaxml->deliveryPoint; $addressMP [] .= $addressmetaxml->city; $addressMP [] .= $addressmetaxml->administrativeArea; $addressMP [] .= $addressmetaxml->postalCode; $addressMP [] .= $addressmetaxml->country; } catch ( yii\base\ErrorException $e ) { } try { $addressMP = array_filter ( $addressMP ); } catch ( yii\base\ErrorException $e ) { } $intellectualRightsxml = $datasetxml->intellectualRights; $irT = [ ]; if($intellectualRightsxml) { try { $irT [] = $intellectualRightsxml->para; $paraXML = $intellectualRightsxml->para; $ulinkXML = $paraXML->ulink; /* if(isset ($ulinkXML)) {$url = $ulinkXML->attributes () [0]; $irT [] = "" . $ulinkXML->citetitle . ""; }*/ } catch ( yii\base\ErrorException $e ) { //Yii::info ( "oups " . $e ); } try { $irT = array_filter ( $irT ); } catch ( Exception $e ) { } } try { $geocoveragexml = $datasetxml->coverage->geographicCoverage->geographicDescription; } catch ( yii\base\ErrorException $e ) { $geocoveragexml = ""; } try { $taxocoveragexml = $datasetxml->coverage->taxonomicCoverage->generalTaxonomicCoverage; } catch ( yii\base\ErrorException $e ) { $taxocoveragexml = ""; } try { $abstract = $datasetxml->abstract->para; } catch ( yii\base\ErrorException $e ) { $abstract = ""; } // Start Core foreach ( $Cores as $Core ) { $catalogNumber = ""; $collectionCode = ""; $collectionID = ""; $institutionCode = ""; $datasetName = ""; $basisOfRecord = ""; $guid = ""; $scientificName = ""; $identifiedBy = ""; $identificationReferences = ""; $identificationRemarks = ""; $dateIdentified = ""; $family = ""; $order = ""; $class = ""; $phylum = ""; $kingdom = ""; $typeStatus = ""; $country = ""; $locality = ""; $locationID = ""; $stateProvince = ""; $islandGroup = ""; $decimalLatitude = ""; $decimalLongitude = ""; $verbatimElevation = ""; $minimumElevationInMeters = ""; $maximumElevationInMeters = ""; $verbatimDepth = ""; $minimumDepthInMeters = ""; $maximumDepthInMeters = ""; $recordedBy = ""; $recordNumber = ""; $fieldNumber = ""; $verbatimEventDate = ""; $eventDate = ""; $sex = ""; $preparations = ""; $individualCount = ""; $lifeStage = ""; $Files = $Core->getElementsByTagName ( 'files' ); foreach ( $Files as $File ) { $FileLocationCore = $File->getElementsByTagName ( 'location' )->item ( 0 )->nodeValue; } $ColumnIDs = $Core->getElementsByTagName ( 'id' ); foreach ( $ColumnIDs as $ColumnID ) { $field_columns_core [0] = $ColumnID->getAttribute ( 'index' ); $idElt = $ColumnID->getAttribute ( 'index' ); } $fields = $Core->getElementsByTagName ( 'field' ); $max = 0; foreach ( $fields as $field ) { $idx = $field->getAttribute ( 'index' ); $field_columns_core [$field->getAttribute ( 'index' )] = $field->getAttribute ( 'term' ); if ($field->getAttribute ( 'index' ) > $max) $max = $field->getAttribute ( 'index' ); if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/catalogNumber') { $catalogNumber = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/collectionCode') { $collectionCode = $field->getAttribute('index'); if($collectionCode == "") { $staticValues_collectionCode = $field->getAttribute('default');} } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/collectionID') { $collectionID = $field->getAttribute('index'); if($collectionID == "") { $staticValues_collectionID = $field->getAttribute('default'); } } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/institutionCode') { $institutionCode = $field->getAttribute('index'); if($institutionCode == "") { $staticValues_institutionCode = $field->getAttribute('default'); } } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/datasetName') { $datasetName = $field->getAttribute('index'); if($datasetName == "") { $staticValues_datasetName = $field->getAttribute('default'); } } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/basisOfRecord') { $basisOfRecord = $field->getAttribute('index'); if($basisOfRecord == "") { $staticValues_basisOfRecord = $field->getAttribute('default'); } } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/occurrenceID') { $guid = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/scientificName') { $scientificName = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identifiedBy') { $identifiedBy = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identificationRemarks') { $identificationRemarks = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identificationReferences') { $identificationReferences = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/dateIdentified') { $dateIdentified = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/family') { $family = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/order') { $order = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/class') { $class = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/phylum') { $phylum = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/kingdom') { $kingdom = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/typeStatus') { $typeStatus = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/country') { $country = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/locality') { $locality = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/locationID') { $locationID = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/islandGroup') { $islandGroup = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/stateProvince') { $stateProvince = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/verbatimElevation') { $verbatimElevation = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/minimumElevationInMeters') { $minimumElevationInMeters = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/maximumElevationInMeters') { $maximumElevationInMeters = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/verbatimDepth') { $verbatimDepth = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/minimumDepthInMeters') { $minimumDepthInMeters = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/maximumDepthInMeters') { $maximumDepthInMeters = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/decimalLatitude') { $decimalLatitude = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/decimalLongitude') { $decimalLongitude = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/recordedBy') { $recordedBy = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/recordNumber') { $recordNumber = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/fieldNumber') { $fieldNumber = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/verbatimEventDate') { $verbatimEventDate = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/eventDate') { $eventDate = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/sex') { $sex = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/preparations') { $preparations = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/individualCount') { $individualCount = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/lifeStage') { $lifeStage = $field->getAttribute('index'); } } if (sizeof ( $field_columns_core ) < $max) foreach ( range ( 0, $max ) as $i ) if (! isset ( $field_columns_core [$i] )) { $field_columns_core [$i] = ""; } // read header first to get column of catalogNumber -> if catalogNumber = required record -> get full row // Yii::info( "try top open " . $folder . " in " . $FileLocationCore . " and look for " . $unitToFind."
" ); $feed_core = 'http://bgbm-import/feed/dwca.cgi' . '?fileStore='. rawurlencode(Yii::$app->params['fileStore']) . '&baseDirectory='. rawurlencode($basedirectory) . '&fileName=' . rawurlencode($occurrenceFile); //Trick17 f�r NHM Pollinators if($_REQUEST ['collectioncode'] == "BMNH(E)") { $feed_core .= '&idIndex=55'; } else { if($guidToFind != "" and $_REQUEST ['collectioncode'] != "BMNH(E)") $idIndex = $OccurrenceID; else $idIndex = $CatalogNoID; $feed_core .= '&idIndex=' . $idIndex; } $feed_core .= '&fieldsTerminatedBy=' . $fieldsTerminatedBy; if($fieldsEnclosedBy != "" && $_REQUEST ['collectioncode'] != "E" && $_REQUEST ['collectioncode'] != "BMNH(E)") { $feed_core .= '&fieldsEnclosedBy=' . rawurlencode($fieldsEnclosedBy); } if($guidToFind != "" and $_REQUEST ['collectioncode'] != "BMNH(E)") $recordToFind = $guidToFind; else $recordToFind = $unitToFind; $feed_core .= '&id=' . rawurlencode($recordToFind) . '&linesTerminatedBy=' .$linesTerminatedBy . '&ignoreHeader=' . $ignoreHeaderLines . '&encoding=' . $encoding; // echo $feed_core; // //does only parse this part if the current thing to display is the DNA part $handle = fopen ( $feed_core, "r" ); if ($handle) { if($fieldsTerminatedBy == ",") { $separator = ","; } else { $separator = "\t"; } $header = fgetcsv ( $handle, 0, $separator); //fopen("aslkdhf==||".implode($header,"@")." - '".""."'"." - '".""."'", "r" ); foreach ( $header as $index => $term ) { if ($term == "catalogNumber") { $ColumnCatalogNumber = $index; } if ($term == "id") { $ColumnIndex = $index; } if ($term == "occurrenceID") { $ColumnOccurrenceID = $index; } //trick17 für Norwegen, Oslo if(!isset($ColumnIndex)) { $ColumnIndex = 0; } if(!isset($ColumnOccurrenceID)) { $ColumnOccurrenceID = 0; } //trick17 für Norwegen, Oslo } if (empty ( $ColumnCatalogNumber )) { //fopen("aslkdhf==||".implode($field_columns_core,"@")." - '", "r" ); $k = array_search ( "http://rs.tdwg.org/dwc/terms/catalogNumber", $field_columns_core ); if ($k) $ColumnCatalogNumber = $k; $k = array_search ( "http://rs.tdwg.org/dwc/terms/occurrenceID", $field_columns_core ); if ($k) $ColumnOccurrenceID = $k; #fopen("aslkdhf==||".$idElt." - '", "r" ); if (isset ( $idElt )) $ColumnIndex = $idElt; else $ColumnIndex = 0; $header = [ ]; foreach ( $field_columns_core as $k => $v ) $tmp = explode ( "/", $v ); $header [$k] = end ( $tmp ); /* * from a forum: The problem is, that end requires a reference, because it modifies the internal representation of the array * (i.e. it makes the current element pointer point to the last element). * The result of explode('/', $ve) cannot be turned into a reference. * This is a restriction in the PHP language, that probably exists for simplicity reasons. */ } $row = 0; $idfound = false; $allIDs = [ ]; //array_push ( $allIDs, $unitToFind ); if (is_array ( $unitToFind )) $allIDs = array_merge ( $unitToFind, $allIDs ); else array_push ( $allIDs, $unitToFind ); $handle2 = fopen ( $feed_core, "r" ); if($fieldsTerminatedBy == ",") { $separator = ","; } else { $separator = "\t"; } while ( ($data = fgetcsv ( $handle2, 0, $separator )) !== FALSE ) { $tmp = 1; $row ++; $idfound = false; if (count ( $data ) > 1) { $currentID = $data [$ColumnCatalogNumber]; if (isset ( $ColumnOccurrenceID )) $currentOccurrenceID = $data [$ColumnOccurrenceID]; else $currentOccurrenceID = ""; if (in_array ( $currentID, $allIDs ) || in_array ( $currentOccurrenceID, $allIDs ) || in_array ( '"'.$currentID.'"', $allIDs) || in_array ('"'.$currentOccurrenceID.'"', $allIDs)) $idfound = true; //fopen("aslkdhf==||".implode($allIDs,"@")." - '".$currentID."'"." - '".$currentOccurrenceID."'", "r" ); if ($idfound) { $ID_Record = $data [$ColumnIndex]; #fopen("aslkdhf==||".implode($field_columns_core,"@")." - '", "r" ); if (Yii::$app->params ['catalogNumberClickable']) $output .= "Catalog Number: " . $data [$catalogNumber] . " "; else $output .= "Catalog Number: " . $data [$catalogNumber] . " "; if (isset ( $data [$collectionCode] )) $output .= $data [$collectionCode]; if (isset ( $staticValues_collectionCode )) { $output .= $staticValues_collectionCode; } if (isset ( $staticValues_collectionID )) { $output .= " (" . $staticValues_collectionID . ")"; } if (isset ( $data [$institutionCode] )) $output .= " (" . $data [$institutionCode] . ")"; if (isset ( $staticValues_institutionCode )) $output .= " (" . $staticValues_institutionCode . ")"; if (isset ( $staticValues_datasetName )) $output .= " (" . $staticValues_datasetName . ")"; $output .= "
"; if (isset ( $data [$basisOfRecord] )) $output .= "Record Basis: " . $data [$basisOfRecord] . "
"; if (isset ( $staticValues_basisOfRecord )) $output .= "Record Basis: " . $staticValues_basisOfRecord . "
"; if (isset ( $data [$guid] )) { if (! (stripos ( $data [$guid], "http" ) === FALSE)) $output .= "GUID/Occurrence ID: " . $data [$guid] . "
"; else $output .= "GUID/Occurrence ID: " . $data [$guid] . "
"; } if (isset ( $data [$scientificName] ) && ! empty ( $data [$scientificName] )) $identification .= "

Identification

Name: " . $data [$scientificName] . "
"; if ((isset ( $data [$family] ) && ! empty ( $data [$family] )) || (isset ( $data [$order] ) && ! empty ( $data [$order] )) || (isset ( $data [$class] ) && ! empty ( $data [$class] )) || (isset ( $data [$phylum] ) && ! empty ( $data [$phylum] )) || (isset ( $data [$kingdom] ) && ! empty ( $data [$kingdom] ))) { $identification .= "Taxonomy (Occurrence): "; if (isset ( $data [$family] ) && ! empty ( $data [$family] )) $identification .= "" . $data [$family] . " (family); "; if (isset ( $data [$order] ) && ! empty ( $data [$order] )) $identification .= "" . $data [$order] . " (order); "; if (isset ( $data [$class] ) && ! empty ( $data [$class] )) $identification .= "" . $data [$class] . " (class); "; if (isset ( $data [$phylum] ) && ! empty ( $data [$phylum] )) $identification .= "" . $data [$phylum] . " (phylum); "; if (isset ( $data [$kingdom] ) && ! empty ( $data [$kingdom] )) $identification .= "" . $data [$kingdom] . " (kingdom); "; $taxonomySet = true; $identification .= "
"; } if ((isset ( $data [$identifiedBy] ) && (strcasecmp ( $data [$identifiedBy], "" ) != 0)) || (isset ( $data [$identificationReferences] ) && (strcasecmp ( $data [$identificationReferences], "" ) != 0)) || (isset ( $data [$identificationRemarks] ) && (strcasecmp ( $data [$identificationRemarks], "" ) != 0))) { // $identification .= "

Identification details

"; if (isset ( $data [$identifiedBy] ) && (strcasecmp ( $data [$identifiedBy], "" ) != 0)) { $identification .= "Identified by: " . $data [$identifiedBy] . "
"; } if (isset ( $data [$dateIdentified] ) && (strcasecmp ( $data [$dateIdentified], "" ) != 0)) { $identification .= "Identified (date): " . $data [$dateIdentified] . "
"; } if (isset ( $data [$identificationReferences] ) && (strcasecmp ( $data [$identificationReferences], "" ) != 0)) { $identification .= "References: " . $data [$identificationReferences] . "
"; } if (isset ( $data [$identificationRemarks] ) && (strcasecmp ( $data [$identificationRemarks], "" ) != 0)) { $identification .= "Remarks: " . $data [$identificationRemarks] . "
"; } if (isset ( $data [$typeStatus] ) && (strcasecmp ( $data [$typeStatus], "" ) != 0)) { $identification .= "Type Status: " . $data [$typeStatus] . "
"; } } $identification .= "
"; if (isset ( $data [$typeStatus] )) { $identification . "Type Status: " . $data [$typeStatus] . ""; } if (isset ( $data [$country] ) || isset ( $data [$locality] ) || isset ( $data [$stateProvince] )) $gathering .= "

Gathering Event

"; if (isset ( $data [$country] ) && $data [$country] != "" ) $gathering .= "Country: " . $data [$country] . "
"; if (isset ( $data [$stateProvince] ) && ! empty ( $data [$stateProvince])) $gathering .= "State/Province: " . $data [$stateProvince] . "
"; if (isset ( $data [$islandGroup] ) && ! empty ( $data [$islandGroup])) $gathering .= "Island Group: " . $data [$islandGroup] . "
"; if (isset ( $data [$locality] )&& ! empty ( $data [$locality])) $gathering .= "Locality: " . $data [$locality] . "
"; if ((isset ($data [$verbatimElevation] )&& ! empty ( $data [$verbatimElevation])) || (isset ($data [$minimumElevationInMeters] )&& ! empty ( $data [$minimumElevationInMeters])) || (isset ($data [$maximumElevationInMeters] )&& ! empty ( $data [$maximumElevationInMeters]))) $gathering .= "Elevation: "; if(isset ($data [$minimumElevationInMeters] )&& ! empty ( $data [$minimumElevationInMeters])) $gathering .= $data [$minimumElevationInMeters] . " m"; if(isset ($data [$maximumElevationInMeters] )&& ! empty ( $data [$maximumElevationInMeters])) $gathering .= " - ". $data [$maximumElevationInMeters] . " m"; if(isset ($data [$verbatimElevation] )&& ! empty ( $data [$verbatimElevation])) $gathering .= " [" . $data[$verbatimElevation] . "]"; $gathering .= "
"; if ((isset ($data [$verbatimDepth] )&& ! empty ( $data [$verbatimDepth])) || (isset ($data [$minimumDepthInMeters] )&& ! empty ( $data [$minimumDepthInMeters])) || (isset ($data [$maximumDepthInMeters] )&& ! empty ( $data [$maximumDepthInMeters]))) $gathering .= "Depth: "; if(isset ($data [$minimumDepthInMeters] )&& ! empty ( $data [$minimumDepthInMeters])) $gathering .= $data [$minimumDepthInMeters] . " m"; if(isset ($data [$maximumDepthInMeters] )&& ! empty ( $data [$maximumDepthInMeters])) $gathering .= " - ". $data [$maximumDepthInMeters] . " m"; if(isset ($data [$verbatimDepth] )&& ! empty ( $data [$verbatimDepth])) $gathering .= " [" . $data [$verbatimDepth] . "]"; $gathering .= "
"; if (isset ( $data [$decimalLatitude] ) || isset ( $data [$decimalLongitude] )) { if (! empty ( $data [$decimalLatitude] ) && ! empty ( $data [$decimalLongitude] )) { $gathering .= "Coordinates (lat|lon): "; if (isset ( $data [$decimalLatitude] )) { Yii::info($data); $gathering .= strval(round(floatval($data [$decimalLatitude]), Yii::$app->params ['coordinatesPrecision'])); // Latitude in Gathering Event section $latitude [] = strval(round(floatval($data [$decimalLatitude]), Yii::$app->params ['coordinatesPrecision'])); // Latitude in Map } $gathering .= " | "; if (isset ( $data [$decimalLongitude] )) { $gathering .= strval(round(floatval($data [$decimalLongitude]), Yii::$app->params ['coordinatesPrecision'])); // Longitude in Gathering Event section $longitude [] = strval(round(floatval($data [$decimalLongitude]), Yii::$app->params ['coordinatesPrecision'])); // Longitude in Map } $gathering .= "

"; } } if (isset ( $data [$fieldNumber] )) if (strcasecmp ( $data [$fieldNumber], "" ) != 0) $gathering .= "Field number: " . $data [$fieldNumber] . "
"; if (isset ( $data [$locationID] )) if (strcasecmp ( $data [$locationID], "" ) != 0) $gathering .= "Location ID: " . $data [$locationID] . "
"; if (isset ( $data [$recordedBy] )) if (strcasecmp ( $data [$recordedBy], "" ) != 0) $gathering .= "Collector(s): " . $data [$recordedBy] . "
"; if (isset ( $data [$recordNumber] )) if (strcasecmp ( $data [$recordNumber], "" ) != 0) $gathering .= "Collector's number: " . $data [$recordNumber] . "
"; if (isset ( $data [$verbatimEventDate] )) if (strcasecmp ( $data [$verbatimEventDate], "" ) != 0) $gathering .= "Collection Date: " . $data [$verbatimEventDate] . "
"; if (isset ( $data [$eventDate] )) if (strcasecmp ( $data [$eventDate], "" ) != 0) $gathering .= "Collection Date: " . $data [$eventDate] . "
"; // PREPARATION SPECIMEN && SEX if (isset ( $data [$sex] )) if (strcasecmp ( $data [$sex], "" ) != 0) $prepSex .= "
Sex: " . $data [$sex] . "
"; if (isset ( $data [$individualCount] )) if (strcasecmp ( $data [$individualCount], "" ) != 0) $prepSex .= "
Individual Count: " . $data [$individualCount] . "
"; if (isset ( $data [$lifeStage] )) if (strcasecmp ( $data [$lifeStage], "" ) != 0) $prepSex .= "
Individual Count: " . $data [$lifeStage] . "
"; if (isset ( $data [$preparations] )) if (strcasecmp ( $data [$preparations], "" ) != 0) $prepSex .= "Preparations: " . $data [$preparations] . "
"; } } } #$ID_Record = ""; fclose ( $handle2 ); // } } // foreach ($Cores as $Core) else echo ("Could not read the file ?
"); } // Start Extensions foreach ( $Extensions as $Extension ) { $encoding = $Core->getAttribute ( 'encoding' ); $fieldTerminatedBy = $Core->getAttribute ( 'fieldsTerminatedBy' ); if($fieldTerminatedBy == ","){ $fieldsTerminatedBy = $fieldTerminatedBy; } else { $fieldsTerminatedBy = "%09"; } $linesTerminatedBy = $Core->getAttribute ( 'linesTerminatedBy' ); $fieldsEnclosedBy = $Core->getAttribute ( 'fieldsEnclosedBy' ); $ignoreHeaderLines = $Core->getAttribute ( 'ignoreHeaderLines' ); $resourceRelationshipID = ""; $relatedResourceID = ""; $relationshipOfResource = ""; $preparationMaterials = ""; $preparationDate = ""; $preparedBy = ""; $preparationType = ""; $concentration = ""; $concentrationUnit = ""; $ratioOfAbsorbance260_230 = ""; $ratioOfAbsorbance260_280 = ""; $qualityCheckDate = ""; $materialSampleType = ""; $preservationType = ""; $preservationDateBegin = ""; $identifier = ""; $DNAThreshold = ""; $percentAboveThreshold = ""; $gelBuffer = ""; $gelConcentration = ""; $gelLadder = ""; $gelStain = ""; $gelStainConcentration = ""; $stainingMethod = ""; $gelRemarks = ""; $permitType = ""; $permitStatus = ""; $permitStatusQualifier = ""; $permitText = ""; $marker = ""; $geneticAccessionNumber = ""; $accessURI = ""; $scientificName = ""; $family = ""; $order = ""; $class = ""; $phylum = ""; $kingdom = ""; $identifiedBy = ""; $identificationReferences = ""; $identificationRemarks = ""; $dateIdentified = ""; $typeStatus = ""; $Files = $Extension->getElementsByTagName ( 'files' ); foreach ( $Files as $File ) { $FileLocationExtension = $File->getElementsByTagName ( 'location' )->item ( 0 )->nodeValue; } $ColumnIDs = $Extension->getElementsByTagName ( 'coreid' ); foreach ( $ColumnIDs as $ColumnID ) { $field_columns_extension [0] = $ColumnID->getAttribute ( 'index' ); $OccurrenceID_extension = $ColumnID->getAttribute ( 'index' ); } $fields = $Extension->getElementsByTagName ( 'field' ); foreach ( $fields as $field ) { if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/resourceRelationshipID') { $resourceRelationshipID = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/relatedResourceID') { $relatedResourceID = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/relationshipOfResource') { $relationshipOfResource = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preparationMaterials') { $preparationMaterials = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preparationDate') { $preparationDate = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preparationBy') { $preparationBy = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preparationType') { $preparationType = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/concentration') { $concentration = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/concentrationUnit') { $concentrationUnit = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_230') { $ratioOfAbsorbance260_230 = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_280') { $ratioOfAbsorbance260_280 = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/qualityCheckDate') { $qualityCheckDate = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/materialSampleType') { $materialSampleType = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preservationType') { $preservationType = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/preservationDateBegin') { $preservationDateBegin = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identifier') { $identifier = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/accessURI') { $accessURI = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/DNAThreshold') { $DNAThreshold = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/percentAboveThreshold') { $percentAboveThreshold = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelBuffer') { $gelBuffer = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelConcentration') { $gelConcentration = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelLadder') { $gelLadder = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelStain') { $gelStain = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelStainConcentration') { $gelStainConcentration = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/stainingMethod') { $stainingMethod = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/gelRemarks') { $gelRemarks = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/permitType') { $permitType = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/permitStatus') { $permitStatus = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/permitStatusQualifier') { $permitStatusQualifier = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/permitText') { $permitText = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/marker') { $marker = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/geneticAccessionNumber') { $geneticAccessionNumber = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/amplificationDate') { $amplificationDate = $field->getAttribute('index'); } else $amplificationDate = ""; if($field->getAttribute('term') == 'http://data.ggbn.org/schemas/ggbn/terms/BOLDProcessID') { $BOLDProcessID = $field->getAttribute('index'); } else $BOLDProcessID = ""; if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/scientificName') { $scientificName = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/family') { $family = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/order') { $order = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/class') { $class = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/phylum') { $phylum = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/kingdom') { $kingdom = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identifiedBy') { $identifiedBy = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identificationReferences') { $identificationReferences = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/identificationRemarks') { $identificationRemarks = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/dateIdentified') { $dateIdentified = $field->getAttribute('index'); } if($field->getAttribute('term') == 'http://rs.tdwg.org/dwc/terms/typeStatus') { $typeStatus = $field->getAttribute('index'); } $field_columns_extension [$field->getAttribute ( 'index' )] = $field->getAttribute ( 'term' ); } // help for debugging foreach($field_columns_core as $field_column_core) { echo $field_column_core."
"; } // read header first to get column of catalogNumber -> if catalogNumber = required record -> get full row $feed_extension = 'http://bgbm-import/feed/dwca.cgi' . '?fileStore='. rawurlencode(Yii::$app->params['fileStore']) . '&baseDirectory='. rawurlencode($basedirectory) . '&fileName=' . rawurlencode($FileLocationExtension) . //'&idIndex=' .$field_columns_extension [0] . // $ColumnID . '&idIndex=' . $OccurrenceID_extension . '&fieldsTerminatedBy=' . $fieldsTerminatedBy; if($fieldsEnclosedBy != "" && $_REQUEST ['collectioncode'] != "E") { $feed_extension .= '&fieldsEnclosedBy=' . rawurlencode($fieldsEnclosedBy); } $feed_extension .= '&id=' . rawurlencode($ID_Record) . '&linesTerminatedBy=' . $linesTerminatedBy . '&ignoreHeader=' . $ignoreHeaderLines . '&encoding=' . $encoding; // echo "
".$feed_extension."
"; if ((fopen ( $feed_extension, "r" )) !== FALSE) { //Yii::info ( "FileLocationExtension: " . $FileLocationExtension ); if($fieldsTerminatedBy == ",") { $separator = ","; } else { $separator = "\t"; } $handle = fopen ( $feed_extension, "r" ); Yii::info ( $feed_extension ); Yii::info ( $handle ); // Yii::info ( "COLUMNID " . $ColumnID ); // Yii::info ( "IDRECORD " . $ID_Record ); $row = 0; while ( ($data = fgetcsv ( $handle, 1000, $separator )) !== FALSE ) { $tmp = 1; $row ++; if (sizeof ( $data ) > 1) { // foreach ( $lines as $dataL ) { // if (strpos ( $line, $ID_Record ) !== false) { // Yii::info ( "line: " . $dataL ); // Yii::info ( "alive: " . $row ); // $data = explode ( $separator, $dataL ); // // while ( ($data = fgetcsv ( $handle, 1000, "\t" )) !== FALSE ) { // $row ++; // if ($data [$ColumnID] == $ID_Record) { // help for debugging foreach ($data as $value) { echo $value. "
"; } if ($FileLocationExtension == "resourcerelationship.txt" || $FileLocationExtension == "resourcerelationship.csv") { #fopen("aslkdhf==||".implode($data,"@")." - '", "r" ); Yii::info($resourceRelationshipID); Yii::info($relatedResourceID); Yii::info($data); /* $relationshipFull = ""; if (isset ( $data [$resourceRelationshipID] )) $relationshipFull = "&" . $data [$resourceRelationshipID]; if (! isset ( $relationshipFull )) $relationshipFull = "&" . $data [$relatedResourceID]; */ $relationshipFull = "&"; if (isset ( $data [$resourceRelationshipID] )) $relationshipFull .= $data [$resourceRelationshipID] . "&" ; if (isset ( $data [$relatedResourceID] )) $relationshipFull .= $data [$relatedResourceID] . "&"; if (isset ( $relationshipFull )) { #fopen("aslkdhf==||".$relationshipFull." - '", "r" ); #$instcode = "123"; $instcode = ""; $collcode = ""; $guidcode = ""; if (strpos($relationshipFull, "&institutionCode=") !== false) { $instcode = explode ( "&", explode ( "&institutionCode=", $relationshipFull ) [1] ) [0]; } if (strpos($relationshipFull, "&collectionCode=") !== false) { $collcode = explode ( "&", explode ( "&collectionCode=", $relationshipFull ) [1] ) [0]; } if (strpos($relationshipFull, "&guid=") !== false) { $guidcode = explode ( "&", explode ( "&guid=", $relationshipFull ) [1] ) [0]; } // $collcode = explode ( "&", explode ( "&collectionCode=", $relationshipFull ) [1] ) [0]; // $guidcode = explode ( "&", explode ( "&guid=", $relationshipFull ) [1] ) [0]; # Problem: There's no catalognumber in relationshipfull. # Question: Is this possible? # Answer 1: If yes, then catch this case here. # Answer 2: If no, the catalognumber doesn't seem to be added in the code above. Need to find its cause above. Yii::info($relationshipFull); if(strpos($relationshipFull, '&catalogNumber=') !== false) { // explodable $catcode = explode ( "&", explode ( "&catalogNumber=", $relationshipFull ) [1] ) [0]; $relation .= "

Relation to " . $catcode . " ($collcode, $instcode)"; if($guidcode != "") { if (strpos($guidcode, "http") !== false && strpos($guidcode, "http") == 0) { $relation .= " [" . $guidcode . "]"; } else { $relation .= " [GUID: " . $guidcode . "]"; } } } else { // not explodable if($guidcode != "") { if (strpos($guidcode, "http") == 0) { $relation .= "

Relation to " . $guidcode . " ($collcode, $instcode)"; } else { $relation .= "

Relation to GUID:" . $guidcode . " ($collcode, $instcode)"; } } } $relation .= " :

"; if (isset ( $data [$relationshipOfResource] )) $relation .= $data [$relationshipOfResource]; } } if ($FileLocationExtension == "preparation.txt" || $FileLocationExtension == "preparation.csv") { if ((isset ( $data [$preparationMaterials] ) && (strcasecmp ( $data [$preparationMaterials], "" ) != 0)) || (isset ( $data [$preparationDate] ) && (strcasecmp ( $data [$preparationDate], "" ) != 0)) || (isset ( $data [$preparedBy] ) && (strcasecmp ( $data [$preparedBy], "" ) != 0)) || (isset ( $data [$preparationType] ) && (strcasecmp ( $data [$preparationType], "" ) != 0))) { if ($sampleType == "DNA") $label = "Extraction"; else $label = "Preparation"; $preparation .= "

" . $label . "

"; $preparation .= isset ( $data [$preparationDate] ) && (strcasecmp ( $data [$preparationDate], "" ) != 0) ? "" . $label . " Date: " . $data [$preparationDate] . "
" : ""; $preparation .= isset ( $data [$preparationMaterials] ) && (strcasecmp ( $data [$preparationMaterials], "" ) != 0) ? "" . $label . " Method: " . $data [$preparationMaterials] . "
" : ""; $preparation .= isset ( $data [$preparedBy] ) && (strcasecmp ( $data [$preparedBy], "" ) != 0) ? "" . $label . " Staff: " . $data [$preparedBy] . "
" : ""; $preparation .= isset ( $data [$preparationType] ) && (strcasecmp ( $data [$preparationType], "" ) != 0) ? "" . $label . " Type: " . $data [$preparationType] . "
" : ""; $preparationType = $data [$preparationType]; } else { $preparation = NULL; if (isset ( $data [$preparationType] )) $material .= "
Preparation Type: " . $data [$preparationType] . ""; } } if ($FileLocationExtension == "materialsample2.txt" || $FileLocationExtension == "materialsample.txt" || $FileLocationExtension == "materialsample.csv") { if ((isset ( $data [$concentration] ) && (strcasecmp ( $data [$concentration], "" ) != 0)) || (isset ( $data [$ratioOfAbsorbance260_230] ) && (strcasecmp ( $data [$ratioOfAbsorbance260_280], "" ) != 0))) { $sample .= "

Quality

"; $sample .= isset ( $data [$concentration] ) && (strcasecmp ( $data [$concentration], "" ) != 0) ? "Concentration: " . $data [$concentration] . " " . $data [$concentrationUnit] . "
" : ""; $sample .= isset ( $data [$ratioOfAbsorbance260_230] ) && (strcasecmp ( $data [$ratioOfAbsorbance260_230], "" ) != 0) ? "Ratio of Absorbance:" . $data [$ratioOfAbsorbance260_230] . "
" : ""; $sample .= isset ( $data [$ratioOfAbsorbance260_280] ) && (strcasecmp ( $data [$ratioOfAbsorbance260_280], "" ) != 0) ? "Ratio of Absorbance:" . $data [$ratioOfAbsorbance260_280] . "
" : ""; $sample .= isset ( $data [$qualityCheckDate] ) && (strcasecmp ( $data [$qualityCheckDate], "" ) != 0) ? "Quality Check Date: " . $data [$qualityCheckDate] . "
" : ""; } else $sample = NULL; if (isset ( $data [$materialSampleType] )) $material .= "
Sample Type / Kind of Unit: " . $data [$materialSampleType] . "
"; } if ($FileLocationExtension == "preservation.txt" || $FileLocationExtension == "preservation.csv") { if ((isset ( $data [$preservationType] ) && (strcasecmp ( $data [$preservationType], "" ) != 0)) || (isset ( $data [$preservationDateBegin] ) && (strcasecmp ( $data [$preservationDateBegin], "" ) != 0))) { $preservation .= "

Sample Preservation(s)

"; $preservation .= isset ( $data [$preservationType] ) && (strcasecmp ( $data [$preservationType], "" ) != 0) ? "Preservation:" . $data [$preservationType] . "
" : ""; $preservation .= isset ( $data [$preservationDateBegin] ) && (strcasecmp ( $data [$preservationDateBegin], "" ) != 0) ? "since:" . $data [$preservationDateBegin] . "
" : ""; } else $preservation = NULL; } if ($FileLocationExtension == "gelimage.txt" || $FileLocationExtension == "gelimage.csv") { if (isset ( $data [$identifier] ) ) { if ($sampleType == "DNA") $label = "Gel image"; $gelimage .= "

" . $label . "

"; $gelimage .= "
"; $gelimage .= isset ( $data [$identifier] ) ? "
" : ""; $gelimage .= "		"; $gelimage .= isset ( $data [$DNAThreshold] ) ? "DNA Threshold:" . $data [$DNAThreshold] . "
" : ""; $gelimage .= isset ( $data [$percentAboveThreshold] ) ? "Percent Above Threshold:" . $data [$percentAboveThreshold] . "
" : ""; $gelimage .= isset ( $data [$gelBuffer] ) ? "Gel Buffer:" . $data [$gelBuffer] . "
" : ""; $gelimage .= isset ( $data [$gelConcentration] ) ? "Gel Concentration:" . $data [$gelConcentration] . "
" : ""; $gelimage .= isset ( $data [$gelLadder] ) ? "Gel Ladder:" . $data [$gelLadder] . "
" : ""; $gelimage .= isset ( $data [$gelStain] ) ? "Gel Stain:" . $data [$gelStain] . "
" : ""; $gelimage .= isset ( $data [$gelStainConcentration] ) ? "Gel Stain Concentration:" . $data [$gelStainConcentration] . "
" : ""; $gelimage .= isset ( $data [$stainingMethod] ) ? "Staining Method:" . $data [$stainingMethod] . "
" : ""; $gelimage .= isset ( $data [$gelRemarks] ) ? "Gel Remarks:" . $data [$gelRemarks] . "
" : ""; $gelimage .= "
"; } else { $gelimage = NULL; } } if ($FileLocationExtension == "permit.txt" || $FileLocationExtension == "permit.csv") { if (isset ( $data [$permitType] ) ) { $permit .= "

Permit(s)

"; $permit .= isset ( $data [$permitType] ) ? "Permit Type:" . $data [$permitType] . "
" : ""; $permit .= isset ( $data [$permitStatus] ) ? "Permit Status:" . $data [$permitStatus] . "
" : ""; $permit .= isset ( $data [$permitStatusQualifier] ) ? "Permit Status Remarks:" . $data [$permitStatusQualifier] . "
" : ""; $permit .= isset ( $data [$permitText] ) ? "Permit Remarks:" . $data [$permitText] . "
" : ""; } else { $permit = NULL; } } if ($FileLocationExtension == "amplification.txt" || $FileLocationExtension == "amplification.csv") { if ((isset ( $data [$marker] ) && (strcasecmp ( $data [$marker], "" ) != 0)) || (isset ( $data [$geneticAccessionNumber] ) && (strcasecmp ( $data [$geneticAccessionNumber], "" ) != 0))) { $sequences = "

Amplifications(s)

"; $sequences .= isset ( $data [$amplificationDate] ) && (strcasecmp ( $data [$amplificationDate], "" ) != 0) ? "Amplification date: " . $data [$amplificationDate] . "
" : ""; $sequences .= isset ( $data [$marker] ) && (strcasecmp ( $data [$marker], "" ) != 0) ? "Marker: " . $data [$marker] . "
" : ""; $sequences .= isset ( $data [$geneticAccessionNumber] ) && (strcasecmp ( $data [$geneticAccessionNumber], "" ) != 0) ? "Genetic Accession Number: ". $data [$geneticAccessionNumber]. "
" : ""; $sequences .= isset ( $data [$BOLDProcessID] ) && (strcasecmp ( $data [$BOLDProcessID], "" ) != 0) ? "BOLD Process ID: ". $data [$BOLDProcessID] . "
" : ""; } else $sequences = NULL; } $multimedia = ""; if ($FileLocationExtension == "multimedia.txt" || $FileLocationExtension == "multimedia.csv") { if ((isset ( $data [$accessURI] ) && (strcasecmp ( $data [$accessURI], "" ) != 0))) { $murl = $data [$accessURI]; if ($murl != "N/A") { if (strpos ( $multimedia, $murl ) === FALSE) { if (strpos ( $murl, "http" ) === FALSE) { $murl = "http://" . $murl; } $multimedia = $multimedia . "  "; } } } else { if ((isset ( $data [$identifier] ) && (strcasecmp ( $data [$identifier], "" ) != 0))) { $murl = $data [$identifier]; if ($murl != "N/A") { if (strpos ( $multimedia, $murl ) === FALSE) { if (strpos ( $murl, "http" ) === FALSE) { $murl = "http://" . $murl; } $multimedia = $multimedia . "  "; } } } } } if ($FileLocationExtension == "identification.txt" || $FileLocationExtension == "identification.csv") { // foreach ($data as $k=>$v) // echo "k and v: ".$k." -- ".$v."
"; if (! empty ( $identification ) && stripos ( $identification, "supplemental information" ) == 0) $identification .= "

Other identification / supplemental information

"; if (isset ( $data [$scientificName] ) && ! empty ( $data [$scientificName] )) $identification .= "Name: " . $data [$scientificName] . "
"; if (! $taxonomySet) if ((isset ( $data [$family] ) && ! empty ( $data [$family] )) || (isset ( $data [$order] ) && ! empty ( $data [$order] )) || (isset ( $data [$class] ) && ! empty ( $data [$class] )) || (isset ( $data [$phylum] ) && ! empty ( $data [$phylum] )) || (isset ( $data [$kingdom] ) && ! empty ( $data [$kingdom] ))) { $identification .= "Taxonomy: "; if (isset ( $data [$family] ) && ! empty ( $data [$family] )) $identification .= "" . $data [$family] . " (family); "; if (isset ( $data [$order] ) && ! empty ( $data [$order] )) $identification .= "" . $data [$order] . " (order); "; if (isset ( $data [$class] ) && ! empty ( $data [$class] )) $identification .= "" . $data [$class] . " (class); "; if (isset ( $data [$phylum] ) && ! empty ( $data [$phylum] )) $identification .= "" . $data [$phylum] . " (phylum); "; if (isset ( $data [$kingdom] ) && ! empty ( $data [$kingdom] )) $identification .= "" . $data [$kingdom] . " (kingdom); "; $identification .= "
"; } if ((isset ( $data [$identifiedBy] ) && (strcasecmp ( $data [$identifiedBy], "" ) != 0)) || (isset ( $data [$identificationReferences] ) && (strcasecmp ( $data [$identificationReferences], "" ) != 0)) || (isset ( $data [$identificationRemarks] ) && (strcasecmp ( $data [$identificationRemarks], "" ) != 0))) { // $identification .= "

Identification details

"; if (isset ( $data [$identifiedBy] ) && (strcasecmp ( $data [$identifiedBy], "" ) != 0)) { $identification .= "Identified by: " . $data [$identifiedBy] . "
"; } if (isset ( $data [$dateIdentified] ) && (strcasecmp ( $data [$dateIdentified], "" ) != 0)) { $identification .= "Identified (date): " . $data [$dateIdentified] . "
"; } if (isset ( $data [$identificationReferences] ) && (strcasecmp ( $data [$identificationReferences], "" ) != 0)) { $identification .= "References: " . $data [$identificationReferences] . "
"; } if (isset ( $data [$identificationRemarks] ) && (strcasecmp ( $data [$identificationRemarks], "" ) != 0)) { $identification .= "Remarks: " . $data [$identificationRemarks] . "
"; } if (isset ( $data [$typeStatus] ) && (strcasecmp ( $data [$typeStatus], "" ) != 0)) { $identification .= "Type Status: " . $data [$typeStatus] . "
"; } } $identification .= "
"; } } } fclose ( $handle ); } } // $output = $relation . $preparation . $sample . $preservation . $sequences; // $dna = "
"; $dataset = ""; if (! empty ( $orga ) || ! empty ( $irT ) || ! empty ( $addressT ) || ! empty ( $addressMP ) || ! empty ( $taxocoveragexml ) || ! empty ( $geocoveragexml )) { $dataset .= "
"; if (! empty ( $orga )) $dataset .= $orga . "
"; if (! empty ( $abstract )) $dataset .= "Description: " . $abstract . "
"; if (! empty ( $addressT )) $dataset .= "Creator of dataset: " . implode ( ", ", $addressT ) . "
"; if (! empty ( $addressMP )) $dataset .= "Metadata Provider: " . implode ( ", ", $addressMP ) . "
"; if (! empty ( $irT )) $dataset .= "Rights: " . implode ( " ", $irT ) . "
"; if (! empty ( $taxocoveragexml )) $dataset .= "Taxonomic coverage: " . $taxocoveragexml . "
"; if (! empty ( $geocoveragexml )) $dataset .= "Geographic coverage: " . $geocoveragexml . "
"; $dataset .= "
"; } if ($sampleType == "DNA") { $dna = "
"; $dna .= $output; $dna .= $relation . "
"; $dna .= $preparation . "
"; $dna .= $preservation . "
"; $dna .= $gelimage . "
"; $dna .= $sample . "
"; $dna .= $permit . "
"; if (! empty ( $dataset )) $dna .= $dataset; $dna .= "
"; if ($preparationType != "" && ! stripos ( " " . $preparationType, "dna" )) $dna = NULL; echo ""; } else $dna = null; if ($sampleType == "specimen" or $sampleType == "unknown") { // $specimen = "
"; $specimen = "
"; $specimen .= $output; $specimen .= $relation; if ($sampleType == "specimen" or $sampleType == "unknown") { $specimen .= $material; $specimen .= $preparation . "
"; $specimen .= $prepSex; $specimen .= $preservation . "
"; } else $specimen .= $prepSex; $specimen .= $permit . "
"; if (! empty ( $dataset )) $specimen .= $dataset; $specimen .= "
"; } else $specimen = null; $header = "
"; $header .= $output; $header .= "
"; if ($sampleType == "culture") { $culture = "
"; $culture .= $output; $culture .= $relation; if ($sampleType == "culture") { $culture .= $material; $culture .= $preparation . "
"; $culture .= $prepSex; $culture .= $preservation . "
"; } else $culture .= $prepSex; $culture .= $permit . "
"; if (! empty ( $dataset )) $culture .= $dataset; $culture .= "
"; } else $culture = null; if ($sampleType == "environmental sample") { $enviro = "
"; $enviro .= $output; $enviro .= $relation; $enviro .= $material; $enviro .= $preparation . "
"; $enviro .= $prepSex; $enviro .= $preservation . "
"; $enviro .= $permit . "
"; if (! empty ( $dataset )) $enviro .= $dataset; $enviro .= "
"; } else { $enviro = null; $taxonlist = null; } //$culture = ""; //$enviro = $specimen; // $tissue = "
"; if ($sampleType == "tissue") { $tissue = "
"; $tissue .= $output; $tissue .= $material; $tissue .= $relation; $tissue .= $preparation . "
"; $tissue .= $preservation . "
"; $tissue .= $permit . "
"; if (! empty ( $dataset )) $tissue .= $dataset; $tissue .= "
"; } // if($preparationType!="" && !stripos(" ".$preparationType,"tissue") && !stripos(" ".$preparationType,"muscle")){ // if( !stripos(" ".$preparationType,"tissue") && !stripos(" ".$preparationType,"muscle") && !stripos(" ".$preparationType,"leaf")){ echo ""; if ($sampleType != "tissue") { $tissue = null; } else { $specimen = null; } if ($sampleType == "environmental sample") $specimen = null; else $enviro = null; if ($sequences != "") $sequences = "
" . $sequences . "
"; $output = "
" . $output . "
"; // echo "HEADER FROM HERE ".$header."

"; // if (is_array ( $unitToFind )) { // Yii::info ( "header part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $header ); // Yii::info ( "tissue part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $tissue ); // Yii::info ( "dna part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $dna ); // Yii::info ( "specimen part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $specimen ); // } else { // Yii::info ( "header part for unit: " . $unitToFind . ": " . $header ); // Yii::info ( "tissue part for unit: " . $unitToFind . ": " . $tissue ); // Yii::info ( "dna part for unit: " . $unitToFind . ": " . $dna ); // Yii::info ( "specimen part for unit: " . $unitToFind . ": " . $specimen ); // } $out = [ "dna" => $dna, "output" => $output, "relation" => $relation, "sample" => $sample, "sequences" => $sequences, "preservation" => $preservation, "preparation" => $preparation, "gelimage" => $gelimage, "permit" => $permit, "specimen" => $specimen, "tissue" => $tissue, "header" => $header, "locality" => $identification . $gathering, "culture" => $culture, "enviro" => $enviro, "taxonlist" => $taxonlist, "latitude" => $latitude, //for mapview "longitude" => $longitude, //for mapview "identification" => $identification, "gathering" => $gathering, "multimedia" => $multimedia, "dataset" => $dataset ]; return $out; } } ?>