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1395
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aaronmk
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#*********************************************************
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# Written by: Bradley University
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# Dr. Steven Dolins
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# Use: Transform and Load Raw Specimen
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# GBIF Data from GBIF file into the
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# Staging Table (StagingRawSpecimen).
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# Version: 2.0
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# Date: November 09, 2009
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#*********************************************************
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<?php
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## ======== Connect to database
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include('connect.php');
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## ======== Spacing for buttons in index.php
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echo "<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>";
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## ======== Identify data file
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$Validation_check = 0;
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$GBIFFile = 'GBIF.txt';
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$duplicateEntries=0;
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$successEntries=0;
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$validation_errors=0;
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$recordCount = 0;
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## ======== Load file as a character array - each entry is one line of text with newline still attached
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$GBIFFile = fopen($GBIFFile, 'r');
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##==== Pull off a single line from file and add it to array ====
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//$line = fgets($GBIFFile); //UNCOMMENT ONLY IF TITLES ARE INCLUDED IN FIRST LINE OF FILE
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while($line = fgets($GBIFFile))
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{
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$line = trim($line);
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$arr = explode("\t", $line);
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$recordCount++;
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## ======== Ensure that data enetered is a full tuple (has all columns associated with GBIF data)
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if(count($arr) != 30)
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{
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reportError(NULL, NULL, $recordCount, "Incomplete tuple, ignored");
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continue;
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}
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## ======== Clean up values in array and check data consistency
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checkArray();
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## ======== Populate an array which holds only the values to be inserted
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$arrayInsert['InstitutionCD'] = $arr[5];
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$arrayInsert['CollectionCD'] = $arr[6];
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$arrayInsert['CatalogNO'] = $arr[7];
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$arrayInsert['DBSourceName'] = "GBIF";
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$arrayInsert['LastDateModified'] = $arr[8];
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$arrayInsert['ScientificName'] = $arr[12];
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$arrayInsert['ScientificNameOriginal'] = $arr[10];
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$arrayInsert['Family'] = $arr[14];
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$arrayInsert['Genus'] = $arr[16];
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$arrayInsert['AuthorOfScientificName'] = $arr[11];
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$arrayInsert['Country'] = $arr[17];
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$arrayInsert['StateProvince'] = $arr[20];
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$arrayInsert['County'] = $arr[19];
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$arrayInsert['MinimumElevationInMeter'] = $arr[26];
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$arrayInsert['MaximumElevationInMeter'] = $arr[27];
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$arrayInsert['LatestDateCollected'] = $arr[4];
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$arrayInsert['Collector'] = $arr[2];
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$arrayInsert['DecimalLatitude'] = $arr[21];
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$arrayInsert['DecimalLongitude'] = $arr[23];
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$arrayInsert['Locality'] = $arr[18];
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$arrayInsert['IdentifiedBy'] = $arr[9];
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$arrayInsert['VerbatimLatitude'] = $arr[22];
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$arrayInsert['VerbatimLongitude'] = $arr[24];
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$arrayInsert['SpecificEpithet'] = $arr[28];
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$arrayInsert['InfraspecificEpithet'] = $arr[29];
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$arrayInsert['GBIFFamilyOriginal'] = $arr[13];
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$arrayInsert['GBIFGenusOriginal'] = $arr[15];
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$arrayInsert['InfraspecificRank'] = $arr[30];
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## ======== Ensure primary key values and not null values (CollectionCD, CatalogNO, InstitutionCD) are not null
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if(is_null($arrayInsert['InstitutionCD']) OR is_null($arrayInsert['CatalogNO']) OR is_null($arrayInsert['InstitutionCD']))
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{
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reportError(NULL, NULL, NULL, "One or more non-null value is NULL");
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continue;
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}
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## ======== Filter out MOBOT and NYBG Data since those are inserted from another file
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if ( strstr($arrayInsert['InstitutionCD'], "MOBOT") or strstr($arrayInsert['InstitutionCD'] , "NYBG"))
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{
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reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], $arrayInsert['InstitutionCD'], "Institution code contains either MOBOT or NYBG");
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continue;
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}
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## ======== Generate SQL code to insert desired information
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$sql = sprintf("INSERT INTO StagingRawSpecimen
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(
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InstitutionCD,
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CollectionCD,
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CatalogNO,
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DBSourceName,
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LastDateModified,
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ScientificName,
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ScientificNameOriginal,
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GBIFFamilyOriginal,
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Family,
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GBIFGenusOriginal,
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Genus,
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AuthorOfScientificName,
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Country,
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StateProvince,
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County,
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MinimumElevationInMeter,
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MaximumElevationInMeter,
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LatestDateCollected,
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Collector,
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DecimalLatitude,
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DecimalLongitude,
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Locality,
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IdentifiedBy,
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VerbatimLatitude,
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VerbatimLongitude,
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SpecificEpithet,
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InfraspecificEpithet,
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InfraspecificRank
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)
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VALUES
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(
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s,
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%s
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)
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",
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insertSQLData($arrayInsert['InstitutionCD']),
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insertSQLData($arrayInsert['CollectionCD']),
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insertSQLData($arrayInsert['CatalogNO']),
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insertSQLData($arrayInsert['DBSourceName']),
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insertSQLData($arrayInsert['LastDateModified']),
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insertSQLData($arrayInsert['ScientificName']),
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insertSQLData($arrayInsert['ScientificNameOriginal']),
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insertSQLData($arrayInsert['GBIFFamilyOriginal']),
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insertSQLData($arrayInsert['Family']),
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insertSQLData($arrayInsert['GBIFGenusOriginal']),
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insertSQLData($arrayInsert['Genus']),
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insertSQLData($arrayInsert['AuthorOfScientificName']),
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insertSQLData($arrayInsert['Country']),
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insertSQLData($arrayInsert['StateProvince']),
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insertSQLData($arrayInsert['County']),
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insertSQLData($arrayInsert['MinimumElevationInMeter']),
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insertSQLData($arrayInsert['MaximumElevationInMeter']),
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insertSQLData($arrayInsert['LatestDateCollected']),
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insertSQLData($arrayInsert['Collector']),
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insertSQLData($arrayInsert['DecimalLatitude']),
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insertSQLData($arrayInsert['DecimalLongitude']),
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insertSQLData($arrayInsert['Locality']),
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insertSQLData($arrayInsert['IdentifiedBy']),
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insertSQLData($arrayInsert['VerbatimLatitude']),
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insertSQLData($arrayInsert['VerbatimLongitude']),
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insertSQLData($arrayInsert['SpecificEpithet']),
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insertSQLData($arrayInsert['InfraspecificEpithet']),
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insertSQLData($arrayInsert['InfraspecificRank'])
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);
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//echo("<br> <br> $sql <br> <br>");
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## ======== Check whether a tuple with the variables you're trying to enter has already been entered (trying to insert duplicate tuple)
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if(mysql_query($sql))
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{
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$successEntries++;
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}
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else if(mysql_errno() == 1062)
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{
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$duplicateEntries++;
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//reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], NULL, mysql_error());
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continue;
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}
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else
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{
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reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], NULL, mysql_error());
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}
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## ======== Validate data entered
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if ($Validation_check) // Validation Check status
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{
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$validation_query = sprintf(
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"SELECT * FROM StagingRawSpecimen WHERE
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CollectionCD %s
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AND CatalogNO %s",
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selectSQLData($arrayInsert['CollectionCD']),
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selectSQLData($arrayInsert['CatalogNO'])
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);
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//echo("<br> <br> $validation_query <br> <br>");
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$validation_result = mysql_query($validation_query) OR reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], NULL, mysql_error());
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if(mysql_num_rows($validation_result) > 1) ## IF more than 1 record has these properties, then NOT UNIQUE
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{
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reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], NULL, "Validation result not unique");
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continue; //error, skip the rest of validation
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}
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if(mysql_num_rows($validation_result) < 1)
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{
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reportError($arrayInsert['CollectionCD'], $arrayInsert['CatalogNO'], NULL, "Validation result does not exist");
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continue; //error, skip the rest of validation
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}
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else //(num_rows == 1)
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{
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| 242 |
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$validation_result_row = mysql_fetch_assoc($validation_result) OR DIE("Error - no result found");
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| 244 |
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$CatalogNO = $arrayInsert['CatalogNO'];
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$CollectionCD = $arrayInsert['CollectionCD'];
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foreach($arrayInsert AS $key => $data)
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{
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| 248 |
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## ======== check if the result found in the database matches that entered (Check both exact string match and numerical equality)
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| 250 |
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if((strcasecmp($validation_result_row[$key], $data) != 0) AND (!checkDifference($data, $validation_result_row[$key], 5)))
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{
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reportError($CollectionCD, $CatalogNO, $key, "Result does not match data entered |--| $data |--| $validation_result_row[$key] |--|");
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}
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}
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| 255 |
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}
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| 256 |
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} //end while loop
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}
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## ======== Display results to user
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| 259 |
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if($duplicateEntries >= 1)
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{
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| 262 |
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echo "<br>" . $duplicateEntries . " record(s) has been skipped, key already exists<br>";
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| 263 |
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}
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| 264 |
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| 265 |
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if($successEntries >= 1)
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| 266 |
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{
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| 267 |
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echo "<br>" . $successEntries . " record(s) has been successfully inserted<br>";
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| 268 |
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}
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| 269 |
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echo("<br> $validation_errors Validation Errors");
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| 270 |
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// =============================
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| 272 |
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// ======== END PROGRAM ========
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| 273 |
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// =============================
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| 274 |
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| 275 |
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| 276 |
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## ======================================
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| 277 |
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## Name: checkArray
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| 278 |
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## Function: Checks the data form the file and formats it for entry into the staging table
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| 279 |
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## Internal Variables:
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| 280 |
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## Global Variables: $arr
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| 281 |
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## Calls Function: None
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| 282 |
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## Called by: Main loop
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## Written by: Andrew Becker, Mark Sheehan
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## Last Modified: 07-22-09
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## =======================================
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| 286 |
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| 287 |
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function checkArray()
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| 288 |
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{
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| 289 |
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global $arr;
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| 290 |
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for($a=0; $a<31; $a++)
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| 291 |
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{
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| 292 |
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if(!(array_key_exists($a, $arr)))
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| 293 |
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{
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| 294 |
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$arr[$a] = ' ';
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| 295 |
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}
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| 296 |
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| 297 |
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## ==== Trim white spaces and newline off of front and end of string (necessary for values at end of line)
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| 298 |
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| 299 |
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$arr[$a] = trim($arr[$a], ' ');
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| 300 |
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| 301 |
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## ==== Replace Empty values ('') with null keyword
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| 302 |
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| 303 |
|
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if($arr[$a] == '' OR $arr[$a] == '\N')
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| 304 |
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{
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| 305 |
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$arr[$a] = NULL;
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| 306 |
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}
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| 307 |
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| 308 |
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if(($a == 4 OR $a == 8) AND $arr[$a] != NULL) ## CHANGED JUN 22 09 - IF date/time AND NOT NULL, then convert it to a form that mysql/PHP recognizes - YYYY-MM-DD HH-MM-SS
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| 309 |
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{
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| 310 |
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if($a == 8)
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| 311 |
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{
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| 312 |
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//==== Actual data in GBIF file in format "MM-DD-YYYY HH:MM"
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| 313 |
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//Start formatting date
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| 314 |
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| 315 |
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$dateFormat = explode(' ', $arr[$a]);
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| 316 |
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$date = $dateFormat[0];
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| 317 |
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$time = $dateFormat[1];
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| 318 |
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$date = explode('-', $date); //break date up into MM DD YYYY
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| 319 |
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$month = str_pad($date[1], 2, '0', STR_PAD_LEFT); //if only entered as 5/27/2008, need it in form 05/27/2008 so need padding on left
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| 320 |
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$day = str_pad($date[2], 2, '0', STR_PAD_LEFT);
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| 321 |
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$year = $date[0];
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| 322 |
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| 323 |
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$time = explode(':', $time);
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| 324 |
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$hour = $time[0];
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| 325 |
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$hour = str_pad($hour, 2, '0', STR_PAD_LEFT); //same issue as above
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| 326 |
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$minute = $time[1];
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| 327 |
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$second = "00"; //seconds not given, assume 00
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| 328 |
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$arr[$a] = sprintf("%s-%s-%s %s:%s:%s", $year, $month, $day, $hour, $minute, $second);
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| 329 |
|
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//echo(" $arr[$a] <br>");
|
| 330 |
|
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}
|
| 331 |
|
|
else if($a == 4)
|
| 332 |
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{
|
| 333 |
|
|
|
| 334 |
|
|
//==== Actual data in GBIF file in format MM/DD/YYYY OR YYYY-MM-DD
|
| 335 |
|
|
|
| 336 |
|
|
if(stripos($arr[$a], '/')) // if in MM/DD/YYYY format
|
| 337 |
|
|
{
|
| 338 |
|
|
$dateFormat = explode('/', $arr[$a]);
|
| 339 |
|
|
$month = str_pad($dateFormat[0], 2, '0', STR_PAD_LEFT);
|
| 340 |
|
|
$day = str_pad($dateFormat[1], 2, '0', STR_PAD_LEFT);
|
| 341 |
|
|
$year = $dateFormat[2];
|
| 342 |
|
|
|
| 343 |
|
|
$arr[$a] = sprintf("%s-%s-%s", $year, $month, $day);
|
| 344 |
|
|
}
|
| 345 |
|
|
else if(stripos($arr[$a], '-')) //if in YYYY-MM-DD format
|
| 346 |
|
|
{
|
| 347 |
|
|
$dateFormat = explode('-', $arr[$a]);
|
| 348 |
|
|
$month = str_pad($dateFormat[1], 2, '0', STR_PAD_LEFT);
|
| 349 |
|
|
$day = str_pad($dateFormat[2], 2, '0', STR_PAD_LEFT);
|
| 350 |
|
|
$year = $dateFormat[0];
|
| 351 |
|
|
|
| 352 |
|
|
$arr[$a] = sprintf("%s-%s-%s", $year, $month, $day);
|
| 353 |
|
|
}
|
| 354 |
|
|
else
|
| 355 |
|
|
{
|
| 356 |
|
|
reportError($arr[6], $arr[7], $arr[$a], "Date format for ||$arr[$a]|| not found.");
|
| 357 |
|
|
}
|
| 358 |
|
|
}
|
| 359 |
|
|
}
|
| 360 |
|
|
else if($a == 26) // if elevation range is given as XXX-YYY in one field instead of as minimum and maximum
|
| 361 |
|
|
{
|
| 362 |
|
|
$minMax = explode('-', $arr[$a]);
|
| 363 |
|
|
if(sizeof($minMax) > 1)
|
| 364 |
|
|
{
|
| 365 |
|
|
$arr[26] = $minMax[0];
|
| 366 |
|
|
$arr[27] = $minMax[1];
|
| 367 |
|
|
}
|
| 368 |
|
|
}
|
| 369 |
|
|
else if ($a == 12) // To get the species and subspeices from the scientific name, Dhaval Shah
|
| 370 |
|
|
{
|
| 371 |
|
|
$spe_subspe = explode(' ',$arr[$a]);
|
| 372 |
|
|
if(sizeof($spe_subspe) > 1 and !(is_numeric($spe_subspe[1])))
|
| 373 |
|
|
{
|
| 374 |
|
|
$arr[28] = trim($spe_subspe[1]);
|
| 375 |
|
|
if(sizeof($spe_subspe) > 3 and !(is_numeric($spe_subspe[2])))
|
| 376 |
|
|
{
|
| 377 |
|
|
|
| 378 |
|
|
if ((strstr($spe_subspe[2], "var") or strstr($spe_subspe[2], "subsp") or strstr($spe_subspe[2], "ssp") or strstr($spe_subspe[2], "sbsp") or strstr($spe_subspe[2], "forma") or strstr($spe_subspe[2], "fo") or strstr($spe_subspe[2], "f") or strstr($spe_subspe[2], "cv")) and (strlen($spe_subspe[2]) < 6))
|
| 379 |
|
|
{
|
| 380 |
|
|
if ( strstr($spe_subspe[2], "ssp"))
|
| 381 |
|
|
{
|
| 382 |
|
|
$spe_subspe[2] = "subsp.";
|
| 383 |
|
|
}
|
| 384 |
|
|
$arr[30] = trim($spe_subspe[2]);
|
| 385 |
|
|
$arr[29] = trim($spe_subspe[3]);
|
| 386 |
|
|
}
|
| 387 |
|
|
else
|
| 388 |
|
|
{
|
| 389 |
|
|
$arr[30] = NULL;
|
| 390 |
|
|
$arr[29] = NULL;
|
| 391 |
|
|
}
|
| 392 |
|
|
}
|
| 393 |
|
|
else
|
| 394 |
|
|
{
|
| 395 |
|
|
$arr[30] = NULL;
|
| 396 |
|
|
$arr[29] = NULL;
|
| 397 |
|
|
}
|
| 398 |
|
|
|
| 399 |
|
|
}
|
| 400 |
|
|
else
|
| 401 |
|
|
{
|
| 402 |
|
|
$arr[28] = NULL;
|
| 403 |
|
|
$arr[29] = NULL;
|
| 404 |
|
|
$arr[30] = NULL;
|
| 405 |
|
|
}
|
| 406 |
|
|
}
|
| 407 |
|
|
}
|
| 408 |
|
|
}
|
| 409 |
|
|
|
| 410 |
|
|
## ========================================
|
| 411 |
|
|
## Name: reportError
|
| 412 |
|
|
## Function: creates a detailed error report in errorLog
|
| 413 |
|
|
## Internal Variables:
|
| 414 |
|
|
## Globals: $recordCount, $GBIFFile
|
| 415 |
|
|
## Calls Function: None
|
| 416 |
|
|
## Called by: Main Loop
|
| 417 |
|
|
## Written by: Mark Sheehan
|
| 418 |
|
|
## Last Updated: 07-22-09
|
| 419 |
|
|
## =======================================
|
| 420 |
|
|
|
| 421 |
|
|
function reportError($CollectionCD, $CatalogNo, $columnName, $Error)
|
| 422 |
|
|
{
|
| 423 |
|
|
GLOBAL $recordCount;
|
| 424 |
|
|
GLOBAL $GBIFFile;
|
| 425 |
|
|
//echo("Creating error log for $CollectionCD | $CatalogNo | $Error <br><br>");
|
| 426 |
|
|
$errorReport = sprintf(
|
| 427 |
|
|
"INSERT INTO ErrorLog (CollectionCD, CatalogNO, RawDataFileName, RawRecordNO, StagingTableName, StagingColumnName, ErrorDescription)
|
| 428 |
|
|
VALUES (%s, %s, %s, %s, %s, %s, %s)",
|
| 429 |
|
|
insertSQLData($CollectionCD),
|
| 430 |
|
|
insertSQLData($CatalogNo),
|
| 431 |
|
|
insertSQLData("GBIFFile.txt"),
|
| 432 |
|
|
insertSQLData($recordCount),
|
| 433 |
|
|
insertSQLData("StagingRawSpecimen"),
|
| 434 |
|
|
insertSQLData($columnName),
|
| 435 |
|
|
insertSQLData($Error)
|
| 436 |
|
|
);
|
| 437 |
|
|
//echo ("<br> $errorReport <br>");
|
| 438 |
|
|
mysql_query($errorReport) OR DIE("Failed to enter log into error report." . mysql_error());
|
| 439 |
|
|
}
|
| 440 |
|
|
|
| 441 |
|
|
## =======================================
|
| 442 |
|
|
## Name: checkDifference
|
| 443 |
|
|
## Function: determines whether the difference between two numbers is close to 0 at given precision
|
| 444 |
|
|
## Internal Variables:
|
| 445 |
|
|
## Globals: None
|
| 446 |
|
|
## Calls Function: None
|
| 447 |
|
|
## Called by: main loop
|
| 448 |
|
|
## Written by: Mark Sheehan
|
| 449 |
|
|
## Last updated: 07-29-09
|
| 450 |
|
|
## ======================================
|
| 451 |
|
|
|
| 452 |
|
|
function checkDifference($firstNum, $secondNum, $precision)
|
| 453 |
|
|
{
|
| 454 |
|
|
if(abs($firstNum - $secondNum) < 2 * pow(10, -$precision))
|
| 455 |
|
|
{
|
| 456 |
|
|
return TRUE;
|
| 457 |
|
|
}
|
| 458 |
|
|
else
|
| 459 |
|
|
{
|
| 460 |
|
|
return FALSE;
|
| 461 |
|
|
}
|
| 462 |
|
|
}
|
| 463 |
|
|
|
| 464 |
|
|
## =======================================
|
| 465 |
|
|
## Name: InsertSQLData
|
| 466 |
|
|
## Function: Formats data to be inserted for SQL insert query
|
| 467 |
|
|
## Internal Variables:
|
| 468 |
|
|
## Globals: None
|
| 469 |
|
|
## Calls Function: None
|
| 470 |
|
|
## Called by: Main Loop
|
| 471 |
|
|
## Written by: Mark Sheehan
|
| 472 |
|
|
## Last Updated: 07-22-09
|
| 473 |
|
|
## ======================================
|
| 474 |
|
|
|
| 475 |
|
|
function InsertSQLData($string)
|
| 476 |
|
|
{
|
| 477 |
|
|
if($string == '' OR $string == NULL)
|
| 478 |
|
|
{
|
| 479 |
|
|
return('NULL');
|
| 480 |
|
|
}
|
| 481 |
|
|
else
|
| 482 |
|
|
{
|
| 483 |
|
|
return(sprintf("'%s'", mysql_real_escape_string($string)));
|
| 484 |
|
|
}
|
| 485 |
|
|
}
|
| 486 |
|
|
|
| 487 |
|
|
## =======================================
|
| 488 |
|
|
## Name: SelectSQLData
|
| 489 |
|
|
## Function: Formats data to be inserted into SQL select query
|
| 490 |
|
|
## Internal Variables:
|
| 491 |
|
|
## Globals: None
|
| 492 |
|
|
## Calls Function: None
|
| 493 |
|
|
## Called by: Main Loop
|
| 494 |
|
|
## Written by: Mark Sheehan
|
| 495 |
|
|
## Last Updated: 07-22-09
|
| 496 |
|
|
## ========================================
|
| 497 |
|
|
|
| 498 |
|
|
function SelectSQLData($string)
|
| 499 |
|
|
{
|
| 500 |
|
|
if($string == '' OR $string == NULL)
|
| 501 |
|
|
{
|
| 502 |
|
|
return("IS NULL");
|
| 503 |
|
|
}
|
| 504 |
|
|
else
|
| 505 |
|
|
{
|
| 506 |
|
|
return(sprintf("= '%s'", mysql_real_escape_string($string)));
|
| 507 |
|
|
}
|
| 508 |
|
|
}
|
| 509 |
|
|
|
| 510 |
|
|
?>
|
