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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'], $arrayInsert['CatalogNO'], NULL, "Validation result does not exist");
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continue; //error, skip the rest of validation
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}
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else //(num_rows == 1)
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{
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$validation_result_row = mysql_fetch_assoc($validation_result) OR DIE("Error - no result found");
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$CatalogNO = $arrayInsert['CatalogNO'];
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$CollectionCD = $arrayInsert['CollectionCD'];
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foreach($arrayInsert AS $key => $data)
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{
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## ======== check if the result found in the database matches that entered (Check both exact string match and numerical equality)
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249
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if((strcasecmp($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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}
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} //end while loop
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}
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## ======== Display results to user
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if($duplicateEntries >= 1)
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{
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echo "<br>" . $duplicateEntries . " record(s) has been skipped, key already exists<br>";
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}
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if($successEntries >= 1)
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{
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echo "<br>" . $successEntries . " record(s) has been successfully inserted<br>";
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}
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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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// =============================
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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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## Global Variables: $arr
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## Calls Function: None
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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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287
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function checkArray()
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{
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global $arr;
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290
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for($a=0; $a<31; $a++)
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{
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292
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if(!(array_key_exists($a, $arr)))
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293
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{
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$arr[$a] = ' ';
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}
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296
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## ==== Trim white spaces and newline off of front and end of string (necessary for values at end of line)
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298
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299
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$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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{
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$arr[$a] = NULL;
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}
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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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{
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if($a == 8)
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{
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//==== Actual data in GBIF file in format "MM-DD-YYYY HH:MM"
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//Start formatting date
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$dateFormat = explode(' ', $arr[$a]);
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$date = $dateFormat[0];
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$time = $dateFormat[1];
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$date = explode('-', $date); //break date up into MM DD YYYY
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$month = str_pad($date[1], 2, '0', STR_PAD_LEFT); //if only entered as 5/27/2008, need it in form 05/27/2008 so need padding on left
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$day = str_pad($date[2], 2, '0', STR_PAD_LEFT);
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$year = $date[0];
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$time = explode(':', $time);
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$hour = $time[0];
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$hour = str_pad($hour, 2, '0', STR_PAD_LEFT); //same issue as above
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$minute = $time[1];
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$second = "00"; //seconds not given, assume 00
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$arr[$a] = sprintf("%s-%s-%s %s:%s:%s", $year, $month, $day, $hour, $minute, $second);
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//echo(" $arr[$a] <br>");
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}
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else if($a == 4)
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{
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//==== Actual data in GBIF file in format MM/DD/YYYY OR YYYY-MM-DD
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if(stripos($arr[$a], '/')) // if in MM/DD/YYYY format
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{
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$dateFormat = explode('/', $arr[$a]);
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$month = str_pad($dateFormat[0], 2, '0', STR_PAD_LEFT);
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$day = str_pad($dateFormat[1], 2, '0', STR_PAD_LEFT);
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$year = $dateFormat[2];
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$arr[$a] = sprintf("%s-%s-%s", $year, $month, $day);
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}
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else if(stripos($arr[$a], '-')) //if in YYYY-MM-DD format
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{
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$dateFormat = explode('-', $arr[$a]);
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$month = str_pad($dateFormat[1], 2, '0', STR_PAD_LEFT);
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$day = str_pad($dateFormat[2], 2, '0', STR_PAD_LEFT);
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$year = $dateFormat[0];
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$arr[$a] = sprintf("%s-%s-%s", $year, $month, $day);
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}
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else
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{
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reportError($arr[6], $arr[7], $arr[$a], "Date format for ||$arr[$a]|| not found.");
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}
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}
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}
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else if($a == 26) // if elevation range is given as XXX-YYY in one field instead of as minimum and maximum
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{
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$minMax = explode('-', $arr[$a]);
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if(sizeof($minMax) > 1)
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{
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$arr[26] = $minMax[0];
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$arr[27] = $minMax[1];
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367
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}
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368
|
}
|
|
369
|
else if ($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
|
?>
|
