PHP - Notice Undefined offset - php

Question

I have an issue in my php script which I don't understand. I know there are several questions regarding this issue but none fits to my issue.
I actually have one input file delimited by tabulation named testfile.txt.
With this txt file, I create a new file named result.txt where I take content of testfile in column 0 and column 7.
When I execute my php script, I get this error:
Notice: Undefined offset: 7
The thing that I don't understand is, my result.txt is well created with data contained in my column 0 and 7 from my testfile.txt. If I do:
echo $dataFromTestFile[7];
I have in output contents in column 7.
So I don't really understand why I have this notice and how to remove it.
Here's my php script:
<?php
if (false !== ($ih = fopen('/opt/lampp/htdocs/ngs/tmp/testfile.txt', 'r'))) {
$oh = fopen('/opt/lampp/htdocs/ngs/tmp/result.txt', 'w');
while (false !== ($dataFromTestFile = fgetcsv($ih,0,"\t"))) {
// this is where I build my new row
$outputData = array($dataFromTestFile[0], $dataFromTestFile[7]);
fputcsv($oh, $outputData);
//echo $dataFromTestFile[7];
}
fclose($ih);
fclose($oh);
}
?>
Sample data of testfile.txt:
Input Errors AccNo Genesymbol Variant Reference Coding Descr. Coding
aaa ddd fdfd dfdf fefefd ref1 fdfdfd fdfdf dfdfde

Answer 1

I suspect this is the line that's causing the error:
$outputData = array($dataFromTestFile[0], $dataFromTestFile[7]);
You are trying to use array elements at specific index without checking if they actually exists.
Also, you are trying to write an array object to the result file, did you mean to create a comma separated value in that file?
Try this:
$source = '/opt/lampp/htdocs/ngs/tmp/testfile.txt';
$result = '/opt/lampp/htdocs/ngs/tmp/result.txt';
if (($handle = fopen($source, "r")) !== FALSE) {
while (($data = fgetcsv($handle, 1000, "\t")) !== FALSE) {
if (isset($data[0]) && isset($data[7])) {
file_put_contents($result, $data[0] .','. $data[7] ."\r\n");
}
}
fclose($handle);
}
Alternatively, you could write the result as a csv like this also:
$sourceFile = '/opt/lampp/htdocs/ngs/tmp/testfile.txt';
$resultFile = '/opt/lampp/htdocs/ngs/tmp/result.txt';
$resultData = array();
// Parse source file
if (($handle = fopen($sourceFile, "r")) !== FALSE) {
while (($data = fgetcsv($handle, 1000, "\t")) !== FALSE) {
if (isset($data[0]) && isset($data[7])) {
$resultData[] = array($data[0], $data[7]);
}
}
fclose($handle);
}
// Write result file
if (sizeof($resultData)) {
$h = #fopen($resultFile, 'w');
if (!$h) {
exit('Failed to open result file for writing.');
}
foreach ($resultData as $resultRow) {
fputcsv($h, $resultRow, ',', '"');
}
fclose($h);
}

Answer 2

make sure the column 7 exists in your testfile.txt - i guess when starting from zero it may be column number 6 - also you can
var_dump($dataFromTestFile)
in order to get the content of the variable - array keys and values might be of interest for your issue