Notice

[Tiago Hori <tiago.hori@xxxxxxxxx>]

Hi Everyone,

I am at loss so I am hoping your wisdom can help me.

I originally had a script that first got a list of terms to be searched
from the file uploaded in the first part. This list is stored in the array
$snp. Every item in $snp occurs once for every entry i have in the table.
The goal is to allow the user to select a set in the file uploaded and get
every entry for a given project, which is entered via POST.

I had originally wrote this in way that it made 3 or 4 calls to the
database and it was way to slow, so I tried to make one call to the
database and put everything in a multidimensional array.

Now, what I have below seems to work, but I get 3notices for every
iteration of the foreach($rows as $ids) and I can't figure out for the life
of me why.

*Notice*: Undefined index: in
*/Applications/MAMP/htdocs/catcnew/snppitv1.php* on line *62*

*Notice*: Undefined index: in
*/Applications/MAMP/htdocs/catcnew/snppitv1.php* on line *63*

*Notice*: Array to string conversion in
*/Applications/MAMP/htdocs/catcnew/snppitv1.php* on line *66*


I guess I would like to know what it is going on out of curiosity and if it
can cause a problem down the road. Also, any suggestions on improvement are
always welcome.

if(isset($_FILES['snps']))
{
    $dir = 'uploads';
    $header = "role\t";
    $filename = $_FILES['snps']['name'];
    if (file_exists("$dir/$filename"))
    {
        die ("A file with this name already exists in the database <br />");
    }
    else
    {
        move_uploaded_file($_FILES['snps']['tmp_name'], "$dir/$filename");
        echo "Uploaded file '$filename' <br />";
        $fh = fopen("$dir/$filename", 'r') or
            die("File does not exist or you lack permission to open it");
    }
    while (!feof($fh))
    {

        $line = fgets($fh);
        $snp[] = trim(preg_replace('/\n/', '', $line));

    }
    foreach ($snp as $loci)
    {
        $header .= $loci . "\t" . $loci . "\t";
    }

}

if(isset($_POST['project']))
{
    $project = sanitizeStrings($_POST['project']);
    $body =  "";

    $query = "SELECT * FROM genotyped WHERE projectid='$project'";
    $result = queryMysql($query);
    if(mysqli_num_rows($result))
    {
        $data = array();
        while($row = mysqli_fetch_row($result))
        {

            $rows[] = $row[2];
            $role[$row[2]] = $row[3];
            $data[$row[2]][$row[6]]['alelleY'] = $row[7];
            $data[$row[2]][$row[6]]['alelleX'] = $row[8];
        }
        $rows = array_unique($rows);
        foreach($rows as $ids)
        {
            $col2 = $role[$ids];
            $alelleX = $alelleY = $content = "";
            foreach($snp as $loci)
            {
                $alelleY = $data[$ids][$loci]['alelleY'];
                $alelleX = $data[$ids][$loci]['alelleX'];
                $content .= "$alelleY\t$alelleX\t";
            }
            $body .= "$ids\t$role\t" . substr($content, 0, -1) . "\n";
        }
    }
}

unlink("$dir/$filename");


?>

T.


-- 
"Education is not to be used to promote obscurantism." - Theodonius
Dobzhansky.

"Gracias a la vida que me ha dado tanto
Me ha dado el sonido y el abecedario
Con él, las palabras que pienso y declaro
Madre, amigo, hermano
Y luz alumbrando la ruta del alma del que estoy amando

Gracias a la vida que me ha dado tanto
Me ha dado la marcha de mis pies cansados
Con ellos anduve ciudades y charcos
Playas y desiertos, montañas y llanos
Y la casa tuya, tu calle y tu patio"

Violeta Parra - Gracias a la Vida

Tiago S. F. Hori. PhD.
Ocean Science Center-Memorial University of Newfoundland