Second submit button not working like first one - php

Question

Right now I am really confused and have been working on this problem for a couple hours now so I thought I would post on here and maybe get some feedback. So I have a program that runs this search tool on a file. The file either comes from user input generated into a file or a user actually uploading the file. I have 2 submit buttons where the first one goes with user generated files and the second one has to do with a user uploading a file.
The problem I have is that I have the same exact code for the second submit button (All that changes is the way the program gets the file) but for some reason by second submit button doesnt work. Nothing is generated and the execution of the search tool does not occur. I know this because there is not an output file created.
I was wondering if someone knows why my second button doesnt perform like the first button....
Here is my code...
<form method="POST", action="/~cs4380sp15grp4/home/blast.php" class="form-inline">
<textarea id="BlastSearch" type="textarea" name="BlastSearch" class="form-control">
Database:
<select id="database" name="database" class="form-control">
<option value="Archaea">Archaea</option>
</select>
Threshold:
<select id="evalue" name="evalue" class="form-control">
<option value="0.0001">0.0001</option>
<option value="0.001">0.001</option>
</select>
Hits:
<select id="hits" name="hits" class="form-control">
<option value="50">50</option>
<option value="100">100</option>
</select>
<button id="run" type="submit" name="submit" class="btn btn-primary"><span class="glyphicon glyphicon-wrench"></span> Run BLAST</button>
<button type="reset" value="Clear" class="btn btn-info">Clear</button>
</form>
<form enctype="multipart/form-data" action="upload.php" method="POST" class="form-inline"/>
<input type="file" name="fileToUpload" id="fileToUpload" class="form-control"/>
<input type="submit" value="upload" name="upload" class="form-control"/>
<input type="reset" value="reset" name="reset" class="form-control"/>
</form>
<form method="POST", action="/~cs4380sp15grp4/home/blast.php" class="form-inline">
<input type="submit" value="submit file" name="submit2" class="form-control"/>
</form>
<?php
//connects to db
//Insert the values into the database
if(isset($_POST['submit'])){
//declare variables to what the user defines them as
$db = $_POST['database'];
$evalue = $_POST['evalue'];
$sequence = $_POST['BlastSearch'];
$hits = $_POST['hits'];
//create a new .fasta file and put the sequence the user wants to search for in that file
$file = 'uploads/'.$mysqli->insert_id.'.fasta';
$header = ">gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)\n";
$current = $header . $_POST['BlastSearch'];
file_put_contents($file, $current);
$userid = $_SESSION['uid'];
//insert the values into the database
$mysqli->query("INSERT INTO `Job` (`uid`, `input`, `status`, `start_time`, `finish_time`) VALUES ('1', '" . $sequence . "', 'running' , NOW(), NOW())");
$mysqli->query("INSERT INTO `BLAST`(`db_name`, `evalue`, `job_id`) VALUES ('" . $db . "','" . $evalue . "', '".$mysqli->insert_id."')") or die(mysqli_error($mysqli));
//execute the BLAST Tool
// Do this execute statement if the user inputs his own sequence. (Use new.fasta)
exec('/students/groups/cs4380sp15grp4/blast/blast-2.2.26/bin/blastall -p blastp -d db -i /students/groups/cs4380sp15grp4/public_html/home/uploads/'.$mysqli->insert_id.'.fasta -m'.$evalue.' -o outputSEQ -v'.$hits.' -b'.$hits);
}
if(isset($_POST['submit2'])){
//declare variables to what the user defines them as
$db = $_POST['database'];
$evalue = $_POST['evalue'];
$sequence = $_POST['BlastSearch'];
$hits = $_POST['hits'];
$userid = $_SESSION['uid'];
//insert the values into the database
$mysqli->query("INSERT INTO `Job` (`uid`, `input`, `status`, `start_time`, `finish_time`) VALUES ('1', '" . $sequence . "', 'running' , NOW(), NOW())");
$mysqli->query("INSERT INTO `BLAST`(`db_name`, `evalue`, `job_id`) VALUES ('" . $db . "','" . $evalue . "', '".$mysqli->insert_id."')") or die(mysqli_error($mysqli));
exec('/students/groups/cs4380sp15grp4/blast/blast-2.2.26/bin/blastall -p blastp -d db -i /students/groups/cs4380sp15grp4/public_html/home/uploads/sample.fasta -m '.$evalue.' -o outputFILE -v'.$hits.' -b'.$hits);
}
$mysqli->close();
?>
I dont understand it. basically the exec function works in the first submit button, but the exec function doesnt work in the second one... I can go into terminal and run the second exec function and it runs perfectly fine. Is it because of the action for the second submit being upload.php? I could see it being that....
EDIT1: I just tried creating a new form specifically for that button and making the action the same as the first submit buttons form. It didnt work though :( any help is appreciated!

Answer 1

Hi there is few issues in your code you pasted.
In first form textarea does not have closing tag.
In third form you have a comma (,) after method="Post"
Your question is about second submit button and you have created 3 forms.

Answer 2

Should that comma after the method=POST be there? I can't actually see why it would make any difference, but it's not going to help. Having multiple forms on a page is valid of course, but it's sometimes better to have just one form and use Javascript behind multiple 'normal' buttons to set the enctype, method, action set and required defaults and then submit the form programatically.

Answer 3

Provide the following hidden inputs in the corresponding forms in order to get the $_POST['submit'] and $_POST['submit2'] in the server side php:
<input type="hidden" value="1" name="submit" />
<input type="hidden" value="1" name="submit2" />
Try this:
<form method="POST", action="/~cs4380sp15grp4/home/blast.php" class="form-inline">
<textarea id="BlastSearch" type="textarea" name="BlastSearch" class="form-control">
Database:
<select id="database" name="database" class="form-control">
<option value="Archaea">Archaea</option>
</select>
Threshold:
<select id="evalue" name="evalue" class="form-control">
<option value="0.0001">0.0001</option>
<option value="0.001">0.001</option>
</select>
Hits:
<select id="hits" name="hits" class="form-control">
<option value="50">50</option>
<option value="100">100</option>
</select>
<input type="hidden" value="1" name="submit" />
<button id="run" type="submit" class="btn btn-primary"><span class="glyphicon glyphicon-wrench"></span> Run BLAST</button>
<button type="reset" value="Clear" class="btn btn-info">Clear</button>
</form>
<form enctype="multipart/form-data" action="upload.php" method="POST" class="form-inline"/>
<input type="file" name="fileToUpload" id="fileToUpload" class="form-control"/>
<input type="submit" value="upload" name="upload" class="form-control"/>
<input type="reset" value="reset" name="reset" class="form-control"/>
</form>
<form method="POST", action="/~cs4380sp15grp4/home/blast.php" class="form-inline">
<input type="hidden" value="1" name="submit2" />
<input type="submit" value="submit file" class="form-control"/>
</form>
<?php
//connects to db
//Insert the values into the database
if(isset($_POST['submit'])){
//declare variables to what the user defines them as
$db = $_POST['database'];
$evalue = $_POST['evalue'];
$sequence = $_POST['BlastSearch'];
$hits = $_POST['hits'];
//create a new .fasta file and put the sequence the user wants to search for in that file
$file = 'uploads/'.$mysqli->insert_id.'.fasta';
$header = ">gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)\n";
$current = $header . $_POST['BlastSearch'];
file_put_contents($file, $current);
$userid = $_SESSION['uid'];
//insert the values into the database
$mysqli->query("INSERT INTO `Job` (`uid`, `input`, `status`, `start_time`, `finish_time`) VALUES ('1', '" . $sequence . "', 'running' , NOW(), NOW())");
$mysqli->query("INSERT INTO `BLAST`(`db_name`, `evalue`, `job_id`) VALUES ('" . $db . "','" . $evalue . "', '".$mysqli->insert_id."')") or die(mysqli_error($mysqli));
//execute the BLAST Tool
// Do this execute statement if the user inputs his own sequence. (Use new.fasta)
exec('/students/groups/cs4380sp15grp4/blast/blast-2.2.26/bin/blastall -p blastp -d db -i /students/groups/cs4380sp15grp4/public_html/home/uploads/'.$mysqli->insert_id.'.fasta -m'.$evalue.' -o outputSEQ -v'.$hits.' -b'.$hits);
}
if(isset($_POST['submit2'])){
//declare variables to what the user defines them as
$db = $_POST['database'];
$evalue = $_POST['evalue'];
$sequence = $_POST['BlastSearch'];
$hits = $_POST['hits'];
$userid = $_SESSION['uid'];
//insert the values into the database
$mysqli->query("INSERT INTO `Job` (`uid`, `input`, `status`, `start_time`, `finish_time`) VALUES ('1', '" . $sequence . "', 'running' , NOW(), NOW())");
$mysqli->query("INSERT INTO `BLAST`(`db_name`, `evalue`, `job_id`) VALUES ('" . $db . "','" . $evalue . "', '".$mysqli->insert_id."')") or die(mysqli_error($mysqli));
exec('/students/groups/cs4380sp15grp4/blast/blast-2.2.26/bin/blastall -p blastp -d db -i /students/groups/cs4380sp15grp4/public_html/home/uploads/sample.fasta -m '.$evalue.' -o outputFILE -v'.$hits.' -b'.$hits);
}
$mysqli->close();
?>