Por mucho que nos guste programar en
Perl, a veces hay que recurrir a otros lenguajes más adecuados para propósitos concretos. Este es el caso de
PHP cuando se trata de realizar interfaces web para nuestros scripts de Perl.
El primer problema que nos surge al pasar a PHP es cómo enviar y recibir datos a través de un formulario web. Los datos enviados los podemos usar para ejecutar en el servidor nuestro script de Perl y generar resultados.
A continuación muestro el ejemplo de un formulario de búsqueda de secuencias DNA o Proteínas:
<?php
// Shows a search input data formulary
function showSearchForm(){
?>
<h3>Search form:</h3></br>
<form enctype="multipart/form-data" action="<?php print $_SERVER['PHP_SELF'] ?>" method="POST">
Search name: <input type="text" name="search_name" size="40" maxlength="127"></br></br>
Email: <input type="text" name="user_email" size="40" maxlength="127"></br></br>
Search input type:
<input type="radio" name="search_type" value="stamp"> DNA
<input type="radio" name="search_type" value="blastp"> Protein
</br></br>
Exclude query from results <input type="checkbox" name="search_exclude" value="yes"></br></br>
Limit number of results per query: <input type="text" name="search_limit" size="2" maxlength="2"></br></br>
Query data or file:</br></br>
<textarea name="query_data" rows="10" cols="67"></textarea>
</br></br>
<input type="file" name="query_file" size="20"></br></br>
Genomes:
<select name="specie" class="selectbutton">
<option value="human">Homo sapiens</option>
<option value="mouse">Mus musculus</option>
<option value="arabidopsis">Arabidopsis thaliana</option>
<option value="rice">Oryza sativa</option>
</select>
</br></br>
<input type="submit" name="search_submitted" value="Search">
</form>
<?php
}
?>
El siguiente paso consistirá en validar los datos introducidos para volver a mostrar el formulario si los datos fueran erróneos. Usaremos la variable especial $_SESSION para guardar los datos enviados con el formulario (almacenados en la variable $_POST). La variable $_SESSION nos permitirá acceder a su contenido si ejecutamos 'session_start()' al comienzo del código PHP. Antes de guardar los datos enviados, borraremos los contenidos anteriores de $_SESSION. Si en vez de enviar un archivo, hemos enviado datos en formato texto, guardaremos estos datos en un archivo temporal ($_SESSION['query_file']). Si faltan datos en algún campo del formulario, crearemos un mensaje de error en $_SESSION['errors'].
<?php
// Validates search form data
function validateSearchData(){
// Stores in $_SESSION variable all the post data and in $_SESSION['errors'] if some important data is missing
// Clear previous $_SESSION values
unset($_SESSION['errors']);
unset($_SESSION['search_name']);
unset($_SESSION['user_email']);
unset($_SESSION['search_type']);
unset($_SESSION['search_exclude']);
unset($_SESSION['search_limit']);
unset($_SESSION['specie']);
unset($_SESSION['output_dir']);
unset($_SESSION['query_file']);
unset($_SESSION['query_data']);
(!empty($_POST['search_name'])) ? $_SESSION['search_name'] = trim($_POST['search_name']) : $_SESSION['errors'][] = 'name for the search';
(!empty($_POST['user_email'])) ? $_SESSION['user_email'] = trim($_POST['user_email']) : $_SESSION['errors'][] = 'email';;
(!empty($_POST['search_type'])) ? $_SESSION['search_type'] = $_POST['search_type'] : $_SESSION['errors'][] = 'search input type';
if (!empty($_POST['search_exclude'])){
($_POST['search_exclude'] == 'yes') ? $_SESSION['search_exclude'] = 1 : $_SESSION['search_exclude'] = 0;
}
(!empty($_POST['search_limit'])) ? $_SESSION['search_limit'] = trim($_POST['search_limit']) : '';
(!empty($_POST['specie'])) ? $_SESSION['specie'] = $_POST['specie'] : '';
// Store the query data into a file inside the /tmp folder
if (!empty($_FILES['query_file']['name']) && !empty($_FILES['query_file']['tmp_name']) && $_FILES['query_file']['size']>0){
$_SESSION['query_file'] = $_FILES['query_file']['tmp_name'];
}elseif (!empty($_POST['query_data'])){
$_SESSION['query_data'] = $_POST['query_data'];
$_SESSION['query_file'] = '/tmp/'.$_SESSION['search_name'].".data";
$file_handle = fopen($_SESSION['query_file'], "w");
fwrite($file_handle, $_POST['query_data']);
fclose($file_handle);
} else{
$_SESSION['errors'][] = 'data or file to process';
}
if (isset($_SESSION['errors'])){
return;
}
}
?>
Finalmente, falta introducir las dos funciones anteriores en un archivo (por ejemplo 'index.php') para que sean leídas e interpretadas por el servidor web. Si los datos del formulario son válidos se ejecutará un pequeño código de Perl, si no se volverá a mostrar el formulario indicando los datos que faltan.
<?php
// Example file of a PHP search formulary with input data validation and script execution
session_start();
?>
<html>
<head>
<title>Search Form</title>
</head>
<body>
<?php
if(!isset($_POST['search_submitted'])){
?><h3>Search form:</h3><?php
showSearchForm();
} else {
validateSearchData();
if (!isset($_SESSION['errors'])){
executeScript();
} else {
?><h3>Search form:</h3><?php
print '<font color="red"><b>Please specify: '.join(', ',$_SESSION['errors']).'.</b></font></br></br>';
unset($_SESSION['errors']);
showSearchForm();
}
}
?>
</body>
</html>
<?php
// Shows an input data formulary filled with previous values
function showSearchForm(){
?>
<form enctype="multipart/form-data" action="<?php print $_SERVER['PHP_SELF'] ?>" method="POST">
Search name: <input type="text" name="search_name" size="40" maxlength="127" <?php ($_SESSION['search_name']) ? print 'value="'.$_SESSION['search_name'].'"' : '' ?> ></br></br>
Email: <input type="text" name="user_email" size="40" maxlength="127" <?php ($_SESSION['user_email']) ? print 'value="'.$_SESSION['user_email'].'"' : '' ?> ></br></br>
Search input type:
<input type="radio" name="search_type" value="stamp" <?php ($_SESSION['search_type'] == 'stamp') ? print 'checked' : '' ?>> DNA
<input type="radio" name="search_type" value="blastp" <?php ($_SESSION['search_type'] == 'blastp') ? print 'checked' : '' ?>> Protein
</br></br>
Exclude query from results <input type="checkbox" name="search_exclude" value="yes" <?php ($_SESSION['search_exclude'] == 'yes') ? print 'checked' : print 'checked' ?>></br></br>
Limit number of results per query: <input type="text" name="search_limit" size="2" maxlength="2" <?php ($_SESSION['search_limit']) ? print 'value="'.$_SESSION['search_limit'].'"' : print 'value="10"'; ?> ></br></br>
Query data or file:</br></br>
<textarea name="query_data" rows="10" cols="67"><?php ($_SESSION['query_data']) ? print $_SESSION['query_data'] : '' ?></textarea>
</br></br>
<input type="file" name="query_file" size="20"></br></br>
Genomes:
<select name="specie" class="selectbutton">
<option value="human" <?php (!isset($_SESSION['specie']) || $_SESSION['specie'] == 'human') ? print 'selected' : '' ?>>Homo sapiens</option>
<option value="mouse" <?php ($_SESSION['specie'] == 'mouse') ? print 'selected' : '' ?>>Mus musculus</option>
<option value="arabidopsis" <?php ($_SESSION['specie'] == 'arabidopsis') ? print 'selected' : '' ?>>Arabidopsis thaliana</option>
<option value="rice" <?php ($_SESSION['specie'] == 'rice') ? print 'selected' : '' ?>>Oryza sativa</option>
</select>
</br></br>
<input type="submit" name="search_submitted" value="Search">
</form>
<?php
}
// Validates search form data
function validateSearchData(){
// Stores in $_SESSION variable all the post data and in $_SESSION['errors'] if some important data is missing
// Clear previous $_SESSION values
unset($_SESSION['errors']);
unset($_SESSION['search_name']);
unset($_SESSION['user_email']);
unset($_SESSION['search_type']);
unset($_SESSION['search_exclude']);
unset($_SESSION['search_limit']);
unset($_SESSION['specie']);
unset($_SESSION['output_dir']);
unset($_SESSION['query_file']);
unset($_SESSION['query_data']);
(!empty($_POST['search_name'])) ? $_SESSION['search_name'] = trim($_POST['search_name']) : $_SESSION['errors'][] = 'name for the search';
(!empty($_POST['user_email'])) ? $_SESSION['user_email'] = trim($_POST['user_email']) : $_SESSION['errors'][] = 'email';;
(!empty($_POST['search_type'])) ? $_SESSION['search_type'] = $_POST['search_type'] : $_SESSION['errors'][] = 'search input type';
if (!empty($_POST['search_exclude'])){
($_POST['search_exclude'] == 'yes') ? $_SESSION['search_exclude'] = 1 : $_SESSION['search_exclude'] = 0;
}
(!empty($_POST['search_limit'])) ? $_SESSION['search_limit'] = trim($_POST['search_limit']) : '';
(!empty($_POST['specie'])) ? $_SESSION['specie'] = $_POST['specie'] : '';
// Store the query data into a file inside the /tmp folder
if (!empty($_FILES['query_file']['name']) && !empty($_FILES['query_file']['tmp_name']) && $_FILES['query_file']['size']>0){
$_SESSION['query_file'] = $_FILES['query_file']['tmp_name'];
}elseif (!empty($_POST['query_data'])){
$_SESSION['query_data'] = $_POST['query_data'];
$_SESSION['query_file'] = '/tmp/'.$_SESSION['search_name'].".data";
$file_handle = fopen($_SESSION['query_file'], "w");
fwrite($file_handle, $_POST['query_data']);
fclose($file_handle);
} else{
$_SESSION['errors'][] = 'data or file to process';
}
if (isset($_SESSION['errors'])){
return;
}
}
// Executes a Perl script and prints the output
function executeScript(){
$output = `perl -e 'print "Hello world\n"'`;
print '<pre>'.$output.'</pre>';
}
?>
