Ahmad's Blog: 2013

Thursday, 5 December 2013

Spreading the Fear: A potential new form of information transmission is discovered

Recently a report was published in the journal Nature Neuroscience about an experiment where mice were taught to associate pain with a scent, and then the fear of this scent was passed on to their offspring and their offspring's litter without them having experienced the pain of the parent or grand-parent themself. If what this research indicates is true, then it could open up the flood gates to a new dimension of genetic research.

The key point to take from this research is that traits can be passed from parent to child and grandchild without there being an alteration of DNA! So there's another form of inheritance! This brings in to question one of the central dogmas in genetics that DNA is the only genetic material (in all species save for a few microbes). If this research is confirmed and an alternative mechanism for information transmission is defined, then it will open up a whole new way of looking at genetics and inheritance of traits, both physical and psychological and also various diseases.

This might be the first time such an idea has been proved without their being confounding genetic and environmental factors that might affect the results and there is evidence of physical changes in the brain too. But before we jump up and down like excited children, we need to be careful and see if the result can be reproduced in other mice strains and in other species. I expect they will.

Here's the article by Nature News: Fearful memories haunt mouse descendants
And the original research papers (pay-walled): Implications of memory modulation for post-traumatic stress and fear disorders by Ryan G Parsons and Kerry J Ressler in Nature Neuroscience 16, 146-153 (2013) doi:10.1038/nn.3296

Wednesday, 30 October 2013

Javascript snippet to HTML encode foreign characters

This Javascript snippet is useful for converting characters in a language like Arabic to HTML Encoding for putting on web pages.

var a = "السلام عليكم"; //Arabic for Peace Be Upon You (Hello)
var h = a.replace(/(.)/g, function($1){
return ($1 == " ") ? $1 : "&#" + $1.charCodeAt() + ";";
});

The variable h now holds السلام عليكم

a.replace(/(.)/g, function($1){
  if ($1 == " ")
    return " ";
  else
    return "&#" + $1.charCodeAt() + ";";
})

"السلام عليكم"

"السلام عليكم"

"السلام عليكم"

"السلام عليكم"

console.log("السلام عليكم".replace(/(.)/g, function($1){
  if ($1 == " ")
    return " ";
  else
    return "&#" + $1.charCodeAt() + ";";
}));

Monday, 28 October 2013

Drupal 7: Referencing Views from inside Panel Pages

Example Scenario: I have created a Panel Page (e.g. Cars) and I want to display a View list of Parts associated with any Car loaded through that Panel page. Each Car node contains a reference (Entity Reference) field (field_parts_ref) to all the parts associated with it.

First, create your View, choose which fields to display, and add a context - select Content: Nid of the Car and on the next page you select Provide default value from the drop down list, select PHP Code from the drop down list, and add the following code:

//get node id of parent passed from the panel and load the node into memory
$nid = $argument->view->args[1];
$node = node_load($nid);
//read the field which has references to the node id's of the child items and add them to $refs
$refs = array();
foreach((array)$node->field_parts_ref['und'] as $t){
if ( ! empty($t['target_id']))
$refs[] = $t['target_id'];
}
//return the array of child item references to the view in a comma-seperated list so it displays only those items
return implode(',', $refs);

Now scroll to the bottom and expand More and check Allow multiple values.

Now you can create your Panel Page. Add your view as a content, but when it shows the interface to configure the View you need to select the Cars ID field in the Node Being Viewed section of the drop down, and make sure the Send arguments check box is checked.

That's it. It was a little tricky to figure this stuff out but I got there in the end, so I hope this gives some clue to anyone trying to get something working.

Tuesday, 1 October 2013

Things that annoy me about OOP in PHP

I've been doing quite a bit of "proper" OOP coding in PHP lately and made a note of common pitfalls I came across. This list is not a complete run-down of what's wrong with OOP PHP. To be honest, save for these pitfalls, proper coding of PHP is actually fun.

1. Having to import every single class you use manually

In Java you say import java.util.*; where the asterisk means everything in that module is available for use in this namespace. Easy to see what's going on and a real timesaver. While using standard PSR-0 autoloading conventions, PHP doesn't have library importing so for every class you use you have to import it or give the full classpath everytime you need to use it. You will often see PHP code with long lists of 'use' statements at the beginning of the file like so:

use mylib\app\util\LoremIpsumGenerator,
mylib\app\config\ConfigLoader,
    anotherlib\tastyphp\orm\TastyORM,
    randomlib\randomhouse\RealRandom;

2. SPL classes have to be referenced with a preceding backslash

Instead of the PHP engine doing a simple search to find a class, first in the namespace of the file, then in the Standard PHP Library namespace, you have to delimit an SPL class with a backslash every time you use it. Why can't I just say "new Exception()" instead of "new \Exception()"? Why do I have to use a backslash everywhere I use an SPL class? It's totally unnecessary and becomes annoying to code and irritating to debug

/**
* Yes, yes, I know I should use instanceof
* but I'm showing another SPL class being used
* @throws \Exception
* @param \Exception|mylib\app\exceptions\MyBaseException
* $exception
*/
public function captureMyExceptionThrowPHPException(\Exception $exception)
{
$rc = new \ReflectionClass($exception);
    if ($rc->isSubclassOf('mylib\app\exceptions\MyBaseException')) throw new \Exception('My Exception: ' . $exception->getMessage());
else throw $exception;
}

3. Lack of object casting

Seriously, why can't I cast one type of object into another, even when the subject is a subclass of the object? I wish it was possible to do this: $e = (\Exception) new mylib\app\exceptions\MyBaseException('My exception'); That would save me a bit of typing and potential buggy code.

Java allows you to upcast an object, meaning a subclass can be easily converted into a parent class, but it is not possible to downcast a parent item into a subclass type. Ideally it should be able to do that but at least it is able to upcast. PHP can't cast anything except it's primitives and two complex types (int|string|float|bool|array|object).

4. Lack of proper documentation for SPL Classes on the PHP.net site

Common SPL Functions are well documented with community supplied code snippets for everything you can imagine so it's easy to copy and paste and you're done. PHP5 SPL Classes are poorly documented, which is a real shame because some crap and procedural code from the PHP4 days has now been re-implemented in a much cleaner, better and faster object oriented way. But you wouldn't know that because of the lack of information in the manual. More work needs to be put into this. More comments with usage examples are necessary. These are provided by the community so please contribute to the project with a comment or an example if you have anything helpful.

Sunday, 23 June 2013

Tortoiseshell-colored cats are usually female

I was reading something about cat behaviour and that reminded me of a fact that I learnt a long time ago, that almost all Tortoiseshell-coloured (black and orange patch) cats are female because of an X-linked gene. I googled it to remind myself of the genetics behind it and found an excellent page that explains it in detail: The genetics of Calico cats

Wednesday, 3 April 2013

Drupal node structure and adding/modifying values for Entity References

Language was left as undefined (und). If you set yours to English or something else then you need to adapt your code accordingly.
Some of these fields are of type Entity Reference. Often, the "value" key is set, but with Entity References it is the "target_id" field that needs setting.
The code to generate this is watchdog('phenotype', print_r(node_load($node_id), true))); And the output is accessible in the logs (Reports > Recent Log Messages).

The problem I was having was how to set an Entity Reference field that can hold unlimited references with a value programatically. First I tried assigning raw reference ids to the field, then I tried array('value' => $nid), but neither of these worked. So after a few hours I did the print_r() of the node above and got the clue to making it work:

$lang = 'und';
$node = node_load($gene_node_id);
foreach ($phenotype_refs as $ref_id)
$node->field_phenotype_ref[$lang][] = array('target_id' => $ref_id);
node_save($node);

And that did it. You need to set the target_id key. So now the Gene node has a list of references to Phenotype nodes.

I hope this saves someone some time.

Tuesday, 19 March 2013

A naturally placed DIV that responsively expands to browser window/viewport height

Have you ever seen those web applications that have a pane on the left hand side and a main body and somehow it fits it all into the size of your browser window (viewport) what ever browser/device you use or screen size you have and it doesn't show your browser's scroll bars? I'm talking about the height of the left pane and the body adjusting automatically to the height of your browser window.

Have you ever tried searching for how they do it? I tried and couldn't find a straight answer. I'm no javascript nerd so I had to figure this out the hard way with trial and error. To save any of you some time here is my solution using a little CSS and some responsive javascript (jQuery):

Scenario:

I have a typical page with a banner at the top and a navigation bar just below it, and I want my web application-style left pane and main body pane to fit into the vertical white space of the page body that is not already occupied by the banner or navigation bar. My HTML looks a little like this:

<!DOCTYPE html>
<html>
<head>
<link rel="stylesheet" href="css.css">
<script src="jquery.js"></script>
<script src="js.js"></script>
</head>
<body>
<div id="container">

<div id="banner"></div>
<div id="nav"></div>

<div id="webapp">
<div id="leftpane"></div>
<div id="mainbody"></div>
</div>

</div>
</body>
</html>

So, for this example, my main concern is the #leftpane div. If you understand the code for that, you can duplicate the approach for the #mainbody. (To be honest, I'm writing this post here before I tackle mainbody next)

The CSS for leftpane is:

#leftpane{
margin:0 auto;
float:left;
border:1px solid darkgreen;
background-color:rgba(0, 0, 150, .15);
vertical-align:top;
width:30%;
overflow-y:auto;
}

Notice there is no mention of position:absolute. That's because this example is NOT about filling the page from top to bottom with the left pane. If you want that kind of information, then google will easily find you that. Instead, what we are doing here is having the top of the div element be in its normal position, while the bottom border of the div will expand vertically depending on the size of the window/viewport. I only care about the height of the div in my example. Widths are managed with width: n% and using min-width:n px, but I will not discuss widths any further.

Anyway. How do we get the leftpane to expand according to size of the window? With a bit of Javascript (jQuery). The javascript below is responsive. When the page first loads it calls the snapLeftpane() function and resizes the leftpane and then if the user makes their window bigger or smaller, it calls the snapLeftpane() function again to resize the leftpane again.

But I set some limits. If the window becomes too small, like if the user is messing about and makes their browser window too small, then it snaps the leftpane to the minimum height allowable. And in the opposite situation, when the user has a huge window, it limits the height of the leftpane to the maximum height allowable, so the web app doesn't look ridiculously disproportioned.

Here's the javascript:

function snapLeftpane(){
    var minHeight = 450,
        maxHeight = 800,
        wHeight = $(window).height();
    var el = $('#leftpane');
    if(el.length){
        var top = el.offset().top + 5;
    if(wHeight >= minHeight && wHeight <= maxHeight) {
        el.height((wHeight - top) + "px");
        console.log('naturally expanding height ' + el.height());
    } else if (wHeight > maxHeight) {
        el.height(maxHeight + "px");
        console.log('set to max height ' + el.height());
    } else if (wHeight < minHeight) {
        el.height(minHeight + "px");
        console.log('set to min height ' + el.height());
    }
    }
}

$(window).on('resize load', function(){snapLeftpane();});

And if you run this code in your browser and play around with the size of the browser window, you will see how it adjusts the height of the left pane accordingly or snaps it to the minimum height or maximum height if you make the window too small or too large. I recommend you modify the min and max heights to your preferences.

That's it. Hope this helps :)

Thursday, 31 January 2013

Automatically Inserting events into Google Calendar using Zend Framework

It's been a while since I posted something on this blog so here is a little problem I sorted out and wanted to share the code to help anyone out there who was planning on doing something similar.

The issue: I had an XML file containing events that needed to be entered into a Google Calendar automatically. I needed my script to log into my Google account and insert the event onto my Calendar. I looked at the Google Calendar API but didn't like it and it required PHP5.3+ according to the instructions and the host I had to get my script working on was PHP5.2. So I went to find another way of solving the problem and found the solution available in the Zend Framework Gdata module. I'm using ZF 1.12 files in my examples. Here is the Calendar documentation.

So, I downloaded the ZF zip archive, but because it's soooo huge, I only took out the files and folders that I needed and stuck them into a 'Zend' folder at the root of my src directory:

/Zend/Feed/
/Zend/Gdata/
/Zend/Http/
/Zend/Loader/
/Zend/Uri/
/Zend/Validate/
/Zend/Exception.php
/Zend/Gdata.php
/Zend/Loader.php/
/Zend/Uri.php
/Zend/Vaildate.php
/Zend/Version.php

Then we need to think how to log into Google to use its services. Zend's Google library has three ways of doing the log in.

For my purpose I did not need anything special. I didn't need a login form or to have an authentication token cookie passed through successive pages. All I needed was to have the same login credentials hard-coded into my script and used for a single script run, so I used the ClientAuth direct login method.

I created a new script at the root of my src directory.

calendar.php

<?php

//Step 1:
//Turn on error reporting so we know what's going on if it doesn't work
//Set your time zone location so your local time is correct and not the server's time zon
//Register the autoloader to automatically load the classes from the Zend Framework when needed

ini_set('display_errors', 1);
ini_set('error_reporting', E_ALL);
date_default_timezone_set('Europe/London');

require_once 'Zend/Loader/Autoloader.php';
$autoloader = Zend_Loader_Autoloader::getInstance();
$autoloader->suppressNotFoundWarnings(false);
$autoloader->setFallbackAutoloader(true);

//Step 2:
//Log into Google
//Create an instance of the Zend_Gdata_Calendar class that we use to send and receive responses from Google Calendar

$email = 'someguy@gmail.com';
$pass = 'monkey';

try {
   $client = Zend_Gdata_ClientLogin::getHttpClient($email, $pass, 'cl'); //cl is to signify the calendar app is what we are using
} catch (Zend_Gdata_App_CaptchaRequiredException $cre) {
    echo 'URL of CAPTCHA image: ' . $cre->getCaptchaUrl() . "\n";
    echo 'Token ID: ' . $cre->getCaptchaToken() . "\n";
} catch (Zend_Gdata_App_AuthException $ae) {
    echo 'Problem authenticating: ' . $ae->exception() . "\n";
}

$gcal = new Zend_Gdata_Calendar($client);

//Step 3:
//Create an event object and use the awesome PHP DateTime class to set the time and duration

$event = $gcal->newEventEntry();
$event->title = $gcal->newTitle('FNP Meeting @ 2030');
$when = $gcal->newWhen();
$startTime = new DateTime('2013-02-01 20:30:00'); //enter your start date and time here
$duration = '30 minutes'; //how long the event is
$when->startTime = $starttime->format(DateTime::RFC3339); //Only Atom-format time is allowed
$when->endTime = $starttime->modify('+' . $duration)->format(DateTime::RFC3339);
$event->when = array($when);
//insert event - the $newEvent variable contains details and the unique id of the inserted event
$newEvent = $gcal->insertEvent($event);

?>

That's it. Simple no?! I only used what I needed but the library offers more options if you care to read the documentation.

The DateTime class can be instantiated with a Unix timestamp as well. In my XML I have the time in a non-standard format and used some PHP code to split it up into individual parts and passed it to the mktime() function. By adding the @ symbol before the timestamp it makes it get parsed correctly by DateTime.

$startTime = new DateTime('@' . mktime((int)$hour, (int)$min, 0, $month, $daynum, $year));

My biggest criticism of this process of inserting events into a Google Calendar in this way is that it is SLOW! Each event insertion requires a http post to the Google server and waiting for the Google server to respond, and if it takes my server 200ms to push the event to Google servers, 100ms for Google to process my query, and 200ms to send the response back, that's 500ms, half a second to carry out a single event insertion. What if I have hundreds of things to insert... sorry, you have to do them one by one - there is no bulk insert API. The alternative is to use some kind of "HTTP multi-threading" approach since PHP doesn't do multi-threading.