Coding standards

WormBase Coding Standards and Style Guide

Quick Reference

Entity	Format
module	CamelCase
method (public)	lowercase, multiple words allowed, separated_by_underscores
method (private)	_lowercase, multiple words allowed, separated_by_underscores
variable (public)
variable (private)
constant	UPPER_CASE

Formatting and whitespace conventions

Function braces

Function braces begin on the line with their operator, and end on their own line indented to the same level.

foreach my $gene (@genes) {
      print "$gene\n";
                         }

# YES!
if (@genes) {
    print join("\n",@genes);
} else {
   print "We don't have any genes!\n";
}

# NO!
if (@genes)
{
    print join("\n",@genes);
} 
else {
   print "We don't have any genes!\n";
}

Hash keys

Hash keys are unquoted unless absolutely necessary. If quotes are necessary, you should change your hash key.

# YES!
$hash{carrot} = 'orange';

# NO!
$hash{'carrot'} = 'orange';

Extra white space

Use carriage return white-space and spaces around operator to improve readability. Avoid excessive use of white space that just increases code length.

# YES!
sub my_function {
   my ($self,@args) = @_;
   
   my $string = join(" ", @args) . ': this is an inane example.';
   return $string;
}

# NO!
sub my_function {
   my($self,@args)=@_;
   
  # Hard to read these lines without space between operators...

   my $string=join(" ", @args).': this is an inane example.';

   return $string;   
   # Why are there carriage returns below here and closing brace? Not necessary.

}

User Interface

Widget and field names

Widget and field names are specified in the application configuration. Since these names auto-vivify to actions -- and map to templates of the same name -- choose them carefully. Likewise, editing them requires changing the name of the template on the file system, too.

Widget names should preferably be short - a single word, and no more than three words. Field names can be more descriptive but no longer than five words.

Default widgets and fields

Identification

Each class should implement a default "Identification" widget. This widget is intended to provide the basic information about a given object. This replaces our non-standard use of Identification, General Information, or General Info in the old structure.

Each Identification widget should minimally include name and common_name. You need only include these fields in the configuration file - they will become automatically available to the appropriate controller. Over-ride common_name in the appropriate model to return the most appropriate common name for an object.

Naming Conventions

Variable names should reflect the content of the variable. Be appropriately verbose so that the variable contents are clear.

Abbreviations and acronyms should be UPPERCASE when used as a name:

print_HTML();

CSS variable names SHOULD follow the same conventions as public class variables.

Private class variables should be written using lowercase with a preceding underscore):

sub _my_private_function {
   my ($self,@args) = @_;
   ...
}

Variables with a large scope SHOULD have globally unambiguous names; ambiguity MAY be distinguished by module membership. Variables with small or private scope MAY have terse names.

Public names SHOULD be as clear as necessary and SHOULD avoid unclear shortenings and contractions:

get_BLAST_hits

NOT

gbh();

Specific Naming Conventions

Iterator variables SHOULD be called "i", "j", "k", etc.

Abbreviations in names SHOULD be avoided.

Files

Class or object-per-file guidelines are not yet determined.

Tabs (set to 4 spaces) SHOULD be used for indentation.

Variables

Variables SHOULD be initialized where they are declared and they SHOULD be declared in the smallest scope possible. A null initialization is acceptable.

Variables MUST never have a dual meaning.

Related variables of the same type CAN be declared in a common statement; unrelated variables SHOULD NOT be declared in the same statement.

Variables SHOULD be kept alive for as short a time as possible.

Loops / iterative declarations

Only loop control statements MUST be included in the "for" loop construction.

Conditionals

Complex conditional expressions SHOULD be avoided; use temporary boolean variables instead.

The nominal case SHOULD be put in the "if" part and the exception in the "else" part of an "if" statement.

Layout

Block statements.

Block layout SHOULD BE as illustrated below:

foreach (@items) {

   doSomething($_);

}

if statements SHOULD have the following form:

if (someCondition) {
    statements;
} elseif (someOtherCondition) {
    statements;
} else {
    statements;
}

for statements SHOULD have the following form:

for (initialization; condition; update) {
    statements;
}

A single statement if-else, while or for MUST NOT be written without brackets, but CAN be written on the same line:

if (condition) { statement; }
while (condition) { statement; }
for (intialization; condition; update){ statement; }

if/unless

conditionals CAN follow the test condition:

print @genes if (@genes > 10);

Whitespace

Conventional operators SHOULD be surrounded by a space (including ternary operators).

In addition:

Commas SHOULD be followed by a space.

Colons MAY be surrounded by a space.

Semi-colons in for statements SHOULD be followed by a space.

Semi-colons SHOULD NOT be preceded by a space.

Function calls and method calls SHOULD NOT be followed by a space. Example: do_something(arguments); // NOT do_something (arguments)

Statements and declarations SHOULD be aligned wherever this enhances readability.

Comments

Tricky code SHOULD not be commented, but rewritten.

All comments SHOULD be written in English.

Comments SHOULD be indented relative to their position in the code, preceding or to the right of the code in question.

Comments SHOULD be included to explain BLOCKS of code, to explain the point of the following block.

Comments SHOULD NOT be included for every single line of code.

Documentation stolen from: Jot wiki

General Information These provide descriptions for the function or object:

summary: A short statement of the purpose of the function or object description: An extended description of the function or object returns: A description of what the function returns (does not include a type) General Function Information function(){

 // summary: Soon we will have enough treasure to rule all of New Jersey.
 // description: Or we could just get a new roomate.
 //        Look, you go find him.  He don't yell at you.
 //        All I ever try to do is make him smile and sing around
 //        him and dance around him and he just lays into me.
 //        He told me to get in the freezer 'cause there was a carnival in there.
 // returns:  Look, a Bananarama tape!

} Object Function Information Has no description of what it returns {

 // summary: Dingle, engage the rainbow machine!
 // description: 
 //        Tell you what, I wish I was--oh my g--that beam,
 //        coming up like that, the speed, you might wanna adjust that.
 //        It really did a number on my back, there. I mean, and I don't
 //        wanna say whiplash, just yet, cause that's a little too far,
 //        but, you're insured, right?

} Function Assembler Information (defineWidget/declare) We can sometimes end up in situations where a function declaration is invisible, being created by the call. In this case, there's no way to associate our comments directly with the function. If you encouter this situation, the data can be associated through the passed object.

Note, this only works if there is no initializer function parameter. If there is, this will be ignored.

dojo.declare(

 "foo",
 null,
 {
   // summary: Phew, this sure is relaxing, Frylock.
   // description: 
   //        Thousands of years ago, before the dawn of
   //        man as we knew him, there was Sir Santa of Claus: an
   //        ape-like creature making crude and pointless toys out
   //        of dino-bones, hurling them at chimp-like creatures with
   //        crinkled hands regardless of how they behaved the
   //        previous year.
   // returns: Unless Carl pays tribute to the Elfin Elders in space.
 }

); Parameters Simple Types If you're only going to be describing the type of the object, you should do it in the main parameter definition block.

function(/*String*/ foo, /*int*/ bar)... Type Modifiers There are some modifiers you can add after the type ? means optional ... means the last parameter repeats indefinitely [] means an array function(/*String?*/ foo, /*int...*/ bar, /*String[]*/ baz)... Full Parameter Descriptions If you want to also add a description, you should move to the initial comment block.

The format for the general information is: *key *Descriptive sentence

The format for paramters and variables is: *key ~type~* Descriptive sentence

Where *key *and ~*type*~ can be surrounded by any non-alphanumeric characters.

function(foo, bar){

 // foo: String
 //        used for being the first parameter
 // bar: int
 //        used for being the second parameter

} Variables Instance variables, prototype variables and external variables can all be defined in the same way. There are many ways that a variable might get assigned to this function, and locating them all inside of the actual function they reference is the best way to not lose track of them, or accidentally comment them multiple times. function foo(){

 // myString: String
 // times: int
 //        How many times to print myString
 // separator: String
 //        What to print out in between myString*
 this.myString = "placeholder text";
 this.times = 5;

} foo.prototype.setString = function(myString){

 this.myString = myString;

} foo.prototype.toString = function(){

 for(int i = 0; i < this.times; i++){
   dojo.debug(this.myString);
   dojo.debug(foo.separator);
 }

} foo.separator = "====="; Variable Comments in an Object The parser takes the comments in between object values and applies the same rules as if they were in the initial comment block: {

 // key: String
 //        A simple value
 key: "value",
 // key2: String
 //        Another simple value

} Return Value Because a function can return multiple types, the types should be declared on the same line as the return statement, and the comment must be the last thing on the line. If all the return types are the same, the parser uses that return type. If they're different, the function is considered to return "mixed".

function(){

 if(arguments.length){
   return "You passed argument(s)"; // String
 }else{
   return false; // Boolean
 }

} Still Up for Discussion Pseudo-Code (implemented)

There are some instances where you might want an object or function to appear in documentation, but not in Dojo, nor in your build. To do this, start a comment block with /*=====. The number of = can be 5 or more. At the moment, this is only useful for declaring an object type that doesn't appear in code.

The parser simply replaces the /*===== and =====*/ with whitespace at the very start, so think of these blocks as if they were commented out.

/*===== module.pseudo.kwArgs = {

 // url: String
 //        The location of the file
 url: "",
 // mimeType: String
 //        text/html, text/xml, etc
 mimeType: ""

} =====*/

function(/*module.pseudo.kwArgs*/ kwArgs){

 dojo.debug(kwArgs.url);
 dojo.debug(kwArgs.mimeType);

} Using the Doctool locally If you are a developer who has marked their code up using this syntax and want to test to make sure it is correct, you can run the doctool yourself locally. See DocParserInstructions for details on how to do so.