@@ -11,6 +11,7 @@ require dirname( __FILE__ ) . '/chemcaster/Registration.php'; require dirname( __FILE__ ) . '/chemcaster/Substance.php'; require dirname( __FILE__ ) . '/chemcaster/Structure.php'; require dirname( __FILE__ ) . '/chemcaster/Execution.php'; +require dirname( __FILE__ ) . '/chemcaster/Component.php'; require dirname( __FILE__ ) . '/chemcaster/Log.php'; require dirname( __FILE__ ) . '/chemcaster/Image.php'; lib/chemcaster.php @@ -9,12 +9,17 @@ */ class Chemcaster_Archive extends Chemcaster_Item { - protected $_links = array( - 'zipfile' => '', - 'index' => '', - 'destroy' => '', - 'registry' => '' - ); + /** + * Archive Compiled + * @var boolean + */ + public $done; + + /** + * archive initiation + * @var datetime + */ + public $created_at; } ?> lib/chemcaster/Archive.php @@ -9,8 +9,9 @@ */ class Chemcaster_Component extends Chemcaster_Item { - protected $_links = array( - 'structure' => '', - 'substance' => '' - ); + /** + * Component Multiplier + * @var number + */ + public $multiplier; } lib/chemcaster/Component.php @@ -9,18 +9,43 @@ */ class Chemcaster_Execution extends Chemcaster_Item implements Iterator, ArrayAccess { - protected $_results = array(); + protected $results = array(); /** * Used by Iterator Interface * @var int */ private $_position = 0; - - protected $_links = array( - 'index' => '', - 'executable' => '' - ); + + /** + * Cursor + * @var string + */ + public $cursor; + + /** + * Reverse + * @var boolean + */ + public $reverse; + + /** + * Max results + * @var number + */ + public $maximum_results; + + /** + * next cursor + * @var string + */ + public $next_cursor; + + /** + * previous cursor + * @var string + */ + public $previous_cursor; /** * Gets the count of items in this index lib/chemcaster/Execution.php @@ -9,7 +9,30 @@ */ class Chemcaster_Image extends Chemcaster_Item { - protected $_links = array( 'imageable' => '' ); + /** + * Width of Image + * @var number + */ + public $width; + + /** + * Height of Image + * @var number + */ + public $height; + + /** + * Media type + * @var string (image/png) + */ + public $format; + + /** + * Base64 encoding + * @var string + */ + public $data; + } ?> lib/chemcaster/Image.php @@ -13,7 +13,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar * Stores the itemized resource links (if any) * @var array */ - protected $_items = array(); + protected $items = array(); /** * Used by Iterator Interface @@ -21,8 +21,6 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ private $_position = 0; - protected $_links = array( 'parent' => '', 'create' => '', 'previous_page' => '', 'next_page' => '' ); - /** * Create method for give index * @param array $args [see api for appropriate keys] @@ -30,12 +28,20 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar * @access public * @throws Chemcaster_CreationException */ - public function create( $args ) + public function create( $args = NULL ) { - $link = $this->_links['create']; + if( FALSE === isset($this->links['create']) ) + { + throw new Chemcaster_MethodNotAllowed("Create not allowed here"); + return; + } + + if( NULL === $args ) $args = new stdClass; + + $link = $this->links['create']; $rep_name = strtolower( $link->getRepresentationName() ); + $json_args = json_encode( array( $rep_name => $args) ); - $ret_json = $this->_transporter->post( $link, $json_args ); if( FALSE === $ret_json ) @@ -62,7 +68,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function size() { - return count( $this->_items ); + return count( $this->items ); } /** @@ -78,7 +84,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function current() { - $link = $this->_items[$this->_position]; + $link = $this->items[$this->_position]; return $this->_factory($link); } @@ -103,7 +109,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function valid() { - return isset( $this->_items[$this->_position] ); + return isset( $this->items[$this->_position] ); } @@ -112,7 +118,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function offsetSet($offset, $value) { - $this->_items[$offset] = $value; + $this->items[$offset] = $value; } /** @@ -120,7 +126,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function offsetExists($offset) { - return isset($this->_items[$offset]); + return isset($this->items[$offset]); } /** @@ -128,7 +134,7 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function offsetUnset($offset) { - unset($this->_items[$offset]); + unset($this->items[$offset]); } /** @@ -136,9 +142,9 @@ class Chemcaster_Index extends Chemcaster_Representation implements Iterator, Ar */ public function offsetGet($offset) { - if( TRUE === isset($this->_items[$offset]) ) + if( TRUE === isset($this->items[$offset]) ) { - $link = $this->_items[$offset]; + $link = $this->items[$offset]; return $this->_factory($link); } else lib/chemcaster/Index.php @@ -17,13 +17,13 @@ class Chemcaster_Item extends Chemcaster_Representation */ public function update( $args ) { - if( FALSE === isset($this->_links['update']) ) + if( FALSE === isset($this->links['update']) ) { throw new Chemcaster_MethodNotAllowed("Update not allowed here"); return; } - $link = $this->_links['update']; + $link = $this->links['update']; $rep_name = strtolower( $link->getRepresentationName() ); $json_args = json_encode( array( $rep_name => $args) ); @@ -54,13 +54,13 @@ class Chemcaster_Item extends Chemcaster_Representation */ public function destroy( ) { - if( FALSE === isset($this->_links['destroy']) ) + if( FALSE === isset($this->links['destroy']) ) { throw new Chemcaster_MethodNotAllowed("Destroy not allowed here"); return; } - $link = $this->_links['destroy']; + $link = $this->links['destroy']; $rep_name = strtolower( $link->getRepresentationName() ); $ret_json = $this->_transporter->delete( $link ); lib/chemcaster/Item.php @@ -9,18 +9,25 @@ */ class Chemcaster_Log extends Chemcaster_Item implements Iterator, ArrayAccess { - protected $_events = array(); + protected $events = array(); /** * Used by Iterator Interface * @var int */ private $_position = 0; - - protected $_links = array( - 'registry' => '', - 'index' => '' - ); + + /** + * Created + * @var datetime + */ + public $created_at; + + /** + * Number of seconds covered by this log + * @var number + */ + public $interval; /** * Gets the count of items in this index lib/chemcaster/Log.php @@ -9,12 +9,11 @@ */ class Chemcaster_Query extends Chemcaster_Item { - protected $_links = array( - 'index' => '', - 'images' => '', - 'executions' => '', - 'registry' => '' - ); + /** + * Query serialization + * @var string + */ + public $serialization; } ?> lib/chemcaster/Query.php @@ -9,11 +9,9 @@ */ class Chemcaster_Registration extends Chemcaster_Item { - protected $_links = array( - 'index' => '', - 'update' => '', - 'destroy' => '', - 'registry' => '', - 'substance' => '' - ); + /** + * Array of templates + * @var array + */ + public $templates = array(); } lib/chemcaster/Registration.php @@ -9,14 +9,15 @@ */ class Chemcaster_Registry extends Chemcaster_Item { - protected $_links = array( - 'service' => '', - 'substances' => '', - 'structures' => '', - 'queries' => '', - 'registrations' => '', - 'index' => '', - 'update' => '', - 'destroy' => '' - ); + /** + * Registry Name + * @var string + */ + public $name; + + /** + * Registry can be deleted + * @var boolean + */ + public $deletable; } lib/chemcaster/Registry.php @@ -19,7 +19,7 @@ class Chemcaster_Representation * Holds array of links. Override in sub classes for specific Representations * @var array */ - protected $_links = array(); + protected $links = array(); /** * Class constructor @@ -55,27 +55,22 @@ class Chemcaster_Representation { foreach( $value as $k => $v ) { - $this->$k = $v; + if( TRUE === is_array($this->$k) ) + foreach( $v as $vv ) + array_push($this->$k, $vv); + else + $this->$k = $v; } } - else if( 'items' === $name ) + else if( TRUE === is_array($value) ) { + $this->$name = array(); foreach( $value as $v ) - $this->_items[] = new Chemcaster_Link($v->name, $v->uri, $v->media_type); + $this->{$name}[] = new Chemcaster_Link($v->name, $v->uri, $v->media_type); } - else if( 'results' === $name) + else { - foreach( $value as $v ) - $this->_results[] = new Chemcaster_Link($v->name, $v->uri, $v->media_type); - } - else if( 'events' === $name) - { - foreach( $value as $v ) - $this->_events[] = new Chemcaster_Link($v->name, $v->uri, $v->media_type); - } - else if( TRUE === isset($this->_links[$name]) ) - { - $this->_links[$name] = new Chemcaster_Link($value->name, $value->uri, $value->media_type); + $this->links[$name] = new Chemcaster_Link($value->name, $value->uri, $value->media_type); } } } @@ -88,9 +83,9 @@ class Chemcaster_Representation */ public function __get( $property ) { - if( TRUE === array_key_exists($property, $this->_links) && '' !== $this->_links[$property] ) + if( TRUE === array_key_exists($property, $this->links) && '' !== $this->links[$property] ) { - $link = $this->_links[$property]; + $link = $this->links[$property]; return $this->_factory( $link ); } else lib/chemcaster/Representation.php @@ -10,10 +10,10 @@ class Chemcaster_Service extends Chemcaster_Representation { /** - * The links for this rep. - * @var array + * Version + * @var string */ - protected $_links = array( 'registries' => '' ); + public $version; /** * Sets up initial connection and returns the Chemcaster_Service object lib/chemcaster/Service.php @@ -9,10 +9,15 @@ */ class Chemcaster_Structure extends Chemcaster_Item { - protected $_links = array( - 'index' => '', - 'images' => '', - 'components' => '', - 'registry' => '' - ); + /** + * Serialization + * @var string + */ + public $serialization; + + /** + * inchi + * @var string + */ + public $inchi; } lib/chemcaster/Structure.php @@ -9,11 +9,15 @@ */ class Chemcaster_Substance extends Chemcaster_Item { - protected $_links = array( - 'index' => '', - 'registry' => '', - 'registration' => '', - 'components' => '', - 'images' => '' - ); + /** + * Substance serialization + * @var string + */ + public $serialization; + + /** + * Substance INCHI + * @var string + */ + public $inchi; } lib/chemcaster/Substance.php @@ -20,7 +20,7 @@ class RegistryTest extends PHPUnit_Framework_TestCase ->will($this->returnValue('{ "registry": { "name": "bar", - "deleteable": false + "deletable": false } }')); @@ -44,9 +44,9 @@ class RegistryTest extends PHPUnit_Framework_TestCase $this->assertSame('bar', $this->registry->name); } - public function testGetDeleteable() + public function testGetDeletable() { - $this->assertSame(false, $this->registry->deleteable); + $this->assertSame(false, $this->registry->deletable); } } tests/RegistryTest.php @@ -20,8 +20,7 @@ class StructureTest extends PHPUnit_Framework_TestCase ->method('get') ->will($this->returnValue('{ "structure": { - "name": "name", - "molfile": "molfile", + "serialization": "serialization", "inchi": "inchi" } }')); @@ -43,14 +42,9 @@ class StructureTest extends PHPUnit_Framework_TestCase $this->assertTrue('Chemcaster_Structure' == get_class($this->structure)); } - public function testStructureName() + public function testStructureSerialization() { - $this->assertSame('name', $this->structure->name); - } - - public function testStructureMolfile() - { - $this->assertSame('molfile', $this->structure->molfile); + $this->assertSame('serialization', $this->structure->serialization); } public function testStructureInchi() tests/StructureTest.php 254d5edb32316415e245b50dbda501ead74846a8 Rob Apodaca rob.apodaca@gmail.com http://github.com/metamolecular/chemcaster-php/commit/c5bf98101f8dd919948311da9fbb23b138c82f9a c5bf98101f8dd919948311da9fbb23b138c82f9a 2009-09-23T20:47:38-07:00 2009-09-23T20:47:38-07:00 Using attributes in sub-classes rather than links 38162a02a818e1f393d53e6aafa64c65c0d6131e Rob Apodaca rob.apodaca@gmail.com