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Merge pull request #22 from lambdacasserole/vertical-pipe-fix

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Restructure SMILES lookup services into chain of responsibility
This commit is contained in:
Saul Johnson
2017-08-27 19:47:29 +01:00
committed by GitHub
parent d4b470023a dd9925adb9
commit 33e5ead455
6 changed files with 412 additions and 120 deletions
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composer.json
+2 -1
View File
@@ -15,7 +15,8 @@
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composer.lock
Generated
+213 -82
View File
@@ -4,7 +4,7 @@
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"LGPL-2.1"
],
"authors": [
{
"name": "Todd Burry",
"email": "todd@vanillaforums.com",
"role": "developer"
}
],
"description": "A jQuery like html dom parser written in php.",
"keywords": [
"dom",
"ganon",
"php"
],
"time": "2016-01-14T20:55:00+00:00"
},
{
"name": "twig/twig",
"version": "v1.34.4",
"source": {
"type": "git",
"url": "https://github.com/twigphp/Twig.git",
"reference": "f878bab48edb66ad9c6ed626bf817f60c6c096ee"
},
"dist": {
"type": "zip",
"url": "https://api.github.com/repos/twigphp/Twig/zipball/f878bab48edb66ad9c6ed626bf817f60c6c096ee",
"reference": "f878bab48edb66ad9c6ed626bf817f60c6c096ee",
"shasum": ""
},
"require": {
"php": ">=5.3.3"
},
"require-dev": {
"psr/container": "^1.0",
"symfony/debug": "~2.7",
"symfony/phpunit-bridge": "~2.7"
"symfony/phpunit-bridge": "~3.3@dev"
},
"type": "library",
"extra": {
"branch-alias": {
"dev-master": "1.24-dev"
"dev-master": "1.34-dev"
}
},
"autoload": {
"psr-0": {
"Twig_": "lib/"
},
"psr-4": {
"Twig\\": "src/"
}
},
"notification-url": "https://packagist.org/downloads/",
@@ -1115,7 +1246,7 @@
"keywords": [
"templating"
],
"time": "2016-05-30T09:11:59+00:00"
"time": "2017-07-04T13:19:31+00:00"
}
],
"packages-dev": [],
src/CactusSmilesConverter.php
+57
View File
@@ -0,0 +1,57 @@
<?php
namespace Avogadrio;
use Condense\Database;
use \GuzzleHttp\Client;
/**
* Provides a conversion service between compound names and SMILES strings that uses a dedicated lookup service.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 06/08/2017
* @package Avogadrio
*/
class CactusSmilesConverter extends SmilesConverter
{
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings that uses a
* dedicated lookup service.
*
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
public function __construct($db = null, $fallback = null) {
parent::__construct($db, $fallback);
}
/**
* @inheritdoc
*/
public function nameToSmiles($name)
{
// Sanitize name for URLs.
$encoded = rawurlencode($name);
// Check if we've got the name cached already.
$cached = $this->getIfCached($encoded);
if ($cached !== null) {
return $cached;
}
// Convert chemical name to SMILES if we can using API.
$client = new Client(['verify' => false, 'exceptions' => false]);
$response = $client->request('GET', "https://cactus.nci.nih.gov/chemical/structure/$encoded/smiles");
// If request was successful.
if ($response->getStatusCode() === 200) {
$smiles = $response->getBody()->getContents();
if (self::isValidSmiles($smiles)) {
$this->cache($encoded, $smiles);
return $smiles;
}
}
return $this->fallback($name); // Fall back.
}
}
src/SmilesConverter.php
+65 -34
View File
@@ -3,16 +3,15 @@
namespace Avogadrio;
use Condense\Database;
use \GuzzleHttp\Client;
/**
* Provides a conversion service between compound names and SMILES strings.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 06/08/2017
* @since 27/08/2017
* @package Avogadrio
*/
class SmilesConverter
abstract class SmilesConverter
{
/**
* The compound name/SMILES cache database.
@@ -21,13 +20,22 @@ class SmilesConverter
*/
private $db;
/**
* The conversion service to fall back to in case of error.
*
* @var SmilesConverter
*/
private $fallback;
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings.
*
* @param Database $db the database in which to cache lookup results
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
public function __construct($db = null) {
protected function __construct($db, $fallback) {
$this->db = $db;
$this->fallback = $fallback;
}
/**
@@ -39,39 +47,62 @@ class SmilesConverter
return $this->db !== null;
}
/**
* Returns true if a given SMILES string is valid, otherwise returns false.
*
* @param string $smiles the SMILES string to check
* @return bool true if the string was valid, otherwise false
*/
protected static function isValidSmiles($smiles) {
return preg_match('/^[a-zA-Z0-9@%=\\\\\/\[\]\.\+\-\_\*\(\)]+$/', $smiles) ? true : false;
}
/**
* Returns a cached SMILES string from its corresponding compound name, if present.
*
* @param string $name the name of the compound to return
* @return string the SMILES structure of the compound, or null if not found
*/
protected function getIfCached($name) {
if ($this->isCacheEnabled()) {
$cachedSmiles = $this->db->get('smiles', 'name', $name);
if ($cachedSmiles !== null) {
return $cachedSmiles;
}
}
return null;
}
/**
* Caches a compound name against its corresponding SMILES string.
*
* @param string $name the compound name
* @param string $smiles the corresponding SMILES string
*/
protected function cache($name, $smiles) {
if ($this->isCacheEnabled()) {
$this->db->insert(['name' => $name, 'smiles' => $smiles]); // Cache name for future.
}
}
/**
* Falls back to another SMILES conversion service.
*
* @param string $name the compound name to convert
* @return null|string the converted compound name or null if not found
*/
protected function fallback($name) {
if ($this->fallback === null) {
return null;
}
return $this->fallback->nameToSmiles($name);
}
/**
* Converts a compound name to SMILES notation.
*
* @param string $name the name of the compound
* @return null|string the SMILES notation for the named compound or null if not found
*/
public function nameToSmiles($name)
{
// Sanitize name for URLs.
$encoded = rawurlencode($name);
// Check if we've got the name cached already.
if ($this->isCacheEnabled()) {
$cachedSmiles = $this->db->get('smiles', 'name', $encoded);
if ($cachedSmiles !== null) {
return $cachedSmiles;
}
}
// Convert chemical name to SMILES if we can using API.
$client = new Client(['verify' => false, 'exceptions' => false]);
$response = $client->request('GET', "https://cactus.nci.nih.gov/chemical/structure/$encoded/smiles");
// If request was successful.
if ($response->getStatusCode() === 200) {
$smiles = $response->getBody()->getContents();
if ($this->isCacheEnabled()) {
$this->db->insert(['name' => $encoded, 'smiles' => $smiles]); // Cache name for future.
}
return $smiles;
}
// Request failed.
return null;
}
public abstract function nameToSmiles($name);
}
src/WikipediaSmilesConverter.php
+71
View File
@@ -0,0 +1,71 @@
<?php
namespace Avogadrio;
use Condense\Database;
use \GuzzleHttp\Client;
use pQuery;
/**
* Provides a conversion service between compound names and SMILES strings that scrapes SMILES strings from Wikipedia.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 27/08/2017
* @package Avogadrio
*/
class WikipediaSmilesConverter extends SmilesConverter
{
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings that scrapes SMILES
* strings from Wikipedia.
*
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
public function __construct($db = null, $fallback = null) {
parent::__construct($db, $fallback);
}
/**
* @inheritdoc
*/
public function nameToSmiles($name)
{
// Sanitize name for URLs.
$encoded = str_replace(' ', '_', $name);
// Check if we've got the name cached already.
$cached = $this->getIfCached($encoded);
if ($cached !== null) {
return $cached;
}
// Get Wikipedia page for compound.
$client = new Client();
$response = $client->request('GET', "https://en.wikipedia.org/wiki/$encoded");
// If there is a page.
if ($response->getStatusCode() === 200) {
// Parse page into DOM.
$page = $response->getBody()->getContents();
$dom = pQuery::parseStr($page);
// Get all hyperlinks.
$links = $dom->select('a');
// Look for the SMILES hyperlink.
foreach ($links as $link) {
if (strstr($link->text(), 'SMILES')) {
$smiles = trim($link->parent->getNextSibling()->text()); // Get actual SMILES string.
if (self::isValidSmiles($smiles)) {
$this->cache($encoded, $smiles);
return $smiles;
}
}
}
}
return $this->fallback($name); // Fall back.
}
}
web/index.php
+4 -3
View File
@@ -5,10 +5,10 @@ require_once __DIR__ . '/../vendor/autoload.php';
use Symfony\Component\HttpFoundation\JsonResponse;
use Symfony\Component\HttpFoundation\Request;
use Symfony\Component\HttpFoundation\Response;
use Symfony\Component\HttpKernel\HttpKernelInterface;
use Condense\Database;
use Avogadrio\SmilesConverter;
use Avogadrio\CactusSmilesConverter;
use Avogadrio\WikipediaSmilesConverter;
use Avogadrio\MoleculeRenderer;
$app = new Silex\Application();
@@ -20,7 +20,8 @@ $app = new Silex\Application();
$config = Spyc::YAMLLoad(__DIR__ . '/../config/config.yaml');
// Services.
$smilesConverter = new SmilesConverter(new Database('names', __DIR__ . '/../db'));
$wikiSmilesConverter = new WikipediaSmilesConverter(new Database('names_wiki', __DIR__ . '/../db'));
$smilesConverter = new CactusSmilesConverter(new Database('names', __DIR__ . '/../db'), $wikiSmilesConverter);
$moleculeRenderer = new MoleculeRenderer($config['sourire_service']);
$moleculeRenderer->setRenderChiralLabels(false); // Disable chiral labels.