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Algorithm of the Week: Aho-Corasick String Matching Algorithm in Haskell
let’s say you have a large piece of text and a dictionary of keywords. how do you quickly locate all the keywords? aho-corasick algorithm diagram well, there are many ways really, you could even iterate through the whole thing and compare words to keywords. but it turns out that’s going to be very slow. at least o(n_keywords * n_words) complexity. essentially you’re making as many passes over the text as your dictionary is big. in 1975 a couple of ibm researchers – alfred aho and margaret corasick – discovered an algorithm that can do this in a single pass. the aho-corasick string matching algorithm . i implemented it in haskell and it takes 0.005s to find 8 different keywords in oscar wilde’s the nightingale and the rose – a 12kb text. a quick naive keyword search implemented in python takes 0.023s . not a big difference practically speaking, but imagine a situation with megabytes of text and thousands of words in the dictionary. the authors mention printing out the result as a major bottleneck in their assessment of the algorithm. yep, printing . the aho-corasick algorithm at the core of this algorithm are three functions: the three functions of aho-corasick algorithm a parser based on a state machine, which maps (state, char) pairs to states and occasionally emits an output. this is called the goto function a failure function, which tells the goto function which state to jump into when the character it just read doesn’t match anything an output function, which maps states to outputs – potentially more than one per state the algorithm works in two stages. it will first construct the goto, failure and output functions. the complexity of this operation hinges solely on the size of our dictionary. then it iterates over the input text to produce all the matches. using state machines for parsing text is a well known trick – the real genius of this algorithm rests in that failure function if you ask me. it makes lateral transitions between states when the algorithm climbs itself into a wall. say you have she and hers in the dictionary. the goto machine eats your input string one character at the time. let’s say it’s already read s h . the next input is an e so it outputs she and reaches a final state. next it reads an r , but the state didn’t expect any more inputs, so the failure function puts us on the path towards hers . this is a bit tricky to explain in text, i suggest you look at the picture from the original article and look at what’s happening. my haskell implementation the first implementation i tried, relied on manully mapping inputs to outputs for the goto, failure and output functions by using pattern recognition. not very pretty, extremely hardcoded, but it worked and was easy to make. building the functions dynamically proved a bit trickier. type goto = map (int, char) int type failure = map int int type output = map int [string] first off, we build the goto function. -- builds the goto function build_goto::goto -> string -> (goto, string) build_goto m s = (add_one 0 m s, s) -- adds one string to goto function add_one::int -> goto -> [char] -> goto add_one _ m [] = m add_one state m (c:rest) | member key m = add_one (frommaybe 0 $ map.lookup key m) m rest | otherwise = add_one max (map.insert key max m) rest where key = (state, c) max = (size m)+1 essentially this builds a flattened prefix tree in a hashmap of (state, char) pairs mapping to the next state. it makes sure to avoid adding new edges to the three as much as possible. the reason it’s not simply a prefix tree are those lateral transitions; doing them in a tree would require backtracking and repeating of steps, so we haven’t achieved anything. once we have the goto function, building the output is trivial. -- builds the output function build_output::(?m::goto) => [string] -> output build_output [] = empty build_output (s:rest) = map.insert (fin 0 s) (list.filter (\x -> elem x dictionary) $ list.tails s) $ build_output rest -- returns the state in which an input string ends without using failures fin::(?m::goto) => int -> [char] -> int fin state [] = state fin state (c:rest) = fin next rest where next = frommaybe 0 $ map.lookup (state, c) ?m we are essentially going over the dictionary, finding the final state for each word and building a hash table mapping final states to their outputs. building the failure function was trickiest, because we need a way to iterate over the depths at which nodes are position in the goto state machine. but we threw that info away by using a hashmap. -- tells us which nodes in the goto state machine are at which traversal depth nodes_at_depths::(?m::goto) => [[int]] nodes_at_depths = list.map (\i -> list.filter (>0) $ list.map (\l -> if i < length l then l!!i else -1) paths) [0..(maximum $ list.map length paths)-1] where paths = list.map (path 0) dictionary we now have a list of lists, that tells us at which depth certain nodes are. -- builds the failure function build_fail::(?m::goto) => [[int]] -> int -> failure build_fail nodes 0 = fst $ mapaccuml (\f state -> (map.insert state 0 f, state)) empty (nodes!!0) build_fail nodes d = fst $ mapaccuml (\f state -> (map.insert state (decide_fail state lower) f, state)) lower (nodes!!d) where lower = build_fail nodes (d-1) -- inner step of building the failure function decide_fail::(?m::goto) => int -> failure -> int decide_fail state lower = findwithdefault 0 (s, c) ?m where (s', c) = key' state $ assocs ?m s = findwithdefault 0 s' lower -- gives us the key associated with a certain state (how to get there) key'::int -> [((int, char), int)] -> (int, char) key' _ [] = (-1, '_') -- this is ugly, being of maybe type would be better key' state ((k, v):rest) | state == v = k | otherwise = key' state rest here we are going over the list of nodes at depths and deciding what the failure should be for each depth based on the failures of depth-1. at depth zero, all failures go to the zeroth state. an important part of this process was inverting the goto hashmap so values point to keys, which is essentially what the key’ function does. finally, we can use the whole algorithm like this: main = do let ?m = fst $ mapaccuml build_goto empty dictionary let ?f = build_fail nodes_at_depths $ (length $ nodes_at_depths)-1 ?out = build_output dictionary print $ ahocorasick text a bit more involved than the usual example of haskell found online, it’s still pretty cool you can see the whole code on github here .
March 19, 2013
by Swizec Teller
· 22,068 Views
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Binding to JSON & XML - Handling Collections
One of EclipseLink JAXB (MOXy)'s strengths is the ability to map an object model to both JSON and XML with a single set of metadata. The one weakness had been that you needed to compromise on the JSON key or XML element for collection properties. I'm happy to say that this issue has been solved in EclipseLink 2.5 (and EclipseLink 2.4.2), and I will demonstrate below with an example. You can try this out today by downloading an EclipseLink 2.5.0 (or EclipseLink 2.4.2) nightly build starting on March 15, 2013 from: http://www.eclipse.org/eclipselink/downloads/nightly.php Domain Model By default a JAXB (JSR-222) implementation will not output a grouping element around collection data. This can be done through the use of the @XmlElementWrapper annotation (see: JAXB & Collection Properties). This grouping element often has a plural name and is a better fit for the key of a JSON array than the repeating element defined by the @XmlElement annotation is. package blog.json.collections; import java.util.*; import javax.xml.bind.annotation.*; @XmlRootElement @XmlType(propOrder={"name", "emailAddresses"}) public class Customer { private String name; private List emailAddresses = new ArrayList(); public String getName() { return name; } public void setName(String name) { this.name = name; } @XmlElementWrapper(name="email-addresses") @XmlElement(name="email-address") public List getEmailAddresses() { return emailAddresses; } public void setEmailAddresses(List<'String> emailAddresses) { this.emailAddresses = emailAddresses; } } Demo We will specify the JSON_WRAPPER_AS_ARRAY_NAME property with a true value to tell MOXy that it should use the grouping element as the name for the JSON array value. Then we will use the same Marshaller to output the same object to both XML and JSON. package blog.json.collections; import java.util.*; import javax.xml.bind.*; import org.eclipse.persistence.jaxb.MarshallerProperties; public class Demo { public static void main(String[] args) throws Exception { Customer customer = new Customer(); customer.setName("Jane Doe"); customer.getEmailAddresses().add("[email protected]"); customer.getEmailAddresses().add("[email protected]"); Map properties = new HashMap(1); properties.put(MarshallerProperties.JSON_WRAPPER_AS_ARRAY_NAME, true); JAXBContext jc = JAXBContext.newInstance(new Class[] {Customer.class}, properties); Marshaller marshaller = jc.createMarshaller(); marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // Output XML marshaller.marshal(customer, System.out); // Output JSON marshaller.setProperty(MarshallerProperties.MEDIA_TYPE, "application/json"); marshaller.marshal(customer, System.out); } } XML Output Below is the XML output from running the demo code. We see that email-addresses is marshalled as the grouping element which contains an email-address element for each item in the collection. Jane Doe [email protected] [email protected] JSON Output The following JSON output is produced from the same metadata. The only difference is that we told MOXy to use the grouping element as the name for JSON array values. { "customer" : { "name" : "Jane Doe", "email-addresses" : [ "[email protected]", "[email protected]" ] } } JAX-RS You can easily use MOXy as your JSON-binding provider in a JAX-RS environment (see: MOXy as your JAX-RS JSON Provider - MOXyJsonProvider). You can specify that the grouping element should be used as the JSON array name with the wrapperAsArrayName property on MOXyJsonProvider. package blog.json.collections; import java.util.*; import javax.ws.rs.core.Application; import org.eclipse.persistence.jaxb.rs.MOXyJsonProvider; public class CustomerApplication extends Application { @Override public Set> getClasses() { HashSet> set = new HashSet>(1); set.add(CustomerService.class); return set; } @Override public Set
March 18, 2013
by Blaise Doughan
· 8,664 Views
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Client For ActiveMQ
This Post explains Topics in Active MQ (Message Broker) with Subscribing and Publishing. For this we will write two java clients. As we did for wso2 Message Broker TopicSubscriber.java to Subcribe for messages TopicPublisher.java to to Publish the messages Let's Start. [1] Get Active MQ from http://activemq.apache.org/download.html [1.1] Start Active MQ from \bin\activemq.bat You can see the started server form http://localhost:8161/admin/ [2] Create Porject "Client" on IDE that you preferred [3] Add activemq-all-5.7.0.jar to lib Dir in the project (activemq-all-5.7.0.jar can be found in root folder) [4] Creat class "TopicSubscriber.java" to Subcribe for messages package simple; import java.util.Properties; import javax.jms.JMSException; import javax.jms.Message; import javax.jms.MessageListener; import javax.jms.Session; import javax.jms.TextMessage; import javax.jms.Topic; import javax.jms.TopicConnection; import javax.jms.TopicConnectionFactory; import javax.jms.TopicSession; import javax.naming.InitialContext; import javax.naming.NamingException; public class TopicSubscriber { private String topicName = "news.sport"; private String initialContextFactory = "" +"org.apache.activemq.jndi.ActiveMQInitialContextFactory"; private String connectionString = "tcp://" +"localhost:61616"; private boolean messageReceived = false; public static void main(String[] args) { TopicSubscriber subscriber = new TopicSubscriber(); subscriber.subscribeWithTopicLookup(); } public void subscribeWithTopicLookup() { Properties properties = new Properties(); TopicConnection topicConnection = null; properties.put("java.naming.factory.initial", initialContextFactory); properties.put("connectionfactory.QueueConnectionFactory", connectionString); properties.put("topic." + topicName, topicName); try { InitialContext ctx = new InitialContext(properties); TopicConnectionFactory topicConnectionFactory = (TopicConnectionFactory) ctx .lookup("QueueConnectionFactory"); topicConnection = topicConnectionFactory.createTopicConnection(); System.out .println("Create Topic Connection for Topic " + topicName); while (!messageReceived) { try { TopicSession topicSession = topicConnection .createTopicSession(false, Session.AUTO_ACKNOWLEDGE); Topic topic = (Topic) ctx.lookup(topicName); // start the connection topicConnection.start(); // create a topic subscriber javax.jms.TopicSubscriber topicSubscriber = topicSession .createSubscriber(topic); TestMessageListener messageListener = new TestMessageListener(); topicSubscriber.setMessageListener(messageListener); Thread.sleep(5000); topicSubscriber.close(); topicSession.close(); } catch (JMSException e) { e.printStackTrace(); } catch (NamingException e) { e.printStackTrace(); } catch (InterruptedException e) { e.printStackTrace(); } } } catch (NamingException e) { throw new RuntimeException("Error in initial context lookup", e); } catch (JMSException e) { throw new RuntimeException("Error in JMS operations", e); } finally { if (topicConnection != null) { try { topicConnection.close(); } catch (JMSException e) { throw new RuntimeException( "Error in closing topic connection", e); } } } } public class TestMessageListener implements MessageListener { public void onMessage(Message message) { try { System.out.println("Got the Message : " + ((TextMessage) message).getText()); messageReceived = true; } catch (JMSException e) { e.printStackTrace(); } } } } [5] Creat class "TopicPublisher.java" to to Publish the messages package simple; import javax.jms.*; import javax.naming.InitialContext; import javax.naming.NamingException; import java.util.Properties; public class TopicPublisher { private String topicName = "news.sport"; private String initialContextFactory = "org.apache.activemq" +".jndi.ActiveMQInitialContextFactory"; private String connectionString = "tcp://localhost:61616"; public static void main(String[] args) { TopicPublisher publisher = new TopicPublisher(); publisher.publishWithTopicLookup(); } public void publishWithTopicLookup() { Properties properties = new Properties(); TopicConnection topicConnection = null; properties.put("java.naming.factory.initial", initialContextFactory); properties.put("connectionfactory.QueueConnectionFactory", connectionString); properties.put("topic." + topicName, topicName); try { // initialize // the required connection factories InitialContext ctx = new InitialContext(properties); TopicConnectionFactory topicConnectionFactory = (TopicConnectionFactory) ctx .lookup("QueueConnectionFactory"); topicConnection = topicConnectionFactory.createTopicConnection(); try { TopicSession topicSession = topicConnection.createTopicSession( false, Session.AUTO_ACKNOWLEDGE); // create or use the topic System.out.println("Use the Topic " + topicName); Topic topic = (Topic) ctx.lookup(topicName); javax.jms.TopicPublisher topicPublisher = topicSession .createPublisher(topic); String msg = "Hi, I am Test Message"; TextMessage textMessage = topicSession.createTextMessage(msg); topicPublisher.publish(textMessage); System.out.println("Publishing message " +textMessage); topicPublisher.close(); topicSession.close(); Thread.sleep(20); } catch (InterruptedException e) { e.printStackTrace(); } } catch (JMSException e) { throw new RuntimeException("Error in JMS operations", e); } catch (NamingException e) { throw new RuntimeException("Error in initial context lookup", e); } } } [6] Firstly Run "TopicSubscriber.java" and then run "TopicPublisher.java" Here is out put from both TopicSubscriber:: Create Topic Connection for Topic news.sport Got the Message : Hi, I am Test Message TopicPublisher:: Use the Topic news.sport Publishing message ActiveMQTextMessage {commandId = 0, responseRequired = false, messageId = ID:Madhuka-THINK-51683-1359787878456-1:1:1:1:1, originalDestination = null, originalTransactionId = null, producerId = null, destination = topic://news.sport, transactionId = null, expiration = 0, timestamp = 1359787878729, arrival = 0, brokerInTime = 0, brokerOutTime = 0, correlationId = null, replyTo = null, persistent = true, type = null, priority = 4, groupID = null, groupSequence = 0, targetConsumerId = null, compressed = false, userID = null, content = null, marshalledProperties = null, dataStructure = null, redeliveryCounter = 0, size = 0, properties = null, readOnlyProperties = false, readOnlyBody = false, droppable = false, text = Hi, I am Test Message} [More] Here is full message that we have send to TopicSubscriber. We can get that any parameter in above. Here is sample to get TimeStamp and ID from JMS message. public class TestMessageListener implements MessageListener { public void onMessage(Message message) { try { System.out.println("Got the Message TimeStamp: " + message.getJMSTimestamp()); System.out.println("Got the Message JMS ID : " + message.getJMSMessageID()); messageReceived = true; } catch (JMSException e) { e.printStackTrace(); } } } Now go to ActiveMQ server at http://localhost:8161/admin/ See that Topic and message count for that topic. Now you time to check more in 'Active MQ'
March 16, 2013
by Madhuka Udantha
· 18,388 Views
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Bring Ruby VCR to Javascript testing with Capybara and puffing-billy
Let’s say you are writing an application in Ruby. You are probably talking to every API under the sun and are happily writing tests to make sure your code isn’t failing. Because you don’t want to rely on 3rd parties or an internet connection to make your tests pass or fail you mock everything with let’s say, Webmock. This also makes your tests much much faster. After all even the fastest internet is much slower than the processor talking to its memory. If you’re too lazy to mock out every API under the sun, you might use VCR to record requests and play them back later. The main advantage being, you don’t have to worry about meticulously reimplementing everything, and you can nuke the recordings at any time to make sure your code still works against the real API. Life is good. Enter Javascript, stage left Then Javascript becomes more and more prominent. Suddenly your application’s logic is shifting from backend to browser and before you know it, most of your tests are pretty irrelevant. You’re fine for a while with Capybara or Cucumber. Launch a headless browser, click around the site from the comfort of RSpec, make sure users see what they’re supposed to. Balance restored. Then you add a payment form. Or something. Suddenly your frontend is talking to an API. In case of Stripe or Balanced it’s even a feature. A great benefit for the user. jQuery(function($) { $('#payment-form').submit(function(event) { var $form = $(this); // Disable the submit button to prevent repeated clicks $form.find('button').prop('disabled', true); Stripe.createToken($form, stripeResponseHandler); // Prevent the form from submitting with the default action return false; }); }); Well that sucks, you’re suddenly back to square one. Your tests take minutes to execute. Your tests fail without an internet connection. Your tests rely on some 3rd party service being up. Your tests suck. Who wants to code when running ~5 tests takes 3 minutes? Nobody. Enter puffing-billy, stage right The problem is that neither Webmock nor VCR can handle requests originating in a browser because they happen in a different thread and they can’t mess around with those. Luckily, a year ago Olly Smith, created puffing-billy. The idea was great – spin up a web proxy, tell your headless browser to use it, when your code makes a request it will go through the proxy, which will try to use a Webmock to handle it, otherwise pass it on to the vast internet. But who wants to mock everything out manually? Over the past few weeks I set upon the task of fixing this problem and restoring sanity to my life. Good tests are transparent to the application and I’ll be damned if I use any of the suggested solutions on the internet like “Well you just put a switch in your code that knows if you’re in a test and then doesn’t talk to Stripe” Screw that. This morning I submitted a pull request to puffing-billy. I added the ability for puffing-billy to behave like it was VCR, but for your browser. When a request is made, it gets cached. The cache is then persisted between sessions, and requests are played back to the browser as needed. It’s not as sophisticated as VCR just yet, but it gets the job done and my test runtime has gone from 3 minutes to just under a minute. That’s a big deal in my book! The caching even understands that some URL’s are needlessly different on every request (social buttons, analytics etc.) so you can configure it to normalize those requests to a single recording that is played back every time. Your tests don’t really rely on gAnalytics working right? And the best thing is, you don’t even have to change your tests. You add something like this in your spec_helper.rb: Billy.configure do |c| c.cache = true c.ignore_params = ["http://www.google-analytics.com/__utm.gif", "http://b.siftscience.com/i.gif", "https://r.twimg.com/jot", "http://p.twitter.com/t.gif", "http://p.twitter.com/f.gif", "http://www.facebook.com/plugins/like.php", "https://www.facebook.com/dialog/oauth", "http://cdn.api.twitter.com/1/urls/count.json"] c.persist_cache = true c.cache_path = 'spec/req_cache/' end # need to call this because of a race condition between persist_cache # being set and the proxy being loaded for the first time Billy.proxy.restore_cache Capybara.javascript_driver = :poltergeist_billy A test for the payment form looks the same as usual: scenario "physical product" do product = start_buying build(:product, :physical, user: @seller, active: true) VCR.use_cassette('Balanced/purchase_with_cc') do within '#new_order' do fill_in 'order_email', with: Faker::Internet.safe_email fill_in_address fill_in_card click_on 'Buy Now' end page.should have_css('#receipt', :visible => true) end validate_receipt product, @seller end Puffing-billy will transparently cache every requests the browser makes and VCR records any requests made by your backend logic. It’s pretty sweet. What do you guys think? I only have 20 days of Ruby experience and the internet has told me it really wants something like this, but I couldn’t find anyone who’s already made it.
March 15, 2013
by Swizec Teller
· 8,096 Views
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From Java to PHP
We are welcoming some new colleagues that come from a Java background in the Onebip team, both from the development and operations field. Here's a primer on learning PHP in this situation, that you may find useful when introducing similar people in your PHP-based projects. The absolute basics Before being able to discuss meaningful matters over PHP code, these pages from the manual should be sent to each interested developer. What is the basic syntax and the available data types of PHP. Primitive types are diffused like in Java, but there's no autoboxing as there is no object equivalent for them. Strings are immutable and one of the most important types. They can be defined with single or double quotes, and their manipulation functions follow the C api. Arrays are the glue of the language, working as lists, sets and maps while wrapped into objects. They can always be traversed with foreach(), and keep an eye on the available functions to avoid rewriting array_search() or sort() by accident. Operators work differently on primitive values and on objects: == is different from === in both these context, but in two ways. Other everyday operators are `.` and `+=`. PHP's object paradigm is borrowed from Java: it supports concrete and abstract classes, interfaces, and the private, protected and public scopes. Type hints (which are actually not hints but strong preconditions) are what is most similar to Java static type safety mechanisms. I personally strongly favors their usage. Namespaces are packages, use statements are imports. However, you don't always have to write them. The deployment model of PHP consists of an interpreter instantiated N times, running on many shared nothing processes. Don't care about: The installation process of Apache and PHP: if you work in a team, you will get good help on that, and you're going to do this only once per project probably. For example, we provide a virtual machine ready for development. The function syntax is also not very useful by itself in 2013, skip directly to objects and their methods. Take a look at anonymous functions, however. Exceptions work mostly as in Java, so don't bother reading about them before coding. Sessions are also evil in web services nowadays, so ignore anything that start with $_SESSION or session_*(): write shared nothing services (that may be restricted to our team and projects.) In general, ignore also low-level APIs like setcookie() or exec() if you already have an higher-level abstraction in the application you're working on, being this abstraction a library or your own code. It's important to know how cookies are transmitted according to HTTP, but coming from another language you already know the protocol. So you write objects that go into a graph At least that's how I see programming these days. However, you have to exit the process sometimes, and PHP provides several APIs for that. The database APIs such as the mongo and PDO extensions, working respectively with MongoDB and relational database. However, if you already use a database abstraction layer, learn just that as there is nothing interesting to see at this lower level. The DateTime object and its cousins, at least know how to call its constructor and the format() method. You should know these APIs exist in order to look them up on demand: json_*() functions, the SimpleXMLElement class, the mcrypt extension and hash_hmac(), mail(). They're just a click away at php.net/function_or_class_name, and I think these names are pretty self-explanatory to tell you when you should read about them. Watch out for: Some topics are always controversial, and get confusing for PHP beginners. Raise your alert level when you feel you're encountering some strange behavior. the difference between == and === comes out often, and it cannot be reduced to "just use === by default" since all primitive types coming from HTTP requests in the classic x-www-form-urlencoded Content-Type are usually strings. php.ini settings may change the output of your application and the actual flow of execution depending on error reporting levels and display options. One never ceases to learn, so when you encounter some problematic directive, take a quick read of the rest of the directives for that extension. Since some people believe web development is the concatenation of strings (it is not), it is tempting to reinvent the wheel; for example, writing functions for composing URLS from paths and query strings. http_build_query() solves that problem as other Composer-ready packages do, so take a look around before starting to implement commodity algorithms yourself. Stack Overflow and the PHP manual itself are good places to start if your problem has been already solved by someone else in the last 10 years. Perform a kata To test your level of proficiency with PHP, execute a small kata with TDD which incidentally will also check your usage of PHPUnit. For example, classic katas are: The Fizz Buzz, maybe with a web interface. The Roman numbers kata: write a function that transforms 42 in XLII. The Game of Life, although it is probably too complex for your first PHP project if you didn't already solve it in another language.
March 13, 2013
by Giorgio Sironi
· 26,751 Views
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In-Memory Data Grids
Introduction The IT buzzword of 2012 is without a doubt Big Data. It’s new and here to stay, and for a good reason. Big data is data that exceeds the processing capacity of conventional database systems. Great examples are CERN with the Large Hadron Collider, whose experiments generate 25 petabytes of data annually, or Walmart, which handles more than one million customer transaction every hour. Problems These vast amounts of data leave us with two problems. Problem 1: To gain value from this data, one must choose an alternative way to process it. The value of big data to an organization falls into two categories: analytical use, and enabling new products. Big data analytics can reveal insights hidden previously by data too costly to process, such as peer influence among customers, revealed by analyzing shoppers’ transactions, social and geographical data. Being able to process every item of data in reasonable time removes the troublesome need for sampling and promotes an investigative approach to data, in contrast to the somewhat static nature of running predetermined reports. Problem 2: The data is too big, moves too fast, or doesn’t fit the strictures of your database architectures. Remember the CERN case where the LHC produces over 25 Petabytes of data annually? No “classic” database architecture or setup is capable of holding these amounts of data. Solutions Fortunately, both problems can be solved by implementing the correct infrastructure and rethinking data storage. There are two critical factors in Big Data environments: size and speed. We already discussed the vast amounts of data and desire to be able to access and process the data fast. The latter is the main differentiator from more traditional data warehouses. Just imagine what you can do when you can access all your data real-time. Enter big data. A common Big Data implementation is an in-memory data grid that lives in a distributed cluster, ensuring both speed, by storing data in-memory, and capacity by using scalability features provided by a cluster. As a bonus, availability is ensured by using a distributed cluster. As for the data storage, there are typically two kinds: in-memory databases and in-memory data grids. But first some background. It is not a new attempt to use main memory as a storage area instead of a disk. In our daily lives there are numerous examples of main memory databases (MMDB), as they perform much faster than disk-based databases. An every day example is a mobile phone. When you SMS or call someone most mobile service providers use MMDB to get the information on your contact as soon as possible. The same applies to your phone. When someone calls you, the caller details are looked up in the contacts application, usually providing a name and sometimes a picture. In memory data grids In Memory Data Grid (IMDG) is the same as MMDB in that it stores data in main memory, but it has a totally different architecture. The features of IMDG can be summarized as follows: Data is distributed and stored on multiple servers. Each server operates in the active mode. A data model is usually object-oriented (serialized) and non-relational. According to the necessity, you often need to add or reduce servers. No traditional database features such as tables. In other words, IMDG is designed to store data in main memory, ensure scalability and store an object itself. These days, there are many IMDG products, both commercial and open source. Some of the most commonly used products are: Hazelcast (http://www.hazelcast.com) JBoss Infinispan (http://www.jboss.org/infinispan) GridGain DataGrid (http://www.gridgain.com/features/in-memory-data-grid/) VMware Gemfire (http://www.vmware.com/nl/products/application-platform/vfabric-gemfire/overview.html) Oracle Coherence (http://www.oracle.com/technetwork/middleware/coherence/overview/index.html) Gigaspaces XAP (http://www.gigaspaces.com/datagrid) Terracotta Enterprise Suite (http://terracotta.org/products/enterprise-suite) Why Memory? The main reasons for using main memory for data storage are once again the two main themes of Big Data: speed and capacity. The processing performance of main memory is 800 times faster than an HDD and up to 40 times faster than an. Moreover, the latest x86 server supports main memory of hundreds of GB per server. It is said that the limit of a traditional processing database’s (OLTP) data capacity is approximately 1 TB and that the OLTP processing data capacity would not increment well. If servers using main memory of 1 TB or larger become more commonly used, you will be able to conduct operations with the entire data placed in main memory, at least in the field of OLTP. IMDG Architecture To use main memory as a storage area, two weak points should be overcome: Limited capacity: involves data that exceeds the maximum capacity of the main memory of the server Reliability: involves data loss in case of a (system) failure. IMDG overcomes the limit of capacity by ensuring horizontal scalability using a distributed architecture, and resolves the issue of reliability through a replication system as part of the grid (or a distributed cluster). Now let’s discuss how an IMDG actually works. First of all, it is important to understand that an IMDG is not the same as an in-memory database, also referred to as MMDB (main memory databases). Typical examples of MMDBs are Oracle TimesTen or Sap Hana. MMDBs are full database products that simply reside in memory. As a result of being a full-blown database, they also carry the weight and overhead of database management features. IMDG is different. No tables, indexes, triggers, stored procedures, process managers etc. Just plain storage. The data model used in IMDG is key-value pairs. A key-value pair is a list with only two parts: a key and a value. The key can be used for storing and retrieving the values in the list. A key can be compared to the index or primary key of a table in a database. Note that IMDG are closely tied to development environments such as Java as the key-value pairs are represented by the structures provided by such a programming environment. Most IMDGs are written in Java, and can only be used within other Java applications. Therefore, the values of key-value pairs can be anything supported by Java, ranging from simple data types such as a string or number, to complex objects. This overcomes the two important hurdles: as you can store complex Java objects as value, there’s no need to translate these objects into a relational datamodel (which is the case in more traditional applications using a database for storage). Furthermore, the seeming limitation of being able to store only one value per key, is actually no limitation at all. Large memory sizes Most of the products introduced above use Java as an implementation language. Java reserves and uses a part of the RAM (internal memory) for dynamic memory allocation. This reserved memory space is called the Java heap. All runtime objects created by a Java application are stored in heap. Using large amounts of data causes two problems. Size limitation: By default, the heap size is 128 MB, but for current business applications, this limit is reached easily. Once the heap is “full”, no new objects can be created and the Java application will show some nasty errors. Performance: It is possible to increase the size of the heap, but this introduces some new problems. When a heap reaches a size of more than 4 gigabytes, Java will have serious issues with memory managements, causing your application to slow down or even freeze. Java has a feature called Garbage Collector, which periodically scans the heap and checks each object if it is still valid and being used. If not, the garbage collector removes the object and defragments the newly available space. The problem is, the larger the heap size, the more work to do for the garbage collector, resulting in performance degradation. Imagine a large bank has a Java application that manages customers, accounts and transactions. We have seen that an IMDG allows the application to store and access all data very quickly by caching it in memory, instead of storing the data in relatively slow databases. Let’s assume the combined data has a size of 40 gigabytes. Storing it in heap is simply not possible, considering the performance penalties of Java’s memory management capabilities. The graph below illustrates the garbage collection pause time when placing cached data in heap: Terracotta’s BigMemory product has a method to overcome these limitations. The method is to use an off-heap memory (direct buffer). Data will not be stored in Java’s heap, but directly in the available internal memory (RAM). Since, this is not subject to Java’s garbage collector, there are no performance penalties. The differences on performance are significant, as can be seen in the graph below: Using off-heap storage has some major benefits: You can use all the available memory on your machine, not just the memory that is allocated to the heap (usually less that 512 Mb). This allows you to store more data in a in-memory data grid, greatly speeding up your application. The heap can be relieved by storing data in native memory, speeding up Java applications as less heap space has to be garbage collected. Clustering, fail over and high availability So far, we have seen IMDG features that are applicable to a single server. However, the real power of IMDG lies in it’s networking and clustering capabilities, providing features as data replication, data synchronization between clients, fail over and high availability. To achieve this, a cluster of servers (or server array) acts a backbone of the infrastructure. Applications (that still can have their own IMDG or off-heap cache) that are connected to the cluster can share, replicate and backup their data with either the cluster or other applications. The graph below depicts a typical setup using Terracotta's BigMemory: The caches on the application servers are usually referred to as “level 1” cache, while the data cache on the server array is referred to as “level 2” cache. There are many different scenarios possible for storing, clustering, synchronizing and replicating data. Covering all these topics goes far beyond the scope of this article. For more information, consult the technical documentation of the product of your choice. Conclusion Big Data brings us some new challenges. First of all, storing and accessing vast amounts of data makes us rethink traditional methods and technologies. Next, there’s the question what to do with all the available data. The potential value for marketing, financial and other businesses is huge. In order to facilitate Big Data, in-memory data grids are considered the best option. IMDGs with off-heap storage are even more powerful, allowing data centric enterprise application to overcome certain limits of the Java platform, such as memory and performance constraints. As the amount of data that (large) companies produce and store, grows exponentially, databases will hit a limit. Accessing your data without a performance penalty simply will not be possible. The answer to this is using an IMDG.
March 13, 2013
by Roy Prins
· 32,687 Views · 5 Likes
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Database Concepts for a java Dev: Database Normalization
In this part, I will be briefing about different types of Database Normalizations using a sample data model. What is Database Normalization? Normalization is the process of efficiently organizing data in the database. Primary Goal of Normalization? Eliminating redundant data & ensuring meaningful data dependencies. Types of Normalization The following are the three most common normal forms in the database normalization process First Normal Form (1NF) Second Normal Form (2NF) Third Normal Form (3NF) Sample Data Model for Demonstration The following data model will be used to demonstrate all the three normal forms First Normal Form (1NF) First Normal Form (1NF) sets the very basic rules for an organized database: Create separate set of tables for each group of related data and identify each row with a unique columns [primary key] or set of columns [composite key] Eliminate duplicate columns from the table The following data model depicts the tables after 1NF rules are applied - Second Normal Form (2NF) Second Normal Form (2NF) further addresses the concept of removing duplicate data: Meet all the requirements of the first normal form Remove subsets of data that apply to multiple rows of a table and place them in separate tables Create relationships between these new tables and their predecessors through the use of foreign keys So basically the objective of the Second Normal Form is to take that is only partly dependent on the primary key and enter that data into another table. The following data model depicts the tables after 2NF rules are applied. Data from EMPLOYEE_TABLE is split into 2 tables – EMPLOYEE_TABLE and EMPLOYEE_HR_TABLE. Similarly data from CUSTOMER_TABLE is moved to CUSTOMER_TABLE and CUSTOMER_ORDER table Third Normal Form (3NF) Third normal form (3NF) goes one large step further: Meet all the requirements of the second normal form. Remove columns that are not dependent upon the primary key. The following data model depicts the tables after 3NF rules are applied. Further state and country details are moved to their own tables because they are not dependent on the primary key. Advantages of Normalizing the Database There are several advantages of normalization - Data can be stored as small atomic pieces Saves space Increases speed Reduces data anomalies Easy maintenance Other parts of this series include: Part 1 – ACID Properties Part 2 – Keys Part 4 – Database Transactions [coming soon] Part 5 – Indexes [coming soon]
March 13, 2013
by Jagadeesh Motamarri
· 10,972 Views · 1 Like
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Maven's Non-Resolvable Parent POM Problem
Need help dealing with Maven's non-resolvable parent problem? Check out this post to learn how.
March 12, 2013
by Roger Hughes
· 463,011 Views · 8 Likes
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Consider Replacing Spring XML Configuration with JavaConfig
Spring articles are becoming a trend on this blog, I should probably apply for a SpringSource position Colleagues of mine sometimes curse me for my stubbornness in using XML configuration for Spring. Yes, it seems so 2000′s but XML has definite advantages: Configuration is centralized, it’s not scattered among all different components so you can have a nice overview of beans and their wirings in a single place If you need to split your files, no problem, Spring let you do that. It then reassembles them at runtime through internal tags or external context files aggregation Only XML configuration allows for explicit wiring – as opposed to autowiring. Sometimes, the latter is a bit too magical for my own taste. Its apparent simplicity hides real complexity: not only do we need to switch between by-type and by-name autowiring, but more importantly, the strategy for choosing the relevant bean among all eligible ones escapes but the more seasoned Spring developers. Profiles seem to make this easier, but is relatively new and is known to few Last but not least, XML is completely orthogonal to the Java file: there’s no coupling between the 2 so that the class can be used in more than one context with different configurations The sole problem with XML is that you have to wait until runtime to discover typos in a bean or some other stupid boo-boo. On the other side, using Spring IDE plugin (or the integrated Spring Tools Suite) definitely can help you there. An interesting alternative to both XML and direct annotations on bean classes is JavaConfig, a former separate project embedded into Spring itself since v3.0. It merges XML decoupling advantage with Java compile-time checks. JavaConfig can be seen as the XML file equivalent, only written in Java. The whole documentation is of course available online, but this article will just let you kickstart using JavaConfig. As an example, let us migrate from the following XML file to a JavaConfig The equivalent file is the following: import java.net.MalformedURLException; import java.net.URL; import javax.swing.Icon; import javax.swing.ImageIcon; import javax.swing.JButton; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; @Configuration public class MigratedConfiguration { @Bean public JButton button() { return new JButton("Hello World"); } @Bean public JButton anotherButton() { return new JButton(icon()); } @Bean public Icon icon() throws MalformedURLException { URL url = new URL("http://morevaadin.com/assets/images/learning_vaadin_cover.png"); return new ImageIcon(url); } } Usage is simpler than simple: annotate the main class with @Configuration and individual producer methods with @Bean. The only drawback, IMHO, is that it uses autowiring. Apart from that, It just works. Note that in a Web environment, the web deployment descriptor should be updated with the following lines: contextClass org.springframework.web.context.support.AnnotationConfigWebApplicationContext contextConfigLocation com.packtpub.learnvaadin.springintegration.SpringIntegrationConfiguration Sources for this article are available in Maven/Eclipse format here. To go further: Java-based container configuration documentation AnnotationConfigWebApplicationContextJavaDoc @ContextConfigurationJavaDoc (to configure Spring Test to use JavaConfig)
March 10, 2013
by Nicolas Fränkel
· 88,788 Views · 1 Like
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Advanced ListenableFuture Capabilities
Last time we familiarized ourselves with ListenableFuture. I promised to introduced more advanced techniques, namely transformations and chaining. Let's start from something straightforward. Say we have our ListenableFuture which we got from some asynchronous service. We also have a simple method: Document parse(String xml) {//... We don't need String, we need Document. One way would be to simply resolve Future (wait for it) and do the processing on String. But much more elegant solution is to apply transformation once the results are available and treat our method as if was always returning ListenableFuture. This is pretty straightforward: final ListenableFuture future = //... final ListenableFuture documentFuture = Futures.transform(future, new Function() { @Override public Document apply(String contents) { return parse(contents); } }); or more readable: final Function parseFun = new Function() { @Override public Document apply(String contents) { return parse(contents); } }; final ListenableFuture future = //... final ListenableFuture documentFuture = Futures.transform(future, parseFun); Java syntax is a bit limiting, but please focus on what we just did. Futures.transform() doesn't wait for underlying ListenableFuture to apply parse() transformation. Instead, under the hood, it registers a callback, wishing to be notified whenever given future finishes. This transformation is applied dynamically and transparently for us at right moment. We still have Future, but this time wrapping Document. So let's go one step further. We also have an asynchronous, possibly long-running method that calculates relevance (whatever that is in this context) of a given Document: ListenableFuture calculateRelevance(Document pageContents) {//... Can we somehow chain it with ListenableFuture we already have? First attempt: final Function> relevanceFun = new Function>() { @Override public ListenableFuture apply(Document input) { return calculateRelevance(input); } }; final ListenableFuture future = //... final ListenableFuture documentFuture = Futures.transform(future, parseFun); final ListenableFuture> relevanceFuture = Futures.transform(documentFuture, relevanceFun); Ouch! Future of future of Double, that doesn't look good. Once we resolve outer future we need to wait for inner one as well. Definitely not elegant. Can we do better? final AsyncFunction relevanceAsyncFun = new AsyncFunction() { @Override public ListenableFuture apply(Document pageContents) throws Exception { return calculateRelevance(pageContents); } }; final ListenableFuture future = //comes from ListeningExecutorService final ListenableFuture documentFuture = Futures.transform(future, parseFun); final ListenableFuture relevanceFuture = Futures.transform(documentFuture, relevanceAsyncFun); Please look very carefully at all types and results. Notice the difference between Function and AsyncFunction. Initially we got an asynchronous method returning future of String. Later on we transformed it to seamlessly turn String into XML Document. This transformation happens asynchronously, when inner future completes. Having future of Document we would like to call a method that requires Document and returns future of Double. If we call relevanceFuture.get(), our Future object will first wait for inner task to complete and having its result (String -> Document) will wait for outer task and return Double. We can also register callbacks on relevanceFuture which will fire when outer task (calculateRelevance()) finishes. If you are still here, the are even more crazy transformations. Remember that all this happens in a loop. For each web site we got ListenableFuture which we asynchronously transformed to ListenableFuture. So in the end we work with a List>. This also means that in order to extract all the results we either have to register listener for each and every ListenableFuture or wait for each of them. Which doesn't progress us at all. But what if we could easily transform from List> to ListenableFuture>? Read carefully - from list of futures to future of list. In other words, rather than having a bunch of small futures we have one future that will complete when all child futures complete - and the results are mapped one-to-one to target list. Guess what, Guava can do this! final List> relevanceFutures = //...; final ListenableFuture> futureOfRelevance = Futures.allAsList(relevanceFutures); Of course there is no waiting here as well. Wrapper ListenableFuture> will be notified every time one of its child futures complete. The moment the last child ListenableFuture completes, outer future completes as well. Everything is event-driven and completely hidden from you. Do you think that's it? Say we would like to compute the biggest relevance in the whole set. As you probably know by now, we won't wait for a List. Instead we will register transformation from List to Double! final ListenableFuture maxRelevanceFuture = Futures.transform(futureOfRelevance, new Function, Double>() { @Override public Double apply(List relevanceList) { return Collections.max(relevanceList); } }); Finally, we can listen for completion event of maxRelevanceFuture and e.g. send results (asynchronously!) using JMS. Here is a complete code if you lost track: private Document parse(String xml) { return //... } private final Function parseFun = new Function() { @Override public Document apply(String contents) { return parse(contents); } }; private ListenableFuture calculateRelevance(Document pageContents) { return //... } final AsyncFunction relevanceAsyncFun = new AsyncFunction() { @Override public ListenableFuture apply(Document pageContents) throws Exception { return calculateRelevance(pageContents); } }; //... final ListeningExecutorService pool = MoreExecutors.listeningDecorator( Executors.newFixedThreadPool(10) ); final List> relevanceFutures = new ArrayList<>(topSites.size()); for (final URL siteUrl : topSites) { final ListenableFuture future = pool.submit(new Callable() { @Override public String call() throws Exception { return IOUtils.toString(siteUrl, StandardCharsets.UTF_8); } }); final ListenableFuture documentFuture = Futures.transform(future, parseFun); final ListenableFuture relevanceFuture = Futures.transform(documentFuture, relevanceAsyncFun); relevanceFutures.add(relevanceFuture); } final ListenableFuture> futureOfRelevance = Futures.allAsList(relevanceFutures); final ListenableFuture maxRelevanceFuture = Futures.transform(futureOfRelevance, new Function, Double>() { @Override public Double apply(List relevanceList) { return Collections.max(relevanceList); } }); Futures.addCallback(maxRelevanceFuture, new FutureCallback() { @Override public void onSuccess(Double result) { log.debug("Result: {}", result); } @Override public void onFailure(Throwable t) { log.error("Error :-(", t); } }); Was it worth it? Yes and no. Yes, because we learned some really important constructs and primitives used together with futures/promises: chaining, mapping (transforming) and reducing. The solution is beautiful in terms of CPU utilization - no waiting, blocking, etc. Remember that the biggest strength of Node.js is its "no-blocking" policy. Also in Netty futures are ubiquitous. Last but not least, it feels very functional. On the other hand, mainly due to Java syntax verbosity and lack of type inference (yes, we will jump into Scala soon) code seems very unreadable, hard to follow and maintain. Well, to some degree this holds true for all message driven systems. But as long as we don't invent better APIs and primitives, we must learn to live and take advantage of asynchronous, highly parallel computations. If you want to experiment with ListenableFuture even more, don't forget to read official documentation.
March 7, 2013
by Tomasz Nurkiewicz
· 23,557 Views · 1 Like
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Sequelize, the JavaScript ORM, in practice
node.js is well-know for its good connectivity with nosql databases. a less know fact is that it's also very efficient with relational databases. among the dozens orms out there in javascript, one stands out for relational databases: sequelize . it's quite easy to learn but there are not many pointers about how to organize model code with this module. here are a few tips we learned by using sequelize in a medium size project. sequelize 101 sequelize claims to supports mysql, postgresql and sqlite. the sequelize docs explain the first steps with the javascript orm. first, initialize a database connection, then a few models, without worrying about primary or foreign keys: var sequelize = new sequelize('database', 'username'[, 'password']) var project = sequelize.define('project', { title: sequelize.string, description: sequelize.text }); var task = sequelize.define('task', { title: sequelize.string, description: sequelize.text, deadline: sequelize.date }); project.hasmany(task); next, create new instances and persist them, query the database, etc. // create an instance var task = task.build({title: 'very important task'}) task.title // ==> 'very important task' // persist an instance task.save() .error(function(err) { // error callback }) .success(function() { // success callback }); // query persistence for instances var tasks = task.all({ where: ['dealdine < ?', new date()] }) .error(function(err) { // error callback }) .success(function() { // success callback }); sequelize uses promises so you can chain error and success callbacks, and it all plays well with unit tests. all that is pretty well documented, but the sequelize documentation only covers the basic usage. once you start using sequelize in real world projects, finding the right way to implement a feature gets trickier. model file structure all the examples in the sequelize documentation show all model declarations grouped in a single file. once a project reaches production size, this is not a viable approach. the alternative is to import models from a module using sequelize.import() . the problem is that relationships rely on several models. when you declare a relationship, models from both sides of the relationship must already be imported. you should not import model files from other model files because of node.js module caching policy (more on that later on); instead, you can define relationships in a standalone file. here is the file structure we've been working with: models/ index.js # import all models and creates relationships phonenumber.js task.js user.js ... and here is how the main models/index.js initializes the entire model: var sequelize = require('sequelize'); var config = require('config').database; // we use node-config to handle environments // initialize database connection var sequelize = new sequelize( config.name, config.username, config.password, config.options ); // load models var models = [ 'phonenumber', 'task', 'user' ]; models.foreach(function(model) { module.exports[model] = sequelize.import(__dirname + '/' + model); }); // describe relationships (function(m) { m.phonenumber.belongsto(m.user); m.task.belongsto(m.user); m.user.hasmany(m.task); m.user.hasmany(m.phonenumber); })(module.exports); // export connection module.exports.sequelize = sequelize; using models in code from other parts of the application, if you need a model class, require the models/index.js instead of the standalone model file. that way, you don't have to repeat the sequelize initialization. var models = require('./models'); var user = models.user; var user = user.build({ first_name: "john", last_name: "doe "}); the problem is, when you require the models/index.js file, node may use a cached version of the module... or not: from nodejs.org : multiple calls to require('foo') may not cause the module code to be executed multiple times. (...) modules are cached based on their resolved filename. since modules may resolve to a different filename based on the location of the calling module (loading from node_modules folders), it is not a guarantee that require('foo') will always return the exact same object, if it would resolve to different files. that means that using require('./models') to get the models may create more than one connection to the database. to avoid that, the models variable must be somehow singleton-esque. this can be easily achieved, if you're using a framework like expressjs , by attaching the models module to the application: app.set('models', require('./models')); and when you need to require a class of the model in a controller, use this application setting rather than a direct import: var user = app.get('models').user; accessing other models sequelize models can be extended with class and instance methods. you can add abilities to model classes, much like in a true activerecord implementation. but a problem arises when adding a method that depends on another model: how can a model access another one? // in models/user.js module.exports = function(sequelize, datatypes) { return sequelize.define('user', { first_name: datatypes.string, last_name: datatypes.string, }, { instancemethods: { counttasks: function() { // how to implement this method ? } } }); }; if the two models share a relationship, there is a way. here, one user has many tasks , that makes the task model accessible through user.associations['tasks'].target . and here is yet another problem: since sequelize doesn't use prototype-based inheritance, how can a user instance gain access to the user class? digging into the sequelize source brings the protected __factory to the light. with all this undocumented knowledge, it is now possible to write the counttasks() instance method: counttasks: function() { return this.__factory.associations['tasks'].target.count({ where: { user_id: this.id } }); } note that task.count() returns a promise, so counttasks() also returns a promise: user.counttasks().success(function(nbtasks) { // do somethig with the user task count }); extending models (a.k.a behaviors) what if you need to reuse several methods across several models? sequelize doesn't have a behavior system per se (or "concerns" in the ruby on rails terminology), although it's quite easy to implement . for now, you're condemned to import common methods before the call to sequelize.define() and use sequelize.utils._.extend() to add it to the instancemethods or classmethods object: // in models/friendlyurl.js module.exports = function(keys) { return { geturl: function() { var ret = ''; keys.foreach(function(key) { ret += this[key]; }) return ret .tolowercase() .replace(/^\s+|\s+$/g, "") // trim whitespace .replace(/[_|\s]+/g, "-") .replace(/[^a-z0-9-]+/g, "") .replace(/[-]+/g, "-") .replace(/^-+|-+$/g, ""); } }; } // in models/user.js var friendlyurlmethods = require('./friendlyurl')(['first_name', 'last_name']); module.exports = function(sequelize, datatypes) { return sequelize.define('user', { first_name: datatypes.string, last_name: datatypes.string, }, { instancemethods: sequelize.utils._.extend({}, friendlyurlmethods, { counttasks: function() { return this.__factory.associations['tasks'].target.count({ where: { user_id: this.id } }); } }); }) }; now the user model instances gain access to a geturl() method: var user = user.build({ first_name: 'john', last_name: 'doe' }); user.geturl(); // 'john_doe' a limitation of this trick is that you must define behaviors before the actual model. this forbids behaviors accessing other models. query series sequelize provides a tool called the querychainer to ease the resynchronization of queries. new sequelize.utils.querychainer() .add(user, 'find', [id]) .add(task, 'findall') .error(function(err) { /* hmm not good :> */ }) .success(function(results) { var user = results[0]; var tasks = results[1]; // do things with the results }); after using it a little, this utility turns out to be very limited. most notably, querychainer executes all queries in parallel by default. and you only get access to the results of the queries in the final callback - no way to pass values from one query to the other. we've found it much more convenient to use a generic resynchronizing module like async , which provides the wonderful async.auto() utility. this method lets you list tasks together with dependencies, and determines which task can be run in parallel, and which must be run in series. async.auto([ user: function(next) { user.find(id).complete(next); }, tasks: ['user', function(next) { tasks.findall({ where: { user_id: user.id } }).complete(next); }] ], function(err, results) { var user = results.user; var tasks = results.tasks; // do things with the results }); notice the complete() method, which is an alternative to the two success() and error() callbacks. complete() accepts a callback with the signature (err, res) , which is more natural in the node.js world, and compatible with async . prefetching one thing orms are usually good at is minimizing queries. sequelize offers a prefetching feature, allowing to group two queries in a single one using a join. for instance, if you want to retrieve a task together with the related user, write the query as follows: task.find({ where: { id: id } }, include: ['user']) .error(function(err) { // error callback }) .success(function(task) { task.getuser(); // does not trigger a new query }); this is another undocumented feature, although the documentation should be updated soon . migrations sequelize provides a migration command line utility. but because it only allows modifying the model using sequelize commands (and not calling any asynchronous method of your own ), this migration command falls short. as of now, we've been handling migrations manually using numbered sql files and a custom utility to run them in order. custom sql queries sequelize is built over database adapters, and as such provides a way to execute arbitrary sql queries against the database. here is an example: var util = require('util'); var query = 'select * from `task` ' + 'left join `user` on `task`.`userid` = `user`.`id` ' + 'where `user`.`last_name` = %s'; var escapedname = sequelize.constructor.utils.escape(last_name); querywithparams = util.format(query, escapedname); sequelize.query(querywithparams, task) .error(function(err) { // error callback }) .success(function(tasks) { task.getuser(); // does not trigger a new query }); sequelize.query() returns a promise just like other query functions. if you provide the model to use for hydration ( task in this case), the query() method returns model instances rather than a simple json. note that you must escape values by hand before concatenating them into the sql query. for strings, sequelize.constructor.utils.escape() is your friend. for integers, util.format('%d') should do the trick. conclusion is sequelize ready for prime time ? almost. the learning curve is made longer by an incomplete documentation, but most of the features required by a production-level orm are there. however, i wouldn't recommend it for production just yet if you're not ready to run on your own fork, since the rate at which prs are merged in the sequelize github repository is low.
March 5, 2013
by Francois Zaninotto
· 52,913 Views · 2 Likes
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MySQL optimizer: ANALYZE TABLE and Waiting for table flush
This post comes from Miguel Angel Nieto at the MySQL Performance Blog. The MySQL optimizer makes the decision of what execution plan to use based on the information provided by the storage engines. That information is not accurate in some engines like InnoDB and they are based in statistics calculations therefore sometimes some tune is needed. In InnoDB these statistics are calculated automatically, check the following blog post for more information: http://www.mysqlperformanceblog.com/2011/10/06/when-does-innodb-update-table-statistics-and-when-it-can-bite/ There are some variables to tune how that statistics are calculated but we need to wait until the gathering process triggers again to see if there is any improvement. Usually the first step to try to get back to the previous execution plan is to force that process with ANALYZE TABLE that is usually fast enough to not cause troubles. Let’s see an example of how a simple and fast ANALYZE can cause a downtime. Waiting for table flush: In order to trigger this problem we need: - Lot of concurrency - A long running query - Run an ANALYZE TABLE on a table accessed by the long running query So first we need a long running query against table t: SELECT * FROM t WHERE c > '%c%'; Then in our efforts to get a better execution plan for another query we run ANALYZE TABLE: mysql> analyze table t; +--------+---------+----------+----------+ | Table | Op | Msg_type | Msg_text | +--------+---------+----------+----------+ | test.t | analyze | status | OK | +--------+---------+----------+----------+ 1 row in set (0.00 sec) Perfect, very fast! But then some seconds later we realize that our application is down. Let’s see the process list. I’ve removed most of the columns to make it clearer: +------+-------------------------+---------------------------------+ | Time | State | Info | | 32 | Writing to net | select * from t where c > '%0%' | | 12 | Waiting for table flush | select * from test.t where i=1 | | 12 | Waiting for table flush | select * from test.t where i=2 | | 12 | Waiting for table flush | select * from test.t where i=3 | | 11 | Waiting for table flush | select * from test.t where i=7 | | 10 | Waiting for table flush | select * from test.t where i=11 | | 11 | Waiting for table flush | select * from test.t where i=5 | | 11 | Waiting for table flush | select * from test.t where i=4 | | 11 | Waiting for table flush | select * from test.t where i=9 | | 11 | Waiting for table flush | select * from test.t where i=8 | | 11 | Waiting for table flush | select * from test.t where i=12 | | 11 | Waiting for table flush | select * from test.t where i=14 | | 10 | Waiting for table flush | select * from test.t where i=6 | | 10 | Waiting for table flush | select * from test.t where i=15 | | 10 | Waiting for table flush | select * from test.t where i=10 | [...] The ANALYZE TABLE runs perfect but after it the rest of the threads that are running a query against that table need to wait. This is because MySQL has detected that the underlying table has changed and it needs to close and reopen it using FLUSH. Therefore the table will be locked until all queries that are using that table finish. There are only two solutions to this situation, wait until the long query finishes or kill the query. Also, we have to take in account that killing a query could cause even more troubles. If we are dealing with a write query on InnoDB the rollback process could take even more time to finish than the original query. On the other hand, if the table is MyISAM there will be no rollback process so all the already updated rows can’t be recovered. This particular example is not only a problem of ANALYZE. Other commands like FLUSH TABLES, ALTER, RENAME, OPTIMIZE or REPAIR can cause threads to wait on “Waiting for tables”, “Waiting for table” and “Waiting for table flush”. Conclusion Before running an ANALYZE table or any other command listed before, check the running queries. If the table that you are going to work on is very used the recommendation is to run it during the low peak of load or a maintenance window.
February 28, 2013
by Peter Zaitsev
· 12,089 Views
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How Expensive is a Method Call in Java?
We have all been there. Looking at the poorly designed code while listening to the author’s explanations about how one should never sacrifice performance over design. And you just cannot convince the author to get rid of his 500-line methods because chaining method calls would destroy the performance. Well, it might have been true in 1996 or so. But since then JVM has evolved to be an amazing piece of software. One way to find out about it is to start looking more deeply into optimizations carried out by the virtual machine. The arsenal of techniques applied by the JVM is quite extensive, but lets look into one of them in more details. Namely method inlining . It is easiest to explain via the following sample: int sum(int a, int b, int c, int d) { return sum(sum(a, b),sum(c, d)); } int sum(int a, int b) { return a + b; } When this code is run, the JVM will figure out that it can replace it with a more effective, so called “inlined” code: int sum(int a, int b, int c, int d) { return a + b + c + d; } You have to pay attention that this optimization is done by the virtual machine and not by the compiler. It is not transparent at the first place why this decision was made. After all – if you look at the sample code above – why postpone optimization when compilation can produce more efficient bytecode? But considering also other not-so obvious cases, JVM is the best place to carry out the optimization: JVM is equipped with runtime data besides static analysis. During runtime JVM can make better decisions based on what methods are executed most often, what loads are redundant, when is it safe to use copy propagation, etc. JVM has got information about the underlying architecture – number of cores, heap size and configuration and can thus make the best selection based on this information. But let us see those assumptions in practice. I have created a small test application which uses several different ways to add together 1024 integers. A relatively reasonable one, where the implementation just iterates over the array containing 1024 integers and sums the result together. This implementation is available in InlineSummarizer.java . Recursion based divide-and-conquer approach. I take the original 1024 – element array and recursively divide it into halves – the first recursion depth thus gives me two 512-element arrays, the second depth has four 256-element arrays and so forth. In order to sum together all the 1024 elements I introduce 1023 additional method invocations. This implementation is attached as RecursiveSummarizer.java . Naive divide-and-conquer approach. This one also divides the original 1024-element array, but via calling additional instance methods on the separated halves – namely I nest sum512(), sum256(), sum128(), …, sum2() calls until I have summarized all the elements. As with recursion, I introduce 1023 additional method invocations in the source code . And I have a test class to run all those samples. The first results are from unoptimized code: As seen from the above, the inlined code is the fastest. And the ones where we have introduced 1023 additional method invocations are slower by ~25,000ns. But this image has to be interpreted with a caveat – it is a snapshot from the runs where JIT has not yet fully optimized the code. In my mid-2010 MB Pro it took between 200 and 3000 runs depending on the implementation. The more realistic results are below. I have ran all the summarizer implementations for more than 1,000,000 times and discarded the runs where JIT has not yet managed to perform it’s magic. We can see that even though inlined code still performed best, the iterative approach also flew at a decent speed. But recursion is notably different – when iterative approach close in with just 20% overhead, RecursiveSummarizer takes 340% of the time the inlined code needs to complete. Apparently this is something one should be aware of – when you use recursion, the JVM is helpless and cannot inline method calls. So be aware of this limitation when using recursion. Recursion aside – method overheads are close to being non-existent. Just 205 ns difference between having 1023 additional method invocations in your source code. Remember, those were nanoseconds (10^-9 s) over there that we used for measurement. So thanks to JIT we can safely neglect most of the overhead introduced by method invocations. The next time when your coworker is hiding his lousy design decisions behind the statement that popping through a call stack is not efficient, let him go through a small JIT crash course first. And if you wish to be well-equipped to block his future absurd statements, subscribe to either our RSS or Twitter feed and we are glad to provide you future case studies. Full disclosure: the inspiration for the test case used in this article was triggered by Tomasz Nurkiewicz blog post .
February 27, 2013
by Nikita Salnikov-Tarnovski
· 13,109 Views
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JDBC: What Resources You Have to Close and When?
I was never sure what resources in JDBC must be explicitely closed and wasn’t able to find it anywhere explained. Finally my good colleague, Magne Mære, has explained it to me: In JDBC there are several kinds of resources that ideally should be closed after use. Even though every Statement and PreparedStatement is specified to be implicitly closed when the Connection object is closed, you can’t be guaranteed when (or if) this happens, especially if it’s used with connection pooling. You should explicitly close your Statement and PreparedStatement objects to be sure. ResultSet objects might also be an issue, but as they are guaranteed to be closed when the corresponding Statement/PreparedStatement object is closed, you can usually disregard it. Summary: Always close PreparedStatement/Statement and Connection. (Of course, with Java 7+ you’d use the try-with-resources idiom to make it happen automatically.) PS: I believe that the close() method on pooled connections doesn’t actually close them but just returns them to the pool. A request to my dear users: References to any good resources would be appreciate.
February 26, 2013
by Jakub Holý
· 27,184 Views
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Solving RPM installation conflicts
This post comes from Ignacio Nin at the MySQL Performance Blog. Lately we’ve had many reports of the RPM packages for CentOS 5 (mostly) and CentOS 6 having issues when installing different combinations of our products, particularly with Percona Toolkit. Examples of bugs related to these issues are lp:1031427 and lp:1051874. These problems arise when trying to install a package from the distribution that is linked against the version of libmysqlclient.so shipped by the distribution (libmysqlclient.so.15 for CentOS 5/libmysqlclient.so.16 for CentOS 6) and a version of Percona Server that depends on another version of libmysqlclient.so, usually more recent. Bug lp:1031427 is an example of this, and shows how the packages would conflict when trying to install libmysqlclient.so. For example, when installing php-mysql alongside PS 5.5 in CentOS 6: # yum -q install Percona-Server-server-55 php-mysql Installing: Percona-Server-server-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 15 M php-mysql x86_64 5.3.3-14.el6_3 updates 79 k Installing for dependencies: Percona-Server-client-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 7.0 M Percona-Server-shared-51 x86_64 5.1.67-rel14.3.506.rhel6 percona 2.8 M Percona-Server-shared-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 787 k Transaction Summary ===================================================================================================================================================== Install 5 Package(s) Is this ok [y/N]: y Transaction Check Error: file /usr/lib64/libmysqlclient.so conflicts between attempted installs of Percona-Server-shared-51-5.1.67-rel14.3.506.rhel6.x86_64 and Percona-Server-shared-55-5.5.29-rel29.4.401.rhel6.x86_64 file /usr/lib64/libmysqlclient_r.so conflicts between attempted installs of Percona-Server-shared-51-5.1.67-rel14.3.506.rhel6.x86_64 and Percona-Server-shared-55-5.5.29-rel29.4.401.rhel6.x86_64 The traditional solution for this situation was to provide a special package, Percona-Server-shared-compat (modeled after upstream’s MySQL-shared-compat) which would contain ALL versions of libmysqlclient.so.* together and wouldn’t conflict. Probably some of you are familiar with this approach. # yum -q install Percona-Server-server-55 Percona-Server-shared-compat php-mysql Installing: Percona-Server-server-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 15 M Percona-Server-shared-compat x86_64 5.5.29-rel29.4.401.rhel6 percona 3.4 M php-mysql x86_64 5.3.3-14.el6_3 updates 79 k Installing for dependencies: Percona-Server-client-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 7.0 M Percona-Server-shared-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 787 k Transaction Summary ===================================================================================================================================================== Install 5 Package(s) Notice how PS-shared-compat installs along the -shared package, providing the older libmysqlclient.so.16 required by php-mysql. However, this has proved non-intuitive and problematic, since the shared-compat package wouldn’t get selected unless explicitely installed — and many of our users would rather have it “just work” without requiring additional knowledge of what the particular workaround was, etc.. We’re now trying a solution in which our -shared packages won’t conflict anymore at libmysqlclient.so, so we are able to install them side-by-side, modelled after the mysql-libs packages provided by CentOS/Redhat. So even if the user wants to install PS 5.5 alongside packages that depend on 5.1/5.0, the -shared packages will work together. For example installing 5.5 and postfix in CentOS: # yum -q install Percona-Server-server-55 postfix Installing: Percona-Server-server-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 19 M postfix x86_64 2:2.3.3-6.el5 base 3.8 M Installing for dependencies: Percona-SQL-shared-50 x86_64 5.0.92-b23.89.rhel5 percona-testing 1.8 M Percona-Server-client-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 9.1 M Percona-Server-shared-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 993 k … and this will install without problems. Additionally, this has the advantage of allowing an upgrade from 5.1 to 5.5 without uninstalling any software that depended on the old version. # rpm -qa | grep ^Percona Percona-Server-client-51-5.1.67-rel14.3.507.rhel6.x86_64 Percona-Server-shared-51-5.1.67-rel14.3.507.rhel6.x86_64 Percona-Server-server-51-5.1.67-rel14.3.507.rhel6.x86_64 In this case only Percona-Server-client-51 and Percona-Server-server-51 need be removed, allowing any package that depends on Percona-Server-shared-51 (providing libmysqlclient.so.16) to remain installed. After the server and client packages are uninstalled, you can install PS 5.5 without conflict. The current package candidates for versions 5.0.92 (which required an update), 5.1.67-14.3 and 5.5.29-29.4 can be tested from the percona-testing repository. We encourage you to try these out and send us your feedback and/or file any bugs you find. Installation instructions for Percona Testing repositories. We’re aiming to include these fixes in our next releases of 5.1 and 5.5. Percona Toolkit users in particular will enjoy this update since it’ll mean no more trouble when installing it from repository!
February 25, 2013
by Peter Zaitsev
· 7,834 Views
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Using R — Package Installation Problems
The post titled Installing Packages described the basics of package installation with R. The process is wonderfully simple when everything goes well. But it can be maddening when it does not. Error messages give a hint as to what went wrong but do not necessarily tell you how to resolve the problem. This post will collect some of the error messages we’ve encountered while installing R packages and describe the reasons for the error and the workarounds we’ve found. 1) Older version of R Warning message: In install.packages(c("sp")) : package ‘sp’ is not available This is the message that you get when the CRAN package you’re interested in requires a more recent version of R than you have. Remember, the default behavior ofinstall.packages() is to grab the latest version of a package. In this case you have to poke around in the “Old sources” link on the CRAN page for that package and use trial-and-error to find an older version of the package that will work with your version of R. You should start by determining what version of R you have: 1 2 $R--version Rversion2.8.1(2008-12-22) This version of R was released at the end of 2008 and any version of the “sp” package released in 2008 should work. At least some of the 2009 releases should also work. Perusing the sp archive, we might try installing version 0.9-37, the last of the 0.9-3x series which was released in May of 2009: 1 2 3 4 $wget http://cran.r-project.org/src/contrib/Archive/sp/sp_0.9-37.tar.gz $sudo CMD INSTALL sp_0.9-37.tar.gz ... $# Success! 2) Unable to execute files in /tmp directory ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual' By default, R uses the /tmp directory to install packages. On security conscious machines, the /tmp directory is often marked as “noexec” in the /etc/fstab file. This means that no file under /tmp can ever be executed. Packages that require compilation or that have self-inflating data will fail with the error above. One such package isRJSONIO. The solution is to set the TMPDIR environment variable which R will use as the compilation directory. For csh shell: 1 2 $mkdir~/tmp $setenv TMPDIR~/tmp And for bash: 1 2 $mkdir~/tmp $export TMPDIR=~/tmp Other problems Please leave comments describing other package installation problems and solutions you’ve encountered to help us build a more complete listing.
February 25, 2013
by Jonathan Callahan
· 4,519 Views
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Removing White Space Around R Figures
When I want to insert figures generated in R into a LaTeX document, it looks better if I first remove the white space around the figure. Unfortunately, R does not make this easy as the graphs are generated to look good on a screen, not in a document. There are two things that can be done to fix this problem. First, you can reduce the white space generated by R. I use the following function when saving figures in R. savepdf <- function(file, width=16, height=10) { fname <- paste("figures/",file,".pdf",sep="") pdf(fname, width=width/2.54, height=height/2.54, pointsize=10) par(mgp=c(2.2,0.45,0), tcl=-0.4, mar=c(3.3,3.6,1.1,1.1)) } The width and height are in centimetres. The ratio is about right for a beamer presentation, and also to fit two figures on an A4 page. Then I use the commands savepdf("filename") # Plotting commands here dev.off() That will generate a pdf figure of about the right size and shape for a document, and with narrow margins of white space, and save it in my figures sub-directory. The second trick is to trim the pdf files so there is no white space left. On a unix system, this is easily achieved as follows. pdfcrop filename.pdf filename.pdf There are probably windows and mac versions of the same, but I haven’t used them. Adobe Acrobat will also crop pdfs, but not from the command line as far as I know. To apply pdfcrop to every file in a directory (using unix), save the following to a file called cropall.sh: #!/bin/bash for FILE in ./*.pdf; do pdfcrop "${FILE}" "${FILE}" done Make the file executable and run it. In my post on Makefiles, I explain how to include pdfcrop within a Makefile. If you just use pdfcrop without first reducing the white space in R, the proportions come out a little odd. So I tend to use both approaches together.
February 24, 2013
by Rob J Hyndman
· 7,498 Views
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Monitoring an IBM JVM with VisualVM
JDK6 update 7 and onward include a tool called VisualVM. VisualVM is a visual tool with monitoring and profiling capabilities for the JVM. With VisualVM you can: Monitor heap usage Monitor CPU usage Monitor Threads Initiate garbage collections Profile CPU and memory And more… Although VisualVM is distributed with the Oracle JDK, it can also be used to monitor IBM JVM’s. VisualVM is not able to connect to the IBM JVM locally. JMX must be used instead. To enable JMX monitoring on the IBM JVM open the WebSphere administrative console and: navigate to: Server -> Server Types -> WebSphere application servers ->[SERVER_NAME] Expand Java and Process Management and click Process definition Click Java Virtual Machine In the Generic JVM arguments field append the following properties: -Djavax.management.builder.initial= -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.authenticate=false -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.port=1099 Restart the server To start monitoring the JVM with VisualVM start VisualVM by navigating to [JDK_HOME]\bin and start jvisualvm.exe (please note that when VisualVM is downloaded as a separate package the executable is called visualvm.exe instead). In VisualVM click File -> Add JMX Connection. Specify localhost:1099 in the connection field and click OK. If everything went OK, you should see the localhost:1099 connection under the Local node in the tree on the left. Double-click this node to start monitoring. See the following screenshot for an example: When using a JMX connection to monitor the JVM please be aware that not all functionality can be used compared to monitoring a local JVM. Profiling memory is for example not possible. The above configuration was tested on: Windows 7 64-bit IBM JDK1.6 64 bit WebSphere Application Server version 7.0 Note: Before JDK6 update 7, VisualVM can also be downloaded separately from http://visualvm.java.net/download.html Note: To actually test if port 1099 is listening for connections use (on Windows) the netstat –a command and check wether the port is present and listening.
February 21, 2013
by Jamie Craane
· 30,935 Views · 1 Like
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Duck Typing in Scala: Structural Typing.
Scala offers a functionality known as Structural Types which allows to set a behaviour very similar to what dynamic languages allow to do when they support Duck Typing (http://en.wikipedia.org/wiki/Duck_typing) The main difference is that it is a type safe, static typed implementation checked up at compile time. This means that you can create a function (or method) that receives an expected duck. But at compile time it would be checked that anything that is passed can actually quack like a Duck. Here is an example. Let’s say we want to create a function that expects anything that can quack like a duck. This is how we would do it in Scala with Structural Typing: def quacker(duck: {def quack(value: String): String}) { println (duck.quack("Quack")) } You can see that in the definition of the function we are not expecting a particular class or type. We are specifying an Structural Type which in this case means that we are expecting any type that has a method with the signature quack(string: String): String. So all the following examples will work with that function: object BigDuck { def quack(value: String) = { value.toUpperCase } } object SmallDuck { def quack(value: String) = { value.toLowerCase } } object IamNotReallyADuck { def quack(value: String) = { "prrrrrp" } } quacker(BigDuck) quacker(SmallDuck) quacker(IamNotReallyADuck) You can see that there is no interface or anything being implemented by any of the three objects we have defined. They simply have to define the method quack in order to work in our function. If you run the code above you get the output: QUACK quack prrrrrp If on the other hand you try to create an object without a quack method and try to call the function with that object you would get a compile error. For example trying to do this: object NoQuaker { } quacker(NoQuaker) You would get the error: error: type mismatch; found : this.NoQuaker.type required: AnyRef{def quack(value: String): String} quacker(NoQuaker) Also, you don’t even need to create a new type or class. You could use AnyRef to create an object with the quack method. Like this: val x = new AnyRef { def quack(value: String) = { "No type needed "+ value } } and you can use that object to call the function: quacker(x) You can also specify in the function that expects the structural type, the the parameter object must respond to more than one method. Like this: def quacker(duck: {def quack(value: String): String; def walk(): String}) { println (duck.quack("Quack")) } There you are saying that any object you pass to the function needs to respond to both methods quack and walk. This is also checked at compile time. Under the covers the use of Structural Types in this way will be handled by reflection. This means that it is a more expensive operation than the standard method call. So use only when it actually makes sense to use it.
February 20, 2013
by Carlo Scarioni
· 42,114 Views · 2 Likes
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Building SOLID Databases: Dependency Inversion and Robust DB Interfaces
Dependency inversion is the idea that interfaces should depend on abstractions not on specifics. According to Wikipedia, the principle states: A. High-level modules should not depend on low-level modules. Both should depend on abstractions. B. Abstractions should not depend upon details. Details should depend upon abstractions. Of course the second part of this principle is impossible if read literally. You can't have an abstraction until you know what details are to be covered, and so the abstraction and details are both co-dependent. If the covered details change sufficiently the abstraction will become either leaky or inadequate and so it is worth seeing these as intertwined to some extent. The focus on abstraction is helpful because it suggests that the interface contract should be designed in such a way that neither side really has to understand any internal details of the other in order to make things work. Both sides depend on well-encapsulated API's and neither side has to worry about what the other side is really doing. This is what is meant by details depending on abstractions rather than the other way around. This concept is quite applicable beyond object oriented programming because it covers a very basic aspect of API contract design, namely how well an API should encapsulate behavior. This principle is first formulated in its current form in the object oriented programming paradigm but is generally applicable elsewhere. SQL as an Abstraction Layer, or Why RDBMS are Still King There are plenty of reasons to dislike SQL, such as the fact that nulls are semantically ambiguous. As a basic disclaimer I am not holding SQL up to be a paragon of programming languages or even db interfaces, but I think it is important to discuss what SQL does right in this regard. SQL is generally understood to be a declarative language which approximates relational mathematics for database access purposes. With SQL, you specify what you want returned, not how to get it, and the planner determines the best way to get it. SQL is thus an interface language rather than a programming language per se. With SQL, you can worry about the logical structure, leaving the implementation details to the db engine. SQL queries are basically very high level specifications of operations, not detailed descriptions of how to do something efficiently. Even update and insert statements (which are by nature more imperative than select statements) leave the underlying implementation entirely to the database management system. I think that this, along with many concessions the language has made to real-world requirements (such as bags instead of sets and the addition of ordering to bags) largely account for the success of this language. SQL, in essence, encapsulates a database behind a mature mathematical, declarative model in the same way that JSON and REST do (in a much less comprehensive way) in many NoSQL db's. In essence SQL provides encapsulation, interface, and abstraction in a very full-featured way and this is why it has been so successful. SQL Abstraction as Imperfect One obvious problem with treating SQL as an abstraction layer in its own right is that one is frequently unable to write details in a way that is clearly separate from the interface. Often storage tables are hit directly, and therefore there is little separation between logical detail and logical interface, and so this can break down when database complexity reaches a certain size. Approaches to managing this problem include using stored procedures or user defined functions, and using views to encapsulate storage tables. Stored Procedures and User Defined Functions Done Wrong Of the above methods, stored procedures and functional interfaces have bad reputations frequently because of bad experiences that many people have with them. These include developers pushing too much logic into stored procedures, and the fact that defining functional interfaces in this way usually produces a very tight binding between database code and application code, often leading to maintainability problems. The first case is quite obvious, and includes the all-too-frequent case of trying to send emails directly from stored procedures (always a bad idea). This mistake leads to certain types of problems, including the fact that ACID-compliant operations may be mixed with non-ACID-compliant ones, leading to cases where a transaction can only be partially rolled back. Oops, we didn't actually record the order as shipped, but we told the customer it was..... MySQL users will also note this is an argument against mixing transactional and nontransactional backend table types in the same db..... However that problem is outside the scope of this post. Additionally, MySQL is not well suited for many applications against a single set of db relations. The second problem, though, is more insidious. The traditional way stored procedures and user defined functions are typically used, the application has to be deeply aware of the interface to the database, but the rollout for these aspects is different leading to the possibility or service interruptions, and a need to very carefully and closely time rollout of db changes with application changes. As more applications use the database, this becomes harder and the chance of something being overlooked becomes greater. For this reason the idea that all operations must go through a set of stored procedures is a decision fraught with hazard as the database and application environment evolves. Typically it is easier to manage backwards-compatibility in schemas than it is in functions and so a key question is how many opportunities you have to create new bugs when a new column is added. There are, of course, more hazards which I have dealt with before, but the point is that stored procedures are potentially harmful and a major part of the reason is that they usually form a fairly brittle contract with the application layer. In a traditional stored procedure, adding a column to be stored will require changing the number of variables in the stored procedure's argument list, the queries to access it, and each application's call to that stored procedure. In this way, they provide (in the absence of other help) at best a leaky abstraction layer around the database details. This is the sort of problem that dependency inversion helps to avoid. Stored Procedures and User Defined Functions Done Right Not all stored procedures are done wrong. In the LedgerSMB project we have at least partially solved the abstraction/brittleness issue by looking to web services for inspiration. Our approach provides an additional mapping layer and dynamic query generation around a stored procedure interface. By using a service locator pattern, and overloading the system tables in PostgreSQL as the service registry, we solve the problem of brittleness. Our approach of course is not perfect and it is not the only possibility. One shortcoming is that our approach is that the invocation of the service locator is relatively spartan. We intend to allow more options there in the future. However one thing I have noticed is the fact that there are far fewer places where bugs can hide and therefore faster and more robust development takes place. Additionally a focus on clarity of code in stored procedures has eliminated a number of important performance bottlenecks, and it limits the number of places where a given change propagates to. Other Important Options in PostgreSQL Stored procedures are not the only abstraction mechanisms available from PostgreSQL. In addition to views, there are also other interesting ways of using functions to accomplish this without insisting that all access goes through stored procedures. In addition these methods can be freely mixed to produce very powerful, intelligent database systems. Such options include custom types, written in C, along with custom operators, functions and the like. These would then be stored in columns and SQL can be used to provide an abstraction layer around the types. In this way SQL becomes the abstraction and the C programs become the details. A future post will cover the use of ip4r in network management with PostgreSQL db's as an example of what can be done here. Additionally, things like triggers and notifications can be used to ensure that appropriate changes trigger other changes in the same transaction or, upon transaction commit, hand off control to other programs in subsequent transactions (allowing for independent processing and error control for things like sending emails). Recommendations Rather than specific recommendations, the overall point here is to look at the database itself as a an application running in an application server (the RDBMS) and design it as an application with an appropriate API. There are many ways to do this, from writing components in C and using SQL as an abstraction mechanism to writing things in SQL and using stored procedures as a mechanism. One could even write code in SQL and still use SQL as an abstraction mechanism. The key point however is to be aware of the need for discoverable abstraction, a need which to date things like ORMs and stored procedures often fill very imperfectly. A well designed db with appropriate abstraction in interfaces, should be able to be seen as an application in its own right, engineered as such, and capable of serving multiple client apps through a robust and discoverable API. As with all things, it starts by recognizing the problems and putting solutions as priorities from the design stage onward.
February 19, 2013
by Chris Travers
· 5,272 Views
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