Data wrangling with Clojure

Clojure is a great language for wrangling data that is either awkwardly-sized or where data needs to be drawn from and stored in different locations.

What does awkward-sized data mean?

I am going to attribute the term “awkward-sized data” to Henry Garner and Bruce Durling. Awkward-sized data is neither big data nor small data and to avoid defining something by what it is not I would define it as bigger than would fit comfortably into a spreadsheet and irregular enough that it is not easy to map onto a relational schema.

It is about hundreds of thousands of data points and not millions, it is data sets that fit into the memory on a reasonably specified laptop.

It also means data where you need to reconcile data between multiple datastores, something that is more common in a microservice or scalable service world where monolithic data is distributed between more systems.

What makes Clojure a good fit for the problem?

Clojure picks up a lot of good data processing traits from its inheritance as a LISP. A LISP after all is a “list processor”, the fundamental structures of the language are data and its key functionality is parsing and processing those data structures into operations. You can serialise data structures to a flat-file and back into memory purely through the reader macro and without the need for parsing libraries.

Clojure has great immutable data structures with great performance, a robust set of data processing functions in its core library, along with parallel execution versions, it has well-defined transactions on data. It is, unusually, lazy be default which means it can do powerful calculations with a minimal amount of memory usage. It has a lot of great community libraries written and also Java compatibility if you want to use an existing Java library.

Clojure also has an awesome REPL which means you have a powerful way of directly interacting with your data and getting immediate feedback on the work you are doing.

Why not use a DSL or a specify datastore?

I will leave the argument as to why you need a general purpose programming language to Tommy Hall, his talk about cloud infrastructure DSLs is equally relevant here. There are things you reasonably want to do and you can either add them all to a DSL until it has every feature of poorly thought-out programming language or you can start directly with the programming language.

For me the key thing that I always want to do is read or write data, either from a datastore, file or HTTP/JSON API. I haven’t come across a single data DSL that makes it easier to read from one datastore and write to another.

Where can I find out more?

If you are interested in statistical analysis a good place to start is Bruce Durling’s talk on Incanter which he gave relatively early in his use of it.

Henry Garner’s talk Expressive Parallel Analytics with Clojure has a name that might scare the hell out of you but, trust me, this is actually a pretty good step-by-step guide to how you do data transformations and aggregations in Clojure and then make them run in parallel to improve performance.

Libraries I like

In my own work I lean on the following libraries a lot.

JSON is the lingua franca of computing and you are going to need a decent JSON parser and serialiser, I like Cheshire because it does everything I need, which is primarily produce sensible native data structures that are as close to native JSON structures as possible.

After JSON the other thing that I always need is access to HTTP. When you are mucking around with dirty data the biggest thing I’ve found frustrating are libraries that throw exceptions whenever you get something other than a status code of 200. clj-http is immensely powerful but you will want to switch off exceptions. clj-http-lite only uses what is in the JDK so makes for easier dependencies, you need to switch off exceptions again. Most of the time the lite library is perfectly usable, if you are just using well-behaved public APIs I would not bother with anything more complicated. For an asynchronous client there is http-kit, if you want to make simultaneous requests async can be a great choice but most of the time it adds a level of complexity and indirection that I don’t think you need. You don’t need to worry about exceptions but do remember to add a basic error handler to avoid debugging heartache.

For SQL I love yesql because it doesn’t do crazy things and instead lets you write and test normal SQL and then use inside Clojure programs. In my experience this is what you want to do 100% of the time and not use some weird abstraction layer. While I will admit to being lazy and frequently loading the queries into the default namespace it is far more sensible to load them via the require-sql syntax.

One thing I have had to do a bit of is parsing and cleaning HTML and I love the library Hickory for this. One of the nice things is that because it produces a standard Clojure map for the content you can use a lot of completely vanilla Clojure techniques to do interesting things with the content.

Example projects

I created a simple film data API that reads content from an Oracle database and simply publishes it as a JSON. This use Yesql and is really just a trivial data transform that makes the underlying data much more usable by other consumers.

id-to-url is a straight-forward piece of data munging but requires internal tier access to the Guardian Content API. Given a bunch of internal id numbers from an Oracle databases we need to check the publication status of the content and then extract the public url for the content and ultimately in the REPL I write the URLs to a flat file.

Asynchronous and Parallel processing

My work has generally been IO-bound so I haven’t really needed to use much parallel processing.

However if you need it then Rich Hickey does the best explanation of reducers and why reduce is the only function you really need in data processing. For transducers (in Clojure core from 1.7) I like Kyle Kingsbury’s talk a lot and he talks about Tesser which seems to be the ultimate library for multicore processing.

For async work Rich, again, does the best explanation of core.async. For IO async ironically is probably the best approach for making the most of your resources but I haven’t yet been in a situation where


Hibernate temporary tables

I was surprised to discover that Hibernate makes use of temporary tables when performing deletes. The creation of the table was triggering an alert in a database monitor for an application. The monitor logged the creation of tables beginning with the prefix HT_ and a name that mirrored that of an entity tablename.

Initially I must admit that I was thrown very far off track and started looking through the schema creation scripts and codebase looking for something, even checking HT as initials against the developer names. Naturally we tried deleting the tables and soon enough they were recreated.

As with a lot of modern programming bugs the answer came through some frustrated Googling and the realisation that HT might stand for Hibernate Table. With that insight in place I was then able to find this excellent explanation of the situation and I get another self-righteous data point in my dislike of ORM.

This temporary table is required for two reasons, firstly because ORM’s do not actually do a proper mapping between the domain concepts of a relational store and objects and secondly because Hibernate wants to create a¬†verisimilitude¬†around the concept of a class hierarchy.

I don’t think there is a better solution than what Hibernate is offering here but I do think it is the wrong problem being solved in a clever way.


Refactoring RDBMS: Adding a new column

So, the requirements change and you now need to record a new piece of information in one of your tables. That’s a pretty easy one, right? Just add a column and you’re laughing.

Well this is probably the way I see this problem solved 100% of the time (Rails migrations and Grails GORM for example) and I actually think it is the worst solution.

When you add a column to a table you should always consider whether you can add a sensible value. Adding a nullable column to a table is a really bad idea. Firstly, it isn’t relational (and it is almost guaranteed to reduce your normal form). Secondly, it is likely to introduce performance problems if the column needs to be searchable. Finally, nullable columns have a higher cost of maintenance as they imply logic (the null state) but don’t define it. The logic as to when the column may be null will always exist outside the schema.

If you can define a sensible default then you might be able to add the column to the table. For example boolean flag fields could be handled this way as long as the historic values can be accurately mapped to, say, false.

This method however falls down if your historical data cannot be truthfully mapped to a default value. If for example the new value represents something you have started to track rather than some brand new piece of information then you cannot truthfully map the historic data to the default value as you don’t know whether the default really applies or not.

For example if you send goods to customers using a regular or overnight delivery method and you need to start tracking the delivery method it would be wrong to map all historic data to the regular delivery. The truth is you don’t know whether a historical order was an overnight delivery or not. If you do map it incorrectly then you will end up skewing all your data and ultimately poison the very data you want to be tracking.

In this case it is far better to simply introduce a relational child table to hold the new information. Using child tables is a more accurate record of the data as a child row will only exist where the data is known. For unknown historic records there will be no child entry and your queries will not need any special cases.

When using child table data like this you can easily separate your data via the EXISTS predicate and in most databases EXISTS is very performant.

I think using child tables to record new information is relational way to solve the problem of adding new columns but it is usually turned down for one of two reasons (there naturally may be others but I’ve only ever heard these used in anger).

Firstly there is the argument that this technique leads to a proliferation of child tables. This is an accurate criticism but unfortunately if you want your database to be accurate and the new information is introduced piecemeal then you do not have a lot of choice. Pretending that you have historic data you don’t actually have doesn’t solve the problem.

One thing that can help this situation is to separate your database into its transaction processing element and its warehousing or archive aspect. In the warehouse the structure of the database might be quite involved but since the accuracy of the data is more important than the simplicity of the data model and the queries tend to be of a reporting or aggregating nature there tends to be less issues with having many tables. Often views can allow you to present a high-level view of the data and introducing null values into the heading of query, while ugly, is more acceptable than breaking normal form in the raw data itself (though god help you if you start joining aggregate views on the gappy data rather than the underlying true state of the data).

The transactional version of the database is then free to reflect the state of the current data model alone rather than the historical permutations. Here the model can be clean and reflect more of the Domain Model although again you want to retain the Relational aspect of the data.

Having separate datastores with different schemas often makes app developers lives easier as well. Usually an application is only concerned with current interactions and not historical transactions. As long as historical data can be obtained as a Service then you have no need to reflect historical schema concerns in your application.

However even if you cannot separate the data there is still little reason to introduce null value columns into the database. ORM often makes the simple assumption that one data entity is one object, but that is simply to make ORM easier. The application persistence layer shouldn’t be allowed to distort the underlying relational data model. If your data isn’t relational or you can’t define a fixed schema, don’t use an RDBMS. Look into things like CouchDB.

In fact some persistence schemes, like JPA, actually allow you to reflect the reality of the relational data by allowing embedded entities in objects. This is a leaky abstraction because from an object point of view there often is very little reason why, say, an Order object contains a Delivery Dispatch Type object.

If you want to avoid the leak then use the Repository pattern to create a true Domain object and be prepared to handle the complexity of transforming the relational data to the object-orientated data within the Repository. Remember that the Repository represents a true boundary in the system: you are hoping to derive real benefits from both the relational representation and the object representation, not screw one in favour of the other.

So please; don’t just wack in another nullable column and then wonder why queries on your database are slow.

Web Applications

Try our new, new services!

So on Friday not one but two long awaited beta service invitations arrived. The first was the announcement of the addition of Jotspot to Google Apps (finally) and the other about the Amazon Simple DB service. Typical buses…

I didn’t have a lot of time this weekend so I plumped for signing up for Google Apps and trying the new wiki functionality as I was hoping for a beefed up version of Pages. The Simple DB service also needs me to beef up my Web Service scripting fu.

It is too early to say much about either service but after signing up for a Google Apps account (apparently you cannot simply drive one off your regular Google Account). I was slightly underwhelmed by the new Google Sites service. It has taken how long to make a basic and acceptable wiki service available?

Still you can have a lot of separate wiki sites and you have a lot of flexibility on how you share and collaborate on them so maybe I need to build up some content first and then try to share it around. I would like to know whether you can hook Analytics up to some Sites content. That would be useful for some of the content that otherwise would go on something like a WordPress page.