rOpenSci | Developing dittodb

Developing dittodb

This post describes a few different aspects behind the scenes of the development of dittodb which recently went through the rOpenSci peer review process and was released to CRAN on 24 July 2020. This isn’t an introduction to the package itself (that’s available on dittodb’s site), but rather a look behind the scenes of the conceiving of the idea, the inspiration for, some of the development of, and history behind dittodb.

🔗 The idea

The idea for dittodb came as a very practical one: at my day job I was working on an R package that interacted with our databases. Though we could test a lot of things, we were struggling with writing good tests for our database interactions. We could technically connect to the actual production database, but that meant that the tests were slow and depended on data that was sometimes changing1. Worst of all: it would mean having to store our database credentials in our Continuous Integration infrastructure.

I had gotten used to using mocked HTTP interfaces with other testing packages (see the section below about how httptest inspired dittodb) and since a database connection is very similar (one sends queries and gets different responses based on those queries) I thought surely someone has already written up an R package for mocking database connections.2 There’s even a standard interface that most database packages use for these interactions!

After a lot of googling and finding nothing, I came to the rOpenSci slack and asked: has anyone seen anything like this? And to my shock, the answer was no. That’s when I started chatting with Mauricio Vargas about what would become dittodb.

🔗 How dittodb was inspired by httptest

At a previous job, I had the opportunity to work with Neal Richardson, the author of httptest and we made extensive use of mocked HTTP interactions while developing the R package. So I had a lot of experience with the patterns of how httptest worked and I even contributed a small pull request. Knowing that the overall flow of the package would be similar gave me a really nice framework to build out dittodb3.

Like testing against a mocked HTTP interface, testing a database connection has two main parts:

  • there’s the request for HTTP or the query for database connections — this specifies what is being requested of the external API or database. For both, there are a number of different actions that return different results. For example, a GET in HTTP land is designed for retrieving some information, an SQL statement that starts with SELECT in database land will return a result that has data of some sort in it.
  • there’s the response for HTTP or the result for database connections — this is the result of whatever the request/query was above. For HTTP interfaces this is frequently a chunk of JSON (alongside some HTTP status codes and other information). With databases the result is frequently a dataframe (especially for SEELCT queries), but can also be lists of information (e.g. list(completed = 1L) after checking the status of a query).

The database package (e.g. RPostgres or RMariaDB) is responsible for taking your query, and using a database driver (which almost always use C or C++ based libraries) send the query, get the response from the database, and then transforming that response into an R-native data type (e.g. a dataframe). To be successful, when it is operating as a mock database, dittodb must be able to match a specific query to a result that is saved to disk (aka a fixture) and return that instead of executing against an actual database. We do this by hashing the query that is sent with dbSendQuery() and then we use that hash to look for the fixture file and read that fixture in when there is a call dbFetch().

To make this a concrete example, say you ran the following code, which mocks a database connection, sends one query, receives the result, and then disconnects:

  con <- dbConnect(...)
  result <- dbSendQuery(
    "SELECT carrier, name FROM airlines LIMIT 1"
  result_df <- dbFetch(result)

Under the hood, during the dbSendQuery() call dittodb takes the select statement, and hashes the query (to ef6317) and returns a result object that will look for the file SELECT-ef6317.R.

Then when you run dbFetch() a few lines later, dittodb looks for the file with the file name SELECT-ef6317.R in each of the mock path directories that have been configured. If it finds one, it will source that file and use that as the result of the fetch. This process is very similar to how httptest works and is one of the main pieces of inspiration that httptest had in the creation of dittodb.

🔗 Main technical challenges

The development process of dittodb had a number of interesting challenges. Two that I will expand on here are our use of method dispatch and class inheritance to make dittodb work as well as use of the trace function for recording fixtures.

🔗 Using method dispatch for good

R is famous for having not one, not two, not three but four object orientation systems.4 The DBI package uses S4 classes extensively. One thing that sets S4 apart from S3 is that S4 allows for formal class inheritance. Though a full description of inheritance is out of scope for this post, the most important point for us is that S4 can inherit methods from their parent classes. To borrow the inheritance metaphor from Advanced R:

Say we have a class 🙂 which inherits from class 😶. If we write a method mouth_shape() for objects of theses classes, we could define one method for each class, so for the 🙂 class which returns the value “smiling” when we call mouth_shape(🙂) and then we could define the same method for class 😶 which returns the value NULL when we call mouth_shape(😶)5. But when we go to define our method eyes() we don’t actually have to define a method for both of the classes, since 🙂 inherits from 😶, we could define the method for 😶 only to return “open” when we call eyes(😶). And now, when we call eyes(🙂) we will get the value “open” even though we did not explicitly write an eyes() method for the 🙂 class. Note that inheritance is directional and we couldn’t do this the other way around: if we only defined an eyes() method for 🙂, we would not automatically get the same behavior for eyes(😶). And if we did want slightly different behavior for these methods, we can always define an eyes() method for the 🙂 class later.

🔗 How this works in dittodb

dittodb makes extensive use of inheritance to serve a mocked database interface during testing: When dittodb is mocking a database connection in testing, instead of a pure connection class DBIConnection, we use a custom class DBIMockConnection which inherits from DBIConnection. This means that we can define custom methods for our DBIMockConnection that don’t actually connect to a database, but use our mocked functionality instead. For example, we defined a dbSendQuery method for the class DBIMockConnection that instead of sending a query, it hashes the query so we know where to look it up when we call dbFetch and returns a result of class DBIMockResult6. And then we defined a dbFetch method for the class DBIMockResult which takes the hash, looks for a file in a fixtures directory with that hash and loads it in, returning that as the fetched results.

Inheritance means that we only have to write custom methods for our DBIMock* classes if the underlying DBI methods call the database. For example, DBI provides a very commonly used method dbGetQuery() which is used to send a query and then fetch the results all at once instead of forcing people to make two calls. But, because the DBI definition for dbGetQuery() calls dbSendQuery() and then dbFetch() we don’t have to write a custom method for dittodb, we can rely on method dispatch and inheritance to do the right thing™️ for us. Easy as 🎂.7

🔗 Using trace in a relatively unorthodox way

Custom classes and inheritance are really great, but what about when we want to interact with a real database and save the results to disk to use later as fixtures? Though many fixtures (especially those that are replicating errant behavior) are best crafted (or edited) by hand so that they are targeted and exercise precise things during tests, it can be convenient to be able to record all of the interactions with a database (especially for hand editing).

We provide functionality to do this with the commands capture_db_requests({...}) which captures the requests made from any expressions wrapped inside, or start_db_capturing() and stop_db_capturing(). For these to work, we wanted to be able to call the standard, native database methods, but at the ends of some of them also execute code to save the fixture objects to disk. We could have used custom classes or mocking like we did above, but that would have required a considerable amount of copying code from other sources to replicate it (and keep it in sync as those packages changed!). Instead, we used trace() which is designed for interactive debugging of calls, but critically for our purposes, it allows us to insert little bits of code to be executed when the function is called (typically at the beginning or at the end).

Here is a (simplified)8 example of what the tracing call looks like when you turn on capturing mode:

    exit = quote({
      .dittodb_env$curr_file_path <- make_path(

What this does is it executes the code inside of the quote({...}) wrapper whenever dbSendQuery() exits it’s call. But critically, with the same environment as inside of dbSendQuery(). So we have access to the statement variable that dbSendQuery() did so that we can hash it. We then save that file path (the statement type, the hash, as well as the current connection’s own path within our mock directories) to a status placeholder (.dittodb_env$curr_file_path) so that we can use that when there is a call to dbFetch() to save the result to the right file.

Using trace in this way was also inspired by httptest which uses it in a similar way. It is certainly a little bit unorthodox, but it works for what we needed to accomplish in dittodb. It lets us capture fixtures with as little custom code as possible, while still working on any database connection that uses DBI.

🔗 What’s in a name?

As the saying goes, naming things is one of the hardest parts of software development. When we first started working on dittodb we called it dbtest. This fit nicely because, as we talked about above, dittodb took a lot of inspiration from httptest, so why not just swap out the bit that was being tested http > db. It was simple and descriptive.9 But there was just one problem, there was already a package with the same name10. Though it wasn’t on CRAN, we still didn’t want to cause confusion. So we set out to think up a different name. Mauricio Vargas had the great idea to name it dittodb.

An illustration of the Pokemon Ditto

Ditto ©Pokémon

The name dittodb takes inspiration from a few sources: The first, and most obvious for developers of a certain age, is the ditto pokemon known for its ability to take on the form of, and impersonate, any other pokemon. Following this, dittodb takes on the form and properties of a database backend, without actually being that database backend. For a different set of (likely non-overlapping with the first) developers dittodb will recall the spirit duplicators used to make duplication of printed materials by making an artifact during the writing process that can be used to make further copies. In some areas these machines were frequently called ditto-machines. dittodb is similar when it is recording fixtures: during the process of interacting with a live database, it makes copies of the responses that can be used to make further copies while running tests as fixtures.

🔗 Resources

🔗 Acknowledgements

dittodb wouldn’t have been possible without the help of a bunch of folks:

  1. And these changes are sometimes for the good, in the case of ETL bugs that we found that were later corrected. ↩︎

  2. In fact, there are multiple packages for testing HTTP interfaces↩︎

  3. With proper attribution, of course. ↩︎

  4. I may be missing some, but even if not now, surely a new one will be made soon enough! ↩︎

  5. There is no mouth, after all. ↩︎

  6. Which, shockingly enough, inherits from DBIResult↩︎

  7. The 🎂 is a lie. It turns out this works for almost all database packages, but some like RPostgreSQL define their own method for dbGetQuery() that doesn’t use dbSendQuery() and dbFetch() internally. To deal with this, we actually created another level of class hierarchy where each database driver has its own custom class (e.g. DBIMockRPostgreSQLConnection) which inherits from both DBIMockConnection and DBIRPostgreSQLConnection so that we can define custom methods for DBI functions like dbSendQuery() for the specific drivers that need them. ↩︎

  8. If you would like to see the full source, see the trace call as well as the function that is called on exit↩︎

  9. Though it should be pointed out, “dbtest” also had the unfortunate property that iOS and macOS auto-correctors would almost constantly “correct” it to “detest”. Though I will admit to being frustrated by bugs that my test suites reveal, detest wasn’t the first thing I wanted associated with this new package. ↩︎

  10. Many thanks to @ma_salmon for pointing this out to us! ↩︎