matt-gardner / util

Some utilities for java and scala, mostly focused on interacting with the filesystem


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A simple collection of utilities that I've slowly been building as I need them for various projects. This is intended to contain things that are likely to be reusable across projects.

The biggest component (or at least the most frequently used and reusable) is FileUtil and related classes. This is an object that abstracts away the interface with the file system, for two purposes: (1) to handle in a simple one-line call some common patterns with interacting with the filesystem, like reading a set of integers from a file. And (2) to allow my code that interacts with the filesystem to be testable, without having to have BufferedReader methods that are the only parts that are tested. I started out with the BufferedReader testing route, and ended up here because it just worked better with all of the things I wanted to test.

Another big piece (new in version 2.1) is functionality for managing experiment pipelines. This lets you specify a number of Steps, with input files and output files, and run a whole pipeline by just telling the last Step to run (which will run whatever other earlier Steps in the pipeline are needed to produce input files that don't already exist). In addition, there's a Metrics class that's mostly reusable for comparing the output of different systems and printing results to the screen (including computing metrics like MAP, and significance tests).

Change log

Version 2.3

  • Added a SubprocessStep to the pipeline code, so that you can easily call out of scala with parts of your pipeline.

Version 2.2.1

  • Switched to using a real logging framework, instead of print statements.

Version 2.2

  • Added parallel execution of substeps in a pipeline, which required adding inProgressFiles. Note that the inProgressFiles help you even if you aren't using parallel execution within a single sbt process (i.e., if runSubstepsInParallel is always false) - if you start several sbt processes that run overlapping pipelines, this will still protect the bits that overlap.

  • Fixed some bugs in the pipeline code

  • Slight change in the API for reading sets and lists of integers from files

Version 2.1

  • Added Travis CI and coveralls integration (as seen by the badges at the top of this README).

  • Added pipeline / workflow functionality, to manage multi-step processes in an experiment workflow.

  • Added significance testing, and some other metric computation (and output) stuff.

  • Added some more parallel file processing.

Version 2.0:

  • Shortened package name from to com.mattg.util. Bumped the version number to 2.0, because this is a breaking change.

Version 1.2.5:

  • Added a parallel count operation for large files.

Version 1.2.4:

  • Added simple methods for reading and writing binary files, and for deleting directories, to FileUtil.

Version 1.2.3:

  • Use trove for immutable dictionaries, trying to further decrease memory usage and increase speed.

  • Trying to get more efficient parsing of large files. Now you can read integers from a TSV file without creating a ton of intermediate strings.

Version 1.2.2:

  • Improved the Index/Dictionary API, so you can have a non-mutable (and thus much more efficient) Dictionary.

Version 1.2.1:

  • Added the ability to enforce a set of options to JsonHelper, plus a minor test fix.

Version 1.2:

  • Moved FileUtil from java to scala, including moving to scala collections. This will mean any code upgrading to this version of the library will likely have to change code, to remove asScala (or add asJava, but why?) when interacting with FileUtil.

  • Allows for parallel processing of files, where we can do some kind of map or flatMap for each line in the file, without having to read the whole file into memory first.

  • Added tests for FileUtil and FakeFileUtil.

Version 1.1:

  • Added my SpecFileReader and JsonHelper, classes that deal with reading specification files in a JSON format, for configuring the behavior of code.