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Hi everyone, welcome back after lunch! I hope you enjoyed your meal. Right now, we are going to start discussing our topic today: high-speed parsing of massive XML data in Ruby. I am Tetsuya Hirota from Japan.
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Today, I'll tell you more about high-speed processing of XML in Ruby. This presentation is an updated version of one I previously delivered at Ruby World Conference 2023 in Japan. First, I was requested to convert data in the BioProject XML file into JSON using Ruby.
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While I was provided with a sample call to do this, the process took me more than four times longer than the sample code suggested. Therefore, I created a method similar to the Python `iterparse()`, which parsed each top-level element individually. This method, combined with Ruby on Ractor, improved performance to be about 30% faster than the original Python sample.
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Today's content will include an introduction, a brief self-introduction, an overview of my company, and an explanation of my project. I will cover what I attempted to achieve and how I created a mechanism similar to Python's `iterparse()` using Ruby.
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My name is Tetsuya Hirota, and I am the CTO at my company. I'm based in Japan, where I spend a lot of time developing applications for bioinformatics. I have been dedicated to our core biotic database development for quite some time.
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In my work, I also teach a programming course focusing on lifelong learning related to bioinformatics. I offer valuable insights into life sciences, including data visualization to help understand what types of operations are demanded by the life science community.
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Today, my focus will be on ongoing development processes for bioinformatics databases. We face challenges related to high-speed parsing of massive XML files.
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The BioProject is a public database that encompasses various bioscience projects. This includes information related to genomes and RNA sequences registered in public databases, along with associated metadata such as papers, experimental conditions, and samples.
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My project involves curating a metacollection about sequence analysis with robust metadata. The format of this project is primarily simple XML files that exceeded 2 gigabytes in size, containing over 700,000 records. The database is continuously growing.
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Researchers often need to perform complex queries on this data. The current limitations mean heavy memory use, consuming around 70 gigabytes when parsing the files.
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Initially, I attempted to parse the BioProject XML using standard methods, which resulted in non-responsive outputs that took over 35 minutes and consumed excessive memory.
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This process is slow because it necessitates loading all objects into memory, and each request searches through the entire dataset. My goal has been to find a more efficient method.
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I explored Python sample codes, which process data in about 8 minutes through incremental loading of individual elements.
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The elements in our database are structured hierarchically with each project element averaging between 100 kilobytes to a few megabytes in size. The XML parser traditionally extracts all elements into memory, creating significant overhead.
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To improve this process, I began leveraging string operations to separate data intelligently and utilize memory more efficiently. Initially, I focused on Ruby's existing capabilities but ran into performance issues, illustrating the importance of implementing solutions that avoid blocking processes.
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I decided to split these tasks into more manageable parts. In the first part, I extracted the primary XML data, followed by the parsing of secondary elements, ensuring that the output was streamlined.
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For outputting JSON, I gathered each project element and processed it before writing it to the resulting file.
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This modular approach allows for much quicker results, reducing processing time significantly.
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Utilizing Ruby on Ractor has enabled concurrent processing, which I found beneficial in optimizing the performance compared to Ruby's conventional parsing methods.
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In the end, I was able to achieve a processing time of about five minutes and thirty-four seconds, which was a significant improvement from the initial methods I tried.
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Moreover, during these tests, I utilized a five CPU setup with 8 gigabytes of RAM, showcasing how resource allocation impacts performance.
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In conclusion, my approach to bioinformatics database processing in Ruby can be optimized greatly. It is essential that we take advantage of Ruby's unique features to sidestep potential bottlenecks.
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I appreciate everyone's attention and I’m ready for any questions you might have.
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Thank you for your interest and participation today! If you have any further queries about the technology or my methodologies, I welcome you to ask.
