skip to main content


Title: Subtle Bugs Everywhere: Generating Documentation for Data Wrangling Code
Data scientists reportedly spend 60 to 80 percent of their time in their daily routines on data wrangling, i.e. cleaning data and extracting features. However, data wrangling code is often repetitive and error-prone to write. Moreover, it is easy to introduce subtle bugs when reusing and adopting existing code, which result not in crashes but reduce model quality. To support data scientists with data wrangling, we present a technique to generate interactive documentation for data wrangling code. We use (1) program synthesis techniques to automatically summarize data transformations and (2) test case selection techniques to purposefully select representative examples from the data based on execution information collected with tailored dynamic program analysis. We demonstrate that a JupyterLab extension with our technique can provide documentation for many cells in popular notebooks and find in a user study that users with our plugin are faster and more effective at finding realistic bugs in data wrangling code.  more » « less
Award ID(s):
1852260
NSF-PAR ID:
10313199
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Proceedings of the 36th IEEE/ACM International Conference on Automated Software Engineering (ASE), Los Alamitos, CA: IEEE Computer Society
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Static analysis tools have demonstrated effectiveness at finding bugs in real world code. Such tools are increasingly widely adopted to improve software quality in practice. Automated Program Repair (APR) has the potential to further cut down on the cost of improving software quality. However, there is a disconnect between these effective bug-finding tools and APR. Recent advances in APR rely on test cases, making them inapplicable to newly discovered bugs or bugs difficult to test for deterministically (like memory leaks). Additionally, the quality of patches generated to satisfy a test suite is a key challenge. We address these challenges by adapting advances in practical static analysis and verification techniques to enable a new technique that finds and then accurately fixes real bugs without test cases. We present a new automated program repair technique using Separation Logic. At a high-level, our technique reasons over semantic effects of existing program fragments to fix faults related to general pointer safety properties: resource leaks, memory leaks, and null dereferences. The procedure automatically translates identified fragments into source-level patches, and verifies patch correctness with respect to reported faults. In this work we conduct the largest study of automatically fixing undiscovered bugs in real-world code to date. We demonstrate our approach by correctly fixing 55 bugs, including 11 previously undiscovered bugs, in 11 real-world projects. 
    more » « less
  2. Coverage-based fault localization has been extensively studied in the literature due to its effectiveness and lightweightness for real-world systems. However, existing techniques often utilize coverage in an oversimplified way by abstracting detailed coverage into numbers of tests or boolean vectors, thus limiting their effectiveness in practice. In this work, we present a novel coverage-based fault localization technique, Grace, which fully utilizes detailed coverage information with graph-based representation learning. Our intuition is that coverage can be regarded as connective relationships between tests and program entities, which can be inherently and integrally represented by a graph structure: with tests and program entities as nodes, while with coverage and code structures as edges. Therefore, we first propose a novel graph-based representation to reserve all detailed coverage information and fine-grained code structures into one graph. Then we leverage Gated Graph Neural Network to learn valuable features from the graph-based coverage representation and rank program entities in a listwise way. Our evaluation on the widely used benchmark Defects4J (V1.2.0) shows that Grace significantly outperforms state-of-the-art coverage-based fault localization: Grace localizes 195 bugs within Top-1 whereas the best compared technique can at most localize 166 bugs within Top-1. We further investigate the impact of each Grace component and find that they all positively contribute to Grace. In addition, our results also demonstrate that Grace has learnt essential features from coverage, which are complementary to various information used in existing learning-based fault localization. Finally, we evaluate Grace in the cross-project prediction scenario on extra 226 bugs from Defects4J (V2.0.0), and find that Grace consistently outperforms state-of-the-art coverage-based techniques. 
    more » « less
  3. null (Ed.)
    Generate-and-validate (G&V) automated program repair (APR) techniques have been extensively studied during the past decade. Meanwhile, such techniques can be extremely time-consuming due to the manipulation of program code to fabricate a large number of patches and also the repeated test executions on patches to identify potential fixes. PraPR, a recent G&V APR technique, reduces such costs by modifying program code directly at the level of compiled JVM bytecode with on-the-fly patch validation, which directly allows multiple bytecode patches to be tested within the same JVM process. However, PraPR is limited due to its unique bytecode-repair design, and is basically unsound/imprecise as it assumes that patch executions do not change global JVM state and affect later patch executions on the same JVM process. In this paper, we propose a unified patch validation framework, named UniAPR, to perform the first empirical study of on-the-fly patch validation for state-of-the-art source-code-level APR techniques widely studied in the literature; furthermore, UniAPR addresses the imprecise patch validation issue by resetting the JVM global state via runtime bytecode transformation. We have implemented UniAPR as a publicly available fully automated Maven Plugin. Our study demonstrates for the first time that on-the-fly patch validation can often speed up state-of-the-art source-code-level APR by over an order of magnitude, enabling all existing APR techniques to explore a larger search space to fix more bugs in the near future. Furthermore, our study shows the first empirical evidence that vanilla on-the-fly patch validation can be imprecise/unsound, while UniAPR with JVM reset is able to mitigate such issues with negligible overhead. 
    more » « less
  4. null (Ed.)
    The first major goal of this project is to build a state-of-the-art information storage, retrieval, and analysis system that utilizes the latest technology and industry methods. This system is leveraged to accomplish another major goal, supporting modern search and browse capabilities for a large collection of tweets from the Twitter social media platform, web pages, and electronic theses and dissertations (ETDs). The backbone of the information system is a Docker container cluster running with Rancher and Kubernetes. Information retrieval and visualization is accomplished with containers in a pipelined fashion, whether in the cluster or on virtual machines, for Elasticsearch and Kibana, respectively. In addition to traditional searching and browsing, the system supports full-text and metadata searching. Search results include facets as a modern means of browsing among related documents. The system supports text analysis and machine learning to reveal new properties of collection data. These new properties assist in the generation of available facets. Recommendations are also presented with search results based on associations among documents and with logged user activity. The information system is co-designed by five teams of Virginia Tech graduate students, all members of the same computer science class, CS 5604. Although the project is an academic exercise, it is the practice of the teams to work and interact as though they are groups within a company developing a product. The teams on this project include three collection management groups -- Electronic Theses and Dissertations (ETD), Tweets (TWT), and Web-Pages (WP) -- as well as the Front-end (FE) group and the Integration (INT) group to help provide the overarching structure for the application. This submission focuses on the work of the Integration (INT) team, which creates and administers Docker containers for each team in addition to administering the cluster infrastructure. Each container is a customized application environment that is specific to the needs of the corresponding team. Each team will have several of these containers set up in a pipeline formation to allow scaling and extension of the current system. The INT team also contributes to a cross-team effort for exploring the use of Elasticsearch and its internally associated database. The INT team administers the integration of the Ceph data storage system into the CS Department Cloud and provides support for interactions between containers and the Ceph filesystem. During formative stages of development, the INT team also has a role in guiding team evaluations of prospective container components and workflows. The INT team is responsible for the overall project architecture and facilitating the tools and tutorials that assist the other teams in deploying containers in a development environment according to mutual specifications agreed upon with each team. The INT team maintains the status of the Kubernetes cluster, deploying new containers and pods as needed by the collection management teams as they expand their workflows. This team is responsible for utilizing a continuous integration process to update existing containers. During the development stage the INT team collaborates specifically with the collection management teams to create the pipeline for the ingestion and processing of new collection documents, crossing services between those teams as needed. The INT team develops a reasoner engine to construct workflows with information goal as input, which are then programmatically authored, scheduled, and monitored using Apache Airflow. The INT team is responsible for the flow, management, and logging of system performance data and making any adjustments necessary based on the analysis of testing results. The INT team has established a Gitlab repository for archival code related to the entire project and has provided the other groups with the documentation to deposit their code in the repository. This repository will be expanded using Gitlab CI in order to provide continuous integration and testing once it is available. Finally, the INT team will provide a production distribution that includes all embedded Docker containers and sub-embedded Git source code repositories. The INT team will archive this distribution on the Virginia Tech Docker Container Registry and deploy it on the Virginia Tech CS Cloud. The INT-2020 team owes a sincere debt of gratitude to the work of the INT-2019 team. This is a very large undertaking and the wrangling of all of the products and processes would not have been possible without their guidance in both direct and written form. We have relied heavily on the foundation they and their predecessors have provided for us. We continue their work with systematic improvements, but also want to acknowledge their efforts Ibid. Without them, our progress to date would not have been possible. 
    more » « less
  5. Automated Program Repair (APR) is one of the most recent advances in automated debugging, and can directly fix buggy programs with minimal human intervention. Although various advanced APR techniques (including search-based or semantic-based ones) have been proposed, they mainly work at the source-code level and it is not clear how bytecode-level APR performs in practice. Also, empirical studies of the existing techniques on bugs beyond what has been reported in the original papers are rather limited. In this paper, we implement the first practical bytecode-level APR technique, PraPR, and present the first extensive study on fixing real-world bugs (e.g., Defects4J bugs) using JVM bytecode mutation. The experimental results show that surprisingly even PraPR with only the basic traditional mutators can produce genuine fixes for 17 bugs; with simple additional commonly used APR mutators, PraPR is able to produce genuine fixes for 43 bugs, significantly outperforming state-of-the-art APR, while being over 10X faster. Furthermore, we performed an extensive study of PraPR and other recent APR tools on a large number of additional real-world bugs, and demonstrated the overfitting problem of recent advanced APR tools for the first time. Lastly, PraPR has also successfully fixed bugs for other JVM languages (e.g., for the popular Kotlin language), indicating PraPR can greatly complement existing source-code-level APR. 
    more » « less