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On the reaction to deprecation of clients of 4+1 popular Java APIs and the JDK

EMPIRICAL SOFTWARE ENGINEERING 2018年第4期23卷 2158-2197页

作者： Sawant, Anand Ashok Robbes, Romain Bacchelli, Alberto Delft Univ Technol SERG Delft Netherlands Free Univ Bozen Bolzano Software & Syst Engn Res Grp SwSE Bolzano Italy Univ Zurich ZEST Zurich Switzerland

application programming interfaces (APIs) are a tremendous resource-that is, when they are stable. Several studies have shown that this is unfortunately not the case. Of those, a large-scale study of API changes in the Pharo Smalltalk ecosystem documented several findings about API deprecations and their impact on API clients. We extend this study, by analyzing clients of both popular third-party Java APIs and the JDK API. This results in a dataset consisting of more than 25,000 clients of five popular Java APIs on GitHub, and 60 clients of the JDK API from Maven Central. This work addresses several short-comings of the previous study, namely: a study of several distinct API clients in a popular, statically-typed language, with more accurate version information. We compare and contrast our findings with the previous study and highlight new ones, particularly on the API client update practices and the startling similarities between reaction behavior in Smalltalk and Java. We make a comparison between reaction behavior for third-party APIs and JDK APIs, given that language APIs are a peculiar case in terms of wide-spread usage, documentation, and support from IDEs. Furthermore, we investigate the connection between reaction patterns of a client and the deprecation policy adopted by the API used.

关键词： application programming interface API usage API popularity Dataset

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The Ruby UCSC API: accessing the UCSC genome database using Ruby

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BMC BIOINFORMATICS 2012年第1期13卷 1-6页

作者： Mishima, Hiroyuki Aerts, Jan Katayama, Toshiaki Bonnal, Raoul J. P. Yoshiura, Koh-ichiro Nagasaki Univ Grad Sch Biomed Sci Dept Human Genet Nagasaki 8528523 Japan Leuven Univ Fac Engn ESAT SCD B-3001 Louvain Belgium IBBT KULeuven Future Hlth Dept Louvain Belgium Univ Tokyo Fac Engn Database Ctr Life Sci Res Org Informat & SystBunkyo Ku Tokyo 1130032 Japan Fdn Ist Nazl Genet Mol Integrat Biol Program I-20122 Milan Italy

Background: The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results: The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions: Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://***/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://***/.

关键词： Ruby application programming interface Genomic Interval Distribute Annotation System Table Class

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Information correspondence between types of documentation for APIs

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EMPIRICAL SOFTWARE ENGINEERING 2020年第5期25卷 4069-4096页

作者： Arya, Deeksha M. Guo, Jin L. C. Robillard, Martin P. McGill Univ Montreal PQ Canada

Documentation for programming languages and their APIs takes many forms, such as reference documentation, blog posts or other textual and visual media. Prior research has suggested that developers switch between reference and tutorial-like documentation while learning a new API. Documentation creation and maintenance is also an effort-intensive process that requires its creators to carefully inspect and organize information, while ensuring consistency across different sources. This article reports on the relationship between information in tutorials and in API reference documentation of three libraries on the topics: regular expressions, unified resource location and Input/Output in the two programming languages, Java and Python. Our investigation reveals that about half of the sentences in the tutorials studied describeAPI Information, i.e. syntax, behaviour, usage and performance of the API, that could be found in the reference documentation. The remaining are tutorial specific use-cases and examples. We also elicited and analyzed six types of correspondences between sentences in tutorials and reference documentation, ranging fromidenticaltoimplied. Based on our findings, we propose a general information reuse pattern as a structured abstraction to represent the systematic integration of information from the reference documentation into a tutorial. We report on the distribution of 38 instances of this pattern, and on the impact of applying the pattern automatically on the existing tutorials. This work lays a foundation for understanding the nature of information correspondence across different documentation types to inform and assist documentation generation and maintenance.

关键词： Software documentation application programming interface Qualitative analysis Exploratory study

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Embedded Middleware and Software Development Kit for Area-Based Distributed Mobile Cache System

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IEEE TRANSACTIONS ON CONSUMER ELECTRONICS 2013年第1期59卷 281-289页

作者： Kasai, Hiroyuki Univ Electrocommun Grad Sch Informat Syst Tokyo 1828585 Japan

A new area-based distributed mobile cache system, a sustainable distributed Geocast technology, enables data caching temporarily in a designated local area using short-range communication technologies such as WiFi and Bluetooth. This system needs no infrastructure network and servers. This caching capability and mechanisms are expected to enhance short-range communications as a time-offset communication in a physical world. For that reason, it is sure to accelerate new location-based communication services. This paper reports a developed middleware for a widespread embedded operating system, and a software development kit with an open application programming interface. This middleware is expected to spur third-party developers to produce widely various applications using this proposed platform. Some pseudo-code is provided. Procedures to use this platform are also explained using an implemented geo-location social game(1).

关键词： Area-based distributed mobile cache Embedded middleware application programming interface Software Development Kit

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A Malware Detection Method Based on Genetic Algorithm Optimized CNN-SENet Network

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IEEE ACCESS 2024年 12卷 160052-160063页

作者： Yang, Zheng Zhu, Hua Li, Zhao Wang, Gang Su, Meng Yunnan Power Grid Co Ltd Elect Power Res Inst Kunming 650200 Peoples R China Kunming Univ Sci & Technol Fac Elect Power Engn Kunming 650500 Peoples R China

In recent years, convolutional neural network (CNN) has achieved great success in the field of network security protection. With the popularization of smart terminals and the gradual increase of power grid informatization and digitization, the protection of power monitoring systems from various cybersecurity threads is a current scientific problem that needs to be solved urgently. To this end, this paper proposes a malware detection method based on genetic algorithm optimization of the CNN-SENet network, which firstly introduces the SENet attention mechanism into the convolutional neural network to enhance the spatial feature extraction capability of the model;then, the application programming interface (API) sequences corresponding to different software behaviors are processed by segmentation and de-duplication, which in turn leads to the sequence feature extraction through the CNN-SENet model;finally, genetic algorithm is used to optimize the hyperparameters of CNN-SENet network to reduce the computational overhead of CNN and to achieve the recognition and classification of different malware at the output layer. The examples under the public dataset containing 8 kinds of malware show that the proposed method is better than the traditional algorithmic model, and can accurately and efficiently achieve malware detection with strong generalization ability.

关键词： application programming interface convolutional neural network convolutional neural network malware detection malware detection network security network security power mobile terminal power mobile terminal SENet attention mechanism SENet attention mechanism SENet attention mechanism

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The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications

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BMC BIOINFORMATICS 2005年第1期6卷 1-7页

作者： Moreland, JL Gramada, A Buzko, OV Zhang, Q Bourne, PE San Diego Supercomp Ctr 9500 Gilman Dr La Jolla CA 92093 USA Univ Calif San Diego Dept Pharmacol 9500 Gilman Dr La Jolla CA 92093 USA

Background: The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web. Results: We describe a new software toolkit - the Molecular Biology Toolkit (MBT;http://***) - that enables fast development of applications for protein analysis and visualization. The toolkit is written in Java, thus offering platform-independence and Internet delivery capabilities. Several applications of the toolkit are introduced to illustrate the functionality that can be achieved. Conclusions: The MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).

关键词： Protein Data Bank application programming interface Class Hierarchy Common Data Model Sequence Viewer

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A high level interface to SCOP and ASTRAL implemented in Python

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BMC BIOINFORMATICS 2006年第1期7卷 1-4页

作者： Casbon, JA Crooks, GE Saqi, MAS Univ London Queen Mary Sch Med & Dent Inst Cell & Mol Sci London EC1 6BQ England Univ Calif Berkeley Dept Plant & Microbial Biol Berkeley CA 94720 USA

Background: Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. Results: We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. Conclusion: The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

关键词： Unify Modelling Language application programming interface Scop Database FASTA File Domain Object

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Affordable Virtual Reality Setup for Educational Aerospace Robotics Simulation and Testing

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JOURNAL OF AEROSPACE INFORMATION SYSTEMS 2020年第1期17卷 66-69页

作者： Shi, Zhenyu McGhan, Catharine L. R. Univ Cincinnati Dept Aerosp Engn AS4SR Lab Cincinnati OH 45221 USA

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API2MoL: Automating the building of bridges between APIs and Model-Driven Engineering

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INFORMATION AND SOFTWARE TECHNOLOGY 2012年第3期54卷 257-273页

作者： Canovas Izquierdo, Javier Luis Jouault, Frederic Cabot, Jordi Garcia Molina, Jesus Ecole Mines Nantes F-44307 Nantes France INRIA F-44307 Nantes France Univ Murcia Fac Informat Dept Comp & Syst E-30071 Murcia Spain

Context: A software artefact typically makes its functionality available through a specialized application programming interface (API) describing the set of services offered to client applications. In fact, building any software system usually involves managing a plethora of APIs, which complicates the development process. In Model-Driven Engineering (MDE). where models are the key elements of any software engineering activity, this API management should take place at the model level. Therefore, tools that facilitate the integration of APIs and MDE are clearly needed. Objective: Our goal is to automate the implementation of API-MDE bridges for supporting both the creation of models from API objects and the generation of such API objects from models. In this sense, this paper presents the API2MoL approach, which provides a declarative rule-based language to easily write mapping definitions to link API specifications and the metamodel that represents them. These definitions are then executed to convert API objects into model elements or vice versa. The approach also allows both the metamodel and the mapping to be automatically obtained from the API specification (bootstrap process). Method: After implementing the API2MoL engine, its correctness was validated using several APIs. Since APIs are normally large, we then developed a tool to implement the bootstrap process, which was also validated. Results: We provide a toolkit (language and bootstrap tool) for the creation of bridges between APIs and MDE. The current implementation focuses on Java APIs, although its adaptation to other statically typed object-oriented languages is straightforward. The correctness, expressiveness and completeness of the approach have been validated with the Swing, SWT and JTwitter APIs. Conclusion: API2MoL frees developers from having to manually implement the tasks of obtaining models from API objects and generating such objects from models. This helps to manage API models in MDE-based so

关键词： application programming interface Model-Driven Engineering Domain-Specific Languages

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fine-GRAPE: fine-grained APi usage extractor - an approach and dataset to investigate API usage

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EMPIRICAL SOFTWARE ENGINEERING 2017年第3期22卷 1348-1371页

作者： Sawant, Anand Ashok Bacchelli, Alberto Delft Univ Technol Mekelweg 4 NL-2628 CD Delft Netherlands

An application programming interface (API) provides a set of functionalities to a developer with the aim of enabling reuse. APIs have been investigated from different angles such as popularity usage and evolution to get a better understanding of their various characteristics. For such studies, software repositories are mined for API usage examples. However, many of the mining algorithms used for such purposes do not take type information into account. Thus making the results unreliable. In this paper, we aim to rectify this by introducing fine-GRAPE, an approach that produces fine-grained API usage information by taking advantage of type information while mining API method invocations and annotation. By means of fine-GRAPE, we investigate API usages from Java projects hosted on GitHub. We select five of the most popular APIs across GitHub Java projects and collect historical API usage information by mining both the release history of these APIs and the code history of every project that uses them. We perform two case studies on the resulting dataset. The first measures the lag time of each client. The second investigates the percentage of used API features. In the first case we find that for APIs that release more frequently clients are far less likely to upgrade to a more recent version of the API as opposed to clients of APIs that release infrequently. The second case study shows us that for most APIs there is a small number of features that is actually used and most of these features relate to those that have been introduced early in the APIs lifecycle.

关键词： application programming interface API usage API popularity Dataset

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