Supporting the grow-and-prune model for evolving software product lines

207 p.Software Product Lines (SPLs) aim at supporting the development of a whole family of software products through a systematic reuse of shared assets. To this end, SPL development is separated into two interrelated processes: (1) domain engineering (DE), where the scope and variability of the system is defined and reusable core-assets are developed; and (2) application engineering (AE), where products are derived by selecting core assets and resolving variability. Evolution in SPLs is considered to be more challenging than in traditional systems, as both core-assets and products need to co-evolve. The so-called grow-and-prune model has proven great flexibility to incrementally evolve an SPL by letting the products grow, and later prune the product functionalities deemed useful by refactoring and merging them back to the reusable SPL core-asset base. This Thesis aims at supporting the grow-and-prune model as for initiating and enacting the pruning. Initiating the pruning requires SPL engineers to conduct customization analysis, i.e. analyzing how products have changed the core-assets. Customization analysis aims at identifying interesting product customizations to be ported to the core-asset base. However, existing tools do not fulfill engineers needs to conduct this practice. To address this issue, this Thesis elaborates on the SPL engineers' needs when conducting customization analysis, and proposes a data-warehouse approach to help SPL engineers on the analysis. Once the interesting customizations have been identified, the pruning needs to be enacted. This means that product code needs to be ported to the core-asset realm, while products are upgraded with newer functionalities and bug-fixes available in newer core-asset releases. Herein, synchronizing both parties through sync paths is required. However, the state of-the-art tools are not tailored to SPL sync paths, and this hinders synchronizing core-assets and products. To address this issue, this Thesis proposes to leverage existing Version Control Systems (i.e. git/Github) to provide sync operations as first-class construct

Deep Learning Software Repositories

Bridging the abstraction gap between artifacts and concepts is the essence of software engineering (SE) research problems. SE researchers regularly use machine learning to bridge this gap, but there are three fundamental issues with traditional applications of machine learning in SE research. Traditional applications are too reliant on labeled data. They are too reliant on human intuition, and they are not capable of learning expressive yet efficient internal representations. Ultimately, SE research needs approaches that can automatically learn representations of massive, heterogeneous, datasets in situ, apply the learned features to a particular task and possibly transfer knowledge from task to task. Improvements in both computational power and the amount of memory in modern computer architectures have enabled new approaches to canonical machine learning tasks. Specifically, these architectural advances have enabled machines that are capable of learning deep, compositional representations of massive data depots. The rise of deep learning has ushered in tremendous advances in several fields. Given the complexity of software repositories, we presume deep learning has the potential to usher in new analytical frameworks and methodologies for SE research and the practical applications it reaches. This dissertation examines and enables deep learning algorithms in different SE contexts. We demonstrate that deep learners significantly outperform state-of-the-practice software language models at code suggestion on a Java corpus. Further, these deep learners for code suggestion automatically learn how to represent lexical elements. We use these representations to transmute source code into structures for detecting similar code fragments at different levels of granularity—without declaring features for how the source code is to be represented. Then we use our learning-based framework for encoding fragments to intelligently select and adapt statements in a codebase for automated program repair. In our work on code suggestion, code clone detection, and automated program repair, everything for representing lexical elements and code fragments is mined from the source code repository. Indeed, our work aims to move SE research from the art of feature engineering to the science of automated discovery

Semantic Web Enabled Software Engineering

Ontologies allow the capture and sharing of domain knowledge by formalizing information and making it machine understandable. As part of an information system, ontologies can capture and carry the reasoning knowledge needed to fulfill different application goals. Although many ontologies have been developed over recent years, few include such reasoning information. As a result, many ontologies are not used in real-life applications, do not get reused or only act as a taxonomy of a domain. This work is an investigation into the practical use of ontologies as a driving factor in the development of applications and the incorporation of Knowledge Engineering as a meaningful activity into modern agile software development. This thesis contributes a novel methodology that supports an incremental requirement analysis and an iterative formalization of ontology design through the use of ontology reasoning patterns. It also provides an application model for ontology-driven applications that can deal with nonontological data sources. A set of case studies with various application specific goals helps to elucidate whether ontologies are in fact suitable for more than simple knowledge formalization and sharing, and can act as the underlying structure for developing largescale information systems. Tasks from the area of bug-tracker quality mining and clone detection are evaluated for this purpose

Code similarity and clone search in large-scale source code data

Software development is tremendously benefited from the Internet by having online code corpora that enable instant sharing of source code and online developer's guides and documentation. Nowadays, duplicated code (i.e., code clones) not only exists within or across software projects but also between online code repositories and websites. We call them "online code clones."' They can lead to license violations, bug propagation, and re-use of outdated code similar to classic code clones between software systems. Unfortunately, they are difficult to locate and fix since the search space in online code corpora is large and no longer confined to a local repository. This thesis presents a combined study of code similarity and online code clones. We empirically show that many code snippets on Stack Overflow are cloned from open source projects. Several of them become outdated or violate their original license and are possibly harmful to reuse. To develop a solution for finding online code clones, we study various code similarity techniques to gain insights into their strengths and weaknesses. A framework, called OCD, for evaluating code similarity and clone search tools is introduced and used to compare 34 state-of-the-art techniques on pervasively modified code and boiler-plate code. We also found that clone detection techniques can be enhanced by compilation and decompilation. Using the knowledge from the comparison of code similarity analysers, we create and evaluate Siamese, a scalable token-based clone search technique via multiple code representations. Our evaluation shows that Siamese scales to large-scale source code data of 365 million lines of code and offers high search precision and recall. Its clone search precision is comparable to seven state-of-the-art clone detection tools on the OCD framework. Finally, we demonstrate the usefulness of Siamese by applying the tool to find online code clones, automatically analyse clone licenses, and recommend tests for reuse

Exploring regularities in software with statistical models and their applications

Software systems are becoming popular. They are used with different platforms for different applications. Software systems are developed with support from programming languages, which help developers work conveniently. Programming languages can have different paradigms with different form, syntactic structures, keywords, and representation ways. In many cases, however, programming languages are similar in different important aspects: 1. They are used to support description of specific tasks, 2. Source codes are written in languages and includes a limit set of distinctive tokens, many tokens are repeated like keywords, function calls, and 3. They follow specific syntactic rules to make machine understanding. Those points also respect the similarity between programming language and natural language. Due to its critical role in many applications, natural language processing (NLP) has been studied much and given many promising results like automatic cross-language translation, speech-to-text, information searching, etc. It is interesting to observe if there are similar characteristics between natural language and programming language and whether techniques in NLP can be reused for programming language processing? Recent works in software engineering (SE) shows that their similarities between NLP and programming language processing and techniques in NLP can be reused for PLP. This dissertation introduces my works with contributions in study of characteristics of programming languages, the models which employed them and the main applications that show the usefulness of the proposed models. Study in both three aspects has drawn interests from software engineering community and received awards due to their innovation and applicability. \u27 I hope that this dissertation will bring a systematic view of how advantage techniques in natural language processing and machine learning can be re-used and give huge benefit for programming language processing, and how those techniques are adapted with characteristics of programming language and software systems

Harnessing customizationinWeb Annotation: ASoftwareProduct Line approach

222 p.La anotación web ayuda a mediar la interacción de lectura y escritura al transmitir información, agregar comentarios e inspirar conversaciones en documentos web. Se utiliza en áreas de Ciencias Sociales y Humanidades, Investigación Periodística, Ciencias Biológicas o Educación, por mencionar algunas. Las actividades de anotación son heterogéneas, donde los usuarios finales (estudiantes, periodistas, conservadores de datos, investigadores, etc.) tienen requisitos muy diferentes para crear, modificar y reutilizar anotaciones. Esto resulta en una gran cantidad de herramientas de anotación web y diferentes formas de representar y almacenar anotaciones web. Para facilitar la reutilización y la interoperabilidad, se han realizado varios intentos durante las últimas décadas para estandarizar las anotaciones web (por ejemplo, Annotea u Open Annotation), lo que ha dado como resultado las recomendaciones de anotaciones del W3C publicadas en 2017. Las recomendaciones del W3C proporcionan un marco para la representación de anotaciones (modelo de datos y vocabulario) y transporte (protocolo). Sin embargo, todavía hay una brecha en cómo se desarrollan los clientes de anotación (herramientas e interfaces de usuario), lo que hace que los desarrolladores vuelvan a re-implementar funcionalidades comunes (esdecir, resaltar, comentar, almacenar,¿) para crear su herramienta de anotación personalizada.Esta tesis tiene como objetivo proporcionar una plataforma de reutilización para el desarrollo de herramientas de anotación web para la revisión. Con este fin, hemos desarrollado una línea de productos de software llamada WACline. WACline es una familia de productos de anotación que permite a los desarrolladores crear extensiones de navegador de anotación web personalizadas, lo que facilita la reutilización de los activos principales y su adaptación a su contexto de revisión específico. Se ha creado siguiendo un proceso de acumulación de conocimientos en el que cada producto de anotación aprende de los productos de anotación creados previamente. Finalmente, llegamos a una familia de clientes de anotación que brinda soporte para tres prácticas de revisión: extracción de datos de revisión sistemática de literatura (Highlight&Go), revisión de tareas de estudiantes en educación superior (Mark&Go), y revisión por pares de conferencias y revistas (Review&Go). Para cada uno de los contextos de revisión, se ha llevado a cabo una evaluación con partes interesadas reales para validar las mejoras de eficiencia y eficacia aportadas por las herramientas de anotación personalizadas en su práctica

On the real world practice of Behaviour Driven Development

Surveys of industry practice over the last decade suggest that Behaviour Driven Development is a popular Agile practice. For example, 19% of respondents to the 14th State of Agile annual survey reported using BDD, placing it in the top 13 practices reported. As well as potential benefits, the adoption of BDD necessarily involves an additional cost of writing and maintaining Gherkin features and scenarios, and (if used for acceptance testing,) the associated step functions. Yet there is a lack of published literature exploring how BDD is used in practice and the challenges experienced by real world software development efforts. This gap is significant because without understanding current real world practice, it is hard to identify opportunities to address and mitigate challenges. In order to address this research gap concerning the challenges of using BDD, this thesis reports on a research project which explored: (a) the challenges of applying agile and undertaking requirements engineering in a real world context; (b) the challenges of applying BDD specifically and (c) the application of BDD in open-source projects to understand challenges in this different context. For this purpose, we progressively conducted two case studies, two series of interviews, four iterations of action research, and an empirical study. The first case study was conducted in an avionics company to discover the challenges of using an agile process in a large scale safety critical project environment. Since requirements management was found to be one of the biggest challenges during the case study, we decided to investigate BDD because of its reputation for requirements management. The second case study was conducted in the company with an aim to discover the challenges of using BDD in real life. The case study was complemented with an empirical study of the practice of BDD in open source projects, taking a study sample from the GitHub open source collaboration site. As a result of this Ph.D research, we were able to discover: (i) challenges of using an agile process in a large scale safety-critical organisation, (ii) current state of BDD in practice, (iii) technical limitations of Gherkin (i.e., the language for writing requirements in BDD), (iv) challenges of using BDD in a real project, (v) bad smells in the Gherkin specifications of open source projects on GitHub. We also presented a brief comparison between the theoretical description of BDD and BDD in practice. This research, therefore, presents the results of lessons learned from BDD in practice, and serves as a guide for software practitioners planning on using BDD in their projects

The Deliverance of Others

The Deliverance of Others is a compelling reappraisal of the idea that narrative literature can expand readers' empathy. What happens if, amid the voluminous influx of otherness facilitated by globalization, we continue the tradition of valorizing literature for bringing the lives of others to us, admitting them into our world and valuing the difference that they introduce into our lives? In this new historical situation, are we not forced to determine how much otherness is acceptable, as opposed to how much is excessive, disruptive, and disturbing? The influential literary critic David Palumbo-Liu suggests that we can arrive at a sense of responsibility toward others by reconsidering the discourses of sameness that deliver those unlike ourselves to us. Through virtuoso readings of novels by J. M. Coetzee, Nadine Gordimer, Kazuo Ishiguro, and Ruth Ozeki, he shows how notions that would seem to offer some basis for commensurability between ourselves and others

Ecophysiology of microbial communities associated with marine sponges Ircinia strobilina and Mycale laxissima

Marine sponges are hosts to many microorganisms that can constitute up to 60% of the sponge biomass. Complex symbiotic interactions may exist between sponges and associated microorganisms. My primary goal was to develop a model sponge system for laboratory studies of complex symbioses between bacteria and marine invertebrates. Two sets of aquaculture systems were designed in order to optimize the conditions for culturing marine sponges Mycale laxissima and Ircinia strobilina. Bacterial communities associated with the sponges were characterized using culture-based and molecular techniques. There was a substantial change in the diversity and composition of bacterial communities upon transfer into aquaculture. This work shows a potential for maintaining healthy marine sponges in closed aquaculture systems, a necessary foundation for using sponges in aquaculture as a laboratory model. There is a limited knowledge of the contributions of bacteria to sponges, and thereby indirectly to the coral reef ecosystem. I examined the role of sponge-associated bacteria in nitrogen fixation. Nitrogen fixation was demonstrated in sponges using nitrogen isotopic composition. The potential for nitrogen fixation by symbionts was assessed by amplification of nifH gene fragments from total DNA and RNA extracted from sponges. Diverse nifH genes were detected, and gene expression studies proved that nifH genes were expressed in sponge-associated bacteria. These nifH transcripts were closely related to cyanobacterial nifH genes. This is the first demonstration of the expression of bacterial genes in sponge symbionts. Cyanobacterial symbionts are likely fixing nitrogen and provide fixed nitrogen to their hosts. Quorum sensing in sponges is hypothesized to play a role in colonization by symbionts and the regulation of symbiosis between sponges and associated bacteria. Alpha- and gamma-proteobacterial isolates were tested for the production of acyl homoserine lactones (AHLs) using diffusion bioassays coupled with thin-layer chromatography fractionation. Isolates affiliated with the Silicibacter-Ruegeria subgroup of the Roseobacteria clade were the main producers of AHLs. These findings demonstrate that sponge associated bacteria show a high incidence of production of complex suites of AHLs involved in cell signaling. This research contributes to the field of sponge microbiology by advancing the understanding of the roles of symbionts and interactions with their hosts