Spectrum-Based Fault Localization in Model Transformations

Model transformations play a cornerstone role in Model-Driven Engineering (MDE), as they provide the essential mechanisms for manipulating and transforming models. The correctness of software built using MDE techniques greatly relies on the correctness of model transformations. However, it is challenging and error prone to debug them, and the situation gets more critical as the size and complexity of model transformations grow, where manual debugging is no longer possible. Spectrum-Based Fault Localization (SBFL) uses the results of test cases and their corresponding code coverage information to estimate the likelihood of each program component (e.g., statements) of being faulty. In this article we present an approach to apply SBFL for locating the faulty rules in model transformations. We evaluate the feasibility and accuracy of the approach by comparing the effectiveness of 18 different stateof- the-art SBFL techniques at locating faults in model transformations. Evaluation results revealed that the best techniques, namely Kulcynski2, Mountford, Ochiai, and Zoltar, lead the debugger to inspect a maximum of three rules to locate the bug in around 74% of the cases. Furthermore, we compare our approach with a static approach for fault localization in model transformations, observing a clear superiority of the proposed SBFL-based method.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-RJunta de Andalucía P12-TIC-186

A bacterial acetyltransferase targets the protein kinase ZIP1, a positive regulator of plant immunity

Pseudomonas syringae is a model bacterial pathogen that penetrates the leaf to reach the plant apoplast, where it replicates causing disease. In order to do that, the pathogen must interfere and suppress a two-tiered plant defense response: PTI (PAMP-Triggered Immunity, or basal resistance) and ETI (Effector-Triggered Immunity). P. syringae uses a type III secretion system to directly deliver effector proteins inside the plant cell cytosol, many of which are known to suppress PTI, some of which are known to trigger ETI, and a handful of which are known to suppress ETI. Bacterial infection can also trigger a systemic plant defense response that protects the plant against additional pathogen attacks known as SAR (Systemic Acquired Resistance). We are particularly interested in the molecular and cellular mechanisms involved in effector-mediated defense evasion by P. syringae, in particular those involved in the suppression of ETI and SAR, and/or mediation of hormone signaling. Here we present data describing effector-mediated interference with plant immunity, by means of acetylation of a key positive regulator of local and systemic responses. Our work identifies a novel plant target for effector function, and characterizes its function. This work illustrates how analyzing the means by which a given effector interferes with its target can provide novel information regarding eukaryotic molecular mechanisms.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. MINECO BIO2015-64391R y FEDE

The bacterial effector HopZ1a acetylates ZIP1 kinase to suppress Arabidopsis defence responses

During the plant-pathogen interaction, disease or resistance are determined in the plant by a series of molecular events. The plant detects Pathogen-Associated Molecular Patterns (PAMPs), such as flagellin, triggering a defence response called PTI (PAMP-Triggered Immunity). Bacterial pathogens can in turn suppress such defence response through the translocation into the plant cell cytosol of virulence proteins, called effectors, via a Type Three Secretion System (T3SS). In resistant plants, intracellular receptors known as R proteins recognize these effectors, triggering a second line of defence, more specific and intense, called ETI (Effector-Triggered Immunity), which usually leads to programmed cell death known as HR (Hypersensitive Response). Pseudomonas syringae is a phytopathogenic bacterium whose virulence depends on a T3SS and its effector repertoire. Some strains include HopZ1a, an unusual effector which is able to suppress in Arabidopsis both local (PTI and ETI), and systemic (SAR, for Systemic Acquired Resistance) defences, by means of its acetyltransferase activity. In resistant Arabidopsis plants, HopZ1a acetylates the ZED1 pseudokinase, which is proposed to function as a decoy mimicking HopZ1a target in the plant: ZED1 modification activates an R-protein (ZAR1) to trigger HopZ1a-dependent ETI. None of the Arabidopsis proteins proposed to date as HopZ1a targets is a kinase, nor fully explains the effector´s defence suppression abilities. In this work we identify an Arabidopsis kinase that functions as a positive regulator of PTI, ETI and SAR, which interacts with HopZ1a and is acetylated by this effector in lysine residues essential for its kinase activity. Further, HopZ1a can specifically suppress the defence phenotypes resulting from ZIP1 expression in Arabidopsis. We propose that ZIP1 acetylation by HopZ1a interferes with its kinase activity, and consequently with positive defence signalling.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Towards the Automation of Metamorphic Testing in Model Transformations

Model transformations are the cornerstone of Model-Driven Engineering, and provide the essential mechanisms for manipulating and transforming models. Checking whether the output of a model transformation is correct is a manual and error-prone task, this is referred to as the oracle problem in the software testing literature. The correctness of the model transformation program is crucial for the proper generation of its output, so it should be tested. Metamorphic testing is a testing technique to alleviate the oracle problem consisting on exploiting the relations between different inputs and outputs of the program under test, so-called metamorphic relations. In this paper we give an insight into our approach to generically define metamorphic relations for model transformations, which can be automatically instantiated given any specific model transformation.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-RJunta de Andalucía TIC-5906Junta de Andalucía P12-TIC-186

Automated inference of likely metamorphic relations for model transformations

Model transformations play a cornerstone role in Model-Driven Engineering (MDE) as they provide the essential mechanisms for manipulating and transforming models. Checking whether the output of a model transformation is correct is a manual and errorprone task, referred to as the oracle problem. Metamorphic testing alleviates the oracle problem by exploiting the relations among di erent inputs and outputs of the program under test, so-called metamorphic relations (MRs). One of the main challenges in metamorphic testing is the automated inference of likely MRs. This paper proposes an approach to automatically infer likely MRs for ATL model transformations, where the tester does not need to have any knowledge of the transformation. The inferred MRs aim at detecting faults in model transformations in three application scenarios, namely regression testing, incremental transformations and migrations among transformation languages. In the experiments performed, the inferred likely MRs have proved to be quite accurate, with a precision of 96.4% from a total of 4101 true positives out of 4254 MRs inferred. Furthermore, they have been useful for identifying mutants in regression testing scenarios, with a mutation score of 93.3%. Finally, our approach can be used in conjunction with current approaches for the automatic generation of test cases.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-RJunta de Andalucía P12-TIC-186

Performance Metamorphic Testing: Motivation and Challenges

Performance testing is a challenging task mainly due to the lack of test oracles, that is, mechanisms to decide whether the performance of a program under a certain workload is either acceptable or poor due to a performance bug. Metamorphic testing enables the generation of test cases in the absence of an oracle by exploiting the relations (so–called metamorphic relations) between the inputs and outputs of multiple executions of the program under test. In the last two decades, metamorphic testing has been successfully used to detect functional faults in a variety of domains, ranging from web services to simulators. However, the applicability of metamorphic testing to detect performance bugs is a topic that remains unexplored. In this vision paper, we introduce Performance Metamorphic Relations (PMRs) as expected relations between the performance measurements of multiple executions of the program under test. We hypothesize that these relations can be turned into assertions for the automated detection of performance bugs removing the need for complex benchmarks and domain experts guidance. As a further benefit, PMRs can be turned into fitness functions to guide search-based techniques on the generation of test data that violate the relations, revealing bugs. This novel idea is motivated with examples and an overview of some of the challenges in this promising topic.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-RMinisterio de Economía, Industria y Competitividad TIN2015-71841-REDJunta de Andalucía P12-TIC-186

A Template–Based Approach to Describing Metamorphic Relations

Metamorphic testing enables the generation of test cases in the absence of an oracle by exploiting relations among different executions of the program under test, called metamorphic relations. In a recent survey, we observed a great variability in the way metamorphic relations are described, typically in an informal manner using natural language. We noticed that the lack of a standard mechanism to describe metamorphic relations often makes them hard to read and understand, which hinders the widespread adoption of the technique. In this paper, we propose a template–based approach for the description of metamorphic relations. The proposed template aims to ease communication among practitioners as well as to contribute to research dissemination. Also, it provides a helpful guide for those approaching metamorphic testing for the first time. For the validation of the approach, we used the proposed template to describe 17 previously published metamorphic relations from different domains and groups of authors, without finding expressiveness problems. We hope that this work eases the diffusion and adoption of metamorphic testing, contributing to the progress of this thriving testing technique.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-RJunta de Andalucía P12-TIC-186

The bacterial effector HopAF1 interacts with Arabidopsis MKK4/5

Pseudomonas syringae is a phytopathogenic bacterium whose virulence depends on a Type III Secretion System and its effector (T3E) repertoire, which is translocated into the host cell cytosol suppressing both basal and effector-triggered Immunity (ETI). HopAF1 is a T3E that suppresses several plant immunity phenotypes, including flg22-induced ethylene (ET) production. HopAF1 is mainly located in the plasma membrane (PM), where it interacts with plant proteins MTN1/2 that participate in ET biosynthesis. However, PM localization is not essential for HopAF1 ability to repress ET accumulation. While seeking for additional HopAF1 interactors in the plant, we have identified MAP kinase kinases MKK4/5. The MAP kinase module including MKK4/5 and MPK3/6 positively regulates 1-aminocyclopropane-1-carboxylic acid synthase (ACS) activity, a rate-limiting and major regulatory step in stress-induced ET production. MKK4/5-dependent phosphorylation directly stabilizes ACS2/6 and indirectly induces ACS transcription. We originally identified HopAF1-MKK4 interaction through an MS-based screening, and have now confirmed it by pull-down and BIFC, while obtaining variable results using FRET-FLIM. Moreover, we are monitoring ACS2/6 expression levels by qRT-PCR, in the presence and absence of HopAF1. We propose that HopAF1 interference with MKK4/5 is likely to contribute to the suppression of ET production, by altering MKK4/5-dependent regulation of ACS activity.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Surface structuring of fused silica with asymmetric femtosecond laser pulse bursts

Fused silica surface structuring has been performed using temporally shaped femtosecond laser pulses. For this purpose we have designed pulse bursts with a triangular intensity envelope and different slope sign and interpulse separation that were experimentally generated using a home-made temporal pulse shaper. We have found that pulse bursts with decreasing intensity envelopes are remarkably more efficient in terms of surface ablation than bursts with increasing intensity envelopes. The results reveal that laser energy coupling in the material is enhanced as the interpulse spacing decreases. A study of the ablation depth using stretched single pulses was carried out and compared to results obtained for pulse bursts with different interpulse spacing. We find that the deepest crater was achieved with bursts of 0.5 ps interpulse separation and decreasing envelope. This pulse form also induced the largest change of the surface reflectivity after irradiation. The results are discussed in terms of how the laser energy coupling efficiency is linked to the temporal pulse shape. © 2013 Optical Society of America.This work has been partially supported by the Spanish TEC2011-22422 project. J. H.-R. acknowledges a grant awarded by the Spanish Ministry of Science and Innovation.Peer Reviewe

Metamorphic Relation Patterns for Query-Based Systems

Searching and displaying data based on user queries is a key feature of most software applications such as information systems, web portals, web APIs, and data analytic platforms. The large volume of data managed by these types of systems, henceforth called query-based systems (QBS), makes them extremely hard to test due to the difficulty to assess whether the output of a query is correct, the so-called oracle problem. Metamorphic testing has proved to be a very effective approach to alleviate the oracle problem in QBS, enabling the detection of bugs in data repositories, large e-commerce sites, and some of the most used software applications worldwide such as Google Search and YouTube. We have observed, however, that the metamorphic relations used to test different types of QBS are very similar, regardless of their domain, since all of them exploit standard query features such as filtering and ordering. Inspired by this finding, in this paper we present a catalogue of metamorphic relation patterns to assist testers in the identification and inference of metamorphic relations in QBS. For the definition of the patterns we resorted to the root of most query languages: relational algebra. We show how the proposed patterns help in the identification of metamorphic relations in the e-commerce platform PrestaShop, the email service Gmail, and the mobile application of video streaming HBO.Comisión Interministerial de Ciencia y Tecnología TIN2015-70560-