Understanding and Mitigating Flaky Software Test Cases

A flaky test is a test case that can pass or fail without changes to the test case code or the code under test. They are a wide-spread problem with serious consequences for developers and researchers alike. For developers, flaky tests lead to time wasted debugging spurious failures, tempting them to ignore future failures. While unreliable, flaky tests can still indicate genuine issues in the code under test, so ignoring them can lead to bugs being missed. The non-deterministic behaviour of flaky tests is also a major snag to continuous integration, where a single flaky test can fail an entire build. For researchers, flaky tests challenge the assumption that a test failure implies a bug, an assumption that many fundamental techniques in software engineering research rely upon, including test acceleration, mutation testing, and fault localisation. Despite increasing research interest in the topic, open problems remain. In particular, there has been relatively little attention paid to the views and experiences of developers, despite a considerable body of empirical work. This is essential to guide the focus of research into areas that are most likely to be beneficial to the software engineering industry. Furthermore, previous automated techniques for detecting flaky tests are typically either based on exhaustively rerunning test cases or machine learning classifiers. The prohibitive runtime of the rerunning approach and the demonstrably poor inter-project generalisability of classifiers leaves practitioners with a stark choice when it comes to automatically detecting flaky tests. In response to these challenges, I set two high-level goals for this thesis: (1) to enhance the understanding of the manifestation, causes, and impacts of flaky tests; and (2) to develop and empirically evaluate efficient automated techniques for mitigating flaky tests. In pursuit of these goals, this thesis makes five contributions: (1) a comprehensive systematic literature review of 76 published papers; (2) a literature-guided survey of 170 professional software developers; (3) a new feature set for encoding test cases in machine learning-based flaky test detection; (4) a novel approach for reducing the time cost of rerunning-based techniques for detecting flaky tests by combining them with machine learning classifiers; and (5) an automated technique that detects and classifies existing flaky tests in a project and produces reusable project-specific machine learning classifiers able to provide fast and accurate predictions for future test cases in that project

Mutations in TOP3A Cause a Bloom Syndrome-like Disorder

Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatal-onset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIα), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIα, and consequently subjects’ cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIα in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis

Characterizing the morbid genome of ciliopathies

Background Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete. Results We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum. Likely causal mutations in previously described ciliopathy genes were identified in 85% (225/265) of the families, adding 32 novel alleles. Consistent with a fully penetrant model for these genes, we found no significant difference in their “mutation load” beyond the causal variants between our ciliopathy cohort and a control non-ciliopathy cohort. Genomic analysis of our cohort further identified mutations in a novel morbid gene TXNDC15, encoding a thiol isomerase, based on independent loss of function mutations in individuals with a consistent ciliopathy phenotype (Meckel-Gruber syndrome) and a functional effect of its deficiency on ciliary signaling. Our study also highlighted seven novel candidate genes (TRAPPC3, EXOC3L2, FAM98C, C17orf61, LRRCC1, NEK4, and CELSR2) some of which have established links to ciliogenesis. Finally, we show that the morbid genome of ciliopathies encompasses many founder mutations, the combined carrier frequency of which accounts for a high disease burden in the study population. Conclusions Our study increases our understanding of the morbid genome of ciliopathies. We also provide the strongest evidence, to date, in support of the classical Mendelian inheritance of Bardet-Biedl syndrome and other ciliopathies

Erratum: Mutations in TOP3A Cause a Bloom Syndrome-like Disorder

Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatal-onset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIα), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIα, and consequently subjects' cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIα in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis

Mutations in TOP3A Cause a Bloom Syndrome-like Disorder

Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatalonset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIa), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIa, and consequently subjects' cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIa in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis

Additional file 1: Figure S1. of Characterizing the morbid genome of ciliopathies

Bar graph showing the percentage of the main features for each distinct ciliopathy syndrome. (PPTX 70 kb

Additional file 2: Table S3. of Characterizing the morbid genome of ciliopathies

Clinical and genomic data for all cases in the study. (XLSX 83 kb

Additional file 6: Table S5. of Characterizing the morbid genome of ciliopathies

Ciliopathy disease burden in the population for each pathogenic variant identified in known ciliopathy genes. (XLSX 19 kb

Additional file 5: Table S4. of Characterizing the morbid genome of ciliopathies

Identification of TXNDC15 interacting proteins using tandem affinity purification (TAP). The list of 224 unique proteins is significantly enriched in known or predicted ciliary proteins. (XLSX 30 kb