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Fact extraction from bash in support of script migration

Ian J. Davis, Richard C. Holt, Ron Mraz
2014 2014 Software Evolution Week - IEEE Conference on Software Maintenance, Reengineering, and Reverse Engineering (CSMR-WCRE)  
Collectively this provides a simple mechanism for altering arbitrary bash scripts so that they use an external XML configuration file, as a first step in the larger exercise of migrating bash scripts to  ...  An open source fact extractor was implemented that determines the dynamic usage made of every variable within an arbitrary bash script.  ...  We have expertise in extracting facts from source code [11] , so we initially thought that we might benefit by developing a bash fact extractor.  ... 
doi:10.1109/csmr-wcre.2014.6747195 dblp:conf/csmr/DavisHM14 fatcat:ssgnehcqora6jftzibga3p5lwq

Using prototyping to choose a bioinformatics workflow management system

Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace, Francis Ouellette
2021 PLoS Computational Biology  
At the heart of RiboViz is an analysis workflow, implemented in a Python script.  ...  RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis.  ...  We thank the Software Sustainability Institute for their support in starting this project.  ... 
doi:10.1371/journal.pcbi.1008622 pmid:33630841 fatcat:3lltosvobrey7o37akej3orwxq

Using rapid prototyping to choose a bioinformatics workflow management system [article]

Michael Jackson, Edward Wallace, Kostas Kavoussanakis
2020 bioRxiv   pre-print
At the heart of RiboViz is an analysis workflow, implemented in a Python script.  ...  RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis.  ...  . ; https://doi.org/10.1101/2020.08.04.236208 doi: bioRxiv preprint possible" motivated our migration to Python from a previous implementation of the analysis 151 as a bash script. 152 However, as our  ... 
doi:10.1101/2020.08.04.236208 fatcat:xzgov53yizb63efaor4ziutn6y

An empirical study of build system migrations in practice: Case studies on KDE and the Linux kernel

Roman Suvorov, Meiyappan Nagappan, Ahmed E. Hassan, Ying Zou, Bram Adams
2012 2012 28th IEEE International Conference on Software Maintenance (ICSM)  
In order to understand the build system migration process, we empirically studied two failed and two successful attempts of build system migration in two major open source projects, i.e.  ...  effective evaluation of build system prototypes; (c) detailed analysis of the first challenge, i.e., requirements gathering for the new build system, which revealed that the failed migrations did not  ...  Transition from v. 1.2 to 2.0 of the Linux kernel saw common build logic extracted into a Rules.make script, and a massive rewrite of other build scripts was carried out between kernel v. 2.2 and 2.4.  ... 
doi:10.1109/icsm.2012.6405267 dblp:conf/icsm/SuvorovNHZA12 fatcat:psic52pprvfdjgqsf7n7aukxia

The Berkeley Phonetics Machine

Ronald L. Sprouse, Keith Johnson
2016 UC Berkeley Phonology Lab Annual Reports  
We also discuss the use of this machine in the Phonology Lab and in phonetics courses.  ...  The overall experience with the machine has been positive, as faculty and graduate students are able to share and execute scripts in a common working environment.  ...  Extracting portions of an audio file and concatenating multiple files are other common operations for this tool in the Phonlab.  ... 
doi:10.5070/p7121040718 fatcat:75wepzno6baqvokabdfiu23or4

ATLAS TDAQ System Administration: Master of Puppets

S Ballestrero, F Brasolin, D Fazio, C Gament, C J Lee, D A Scannicchio, M S Twomey
2017 Journal of Physics, Conference Series  
The previous method of configuring these servers, using Quattor and a hierarchical scripts system was cumbersome and restrictive.  ...  Various configuration management systems were evaluated, though in the end, Puppet was chosen as the application of choice and was the first such implementation at CERN.  ...  Once the computer had booted, a complicated system of hierarchical bash scripts called "BootWithMe" (BWM) was used to configure each node, based on the requirements of each sub-detector.  ... 
doi:10.1088/1742-6596/898/8/082002 fatcat:m2suwfrxcnbvdg7p7xxfhchfwi

Contents

2014 2014 Software Evolution Week - IEEE Conference on Software Maintenance, Reengineering, and Reverse Engineering (CSMR-WCRE)  
Schneider -University of Saskatchewan, Canada . . . . . . . . 358 Fact Extraction from Bash in Support of Script Migration Ian J. Davis, Richard C.  ...  Gyimóthy -MTA-SZTE Research Group on Artificial Intelligence, Hungary; University of Szeged, Hungary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 In Medio Stat Virtus: Extract  ... 
doi:10.1109/csmr-wcre.2014.6747155 fatcat:m3kgepp4yvexxjdsvuoioprftm

XUTools: Unix Commands for Processing Next-Generation Structured Text

Gabriel A. Weaver, Sean W. Smith
2012 USENIX Large Installation Systems Administration Conference  
In this paper, we propose eXtended Unix text-processing tools (xutools) and present implementations that enable practitioners to extract (xugrep), count (xuwc), and compare (xudiff) texts in terms of language-specific  ...  We motivate, design, and evaluate our tools around realworld use cases from network and system administrators, security consultants, and software engineers from a variety of domains including the power  ...  This work was supported in part by the TCIPG project from the DOE (under grant DE-OE0000097). Views are the authors' alone.  ... 
dblp:conf/lisa/WeaverS12 fatcat:sfosfkmnifh7tafq5mhbb663ru

Handling Duplicates in Dockerfiles Families: Learning from Experts

Mohamed A. Oumaziz, Jean-Remy Falleri, Xavier Blanc, Tegawende F. Bissyande, Jacques Klein
2019 2019 IEEE International Conference on Software Maintenance and Evolution (ICSME)  
We show that duplicates in Dockerfiles are frequent in our corpus, that maintainers are aware of their existence, are frequently facing them and have a mixed opinion regarding them (error-prone when not  ...  In some situations, Dockerfiles family maintainers have to propagate a change to several, if not all, Dockerfiles of the family (for instance a bugfix applying on all Dockerfiles targeting Python 2.7).  ...  Listing 11 is an extract from the OpenJDK project's update script (written in bash). In this example, we see that a loop is used to generate the Dockerfiles for all versions of OpenJDK.  ... 
doi:10.1109/icsme.2019.00086 dblp:conf/icsm/OumazizF0BK19 fatcat:2ipfdnbt25hf7n32tc4htb2hca

From Scripted HPC-Based NGS Pipelines to Workflows on the Cloud

Jacek Cala, Yaobo Xu, Eldarina Azfar Wijaya, Paolo Missier
2014 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing  
In this paper we describe our initial experiences in the Cloud-e-Genome project with moving the whole exome sequencing pipeline from the scripted HPC-based solution to a workflow enactment system running  ...  Despite the effort it involved to wrap all required tools in the form of workflow blocks and the restrictions of the dataflow model used to represent workflows we expect the migration to significantly  ...  ACKNOWLEDGMENT This work is sponsored by Biomedical Research Centre, National Institute for Health and Research and a grant from Windows Azure Research programme.  ... 
doi:10.1109/ccgrid.2014.128 dblp:conf/ccgrid/CalaXWM14 fatcat:vkkuscziqbb47nfa3fxauykata

A job monitoring system for the LCG computing grid

Ahmad Hammad, T. Harenberg, D. Igdalov, P. Mattig, D. Meder-Marouelli, P. Ueberholz
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
Both components are currently integrated in the computing environment for generating data for the DØ Experiment. In this paper we want to describe the basic components of the job monitoring software.  ...  Such a system can give information about the status of the user job as well as the worker node in parallel while a user job is running.  ...  All commands of the job script are extracted and replaced by a python script called my pipe taking a command including its parameters as argument (''job wrapper'' in figure 4).  ... 
doi:10.1109/ipdps.2006.1639659 dblp:conf/ipps/HammadHIMMU06 fatcat:o75rjncf3ng7roh2kfx3hjdz6a

ESO's User Portal: lessons learned

A. M. Chavan, L. E. Tacconi-Garman, M. Peron, F. Sogni, D. Dorigo, P. Nass, N. Fourniol, D. Sforna, K. Haggouchi, M. Dolensky, Roger J. Brissenden, David R. Silva
2008 Observatory Operations: Strategies, Processes, and Systems II  
ESO introduced a User Portal for its scientific services in November 2007.  ...  The project faced and overcame a number of challenging hurdles between inception and deployment, and ESO learned a number of useful lessons along the way.  ...  We needed a script to extract the raw institution information from the user databases into the spreadsheets, and another script to load the spreadsheets back into the User Portal database.  ... 
doi:10.1117/12.789348 fatcat:dxollethsnduvb3l42f56ddgwi

On Cloud deployment of digital preservation environments

Daniel Pop, Marian Neagul, Dana Petcu
2014 IEEE/ACM Joint Conference on Digital Libraries  
One of the migration expectations is the scalability of digital preservation architectures in Cloud environments.  ...  After presenting some architectural considerations of a scalable deployment system, we detail the prototype developed within a support platform, namely SCAPE.  ...  Acknowledgments The work reported in this paper is partially funded by the European Commission FP7 Programme by grants no. 270137 (SCAPE -Scalable Preservation Environments) and 284595 (HOST -High Performance  ... 
doi:10.1109/jcdl.2014.6970216 dblp:conf/jcdl/PopNP14 fatcat:mfbyak7vizcl5acm55ejguhg7y

APPLICATION MIGRATION EFFORT IN THE CLOUD

Stefan Kolb, Jörg Lenhard, Guido Wirtz
2015 Services Transactions on Cloud Computing  
In this case study, we analyze the feasibility of the migrations in terms of portability and the effort of the migrations.  ...  A leading trend is the adoption of Platform as a Service to support rapid application deployment.  ...  We also appreciate the support given by the selected vendors.  ... 
doi:10.29268/stcc.2015.0009 fatcat:v76lrfvthvhubgvmkyru532w7m

APPLICATION MIGRATION EFFORT IN THE CLOUD

2015 Services Transactions on Cloud Computing  
In this case study, we analyze the feasibility of the migrations in terms of portability and the effort of the migrations.  ...  A leading trend is the adoption of Platform as a Service to support rapid application deployment.  ...  We also appreciate the support given by the selected vendors.  ... 
doi:10.29268/stcc.2015.3.4.1 fatcat:oth622fkgjchteadpcwkz2vexu
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