scholarly journals Constructing Workflows from Script Applications

2012 ◽  
Vol 20 (4) ◽  
pp. 359-377 ◽  
Author(s):  
Mikołaj Baranowski ◽  
Adam Belloum ◽  
Marian Bubak ◽  
Maciej Malawski
Keyword(s):  
Programming Languages ◽  
Source Code ◽  
General Purpose ◽  
Control Flow ◽  
Scientific Workflows ◽  
Collaborative Programming ◽  
Execution Environment ◽  
Grid Infrastructures ◽  
Grid Application ◽  
High Level

For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.

A REUSE-ORIENTED WORKFLOW DEFINITION LANGUAGE

2003 ◽  
Vol 12 (01) ◽  
pp. 1-36 ◽  
Author(s):  
MARIE JOSÉ BLIN ◽  
JACQUES WAINER ◽  
CLAUDIA BAUZER MEDEIROS
Keyword(s):  
Programming Languages ◽  
Building Blocks ◽  
Database Systems ◽  
Exception Handling ◽  
Control Flow ◽  
New Formalism ◽  
Definition Of ◽  
High Level ◽  
And Control ◽  
High Degree

This paper presents a new formalism for workflow process definition, which combines research in programming languages and in database systems. This formalism is based on creating a library of workflow building blocks, which can be progressively combined and nested to construct complex workflows. Workflows are specified declaratively, using a simple high level language, which allows the dynamic definition of exception handling and events, as well as dynamically overriding workflow definition. This ensures a high degree of flexibility in data and control flow specification, as well as in reuse of workflow specifications to construct other workflows. The resulting workflow execution environment is well suited to supporting cooperative work.

scholarly journals Pembangunan Perangkat Lunak PuniEdit (Perangkat Lunak Editor untuk Multi Language Programming)

2019 ◽  
Author(s):  
Budiman
Keyword(s):  
Programming Languages ◽  
Programming Language ◽  
Source Code ◽  
Computer Software ◽  
Object Oriented ◽  
Object Oriented Programming ◽  
Text Editor ◽  
Development Environment ◽  
Integrated Development ◽  
High Level

During this period continued to develop computer software, programming language was no exception. At the start of the era of low level programming languages, then developed a high level programming language. It is characterized by the appearance of a method of programming offered by a programming language, that is, object-oriented programming (OOP). IDE (Integrated Development Environment) is a computer program that has some facilities that are required in the development of the software. The purpose of the IDEA is to provide all the necessary utilities in building software. As for the type of software text editor that can be used to manipulate the source code hereinafter referred to as the source code of programming languages such as Ultraedit, JediEdit, ClearEdit, cEdit, the Golden Pen, and so on. PuniEdit software is a text-based editor software that can simplify the user through correction, insertion, and modification of the source code. PuniEdit software is built using Borland Delphi 7.0 and SynEdit component. This software can be used for the Pascal programming language, C++ and HTML. In addition, the software PuniEdit can perform management of the token. This PuniEdit software, the user can clearly see every occurrence of the type of token as keywords (reserved word), identifier, operator, and so on.Keywords: Source code, programming language, source code is scanned.

scholarly journals fastp: an ultra-fast all-in-one FASTQ preprocessor

2018 ◽  
Author(s):  
Shifu Chen ◽  
Yanqing Zhou ◽  
Yaru Chen ◽  
Jia Gu
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Programming Languages ◽  
Source Code ◽  
Data Filtering ◽  
Quality Filtering ◽  
Downstream Analysis ◽  
High Level ◽  
Unique Molecular Identifier ◽  
Adapter Trimming

AbstractMotivationQuality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming, and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g., Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.ResultsWe developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality cutting, and many other operations with a single scan of the FASTQ data. It also supports unique molecular identifier preprocessing, poly tail trimming, output splitting, and base correction for paired-end data. It can automatically detect adapters for single-end and paired-end FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.Availability and ImplementationThe open-source code and corresponding instructions are available at https://github.com/OpenGene/[email protected]

Development and Application of Planar Computational General-Purpose Constrained Multibody Simulations in MATLAB With Simple Graphical/Visualization Capability

2015 ◽  
Author(s):  
J. R. Dye ◽  
Y. Y. Tay ◽  
H. M. Lankarani
Keyword(s):  
Programming Languages ◽  
Equations Of Motion ◽  
Source Code ◽  
Data Entry ◽  
General Purpose ◽  
Integration Scheme ◽  
Double Pendulum ◽  
Time Step ◽  
Code Structure ◽  
Matlab Programming

This study demonstrates the implementation and advantages in utilizing the Matlab programming environment for general-purpose simulations of constrained planar dynamic and kinematic multibody mechanical systems. Many currently available tools have a focus and can have limited flexibility through difficulty in data entry, limited access to source code, analysis of data or use of programming languages not readily taught. A Matlab source code is created, which includes the use of Microsoft Excel and GUI’s created in GUIDE that allow a user to construct, simulate and analyze multibody systems in Matlab. This technique allows the user to utilize any of Matlab toolboxes for unique problems or integrate the base program into a Simulink environment. An overview of the general code structure and multibody kinematics and dynamics equations used are shown in this paper. For kinematic simulations, the system’s Cartesian coordinates are found by finding the roots of the constraints vector at each time step. For the dynamic systems, the solver uses a numerical integration scheme with augmented form of the constrained equations of motion to solve for the system’s accelerations. Examples are presented demonstrating the benefits of using the Matlab environment and the flexibility to easily expand the code to simulate unique problems. These examples include an Ackermann steering for automotive applications and a double pendulum at the influence of gravity. The last example shows how a custom function can be created to inject forces into the dynamic solver in order to simulate a structural beam at the influence of a heavy pendulum.

AN ABSTRACT, SHARED AND PERSISTENT DATA STRUCTURE FOR SUPPORTING DATABASE MANAGEMENT AND MULTILINGUAL NATURAL LANGUAGE PROCESSING

1993 ◽  
Vol 03 (03) ◽  
pp. 369-382 ◽  
Author(s):  
CUI ZHANG ◽  
RICHARD F. WALTERS
Keyword(s):  
Data Structure ◽  
Programming Languages ◽  
Language Processing ◽  
Database Management ◽  
English Language ◽  
Database Systems ◽  
General Purpose ◽  
Programming Environment ◽  
Persistent Data ◽  
High Level

Neither today’s general purpose programming environment nor high-level programming languages, including those designed for AI purposes, provide adequate support for database systems. Furthermore, non-English language databases are difficult to treat either in existing database systems or with current high-level languages, because they require culture-sensitive operations on multiple foreign character sets. In this paper, we present an abstract, shared and persistent data structure, called HL+, capable of supporting database management applications. We also describe the means for coping with the aforementioned problems by accessing HL+ features of database management from high-level programming languages with an extensible programmable high-level language interface. Extensions to the data structure to accommodate processing of multiple foreign character strings are also described, and examples of multilingual applications are given.

scholarly journals X-Switch: An Efficient , Multi-User, Multi-Language Web Application Server

2010 ◽  
Vol 44 ◽  
Author(s):  
Mayumbo Nyirenda ◽  
Hussein Suleman ◽  
Andrew Maunder ◽  
Reinhardt Van Rooyen
Keyword(s):  
Resource Management ◽  
Web Application ◽  
Web Applications ◽  
General Purpose ◽  
Application Server ◽  
Switch System ◽  
Execution Environment ◽  
And Performance ◽  
High Level ◽  
Application Execution

Web applications are usually installed on and accessed through a Web server. For security reasons, these Web servers generally provide very few privileges to Web applications, defaulting to executing them in the realm of a guest ac- count. In addition, performance often is a problem as Web applications may need to be reinitialised with each access. Various solutions have been designed to address these security and performance issues, mostly independently of one another, but most have been language or system-specic. The X-Switch system is proposed as an alternative Web application execution environment, with more secure user-based resource management, persistent application interpreters and support for arbitrary languages/interpreters. Thus it provides a general-purpose environment for developing and deploying Web applications. The X-Switch system's experimental results demonstrated that it can achieve a high level of performance. Further- more it was shown that X-Switch can provide functionality matching that of existing Web application servers but with the added benet of multi-user support. Finally the X-Switch system showed that it is feasible to completely separate the deployment platform from the application code, thus ensuring that the developer does not need to modify his/her code to make it compatible with the deployment platform.

scholarly journals Novel Code Plagiarism Detection Based on Abstract Syntax Tree and Fuzzy Petri Nets

2019 ◽  
Vol 1 (1) ◽  
pp. 46-56 ◽  
Author(s):  
Victor R. L. Shen
Keyword(s):  
Programming Languages ◽  
Source Code ◽  
Learning Performance ◽  
Abstract Syntax ◽  
Plagiarism Detection ◽  
Abstract Syntax Tree ◽  
Source Codes ◽  
Syntax Tree ◽  
Fuzzy Petri Nets ◽  
High Level

Those students who major in computer science and/or engineering are required to design program codes in a variety of programming languages. However, many students submit their source codes they get from the Internet or friends with no or few modifications. Detecting the code plagiarisms done by students is very time-consuming and leads to the problems of unfair learning performance evaluation. This paper proposes a novel method to detect the source code plagiarisms by using a high-level fuzzy Petri net (HLFPN) based on abstract syntax tree (AST). First, the AST of each source code is generated after the lexical and syntactic analyses have been done. Second, token sequence is generated based on the AST. Using the AST can effectively detect the code plagiarism by changing the identifier or program statement order. Finally, the generated token sequences are compared with one another using an HLFPN to determine the code plagiarism. Furthermore, the experimental results have indicated that we can make better determination to detect the code plagiarism.

scholarly journals Control Flow Graph Embedding Based on Multi-Instance Decomposition for Bug Localization

2020 ◽  
Vol 34 (04) ◽  
pp. 4223-4230
Author(s):  
Xuan Huo ◽  
Ming Li ◽  
Zhi-Hua Zhou
Keyword(s):  
Programming Languages ◽  
Software Maintenance ◽  
Source Code ◽  
Control Flow ◽  
Control Flow Graph ◽  
Bug Localization ◽  
Flow Graph ◽  
Bug Reports ◽  
Bug Report ◽  
Sequential Nature

During software maintenance, bug report is an effective way to identify potential bugs hidden in a software system. It is a great challenge to automatically locate the potential buggy source code according to a bug report. Traditional approaches usually represent bug reports and source code from a lexical perspective to measure their similarities. Recently, some deep learning models are proposed to learn the unified features by exploiting the local and sequential nature, which overcomes the difficulty in modeling the difference between natural and programming languages. However, only considering local and sequential information from one dimension is not enough to represent the semantics, some multi-dimension information such as structural and functional nature that carries additional semantics has not been well-captured. Such information beyond the lexical and structural terms is extremely vital in modeling program functionalities and behaviors, leading to a better representation for identifying buggy source code. In this paper, we propose a novel model named CG-CNN, which is a multi-instance learning framework that enhances the unified features for bug localization by exploiting structural and sequential nature from the control flow graph. Experimental results on widely-used software projects demonstrate the effectiveness of our proposed CG-CNN model.

scholarly journals An Algorithm-Adaptive Source Code Converter to Automate the Translation from Python to Java

2021 ◽  
Author(s):  
Eric Jin ◽  
Yu Sun
Keyword(s):  
United States ◽  
Computer Science ◽  
Programming Languages ◽  
Error Rate ◽  
Source Code ◽  
Qualitative Evaluation ◽  
General Purpose ◽  
Huge Number ◽  
Code Converter

In the fields of computer science, there exist hundreds of different programming languages. They often have different usage and strength but also have a huge number of overlapping abilities [1]. Especially the kind of general-purpose coding language that is widely used by people, for example Java, Python and C++ [2]. However, there is a lack of comprehensive methods for the conversion for codes from one language to another [3], making the task of converting a program in between multiple coding languages hard and inconvenient. This paper thoroughly explained how my team designs a tool that converts Python source code into Java which has the exact same function and features. We applied this converter, or transpiler, to many Python codes, and successfully turned them into Java codes. Two qualitative experiments were conducted to test the effectiveness of the converter. 1. Converting Python solutions of 5 United States Computer Science Olympic (USACO) problems into Java solutions and conducting a qualitative evaluation of the correctness of the produced solution; 2. converting codes of various lengths from 10 different users to test the adaptability of this converter with randomized input. The results show that this converter is capable of an error rate less than 10% out of the entire code, and the translated code can perform the exact same function as the original code.

scholarly journals Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Maciej Malawski ◽  
Kamil Figiela ◽  
Marian Bubak ◽  
Ewa Deelman ◽  
Jarek Nabrzyski
Keyword(s):  
Programming Languages ◽  
Cost Optimization ◽  
Workflow Management ◽  
Resource Planning ◽  
General Purpose ◽  
Scientific Workflows ◽  
Workflow Execution ◽  
Amazon Ec2 ◽  
Deadline Constraints ◽  
The Cost

This paper presents a cost optimization model for scheduling scientific workflows on IaaS clouds such as Amazon EC2 or RackSpace. We assume multiple IaaS clouds with heterogeneous virtual machine instances, with limited number of instances per cloud and hourly billing. Input and output data are stored on a cloud object store such as Amazon S3. Applications are scientific workflows modeled as DAGs as in the Pegasus Workflow Management System. We assume that tasks in the workflows are grouped into levels of identical tasks. Our model is specified using mathematical programming languages (AMPL and CMPL) and allows us to minimize the cost of workflow execution under deadline constraints. We present results obtained using our model and the benchmark workflows representing real scientific applications in a variety of domains. The data used for evaluation come from the synthetic workflows and from general purpose cloud benchmarks, as well as from the data measured in our own experiments with Montage, an astronomical application, executed on Amazon EC2 cloud. We indicate how this model can be used for scenarios that require resource planning for scientific workflows and their ensembles.

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