Tommy's Scriptinator 3000 TM

Quick Start

note beforehand

it is possible to run the program using the .jar file. If doing so, be aware that the program was compiled using the Bash Script StyleSheet. In this early version it is not yet possible to change the style in the compiled version. If you desire changing the style sheet, then make sure you have install at least JDK 9 (http://www.oracle.com/technetwork/java/javase/downloads/jdk9-downloads-3848520.html). Download the github repository using "git clone https://github.com/TommyClausner/Scriptinator". Navigate to /src. There you can modify the StyleSheet.java Afterwards run "javac Scriptinator.java". To start the program use "java Scriptinator"

now really the quick start

After opening the application a window will appear exposing a button panel on the top edge.

• You can create a new node by double clicking the window at some free position.
• Once a node appeared you can view and manipulate it's properties by double clicking it
• Connect two nodes by first selecting the from node by single clicking it and then selecting the to node by single clicking it. You can remove a node by redoing the above operation.
• click the "S" button to save a pipeline
• click the "L" button to load a pipeline
• click the "P" button to make a runnable pipeline
• click the "X" button to exit
• click the "/" button to clear the pipeline
• "!" and "?" open the about and help window

Hello World example

• open Tommy'y Scriptinator 3000 TM
• double click at a random position
• double click the icon that just appeared
• select load script
• navigate to the example scripts folder further to the hello world example and select "Hello.sh"
• you will notice a change in the properties window
• if desired change within the "Input" section which language should be selected (coded in the Languages.txt file)
• click Confirm and Close
• repeat the above procedure, but select the "World.sh"
• connect the two scripts by selecting the hello script first and afterwards the world script by single clicking them
• you will see a connection line appearing being thicker at the "hello end"
• click P in the main button panel
• select a folder where to store the pipeline
• choose a name
• copy the "Language.txt" into the pipeline folder
• execute yourpipeline file by typing "sh yourpipeline.sh"
• congrats you've just created your first pipeline

Note that you can also load the prepared hello world pipeline "HelloWorld.pipe", that has all steps above already set up.

Main Purpose

Tommy's Scriptinator 3000 TM aims to provide an interface between code line programming and graphical user interfaces. This can become especially handy in science, where users in general are less skilled in using multiple programming languages. E.g. students entering the field are often confronted with analysis scripts that are stitched together by another person and spend often a significant amount of time figuring out the workflow. This is where Tommy's Scriptinator 3000 TM slips in.

Scripts can be prepared such that main I/O variables and different additional parameters can be defined in a classical graphical user interface (GUI). Furthermore those scripts can be daisy chained to create analysis pipelines.

Once a pipeline was created it can be shared with anyone using Tommy's Scriptinator 3000 TM. Thus, making it the ideal solution for sharing scripts and communicating dependencies.

main functions

When starting up Tommy's Scriptinator 3000 TM the main playground shows up with the main control buttons located at the top centre of the panel.

main button panel:

• "/" removes all scripts from the playground

• "S" saves the current pipeline to hard drive using the .pipe extension

• "L" loads pipelines using the .pipe extension

• "P" creates a runnable pipeline (will be explained later)

• "!" calls the "About" information window

• "?" shows this document

• "X" closes the application

creating a new script

A new script can be created by double clicking somewhere on the playground. A round icon having a random colour will appear at the respective location. This Icon represents your script. At the moment of creation it will be a default "unknown" script. Double clicking the script lists all features of the script and allows for modification (will be explained later). Further the script icon can be dragged to any location desired.

connecting two scripts

Two scripts can be connected by single clicking a script providing the from connection and afterwards single clicking the script to which the first script is connected to. When repeating the exact same procedure the connection is removed. Internally each script stores all connections it has from other scripts (rather than to). Outgoing connections are symbolized by the thicker end of the connection line whereas the opposite is true for incoming connections. In other words the connection goes from thick to thin.

Style Sheet

The default Scriptinator style sheet was created for being used with Bash scripts. However by creating the respective style sheet for a different language would make the program compatible to that as well. All functions are set up in a general way such that according to the style sheet the environment is built.

Note that the StyleSheet includes parameters for skipping confirmation dialogs. Make sure that this settings are defined in accordance with the desired behavior.

modifying script properties

If a script was created, it accepts double clicks to expose the properties window. Depending on how the style sheet was set up, the default or template script will be displayed.

The different sections of the properties window contain:

Input All input variables (to be used by the script) are defined here. Thereby the style convention is derived from the settings in the style sheet. Variables defined here can be e.g. used later in the script. Hence file paths or often changed parameters are good candidates for find their places here.

Output All input variables (to be produced by the script) are defined here. Thereby the style convention is derived from the settings in the style sheet. Variables defined here can be e.g. used to provide an output path for the script to save results.

Misc All miscellaneous variables (to be used by the script) are defined here. This could be parameters or an additional waiting time (if that makes sense within the pipeline)

General This section contains information that is internally used by Tommy's Scriptinator 3000 TM. Thereby:

• label refers to how the file is internally called

• file refers to the absolute path, where the file is stored

• useqsub is a boolean statement whether to use qsub

• shortLabel is what will be displayed as an overlay on to of the round icons on the playground

Note that those variables must be defined language specific as well.

Qsub Parameters for the use of qsub.

Script Settings In the left column of this sections the number of variables for the respective section can be variated. Note that all variables defined will go into the file header.

Within the right column the control buttons are located.

• Load Script will spawn a dialog to select a script in the defined language. If the script already has a valid header, then this information will update the existing panel information.

• Confirm and Close closes the Properties window and sets the parameters in the defined way.

• Write to file creates a runnable script in the respective language, including the header information wrapped in language specific comments.

• Cancel closes the Properties window and reverts the state to it's original state

• Delete Script closes the Properties window and deletes Script node

Code All code elements that were part of the sourced script, but not of the header are displayed here. Changes for instance in variable naming in the header section could be applied directly to the code in here.

Qsub support

If qsub support was enabled (setting useqsub to true) than a white indicator ring around the script icon will appear to indicate qsub support. This means that a predefined template script must be provided next to the main function. The default name is "RunOnQsubTemplate.sh"

The P option

This function is used to create executable pipelines. Choosing the P or Pipe it! option in the main menu, will cause a dialog to spawn asking to select the folder where the pipeline is going to be saved.

After that all scripts that were displayed on the playground will be equipped with a header and copied to the respective pipeline folder in the language specific format. Furthermore a runnable pipeline is create. That is a file in the respective language format that calls all copied scripts in the correct order. This means that the hierarchy implicated by the connection lines on the playground will be inferred and scripts will be ordered such that a script that is connected to will be called prior to a script that is connected from.

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License:

All contents within this repository are distributed under the GPL-3.0 license.

Copyright (C) 2018, Tommy Clausner, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands DCCN

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remark for those who need it:

Tommy's Scriptinator 3000 TM is not a registered trade mark. The name is a funny reference to the computer game "Thimbleweed Park".