Application Repository Content

This document contains a description of files that can or should be present in an application repository

Application Definition (Required)

A JSON file named appDefinition.json. Contains information that specifies inputs and outputs of the application and how the application should be run.

Options

scriptLanguage - name of the scripting language in which the application is written. Currently only one language is available:
- MATLAB - MATLAB programming language. This applies also to Octave applications
executableScriptName - name of the application executable file
functionName - name of main function used to execute the application
inputFiles (Optional) - input files that are needed by the application. For each input file defined here, the application panel will show a button to choose the location of that file. When the application is run the input files will be read into a MATLAB variable and passed as arguments to the main executable function. The order in which the inputs are passed to the function is described in Executable Script section. Each input file is defined by:
- dataType - data type of the input
- multiplicity - how many inputs of that type are expected (written as string value). Defines minimum required number and maximum allowed number of inputs. Depending on these values the user will be allowed to select one file, multiple files or none at all, and won't be able to run the application if the minimal required number of files is not chosen. Depending on what multiplicity is given the input(s) might be passed to the main function in a different way:
  - one file - written as "1", or "[1, 1]" - exactly one input file of this type is required. When the application is run this file will be read to a MATLAB variable and this variable will be passed directly as argument to the main function
  - other number - there might be many inputs of this type, or none at all. When the application is run these files will be read to MATLAB variables and they will packed into a single cell array before it will be passed as argument to the main function. The variables in the cell array are not guaranteed to be in any specific order. Options:
    - ? - zero or one. The input is optional, there can be at most one input file
    - * - zero or more. The input is optional and there is no upper limit of how many input files there can be
    - + - one or more. At least one file is required and there is no upper limit of how many input files there can be
    - n - exactly n input files are expected - no more, no less
    - [n, m] - there should be at least n input files and at most m input files
inputParameters (Optional) - simple input parameters that should be entered by the user. For each parameter defined here, the application panel will show input form where the user can enter the value of the parameter. When the application is run the parameters' values will be passed as arguments to the main executable function. The order in which the parameters are passed to the function is described in Executable Script section. When adding a parameter you have to specify what kind of value it should have. The available options are:
- TEXT - a text value
- BOOLEAN - a true or false value
- DOUBLE - a real number value
- INTEGER - an integer value
- TIME - a date value
outputs - list of outputs generated by the application. The outputs defined here should be returned as output variables by the main executable function. After the function is run each of these outputs will be saved as a mat file and returned as a result of the application. Each output is defined by:
- dataType - data type that this output file should have
- fileName - name of the file under which this output should be saved
requiredTools - list of programs or tools that are needed to run the application. At least one value should be present - the script interpreter. Available options are:
- matlab - the MATLAB interpreter
- matlab-signal_processing_toolbox - signal processing toolbox. Usable only with MATLAB
- matlab-image_processing_toolbox - image processing toolbox. Usable only with MATLAB
- octave - the Octave interpreter
- octave-4.2.1 - the Octave interpreter in version 4.2.1
requiredComputationResources (Optional) - a map defining what computational resources should be available to the application. Available options are:
- COMPUTATION_TIME - maximum time that an application needs for the computation (in minutes). If not specified it defaults to 30 minutes
- MEMORY - maximum memory that an application needs for the computation (in gigabytes). If not specified it defaults to 2GB
- CPU_COUNT - number of processors that should be available to the application. If not specified it defaults to 1

Sample file

{
  "scriptLanguage":"MATLAB",
  "executableScriptName":"sampleScriptName.m",
  "functionName":"sampleScriptName",
  "inputFiles":[
    {
      "dataType":"double_vector",
      "multiplicity":"1"
    }
  ],
  "inputParameters":[
    "DOUBLE",
    "TEXT"
  ],
  "outputs":[
    {
      "dataType":"double_vector",
      "fileName":"output.mat"
    }
  ],
  "requiredComputationResources":{
    "COMPUTATION_TIME":5
  },
  "requiredTools":[
    "octave"
  ]
}

Executable Script (Required)

The main script of the application that is the entry point of the application. The name of the script file should be the same as executableScriptName defined in the application definition file and the script should contain a function that has the same name as the functionName. The main function should have the same number of inputs and outputs as defined in the application definition file. The names of the input and output variables are irrelevant. For example, if the application definition contains:

"functionName": "sampleFunctionName",
"inputParameters": ["TEXT", "DOUBLE"],
"inputFiles": [{ "dataType" : "integer_vector", "multiplicity" : "1"},  { "dataType" : "string_vector", "multiplicity" : "1"}],
"outputs": [{ "dataType" : "double_vector", "fileName" : "output1.mat"},  { "dataType" : "boolean_vector", "fileName" : "output2.mat"}]

the executable script could look like that:

function [out1, out2] = sampleFunctionName(in1, int2, int3, in4)
  out1 = [];
  out2 = logical([]);
end

The order of inputs and outputs corresponds to the order in which they are defined in the application definition file, with the note that inputFiles variables come before inputParameters variables. For the above example the order of variables would be as follows:

in1 - corresponds to the input file with type 'integer_vector'
in2 - corresponds to the input file with type 'string_vector'
in3 - corresponds to the input parameter with type TEXT
in4 - corresponds to the input parameter with type DOUBLE
out1 - corresponds to the output with type 'double_vector'
out2 - corresponds to the output with type 'boolean_vector'

Application Description (Optional)

A JSON file named appDescription.json. Defines how the application will be described in the Applications page inside the EPISODES platform, and how a workspace directory will be named when the application is created. This file is optional - if it is not present the required fields - shortName and name - will be filled with the name of the repository, and all other fields will be left empty.

Options

shortName (Required) - short name of the application. The short name will be used for creating application directory within the workspace. It is not recommended to include special characters in the application name, some of them are not allowed
lastUpdate - a date when the application was last updated, written In format "dd-MM-yyyy HH:mm:ss"
references - links to additional resources that can be displayed with the application (e.g. user guide). It is a map where the key will be the text of the link and the value will be its web address (URL)
categories - categories to which the application can be assigned. It is advisable to use the categories already present within the portal. However, you can also add your own
keywords - keywords that match the application. If relevant, use the keywords already defined within the portal, but add also your own, to describe the application best
hidden - if this application should be visible in the EPISODES platform
translations - a map that contains translations of descriptions that are subject to internationalization. The key of the map is the language of the translation written as a two letter language code, e.g. "en", or "pl" and the value contains the translated descriptions written in that language. There should be at least one language present - "en". The available description fields are:
- name (Required) - full name of the application, that will be visible on the application list. May contain spaces.
- description - longer description of the application. May contain HTML tags, including links. May also include the input or output type name written as ${D__data_type}, where "data_type" is the data type of the input or output file - this will be filled with a full name of this data type that will be automatically translated into an appropriate language (if that translation is available)
- license - license used for publishing the application. If you wish your application to be open to other users, include a license here. You might also include it as a LICENCE.txt file in your code repository
- author - author of the application, may contain your name, institution and/or project affiliation.
- citation - citations (articles) related to the application (e.g. the algorithms it uses). A generic portal and its application part is added to the citations, therefore, include here only citations related solely to this application.
- inputsDescription - description of the application inputs. May contain HTML tags, including links. By default it should include listing of the types of inputs, but adding more detailed description is advisable. Input types should be written as ${D__data_type}, where "data_type" is the data type of the input file
- resultsDescription - description of the application results. May contain HTML tags, including links. By default it should include listing of the types of outputs, but adding more detailed description is advisable. Output types should be written as ${D__data_type}, where "data_type" is the data type of the output file
- computationalCharacteristic - description of the features of the application that might have impact on its computation time or other resources consumption.

Sample file

{
  "shortName":"AppDir",
  "references":{
    "User Guide":"https://docs.cyfronet.pl/pages/viewpage.action?pageId=somepage"
  },
  "lastUpdate":"28-02-2021 20:50:12",
  "categories":[
    "Category"
  ],
  "keywords":[
    "keyword1",
    "keyword2"
  ],
  "hidden":false,
  "translations":{
    "en":{
      "name":"Application name",
      "description":"Longer description containing some ${D__data_types} and <a href='#app:AppId'>links</a>.",
      "license":"Sample licence",
      "author":"Sample author",
      "citation":"Sample citation",
      "inputsDescription":"${D__data_type}",
      "resultsDescription":"${D__other_data_type}",
      "computationalCharacteristic":"Description of computational characteristic"
    },
    "pl":{
      "name":"Aplikacja",
      "description":"Dłuższy opis z ${D__data_types} i <a href='#app:AppId'>linkiem</a>.",
      "license":"Licencja",
      "author":"Autor",
      "citation":"Cytacje",
      "inputsDescription":"${D__data_type}",
      "resultsDescription":"${D__other_data_type}",
      "computationalCharacteristic":"Opis charakterystyki obliczeniowej"
    }
  }
}

Other Files

You are free to add any other files to the repository if you wish. You can, for example, include additional script files to help better organize the code, or you can add some supplementary files like a readme or a license file.