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This document contains a description of files that can or should be present in an application repository. Note that instead of preparing the files manually you can also use a dedicated application creation wizard that is available on the EPISODES platform.

Table of Contents

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Application Definition (Required)

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

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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 (see Data Types section below)
- typeLabel (Optional) - a name distinguishing this input file from others. Allows to have multiple input files with the same data type. Each input file with different type label will be treated as a separate input and 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
- as a separate argument
- multiplicity - how many inputs of that type are expected (written as string value). Defines minimum required number and maximum allowed number of inputs. The portal validates if the user selected the minimal required number of input files, and if not it will forbid the application from being run. Depending on what multiplicity is given the input(s) might be passed to the main function in a different way (see Input Multiplicity section). The possible values are:
  - ? - 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
  Thats how the input paramters will look like when they are presented as input forms in the application panel:
- Image Added

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 (see Data Types section below)
- 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. Please contact us if you need any other tools, or toolboxes, or if you require a specific version of a Matlab or Octave interpreter. Available options are:
- matlab - the MATLAB interpreter. By default one of these versions will be used: 2019b or 2021a (this is subject to change).
- matlab-signal_processing_toolbox - signal processing toolbox. Usable only with MATLAB
- matlab-image_processing_toolbox - image
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 4.2.1octave - the Octave interpreter. By default one of these versions will be used: 3.8.1 or 4.2.1 (this is subject to change)
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

...

Code Block

language	js

{
  "scriptLanguage":"MATLAB",
  "executableScriptName":"sampleScriptName.m",
  "functionName":"sampleScriptName",
  "inputFiles":[
    {
      "dataType":"double_vector",
      "multiplicity":"1",
    }
  ],
  "typeLabel": "label"
    }
  ],
  "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:

Code Block

language	js

"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:

Code Block
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:

...

Optional Fields

If a field is marked as 'Optional' it means that it doesn't have to be present in the file. For example, the above example without any optional fields would like like this:

Code Block

language	js

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

Data Types

The data type field that is present in input and output definition must contain a name of one of predefined data types. The most commons types are:

double_vector - a vector of real number values
time_vector - a vector of date values
integer_vector - a vector of integer values
boolean_vector - a vector of boolean values
string_vector - a vector of text values
catalog - a seismic catalog
seed - a SEED file
fullseed - a SEED file containing both data records and station information
miniseed - a SEED file that contains only data record

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:

Code Block

language	js

"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:

Code Block

function [outputDoubleValues, outputBooleanValues] = sampleFunctionName(intValues, stringValues, text, multiplicator)
  outputDoubleValues = double(intValues) * multiplicator;
  outputBooleanValues = strcmp(stringValues, text);
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:

intValues - corresponds to the input file with type 'integer_vector'
stringValues - corresponds to the input file with type 'string_vector'
text - corresponds to the input parameter with type TEXT
multiplicator - corresponds to the input parameter with type DOUBLE
outputDoubleValues - corresponds to the output with type 'double_vector'
outputBooleanValues - corresponds to the output with type 'boolean_vector'

Input Multiplicity

Depending on what multiplicity is given the input(s) might be passed to the main function in a different way:

multiplicity is set to exactly one input file - 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
any other multiplicity - 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. This is done by design, inputs of the same data type and non-singular multiplicity are undistinguishable from each other. If you need to have a few inputs with the same data type, and you need to be able to distinguish between them use typeLabel instead.

...

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.

...

Code Block

language	js

{
  "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 ${D__data_types} and <a href='#app:AppId'>links</a>.",
      "license":"Sample licence",
      "author":"Sample author",
      "citation":"Sample citationcitations",
      "inputsDescription":"${D__data_type}",
      "resultsDescription":"${D__other_data_type}",
      "computationalCharacteristic":"Description of computational characteristic"
    },
    "pl":{
      "name":"Aplikacja",
      "description":"Dłuższy opis z ${D__data_types} i <a href='#app:AppId'>linkiem</a>.",
      "license":"Licencja",
      "author":"Autor",
      "citation":"CytacjeRerefencje do artykułów",
      "inputsDescription":"${D__data_type}",
      "resultsDescription":"${D__other_data_type}",
      "computationalCharacteristic":"Opis charakterystyki obliczeniowej"
    }
  }
}

...

Versions Compared

Old Version 1

New Version 2

Key

Application Definition (Required)

Executable Script (Required)

Optional Fields

Data Types

Executable Script (Required)

Input Multiplicity

Application Description (Optional)