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General Information

When used by the public or a private NDEx server:

  • This application is invoked using the NDEx batch/network/export REST API function.
  • After the batch process runs, the task/file REST API function will download the resultant output file.
  • You can then import the downloaded file into applications that accept .csv/.tsv/.txt files as input.

When used from a Terminal or Command-line:

  • Input originates from a JSON-formatted NDEx CX network file that you downloaded to your local file system using the NDEx Webapp front-end, or through the NDEx REST API.
  • This application is run in a Terminal or Command/PowerShell shell using parameter options that specify the input and output filenames and the file-type you want.
  • The output file can then be imported into applications that accept .csv/.tsv/.txt files as input.

Running the Application

The executable program containing all dependencies is named morphcx.jar.
A zip or tar file of this asset is obtained using this repository's Releases function. Download the file by clicking on the appropriate asset file link.

The executable file should be placed in a directory pointed to by the Java CLASSPATH environment variable or in the current directory. If the program is not found, it is likely Java is not installed or is incorrectly configured.

The program is a Java executable, thus the Java JRE 8 or JDK 8 must be installed on your computer. To test if Java is installed, enter the following on the Terminal or Command-line/PowerShell prompt:

java -version

Execute the program in a Terminal or Command/Powershell shell using the following general format.

java -jar morphcx.jar [option-1, option-n...]

Valid options are documented in Parameter Options section below. Default values are assumed if none are specified.

A few sample CX networks are provided in the target/sample-networks directory. They let you quickly test whether this application has been installed correctly. For a quick test, copy the entire ${project}/targetdirectory and sub-directories onto your workstation, make it the current directory, and enter the following from a Terminal or Command-line prompt:

java -jar morphcx.jar -c tsv -i sample-networks/LBC_FILTERED_ERK_AKT.json -o sample-networks/LBC_FILTERED_ERK_AKT.tsv

... which will result in sample-networks/LBC_FILTERED_ERK_AKT.tsv being produced in the sample-networks directory.

Parameter Options

When executing this application in a Terminal or Command/Powershell shell, the input and output files should be specified, either by using command-line parameters or by IO redirection. Default values are assumed for missing parameters.

When configuring this application to be run as an NDEx server batch process, use the -S or --server command-line parameter options without specifying the input or output command-line parameters.
These command-line parameter options force all input and output to use the system standard input and output, respectively.

IO Redirection

IO redirection is commonly used by SysOps engineers and is less intuitive than using conventional parameters. Nevertheless, IO redirection can be quite useful when executing this application within a script. Examples of IO redirection are found in the link immediately below.

Running as an NDEx Server Process

An NDEx server administrator can configure this application to run as an Exporter in the ImporterExporter tag of the NDEx configuration file. Several exporter names can be created, one designated for each output file-type and optional parameter options. Instructions are found in the link that follows.

Notes for Developers

A fully built executable binary .jar file is found in the ${project}/target directory of this repository.
However, for those who prefer to build their own executables from scratch, instructions to do this are found at the link below.