NBIA data retriever CLI

A command line replacement of NBIA data retriever. Forked from ygidtu/NBIA_data_retriever_CLI.

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Install Dependencies

Since the scripts are written in go, some dependencies need to be installed before running build.sh:

sudo apt install golang-go

go get -v github.com/voxelbrain/goptions
go get -v github.com/rs/zerolog/log

After running build.sh, three files (nbia_cli_linux_amd64, nbia_cli_darwin and nbia_cli_win64.exe) are built in the directory. Assuming one wants to run the NBIA command line data retriever on linux, after the previous step one can go on and simply run nbia_cli_linux_amd64 with the syntax that follows (see the "Command Line Usage" section for details):

./nbia_cli_linux_amd64 --input ../data/path_to_manifest/NBIA-manifest-xxxxxxxxxxx.tcia --output ../data/path_to_output/

Command Line Usage

Usage: nbia_cli_xxxx [global options]                                       
                                                                              
Global options:                                                               
        -i, --input   Path to tcia file                                       
        -o, --output  Output directory, or output file when --meta enabled (default: downloads)                                                             
        -x, --proxy   Proxy                                                   
        -t, --timeout Due to limitation of target server, please set this time out value as big as possible (default: 1200000)                               
        -p, --process Start how many download at same time (default: 1)       
        -m, --meta    Get Meta info of all files                              
        -v, --version Show version                                            
            --debug   Show debug info                                         
            --help    Show this help

The aforementioned TCIA (NBIA-manifest-xxxxxxxxx.tcia) file can be obtained directly from the dataset page on The TCIA website.

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Known Issues

Known issues:

• The public.cancerimagingarchive.net/nbia-download/servlet use POST to transfer data from server to local, the connection may be terminated even before the download is complete. Therefore, PLEASE set timeout as huge as possible
• progress bar is a mess when using multiple process
• I do not have a account of NBIA, therefore this program could not handle the restricted data for now.