Download steps

    Created: April 7, 2015;  Last updated: November 15, 2017

    JGA data use request

    Apply data use request to National Bioscience Database Center (NBDC) with the JGA Study (e.g., JGAS00000000025) and Dataset (e.g., JGAD00000000025) accession numbers.

    Approved users should follow the NBDC Security Guidelines for Human Data (for Data Users).

    NBDC will notify user ID and password to approved users. The download account will expire in two weeks after assignment.

    This page explains how to use the JGA data.

    Download data by using the GUI tool

    JGA GUI download tool

    Download the JGA GUI download tool (last updated: 2017-11-16,v3.4.0).

    Use this tool in Java 8. This tool does not work in Java 7.

    Windows

    JGA download tool for Windows

    Run the tool by clicking the "bat" file in the folder.

    Unix

    JGA download tool for Unix

    Run the tool by executing the sh file in the directory.

    Use "Java SE Development Kit 8" and not OpenJDK.

    Login

    Run the JGA tool and login the JGA system with user ID and password notified by NBDC.

    JGA submission and download tool is the same software behave in different mode according to the account used.

    Login the JGA tool
    Login the JGA tool

    The left window is your local computer and the right window is the secure JGA file server.

    In the right window, data sets approved to use are listed. Check the data sets you want to download. Total number of files and size are displayed at below.

    Select data sets to download

    Click the [Download] button and the tool download and decrypt the data sets. The number of parallel download can be adusted from 1-5 at "Parallel Download count".

    When this process finishes, decrypted data set are downloaded to your local computer.

    In the created directory with data set accession number, the metadata XML and data files have been downloaded.

    metadata XML and data files

    You can expand the directory tree by clicking the arrowhead left to the dataset directory icon. By selecting each data directory and file, you can download individual files.

    Download data set

    Download via a proxy server

    To use the tool via the proxy server, you need to set the name and port number of the proxy server.

    Edit the "proxy.properties" file in the tool folder and enter the name (server=) and port number (port=) of the proxy server.

    # Enter the server name and port number of the proxy server 
      to connect the JGA server via the proxy.
    # For example:
    # server=proxy.example.ac.jp
    # port=8080
    server=
    port=
    

    After login, when the proxy requires user authentication, enter the authentication information in the displayed window. The v3.2.0 (2016-11-17) tool is compatible with the BASIC authentication but not with the Digest authentication.

    View metadata in website

    Users can view JGA metadata also in website.

    From the "JGA studies" page, move to the JGA datasets page.

    JGA studies

    Select data sets with data use permission.

    Select data sets to view metadata

    As in the JGA tool, login the website by using user ID and password notified by NBDC.

    Login with data use account

    Users can view metadata in the website after login.

    Users can view metadata in the website after login

    Logout from the metadata view site

    Access to the metadata view site is limited to 1 from same account. After viewing metadata, do NOT close your browser but logout at right-top "Logout".
    When an error "Maximum sessions of 1 for this principal exceeded" is displayed, login again after 30 min interval.

    After viewing metadata, do NOT close your browser but logout at right-top "Logout".

    Logout from metadata view site

    The following error is displayed when access from single account exceeds "1". Login again after 30 min interval.

    Error when access from single account exceeds 1

    Data file transfer by hard disk

    For all hard drive request please contact JGA team and let us know the permitted datasets you would like to have transferred.

    If you would like the data in hard disk, please prepare the USB hard disk drive (filesystem should be NTFS, ext3 or ext4) with enough space for the approved dataset. Be sure to virus check the entire filesystem and send us the empty drive.

    Please send your disk to the following address. Be sure to label your disk.

    Postal code: 411-8540
    Kodama Yuichi
    1111 Yata, Mishima, Shizuoka 411-8540, Japan
    Phone:+81-55-981-6853

    Download data by using the CUI tool

    JGA CUI download tool

    Download the JGA CUI download tool (Last updated: 2017-11-16, v3.4.0). At present, only the Unix tool is available.

    Unix

    Unix JGA tool

    Login

    Run the JGA tool in the tool directory.

    $ ./JgaDownload.sh  
    

    Login with the user name and password notified by NBDC.

    JGA login user name : 
    JGA Login Password  : 
    

    The user name and password can be configured.

    $ . ./JgaSetUser.sh
    or
    $ source ./JgaSetUser.sh
    

    Configure the user name and password.

    JGA login user name : 
    JGA Login Password  : 
    

    After configuration, run the tool.

    Download via the proxy server

    Configure the proxy server and port by editting the proxy.properties file. Execute as below for the proxy BASIC authentification.

    $ . ./JgaSetProxyUser.sh
    or
    $ source ./JgaSetProxyUser.sh
    

    Enter the user name and password for the proxy.

    Proxy server user name : 
    Proxy server password  : 
    

    After configuration, run the tool. The tool dose not handle the Digest authentification.

    Command line options and arguments.

    -h,--help
    -v,--version
    -l,--list {datasets|}
    -f,--files [/metadata]
    -d,--download 
    -i,--download-list 
    -q,--quiet
    -o,--output-dir 
    

    List approved Dataset, object and data files

    List all approved Datasets.

    $ sh JgaDownload.sh --list datasets
    accession       size
    JGAD00000000002 14.35KB
    JGAD00000000003 15.37KB
    JGAD00000000004 31.77KB
    

    List all Data/Analysis objects in the approved Dataset.

    $ sh JgaDownload.sh --list JGAD00000000004
    accession       size
    JGAR00000000004 19
    JGAR00000000005 19576
    JGAZ00000000004 25
    JGAZ00000000005 5066
    

    List data and metadata files in the approved Dataset.

    $ ./JgaDownload.sh --files JGAD00000000004
    file                                                 size
    JGAD00000000004/JGAR00000000004/Data-Test1-1.txt     19
    JGAD00000000004/JGAR00000000005/Data-Test2-1.txt     4635
    JGAD00000000004/JGAR00000000005/Data-Test2-2.txt     14941
    JGAD00000000004/JGAZ00000000004/Analysis-Test1-1.txt 25
    JGAD00000000004/JGAZ00000000005/Analysis-Test2-1.txt 1943
    JGAD00000000004/JGAZ00000000005/Analysis-Test2-2.txt 3123
    
    $ ./JgaDownload.sh --files JGAD00000000004/metadata
    file                                                    size
    JGAD00000000004/metadata/JGAD00000000004.analysis.xml   2145
    JGAD00000000004/metadata/JGAD00000000004.dac.xml        274
    JGAD00000000004/metadata/JGAD00000000004.data.xml       1121
    JGAD00000000004/metadata/JGAD00000000004.dataset.xml    917
    JGAD00000000004/metadata/JGAD00000000004.experiment.xml 1375
    JGAD00000000004/metadata/JGAD00000000004.policy.xml     536
    JGAD00000000004/metadata/JGAD00000000004.sample.xml     447
    JGAD00000000004/metadata/JGAD00000000004.study.xml      1035
    
    $ ./JgaDownload.sh --files JGAR00000000005
    file                                             size
    JGAD00000000004/JGAR00000000005/Data-Test2-1.txt 4635
    JGAD00000000004/JGAR00000000005/Data-Test2-2.txt 14941
    

    Download files to the specified directory.

    $ ./JgaDownload.sh --download-list samplelist.txt --output-dir /tmp