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Tool

Overview

The ImmPort File Download Tool is a ZIP package which contains two directories:

  • bin
  • aspera

The bin directory contains a bash shell script downloadImmportData.sh, referred to as the File Download Tool is designed to automate the authentication, authorization and downloading of files from the ImmPort Data Browser web site. Details on how to use the downloadImmPortData.sh tool are are available below.

In addition a Python file immport_download.py file is included to demonstrate how you can use Python to automate downloading files and using the Download and Query API.

The aspera directory contains software made available from Aspera. Aspera has developed software to transfer large files at high rates of speeds, faster than normal FTP, and is used by many scientific sites to support downloading of files.

Download Tool

The File Download Tool distribution can be obtained from HERE. Then unzip the contents of the zip package and cd to the immport-data-download-tool directory.

If you execute the bin/downloadImmPortData.sh script without any parameters it will display useful information on the parameters available and other options. (check the Response tab)

unzip immport-data-download-tool.zip
cd immport-data-download-tool
./bin/downloadImmportData.sh
Download Tool Help
usage: downloadImmportData.sh username password file | --manifest-file=filename [ --verbose | --debug ]
       downloadImmportData.sh --clean

where

  username = ImmPort username
  password = ImmPort password
  file     = Name of file or directory to be downloaded (e.g. /ALLSTUDIES/ALLSTUDIES-DR22_table_count.txt). If this parameter is not specified, then the --manifest-file option must be specified.

  --manifest-file=filename = A manifest file containing the list of files and directories to be downloaded. The filename can be either a text file or a JSON file.  If it is a text file, it must contain one file or directory name per line.  If it is a JSON file, it must have a .json file extension AND conform to the output of the ImmPort Shared Data Query API.  If this option is not specified, then parameter file must be specified.

  --verbose = run in verbose mode
  --debug   = run in debug mode (for troubleshooting purposes)
  --clean   = clean output, error, and log files
  --version = version of immport-data-download-tool

Examples

Download a Result File

./bin/downloadImmportData.sh "REPLACE_WITH_USERNAME" "REPLACE_WITH_PASSWORD" "/SDY1/ResultFiles/Flow_cytometry_result/02054141.001.52628.fcs"
Review Download Result
USER> ls -lt SDY1/ResultFiles/Flow_cytometry_result
total 240
-rw-r--r-- 1 USER USER 242048 Apr 20  2017 02054141.001.52628.fcs

USER> ls -lt log
total 64
-rw-rw---- 2 USER USER 31303 Jun 14 15:13 aspera-scp-transfer.0.log
-rw-rw---- 2 USER USER 31303 Jun 14 15:13 aspera-scp-transfer.log

Download Multiple Files using a Manifest File

Manifest File

SDY1/ResultFiles/Flow_cytometry_result/02054141.001.52628.fcs
SDY1/ResultFiles/Flow_cytometry_result/02054142.001.52644.fcs
SDY1/ResultFiles/Flow_cytometry_result/02054151.001.52646.fcs 

./bin/downloadImmportData.sh "REPLACE_WITH_USERNAME" "REPLACE_WITH_PASSWORD" --manifest-file=manifest.txt

Create JSON Manifest File - Download Files

For this example, we will create a Shell script to run multiple commands. The first 2 commands execute a query against the filePath endpoint to create a manifest file in JSON format. This manifest file is then used a input to the dowload tool.

#!/bin/bash

#
# Get an ImmPort token to access the ImmPort Shared Data Query API
#
export token=`curl -X POST https://immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`

#
# Create a JSON file containing the output of the ImmPort Shared Data Query API
#
curl -k -H "Authorization: bearer $token" "https://immport.org/data/query/result/filePath?studyAccession=SDY208" > manifest.json

#
# Call the Download Tool and pass the JSON file created above as the manifest file
#
./bin/downloadImmportData.sh "REPLACE_WITH_USERNAME" "REPLACE_WITH_PASSWORD" --manifest-file=manifest.json

The file contents of the JSON file created by the filePath API is quite verbose. The downloadImmPortData.sh knows how to parse this JSON output and removes duplicate file names before downloading the files. Below is an example of a stripped down version of a JSON manifest file, duplicate file names removed automatically.

Sample Stripped Down JSON Manifest
[
  {
    "filePath" : "/SDY208/ResultFiles/Virus_neutralization_result/Virus_Neutralization_Results.388647.txt"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Virus_neutralization_result/Virus_Neutralization_Results.388647.txt"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Virus_neutralization_result/Virus_Neutralization_Results.388647.txt"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Virus_neutralization_result/Virus_Neutralization_Results.388647.txt"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Image_Histology_result/DK11-M-Histo.388650.pdf"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Image_Histology_result/DK11-M-Histo.388650.pdf"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Image_Histology_result/DK11-M-Histo.388650.pdf"
  },
  {
    "filePath" : "/SDY208/ResultFiles/Image_Histology_result/DK11-M-Histo.388650.pdf"
  }
]
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