chrs

chrs is a command-line client for ChRIS. It can upload files to ChRIS library, download files from ChRIS, and can run and feeds (computational experiments) on ChRIS.

Installation

There are two ways to install chrs.

Download

Pre-compiled binaries are automatically built and uploaded to Github Releases. Get the latest version here:

https://github.com/FNNDSC/chrs/releases/latest

This is the easiest installation method, however there is no mechanism for automatic updates.

Get from Crates.io

Use cargo to get and build the package from crates.io:

cargo install chrs

If necessary, add the bin folder to $PATH:

echo 'export PATH=$HOME/.cargo/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

Using chrs

Run chrs --help for usage information.

Note: when specifying URLs, they should be to the backend API, not the front-end. E.g. instead of https://app.chrisproject.org/feeds/1520, the correct URL would be https://cube.chrisproject.org/api/v1/1520/.

Overview

chrs --address https://cube.chrisproject.org/api/v1/ --username chris --password chris1234 login
chrs upload my_data/

chrs login

chrs login saves authentication tokens securely using your keyring. Logging into multiple different instances of ChRIS is supported, or as different users on the same ChRIS instance.

# log in, type username and password interactively
chrs --address https://cube.chrisproject.org/api/v1/ login

# log in without using keyring and non-interactively, useful for automation
chrs --address https://cube.chrisproject.org/api/v1/ --username test-user login --no-keyring --password-stdin <<< "$PASSWORD"

chrs logout

Remove previously saved authentication token(s).

# remove saved logins for cube.chrisproject.org
chrs --address https://cube.chrisproject.org/api/v1/ logout

# remove all saved logins
chrs logout

chrs tree PATH

List files and directories in ChRIS.

$ chrs tree -L 4 chris/feed_1443
chris/feed_1443
└── pl-dircopy_5827
    ├── data
    │   ├── output.meta.json
    │   ├── input.meta.json
    │   └── aparc.a2009saseg.mgz
    └── pl-mgz2LUT_report_5836
        └── data
            ├── output.meta.json
            ├── mgz2LUT_report.pdf
            ├── mgz2LUT_report.html
            └── input.meta.json

$ chrs tree -L 4 --full chris/feed_1443
chris/feed_1443
└── pl-dircopy_5827
    ├── data
    │   ├── chris/feed_1443/pl-dircopy_5827/data/output.meta.json
    │   ├── chris/feed_1443/pl-dircopy_5827/data/input.meta.json
    │   └── chris/feed_1443/pl-dircopy_5827/data/aparc.a2009saseg.mgz
    └── pl-mgz2LUT_report_5836
        └── data
            ├── chris/feed_1443/pl-dircopy_5827/pl-mgz2LUT_report_5836/data/output.meta.json
            ├── chris/feed_1443/pl-dircopy_5827/pl-mgz2LUT_report_5836/data/mgz2LUT_report.pdf
            ├── chris/feed_1443/pl-dircopy_5827/pl-mgz2LUT_report_5836/data/mgz2LUT_report.html
            └── chris/feed_1443/pl-dircopy_5827/pl-mgz2LUT_report_5836/data/input.meta.json

chrs upload FILE...

Upload files and run workflows.

# upload some files
chrs upload one_file.txt another_file.txt

# upload all files in a directory
chrs upload my_data/

# upload directory and create a feed with the name "Tractography Study"
chrs upload --feed "Tractography Study" my_data/

# upload directory, create a feed, and run a workflow
chrs upload --feed "Surface Extraction" \
            --pipeline "Fetal Brain Surface Extraction v1.0.0" \
            my_data/

chrs download SRC [DST]

Download files from ChRIS.

# download all files created by a feed number 15 into the current directory
chrs download https://cube.chrisproject.org/api/v1/15/files/

# download the output of plugin instance 30, but save the files to a
# directory called "my_outputs" instead of something like
# "<username>/feed_15/pl-dircopy_5550/pl-pfdicom_tagExtract_5551/data/...",
chrs download --shorten https://cube.chrisproject.org/api/v1/plugins/instances/5551/files/ my_outputs

# download files from ChRIS given a path
chrs download chris/uploads/fetal_dataset
chrs download SERVICES/PACS/orthanc/9cfafb0-DIXON_SHANNON_ANON-20140701

chrs pipeline-file add

Uploads a file-representation of a ChRIS pipeline. Supported file formats are:

• JSON (plugin_tree may be either a string (canonical) or an object)
• YAML

chrs pipeline-file add chris/tests/data/pipelines/fetal_brain_reconstruction_expanded.json

chrs pipeline-file convert

Convert between supported pipeline file formats.

chrs pipeline-file convert pipeline.json pipeline.yml