chrs

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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:

shell cargo install chrs

If necessary, add the bin folder to $PATH:

shell 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

shell 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.

```shell

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).

```shell

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.

```shell $ chrs tree -L 4 chris/feed1443 chris/feed1443 └── pl-dircopy5827 ├── data │ ├── output.meta.json │ ├── input.meta.json │ └── aparc.a2009saseg.mgz └── pl-mgz2LUTreport5836 └── data ├── output.meta.json ├── mgz2LUTreport.pdf ├── mgz2LUT_report.html └── input.meta.json

$ chrs tree -L 4 --full chris/feed1443 chris/feed1443 └── pl-dircopy5827 ├── data │ ├── chris/feed1443/pl-dircopy5827/data/output.meta.json │ ├── chris/feed1443/pl-dircopy5827/data/input.meta.json │ └── chris/feed1443/pl-dircopy5827/data/aparc.a2009saseg.mgz └── pl-mgz2LUTreport5836 └── data ├── chris/feed1443/pl-dircopy5827/pl-mgz2LUTreport5836/data/output.meta.json ├── chris/feed1443/pl-dircopy5827/pl-mgz2LUTreport5836/data/mgz2LUTreport.pdf ├── chris/feed1443/pl-dircopy5827/pl-mgz2LUTreport5836/data/mgz2LUTreport.html └── chris/feed1443/pl-dircopy5827/pl-mgz2LUTreport_5836/data/input.meta.json ```

chrs upload FILE...

Upload files to my ChRIS Library.

```shell

upload some files

chrs upload onefile.txt anotherfile.txt

upload all files in a directory

chrs upload my_data/ ```

chrs download SRC [DST]

Download files from ChRIS.

```shell

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

"/feed15/pl-dircopy5550/pl-pfdicomtagExtract5551/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/fetaldataset chrs download SERVICES/PACS/orthanc/9cfafb0-DIXONSHANNON_ANON-20140701 ```

chrs pipeline-file add

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

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

chrs pipeline-file convert

Convert between supported pipeline file formats.

shell chrs pipeline-file convert pipeline.json pipeline.yml