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 four ways to install chrs
.
Direct Download
You can download chrs
from
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.
Using Pip
chrs
is published to PyPi using
PyO3/maturin. Installing chrs
using pip
will be preferable for users who are already comfortable with Python.
pip install --user chrs
If necessary, add the bin
folder to $PATH
:
echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc
cargo binstall
cargo binstall
is a convenient solution
for installing pre-compiled binaries using cargo
as a package manager. First install rust-binstall,
then run
cargo binstall chrs
Build from source from crates.io
Use cargo to get and build the package from source, 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 switch
Switch between saved logins.
# interactive prompt, use arrow keys to choose
chrs switch
jennings http://cube-next.tch.harvard.edu/api/v1/
jenni http://cube-next.tch.harvard.edu/api/v1/
rudolph http://cube-next.tch.harvard.edu/api/v1/
> jennydaman https://cube.chrisproject.org/api/v1/
chris https://cube.chrisproject.org/api/v1/
# non-interactive usage
chrs switch --username jennydaman --address https://cube.chrisproject.org/api/v1/
chrs feeds
List or search existing feeds.
$ chrs feeds
COVID-NET analysis on patient ABCD chris/feed_1891
SPL visualization chris/feed_1890
LLD test 3 chris/feed_1889
Subplate surfaces surface_fit parameter schedule jennings/feed_1888
Preprocess data from henry jennings/feed_1887
chrs ls PATH
List files and directories in ChRIS.
# by default, folder names appear as feed names or plugin instance titles
$ chrs ls --tree -L 4 chris/feed_1443
chris/Segmented volume data analysis
└── pl-dircopy_5827
├── data
│ ├── output.meta.json
│ ├── input.meta.json
│ └── aparc.a2009saseg.mgz
└── generate volume report
└── data
├── output.meta.json
├── mgz2LUT_report.pdf
├── mgz2LUT_report.html
└── input.meta.json
$ chrs ls --tree -L 4 --full --raw chris/feed_1443
chris/feed_1443
└── chris/feed_1443/pl-dircopy_5827
├── 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
└── chris/feed_1443/pl-dircopy_5827/pl-mgz2LUT_report_5836
└── chris/feed_1443/pl-dircopy_5827/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
# download data from all plugin instances of a feed to the same folder,
# effectively joining their outputs into one directory
chrs download --flatten chris/feed_14 feed14_outputs
chrs run-latest
Run a ChRIS plugin (i.e. create a plugin instance) by name.
# run pl-mri10yr06mo01da_normal (fs-type) to create a new ChRIS feed
chrs run-latest pl-mri10yr06mo01da_normal
# run pl-mri-preview (ds-type) after plugin instance id=56, with option --units-fallback mm
chrs run-latest --memory-limit 2Gi --compute-resource-name moc --previous-id 56 pl-mri-preview -- --units-fallback mm
Note: since plugin version is not specified when using chrs run-latest
,
the parameters are subject to change. chrs run
(not yet implemented)
is preferable for the sake of reproducibility.
A plugin's parameters help can be viewed, e.g. for pl-mri-preview
,
by running chrs plugin-help pl-mri-preview
chrs get
Make an authenticated HTTP GET request.
As chrs
is still under development, many functions are still unavailable.
Advanced users can use chrs get
to query the CUBE API directly.
# example: list plugins used in feed 12
cargo run -- get https://cube.chrisproject.org/api/v1/12/plugininstances/ | jq -r '.results[] | .plugin_name'
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
Feedback
Please report bugs and/or request features here: https://github.com/FNNDSC/chrs/issues **