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

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.

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 switch`

Switch between saved logins.

```shell

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.

shell $ 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.

```shell

by default, folder names appear as feed names or plugin instance titles

$ chrs ls --tree -L 4 chris/feed1443 chris/Segmented volume data analysis └── pl-dircopy5827 ├── data │ ├── output.meta.json │ ├── input.meta.json │ └── aparc.a2009saseg.mgz └── generate volume report └── data ├── output.meta.json ├── mgz2LUTreport.pdf ├── mgz2LUTreport.html └── input.meta.json

$ chrs ls --tree -L 4 --full --raw chris/feed1443 chris/feed1443 └── chris/feed1443/pl-dircopy5827 ├── 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 └── chris/feed1443/pl-dircopy5827/pl-mgz2LUTreport5836 └── chris/feed1443/pl-dircopy5827/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-mgz2LUTreport5836/data/input.meta.json ```

`chrs upload FILE...`

Upload files and run workflows.

```shell

upload some files

chrs upload onefile.txt anotherfile.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.

```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

download data from all plugin instances of a feed to the same folder,

effectively joining their outputs into one directory

chrs download --flatten chris/feed14 feed14outputs ```

`chrs run-latest`

Run a ChRIS plugin (i.e. create a plugin instance) by name.

```shell

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.

```shell

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

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

Feedback

Please report bugs and/or request features here: https://github.com/FNNDSC/chrs/issues

chrs

Installation

Download

Get from Crates.io

Using chrs

Overview

chrs login

log in, type username and password interactively

log in without using keyring and non-interactively, useful for automation

chrs logout

remove saved logins for cube.chrisproject.org

remove all saved logins

chrs switch

interactive prompt, use arrow keys to choose

non-interactive usage

chrs feeds

chrs ls PATH

by default, folder names appear as feed names or plugin instance titles

chrs upload FILE...

upload some files

upload all files in a directory

upload directory and create a feed with the name "Tractography Study"

upload directory, create a feed, and run a workflow

chrs download SRC [DST]

download all files created by a feed number 15 into the current directory

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/...",

download files from ChRIS given a path

download data from all plugin instances of a feed to the same folder,

effectively joining their outputs into one directory

chrs run-latest

run pl-mri10yr06mo01da_normal (fs-type) to create a new ChRIS feed

run pl-mri-preview (ds-type) after plugin instance id=56, with option --units-fallback mm

chrs get

example: list plugins used in feed 12

chrs pipeline-file add

chrs pipeline-file convert

Feedback

Using `chrs`

`chrs login`

`chrs logout`

`chrs switch`

`chrs feeds`

`chrs ls PATH`

`chrs upload FILE...`

`chrs download SRC [DST]`

`chrs run-latest`

`chrs get`

`chrs pipeline-file add`

`chrs pipeline-file convert`