CLI Client

chrs is the command-line client for ChRIS. It is useful for scripting as well as efficiency for file uploads and downloads.

Overview

Using chrs you can manage files and run analyses in ChRIS.

First, create a ChRIS user account at https://app.chrisproject.org/signup and install chrs. After that, you will be able to follow along with this section as a tutorial.

Logging In

First, we need to log in. By default, chrs uses "keyring" (secure) storage to save your login token.

# login to a ChRIS backend
$ chrs login --cube https://cube.chrisproject.org/api/v1/ --ui https://app.chrisproject.org
username: rudolph
password: [hidden]

Uploading Files

Now that we are logged in, we can get to work by uploading some files. To upload a directory of DICOMs:

# upload specific files
$ chrs upload --feed 'Example Feed Name' ./001.dcm ./002.dcm

# upload specific files by pattern
$ chrs upload --feed 'Example Feed Name' ./*.dcm

# or, upload directory
$ chrs upload --feed 'Example Feed Name' .

Searching for Analyses

Now that we have some data to work with, what can we do? Search for plugins/pipelines to run with the chrs search command, followed by chrs describe to get the usage:

# show *all* available plugins and pipelines
$ chrs search

# search for plugins and pipelines matching the query "dcm"
$ chrs search "dcm"
plugin/88     pl-img2dcm@1.0.10
plugin/87     pl-img2dcm@1.0.12
plugin/86     pl-img2dcm@1.2.0
plugin/85     pl-img2dcm@1.2.2
plugin/98     pl-dcm2mha_cnvtr@1.0.0
plugin/97     pl-dcm2mha_cnvtr@1.1.14
plugin/96     pl-dcm2mha_cnvtr@1.1.16
plugin/95     pl-dcm2mha_cnvtr@1.1.18
plugin/17     pl-dcm2mha_cnvtr@1.2.22
plugin/127    pl-dcm2niix@0.1.0
plugin/9      pl-dcm2niix@1.0.0

# print information and help about a command
$ chrs describe pl-dcm2niix@1.0.0
pl-dcm2niix: dcm2niix (plugin/9)
https://app.chrisproject.org/plugin/9

             Version: 1.0.0
               Image: fnndsc/pl-dcm2niix:1.0.0
             License: MIT
                Code: https://github.com/FNNDSC/pl-dcm2niix
   Compute Resources: NERC-other, NERC

Usage: dcm2niixw [OPTIONS] [incoming]...

Arguments:
  [incoming]...  Plugin instance or feed to use as input for this plugin

Options:
  -b, --b <string>  BIDS sidecar [choices: y, n, o]
  -d, --d <int>     directory search depth. Convert DICOMs in sub-folders of in_folder? [choices: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
  -f, --f <string>  filename (%%a=antenna (coil) name, %%b=basename, %%c=comments, %%d=description, %%e=echo number, %%f=folder name, %%g=accession number, %%i=ID of patient, %%j=seriesInstanceUID, %%k=studyInstanceUID, %%m=manufacturer, %%n=name of patient, %%o=mediaObjectInstanceUID, %%p=protocol, %%r=instance number, %%s=series number, %%t=time, %%u=acquisition number, %%v=vendor, %%x=study ID; %%z=sequence name;)
  -m, --m <string>  merge 2D slices from same series regardless of echo, exposure, etc. [no, yes, auto] [choices: n, y, 0, 1, 2]
  -v, --v <string>  verbose [no, yes, logorrheic] [choices: n, y, 0, 1, 2]
  -x, --x <string>  crop 3D acquisitions [choices: y, n, i]
  -z, --z <string>  gz compress images [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D] [choices: y, o, i, n, 3]

Running an Analyses

Let's run pl-dcm2niix on our uploaded data to convert DICOM to NIFTI.

# simple usage
$ chrs run --title "DICOM to NIFTI simple" pl-dcm2niix

# advanced usage
$ chrs run --title "DICOM to NIFTI simple" --memory-limit 4Gi   pl-dcm2niix@1.0.0       --      -b n -v y
#          |________________________________________________|   |______________|        ^^      |________|
#                            chrs options                       plugin/pipeline name  Separator   plugin parameters

tip

Plugin parameters should be listed after the optional -- separator.

Check what we have so far with the chrs status command:

$ chrs status

▲ Example Feed Name  (feed/10)
  |
  |    created: Tue, 12 Mar 2024 10:19:46 -0400
  |   modified: Tue, 12 Mar 2024 10:19:46 -0400
  |
  |   finished: 2  pending: 0  running: 1  errors: 0

――――――――――――――――――――――――――――――――――――――――
● File upload from chrs  (plugininstance/45)
| ghcr.io/fnndsc/pl-dircopy:2.1.2 dircopy --dir=chris/uploads/chrs-upload-tmp-
|     1710253185164
|
● pl-unstack-folders  (plugininstance/46)
| fnndsc/pl-unstack-folders:1.0.0 unstack
|
● DICOM to NIFTI simple  (plugininstance/47)
  fnndsc/pl-dcm2niix:1.0.0 dcm2niixw -b=n -v=y

To see the logs, run chrs logs:

$ chrs logs
Converting /share/incoming/0001-1.3.12.2.1107.5.2.19.45152.2013030808110258929186035.dcm
# -- logs truncated --

Downloading Files

What files did we get? Find out by running

chrs ls

Output files can be downloaded by running chrs download.

# download the current data
chrs download

# be specific about what to download
chrs download 'feed/Example Feed Name'

# be specific about what to download and where to save it
chrs download 'feed/Example Feed Name' output_data

Referring to Previous Jobs

What if we need to rerun pl-dcm2niix with a different set of parameters? Currently, our feed looks like this:

pi/45  "File upload from chrs"
  |
pi/46  `pl-unstack-folders`
  |
pi/47  "DICOM to NIFTI simple"

We need to tell chrs run that we want the input for the next job to be pi/46 instead of pi/47. By default, chrs run will assume the input directory is your most recent output, which is pi/47 in this case. To specify the "second to most recent output" of our analysis, we can refer to it by ID:

chrs run --title "Convert DICOM to NIFTI with gz compression" pl-dcm2niix -- -z y pi/47

Or more conveniently, we can refer to the "second to most recent output" as ..:

chrs run --title "Convert DICOM to NIFTI with gz compression" pl-dcm2niix -- -z y ..

Now, our tree looks like

    pi/45  "File upload from chrs"
      |
      |
    pi/46  `pl-unstack-folders`
    /  \
   /    \
  |      |
  |    pi/48  "Convert DICOM to NIFTI with gz compression" (new)
  |
pi/47  "DICOM to NIFTI simple"

Joining Branches

Now I want to run another plugin, pl-mri-preview on the outputs of both pi/47 and pi/48. ChRIS plugins only accept a single input directory, so chrs run will merge multiple input directories into one before running.

chrs run --title "Create PNG figures" pl-mri-preview "DICOM to NIFTI simple" "Convert DICOM to NIFTI with gz compression"

Now, our tree looks like

    pi/45  "File upload from chrs"
      |
      |
    pi/46  `pl-unstack-folders`
    /  \
   /    \
  |      |
  |    pi/48  "Convert DICOM to NIFTI with gz compression"
  |      |
pi/47    |    "DICOM to NIFTI simple"
  |      |
   \    /
    \ /
    pi/49  "Merge of ..."
     |
     |
    pi/50  "Create PNG figures"

Notice the flexibility in how we specify arguments: input arguments can be:

by ID, e.g. pi/47 or plugininstance/47
by feed ID, e.g. feed/10
by title, e.g. "DICOM to NIFTI simple"
unspecified (work on the most recent)

To learn more about how this works, read about the concepts.

Overview​

Logging In​

Uploading Files​

Searching for Analyses​

Running an Analyses​

Downloading Files​

Referring to Previous Jobs​

Joining Branches​