Flywheel BIDS Client
Project description
bids-client
Overview
The BIDS Client has three components:
- Upload (Import)
- Curate
- Export
Below is more information about each of the components.
[This information is old and may not be correct.]
Build the image
The following command will build the docker image containing all BIDS Client components.
git clone https://gitlab.com/flywheel-io/public/bids-client
cd bids-client
docker build -t flywheel/bids-client .
Upload
The upload script (upload_bids.py) takes a BIDS dataset and uploads it to Flywheel.
Flywheel CLI
NOTE: This requires the Flywheel CLI.
The upload script has been integrated into the flywheel cli as
fw import bids [folder] [group] [project] [flags]
Docker Script
A docker script has been provided to simplify the below process. To run:
./docker/upload.sh \
/path/to/BIDS/dir/in/container \
--api-key '<PLACE YOUR API KEY HERE>' \
--type 'Flywheel' \
-g '<PLACE GROUP ID HERE>'
An optional project flag can also be given if the given BIDS directory is not at the project level.
-p '<PLACE PROJECT LABEL HERE>'
Run Docker image locally
Startup container
docker run -it --rm \
-v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \
flywheel/bids-client /bin/bash
Run the upload script
python /code/upload_bids.py \
--bids-dir /path/to/BIDS/dir/in/container \
--api-key '<PLACE YOUR API KEY HERE>' \
--type 'Flywheel' \
-g '<PLACE GROUP ID HERE>'
Curate
Gear
The BIDS Curation step (curate_bids.py) has been transformed into a gear for better usability. The git repo for the gear is here: https://gitlab.com/flywheel-io/flywheel-apps/curate-bids
Docker Script
Run it using the docker script
./docker/curate.sh \
--api-key '<PLACE YOUR API KEY HERE>' \
-p '<PLACE PROJECT LABEL HERE>' \
[optional flags]
Flags:
--reset Reset BIDS data before running
--template-file Template file to use
To standardize how a project is curated, follow this Jupyter notebook
Export
The export script (export_bids.py) takes a curated dataset within Flywheel and downloads it to local disk.
Flywheel CLI
NOTE: This requires the Flywheel CLI.
Usage:
fw export bids [dest folder] [flags]
Flags:
-h, --help help for bids
-p, --project string The label of the project to export
--source-data Include sourcedata in BIDS export
Docker Script
To run
./docker/export.sh \
/path/to/BIDS/dir/in/container \
--api-key '<PLACE YOUR API KEY HERE>' \
-p '<PLACE PROJECT LABEL HERE>'
Run Docker image locally
Startup container
docker run -it --rm \
-v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \
flywheel/bids-client /bin/bash
Run the export script
python /code/export_bids.py \
--bids-dir /path/to/BIDS/dir/in/container \
--api-key '<PLACE YOUR API KEY HERE>' \
-p '<PROJECT LABEL TO DOWNLOAD>'
Testing and contributing
- Build the test container and run the tests
./tests/bin/docker-test.sh
- If you want to drop into the container:
./tests/bin/docker-test.sh -B -s # "-B" prevents building, "-s" run the shell
docker container ls
- Find the container name
docker run -ti exec <container name>
- Inside the container, run the tests:
/src/tests/bin/tests.sh
-
If you are using PyCharm as your IDE, you can build the docker image as above. Add the interpreter, making note of the python path (by dropping in the container and
which python
). Edit the configurations (top toolbar by debugging) to have the API key made available to the docker image. To do so, add to the container settings. Your home directory/.config/flywheel/user.json should point to /root/.config/flywheel/user.json in the container. N.B. Relative or path expansions don't work. From there, you should be able to debug whichever tests you desire. -
Setting conditional breakpoints in PyCharm: Click on the link to set a breakpoint. Right click to add a condition. As an example, one of the handiest spots to debug is
bidsify_flywheel
line 139. Add a condition like: ("file" in context) and (rule.id == "reproin_func_file") and ("task-bart" in context["acquisition"].data["label"]) and debug. All the tests will continue to run until that condition is satisfied. Then, you can step through.
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