flywheel-bids 1.2.33
Flywheel BIDS Client
Requires Python: <4,>=3.11
Keywords: BIDS, Flywheel, SDK, flywheel

<!-- markdownlint-configure-file { "MD024": { "siblings_only": true } } -->

# 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.

```bash
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

```bash
fw import bids [folder] [group] [project] [flags]
```

### Docker Script

A docker script has been provided to simplify the below process. To run:

```bash
./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.

```bash
    -p '<PLACE PROJECT LABEL HERE>'
```

### Run Docker image locally

Startup container

```bash
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

```bash
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

```bash
./docker/curate.sh \
    --api-key '<PLACE YOUR API KEY HERE>' \
    -p '<PLACE PROJECT LABEL HERE>' \
    [optional flags]
```

Flags:

```bash
  --reset               Reset BIDS data before running
  --template-file       Template file to use
```

To standardize how a project is curated, follow this [Jupyter notebook](https://gitlab.com/flywheel-io/scientific-solutions/tutorials/notebooks/bids-sidecar-standardization/-/blob/main/BIDS_sidecar_hierarchy_curator.ipynb)

## 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:

```bash
fw export bids [dest folder] [flags]
```

Flags:

```bash
  -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

```bash
./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

```bash
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

```bash
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

```bash
./tests/bin/docker-test.sh
```

- If you want to drop into the container:

```bash
./tests/bin/docker-test.sh -B -s   # "-B" prevents building, "-s" run the shell
docker container ls
```

1. Find the container name
2. `docker run -ti exec <container name>`
3. 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.