flywheel-bids


Nameflywheel-bids JSON
Version 1.2.10 PyPI version JSON
download
home_pagehttps://gitlab.com/flywheel-io/public/bids-client
SummaryFlywheel BIDS Client
upload_time2024-02-13 19:52:35
maintainer
docs_urlNone
authorFlywheel
requires_python>=3.8,<4.0
licenseMIT
keywords flywheel flywheel bids sdk
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            <!-- 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
```

## 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.

            

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    "description": "<!-- markdownlint-configure-file { \"MD024\": { \"siblings_only\": true } } -->\n# bids-client\n\n## Overview\n\nThe BIDS Client has three components:\n\n- Upload (Import)\n- Curate\n- Export\n\nBelow is more information about each of the components.\n\n[This information is old and may not be correct.]\n\n### Build the image\n\nThe following command will build the docker image containing all BIDS Client components.\n\n```bash\ngit clone https://gitlab.com/flywheel-io/public/bids-client\ncd bids-client\ndocker build -t flywheel/bids-client .\n```\n\n## Upload\n\nThe upload script (upload_bids.py) takes a BIDS dataset and uploads it to Flywheel.\n\n### Flywheel CLI\n\nNOTE: This requires the Flywheel CLI.\n\nThe upload script has been integrated into the flywheel cli as\n\n```bash\nfw import bids [folder] [group] [project] [flags]\n```\n\n### Docker Script\n\nA docker script has been provided to simplify the below process.\nTo run:\n\n```bash\n./docker/upload.sh \\\n    /path/to/BIDS/dir/in/container \\\n    --api-key '<PLACE YOUR API KEY HERE>' \\\n    --type 'Flywheel' \\\n    -g '<PLACE GROUP ID HERE>'\n```\n\nAn optional project flag can also be given if the given BIDS directory is not at the\nproject level.\n\n```bash\n    -p '<PLACE PROJECT LABEL HERE>'\n```\n\n### Run Docker image locally\n\nStartup container\n\n```bash\ndocker run -it --rm \\\n    -v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \\\n     flywheel/bids-client /bin/bash\n```\n\nRun the upload script\n\n```bash\npython /code/upload_bids.py \\\n    --bids-dir /path/to/BIDS/dir/in/container \\\n    --api-key '<PLACE YOUR API KEY HERE>' \\\n    --type 'Flywheel' \\\n    -g '<PLACE GROUP ID HERE>'\n```\n\n## Curate\n\n### Gear\n\nThe BIDS Curation step (curate_bids.py) has been transformed into a gear for better usability.\nThe git repo for the gear is here: <https://gitlab.com/flywheel-io/flywheel-apps/curate-bids>\n\n### Docker Script\n\nRun it using the docker script\n\n```bash\n./docker/curate.sh \\\n    --api-key '<PLACE YOUR API KEY HERE>' \\\n    -p '<PLACE PROJECT LABEL HERE>' \\\n    [optional flags]\n```\n\nFlags:\n\n```bash\n  --reset               Reset BIDS data before running\n  --template-file       Template file to use\n```\n\n## Export\n\nThe export script (export_bids.py) takes a curated dataset within Flywheel and\ndownloads it to local disk.\n\n### Flywheel CLI\n\nNOTE: This requires the Flywheel CLI.\n\nUsage:\n\n```bash\nfw export bids [dest folder] [flags]\n```\n\nFlags:\n\n```bash\n  -h, --help             help for bids\n  -p, --project string   The label of the project to export\n      --source-data      Include sourcedata in BIDS export\n```\n\n### Docker Script\n\nTo run\n\n```bash\n./docker/export.sh \\\n    /path/to/BIDS/dir/in/container \\\n    --api-key '<PLACE YOUR API KEY HERE>' \\\n    -p '<PLACE PROJECT LABEL HERE>'\n```\n\n### Run Docker image locally\n\nStartup container\n\n```bash\ndocker run -it --rm \\\n    -v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \\\n     flywheel/bids-client /bin/bash\n```\n\nRun the export script\n\n```bash\npython /code/export_bids.py \\\n    --bids-dir /path/to/BIDS/dir/in/container \\\n    --api-key '<PLACE YOUR API KEY HERE>' \\\n    -p '<PROJECT LABEL TO DOWNLOAD>'\n```\n\n## Testing and contributing\n\n- Build the test container and run the tests\n\n```bash\n./tests/bin/docker-test.sh\n```\n\n- If you want to drop into the container:\n\n```bash\n./tests/bin/docker-test.sh -B -s   # \"-B\" prevents building, \"-s\" run the shell \ndocker container ls\n```\n\n1) Find the container name\n2) ```docker run -ti exec <container name>```\n3) Inside the container, run the tests:\n    ```/src/tests/bin/tests.sh```\n\n- If you are using PyCharm as your IDE, you can build the docker image as above. Add\nthe interpreter, making note of the python path (by dropping in the container and\n`which python`). Edit the configurations (top toolbar by debugging) to have the API key\nmade available to the docker image. To do so, add to the container settings. Your home\ndirectory/.config/flywheel/user.json should point to /root/.config/flywheel/user.json\nin the container. N.B. Relative or path expansions don't work. From there, you should\nbe able to debug whichever tests you desire.\n\n- Setting conditional breakpoints in PyCharm:\nClick on the link to set a breakpoint. Right click to add a condition. As an example,\none of the handiest spots to debug is `bidsify_flywheel` line 139. Add a condition\nlike: (\"file\" in context) and (rule.id == \"reproin_func_file\") and (\"task-bart\" in\ncontext[\"acquisition\"].data[\"label\"]) and debug. All the tests will continue to run\nuntil that condition is satisfied. Then, you can step through.\n",
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