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توضیحات

Flywheel BIDS Client

ویژگی	مقدار
سیستم عامل	-
نام فایل	flywheel-bids-1.1.5
نام	flywheel-bids
نسخه کتابخانه	1.1.5
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Flywheel
ایمیل نویسنده	support@flywheel.io
آدرس صفحه اصلی	https://gitlab.com/flywheel-io/public/bids-client
آدرس اینترنتی	https://pypi.org/project/flywheel-bids/
مجوز	MIT

# bids-client ## Overview The BIDS Client has three components: - Upload (Import) - Curate - Export Below is more information about each of the components. ### 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.

نیازمندی

مقدار	نام
>=15.8.0,<16.0.0	flywheel-sdk
>=16.8.0,<17.0.0	flywheel-sdk
>=0.6.0,<0.7.0	flywheel-gear-toolkit
>=0.18.2	future
>=3.2.0	jsonschema
>=1.0.0	rtstatlib
>=1.26.4	urllib3

زبان مورد نیاز

مقدار	نام
>=3.8,<4.0	Python

نحوه نصب

نصب پکیج whl flywheel-bids-1.1.5:

pip install flywheel-bids-1.1.5.whl

نصب پکیج tar.gz flywheel-bids-1.1.5:

pip install flywheel-bids-1.1.5.tar.gz