<!-- 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.
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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\nTo 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)\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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