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‎.github/workflows/validate_and_release.yml

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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools
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pip install linkml astor pre-commit
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pip install git+https://github.com/ReproNim/reproschema-py.git
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- name: Generate pydantic using linml and fixing it with reproschema specific script
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run: |
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gen-pydantic --pydantic-version 2 linkml-schema/reproschema.yaml > reproschema_model.py
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python scripts/fix_pydantic.py reproschema_model.py
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pre-commit run --files reproschema_model.py || true
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- name: Generate jsonld format using linkml
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run: |
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gen-jsonld --context https://raw.githubusercontent.com/ReproNim/reproschema/main/contexts/reproschema linkml-schema/reproschema.yaml > reproschema.jsonld
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- name: Generate n-triples and turtle formats using reproschema
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run: |
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reproschema convert --format n-triples reproschema.jsonld > reproschema.nt
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reproschema convert --format turtle reproschema.jsonld > reproschema.ttl
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- name: Make a release
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run: |
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echo "Making a release ${{ inputs.version }}"
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mkdir releases/${{ inputs.version }}
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cp contexts/reproschema releases/${{ inputs.version }}/base
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cp contexts/reproschema releases/${{ inputs.version }}/reproschema
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mv reproschema_model.py releases/${{ inputs.version }}/reproschema_model.py
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mv reproschema.jsonld releases/${{ inputs.version }}/reproschema.jsonld
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mv reproschema.nt releases/${{ inputs.version }}/reproschema.nt
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mv reproschema.ttl releases/${{ inputs.version }}/reproschema.ttl
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# python scripts/makeRelease.py ${{ inputs.version }}
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- name: Open pull requests to add files

‎.gitignore

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activities/.DS_Store
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protocols/.DS_Store
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__pycache__
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.idea/
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local_data

‎.gitmodules

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[submodule "library"]
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path = library
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url = https://github.com/ReproNim/reproschema-library.git
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datalad-url = https://github.com/ReproNim/reproschema-library.git

‎docs/FAQ.md

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**🛠 Work in progress 🛠**
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-->
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### How can I visualize the schema for a `protocol` or an `activity`?
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If you want to see what the assessment that are already supported by the ReproSchema would look like using our ReproSchema user-interface, you can visualize them directly on [schema.repronim.org](https://schema.repronim.org/rl).
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If you just want to view a protocol or activity you are developing using the `reproschema-ui`,
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you can pass the URL of the schema to the `url` query parameter like this:
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```https://schema.repronim.org/ui/#/?url=url-to-your-schema```
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If you are hosting a schema on github, make sure that you are passing the URL of the **raw** content of the schema.
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For example, our demo protocol can be accessed at this URL:
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[https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema)
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But to get access to the raw content of that file you must click on the `Raw` button
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once you have opened that page on github that will open this URL:
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[https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema).
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If you want to visualize the graph represented by the JSON-LD file,
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we explain how to do this in [From JSON to JSON-LD](#from-json-to-json-ld).
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### Which assessments tools will/are supporting this standard?
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At the moment, all the assessments that support this standard are listed in [this folder](https://github.com/ReproNim/reproschema-library/tree/master/activities) or the [reproschema-library repository](https://github.com/ReproNim/reproschema-library).
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The ReproSchema is also used to develop a checklist to [improve methods and results reporting in neuroimaging](https://github.com/ohbm/cobidas).
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## Linked data and semantic web
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## What is the semantic web?

‎docs/how-to/validation.md

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# Validation
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### Validating your schema
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If you want to validate a schema you have created:
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- install the reproschema python tools
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```bash
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pip install reproschema
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```
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- run its `validate` command
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```bash
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reproschema --log-level DEBUG validate PATH_TO_VALIDATE
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```
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!!! note
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You can validate a single file or all the files in a folder and its subfolder.
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### Automating validation
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If you are hosting your schema on a github repository,
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you can automate its validation with a with GitHub CI workflow.
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For example if your repository is structured like this:
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```text
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├── protocols
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│ └── protocol-1.jsonld
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├── activities
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│ ├── items
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│ │ └── item-1.jsonld
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│ └── activity-1.jsonld
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└── README.md
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```
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create a `.github/workflows/validate.yml` file in this repository.
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```text hl_lines="1-3"
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├── .github # hidden github folder
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│ └── workflows
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│ └── validate.yml # file the actions used to validate your schema
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├── protocols
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│ └── protocol-1.jsonld
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├── activities
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│ ├── items
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│ │ └── item-1.jsonld
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│ └── activity-1.jsonld
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└── README.md
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```
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Content of `validate.yml`:
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```yaml
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name: validation
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on:
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push:
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branches: [ main ]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools
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pip install reproschema-py
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- name: validate
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run: |
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reproschema validate protocols
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reproschema validate activities
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```
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!!! note
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Note that if you have created your schema
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using the [reproschema cookie cutter](../user-guide/create-new-protocol.md)
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then a validation workflow should already be included in your repository.

‎docs/how-to/visualize.md

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# Visualize
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If you want to visualize the graph represented by the JSON-LD file,
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we explain how to do this in [From JSON to JSON-LD](../FAQ.md#from-json-to-json-ld).
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If you want to visualize the protocol or the activity you have created as a web form,
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you can use the [reproschema-ui](https://github.com/ReproNim/reproschema-ui) to preview it.
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To do so you can pass the URL to your protocol or activity as a query
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to the [reproschema-ui app](https://www.repronim.org/reproschema-ui/)
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```https://www.repronim.org/reproschema-ui/#/?url=url-to-your-schema```
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If you are hosting a schema on github, make sure that you are passing the URL of the **raw** content of the schema.
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For example, our demo protocol can be accessed at this URL:
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[https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://github.com/ReproNim/reproschema-demo-protocol/blob/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema)
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But to get access to the raw content of that file you must click on the `Raw` button
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once you have opened that page on github that will open this URL:
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[https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema).
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So in the end the URL to preview this protocol as a web form would be:
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[https://www.repronim.org/reproschema-ui/#/?url=https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema](
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https://www.repronim.org/reproschema-ui/#/?url=https://raw.githubusercontent.com/ReproNim/reproschema-demo-protocol/7ed1ae49279f75acdd57380fff1f8aaff2c7b511/reproschema_demo_protocol/reproschema_demo_protocol_schema)

‎docs/library.md

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---
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hide:
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- toc
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---
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# Reproschema library
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At the moment, all the assessments that support this standard are listed in [this folder](https://github.com/ReproNim/reproschema-library/tree/master/activities) of the [reproschema-library repository](https://github.com/ReproNim/reproschema-library).
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For convenience we are listing them in the table below.
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If you want to see those different tools in action using our user interface,
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you can explore them on [schema.repronim.org/](https://schema.repronim.org/rl/).
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{{ MACROS___library_table() }}

‎docs/project-structure.md

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items from this library, knowing that the information is tracked in your protocol.
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All assessments are listed in [the `activity` folder](https://github.com/ReproNim/reproschema-library/tree/master/activities)
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and are served [here](https://schema.repronim.org/rl/) if you want to visualize
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them.
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and are served [here](https://schema.repronim.org/rl/) if you want to visualize them.
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- **Standard Alignment:** Each element in the library aligns with the ReproSchema framework, ensuring uniformity in terms and structure and upholding validation protocols for consistency across the ecosystem.
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- **Research Protocol Integration:** Researchers can utilize these assessments in various combinations to align with specific protocol needs, customizing their application per study objectives. This process can be integrated using the reproschema-protocol-cookiecutter for constructing user interfaces.

‎docs/tutorials/collecting-demographics-information.md

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