brainstem-python-api-tools 0.2.0__tar.gz → 2.0.0__tar.gz

brainstem_python_api_tools-2.0.0/PKG-INFO

@@ -0,0 +1,179 @@
+Metadata-Version: 2.4
+Name: brainstem_python_api_tools
+Version: 2.0.0
+Summary: A Python toolset for interacting with the BrainSTEM API.
+Author-email: BrainSTEM Team <petersen.peter@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/brainstem-org/brainstem_python_api_tools
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.28
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Dynamic: license-file
+
+# BrainSTEM Python API Tools
+
+The `brainstem_python_api_tools` is a Python toolset for interacting with the [BrainSTEM](https://www.brainstem.org/) API, designed for researchers and developers working with neuroscience data.
+
+## Installation
+You can install the package using `pip`:
+```bash
+pip install brainstem_python_api_tools
+```
+
+## Authentication
+
+Authentication uses a **browser-based device authorization flow** that supports two-factor authentication (2FA). No credentials are entered into the tool itself.
+
+```python
+from brainstem_api_tools import BrainstemClient
+
+# First run: opens a browser window for secure login.
+# The token is cached at ~/.config/brainstem/token and reused automatically.
+client = BrainstemClient()
+```
+
+To skip the browser flow, pass a token directly:
+```python
+client = BrainstemClient(token="YOUR_TOKEN")
+```
+
+For headless environments (no browser available):
+```python
+client = BrainstemClient(headless=True)  # prints a URL + code to enter manually
+```
+
+To connect to a different server (e.g. a local development instance):
+```python
+client = BrainstemClient(url="http://127.0.0.1:8000/")
+```
+
+> **Security note:** The cached token file is stored with owner-read-only permissions (`0600`). Treat it like a password and do not commit it to version control.
+
+## Getting Started
+To get started with the BrainSTEM API tools, please refer to the tutorial script provided:
+
+- **Tutorial:** `brainstem_api_tutorial.py`
+
+The tutorial demonstrates how to:
+
+- **Authenticate:** Load the client and authenticate via your browser.
+- **Load Data:** Load sessions and filter data using flexible options.
+- **Paginate:** Retrieve large datasets using `limit` / `offset` or `load_all=True`.
+- **Convenience Loaders:** Use `load_session()`, `load_subject()`, etc. for common queries.
+- **Update Entries:** Modify existing records and update them in the database.
+- **Create Entries:** Submit new data entries with required fields.
+- **Delete Entries:** Remove records by ID.
+- **Load Public Data:** Access public projects and data using the public portal.
+
+## Example Usage
+```python
+from brainstem_api_tools import BrainstemClient
+
+client = BrainstemClient()
+
+# Load sessions sorted by name
+response = client.load('session', sort=['name'])
+print(response.json())
+
+# Filter and include related data
+response = client.load(
+    'session',
+    filters={'name.icontains': 'Rat'},
+    sort=['-name'],
+    include=['projects'],
+)
+
+# Paginate results (manual)
+page2 = client.load('session', limit=20, offset=20).json()
+
+# Auto-paginate — fetches every page and returns a merged dict
+all_sessions = client.load('session', load_all=True)
+
+# Convenience loaders — sensible defaults with named filter kwargs
+# load_session embeds dataacquisition, behaviors, manipulations, epochs
+sessions = client.load_session(name='Rat', load_all=True)
+
+# load_subject embeds procedures and subjectlogs
+subjects = client.load_subject(sex='M', projects='<project-uuid>', load_all=True)
+
+# load_project embeds sessions, subjects, collections, cohorts
+projects = client.load_project(name='MyProject')
+
+# load_behavior / load_dataacquisition / load_manipulation scope by session UUID
+behaviors = client.load_behavior(session='<session-uuid>', load_all=True)
+
+# load_procedure scopes by subject UUID
+procedures = client.load_procedure(subject='<subject-uuid>', load_all=True)
+
+# Create a record
+client.save('session', data={'name': 'New session', 'projects': ['<project-uuid>']})
+
+# Update a record
+client.save('session', id='<session-uuid>', data={'description': 'updated'})
+
+# Delete a record
+client.delete('session', id='<session-uuid>')
+```
+
+## Command-line Interface
+
+After installation a `brainstem` command is available in your shell.
+
+### Authentication
+```bash
+# Authenticate (opens browser) and cache token
+brainstem login
+
+# Headless — prints URL + code instead of opening browser
+brainstem login --headless
+
+# Connect to a local dev server
+brainstem login --url http://127.0.0.1:8000/
+
+# Remove cached token
+brainstem logout
+```
+
+### Loading data
+```bash
+# Load all sessions (private portal)
+brainstem load session
+
+# Filter, sort and embed related data
+brainstem load session --filters name.icontains=Rat --sort -name --include projects
+
+# Load a single record by UUID
+brainstem load session --id <uuid>
+
+# Manual pagination
+brainstem load session --limit 20 --offset 20
+
+# Public portal
+brainstem load project --portal public
+```
+
+### Creating and updating records
+```bash
+# Create a new session
+brainstem save session --data '{"name":"New session","projects":["<uuid>"]}'
+
+# Update an existing record
+brainstem save session --id <uuid> --data '{"description":"updated"}'
+```
+
+### Deleting records
+```bash
+brainstem delete session --id <uuid>
+```
+
+All subcommands accept `--token`, `--headless`, and `--url` to override defaults.
+
+## Contributing
+Contributions are welcome! Feel free to open issues or submit pull requests on GitHub.
+
+## License
+This project is licensed under the MIT License. See the `LICENSE` file for more details.

brainstem_python_api_tools-2.0.0/README.md

@@ -0,0 +1,163 @@
+# BrainSTEM Python API Tools
+
+The `brainstem_python_api_tools` is a Python toolset for interacting with the [BrainSTEM](https://www.brainstem.org/) API, designed for researchers and developers working with neuroscience data.
+
+## Installation
+You can install the package using `pip`:
+```bash
+pip install brainstem_python_api_tools
+```
+
+## Authentication
+
+Authentication uses a **browser-based device authorization flow** that supports two-factor authentication (2FA). No credentials are entered into the tool itself.
+
+```python
+from brainstem_api_tools import BrainstemClient
+
+# First run: opens a browser window for secure login.
+# The token is cached at ~/.config/brainstem/token and reused automatically.
+client = BrainstemClient()
+```
+
+To skip the browser flow, pass a token directly:
+```python
+client = BrainstemClient(token="YOUR_TOKEN")
+```
+
+For headless environments (no browser available):
+```python
+client = BrainstemClient(headless=True)  # prints a URL + code to enter manually
+```
+
+To connect to a different server (e.g. a local development instance):
+```python
+client = BrainstemClient(url="http://127.0.0.1:8000/")
+```
+
+> **Security note:** The cached token file is stored with owner-read-only permissions (`0600`). Treat it like a password and do not commit it to version control.
+
+## Getting Started
+To get started with the BrainSTEM API tools, please refer to the tutorial script provided:
+
+- **Tutorial:** `brainstem_api_tutorial.py`
+
+The tutorial demonstrates how to:
+
+- **Authenticate:** Load the client and authenticate via your browser.
+- **Load Data:** Load sessions and filter data using flexible options.
+- **Paginate:** Retrieve large datasets using `limit` / `offset` or `load_all=True`.
+- **Convenience Loaders:** Use `load_session()`, `load_subject()`, etc. for common queries.
+- **Update Entries:** Modify existing records and update them in the database.
+- **Create Entries:** Submit new data entries with required fields.
+- **Delete Entries:** Remove records by ID.
+- **Load Public Data:** Access public projects and data using the public portal.
+
+## Example Usage
+```python
+from brainstem_api_tools import BrainstemClient
+
+client = BrainstemClient()
+
+# Load sessions sorted by name
+response = client.load('session', sort=['name'])
+print(response.json())
+
+# Filter and include related data
+response = client.load(
+    'session',
+    filters={'name.icontains': 'Rat'},
+    sort=['-name'],
+    include=['projects'],
+)
+
+# Paginate results (manual)
+page2 = client.load('session', limit=20, offset=20).json()
+
+# Auto-paginate — fetches every page and returns a merged dict
+all_sessions = client.load('session', load_all=True)
+
+# Convenience loaders — sensible defaults with named filter kwargs
+# load_session embeds dataacquisition, behaviors, manipulations, epochs
+sessions = client.load_session(name='Rat', load_all=True)
+
+# load_subject embeds procedures and subjectlogs
+subjects = client.load_subject(sex='M', projects='<project-uuid>', load_all=True)
+
+# load_project embeds sessions, subjects, collections, cohorts
+projects = client.load_project(name='MyProject')
+
+# load_behavior / load_dataacquisition / load_manipulation scope by session UUID
+behaviors = client.load_behavior(session='<session-uuid>', load_all=True)
+
+# load_procedure scopes by subject UUID
+procedures = client.load_procedure(subject='<subject-uuid>', load_all=True)
+
+# Create a record
+client.save('session', data={'name': 'New session', 'projects': ['<project-uuid>']})
+
+# Update a record
+client.save('session', id='<session-uuid>', data={'description': 'updated'})
+
+# Delete a record
+client.delete('session', id='<session-uuid>')
+```
+
+## Command-line Interface
+
+After installation a `brainstem` command is available in your shell.
+
+### Authentication
+```bash
+# Authenticate (opens browser) and cache token
+brainstem login
+
+# Headless — prints URL + code instead of opening browser
+brainstem login --headless
+
+# Connect to a local dev server
+brainstem login --url http://127.0.0.1:8000/
+
+# Remove cached token
+brainstem logout
+```
+
+### Loading data
+```bash
+# Load all sessions (private portal)
+brainstem load session
+
+# Filter, sort and embed related data
+brainstem load session --filters name.icontains=Rat --sort -name --include projects
+
+# Load a single record by UUID
+brainstem load session --id <uuid>
+
+# Manual pagination
+brainstem load session --limit 20 --offset 20
+
+# Public portal
+brainstem load project --portal public
+```
+
+### Creating and updating records
+```bash
+# Create a new session
+brainstem save session --data '{"name":"New session","projects":["<uuid>"]}'
+
+# Update an existing record
+brainstem save session --id <uuid> --data '{"description":"updated"}'
+```
+
+### Deleting records
+```bash
+brainstem delete session --id <uuid>
+```
+
+All subcommands accept `--token`, `--headless`, and `--url` to override defaults.
+
+## Contributing
+Contributions are welcome! Feel free to open issues or submit pull requests on GitHub.
+
+## License
+This project is licensed under the MIT License. See the `LICENSE` file for more details.

{brainstem_python_api_tools-0.2.0 → brainstem_python_api_tools-2.0.0}/brainstem_api_tools/__init__.py

@@ -1 +1,3 @@
-from .brainstem_api_client import BrainstemClient, ModelType, PortalType
+from .brainstem_api_client import BrainstemClient, ModelType, PortalType, AuthenticationError
+
+__version__ = "2.0.0"