plantdb_client

plantdb.client.plantdb_client

PlantDB Client Module

A client library for interacting with the PlantDB API, providing a streamlined interface for managing plant-related data including scans, filesets, and associated metadata.

Key Features

• Scan Management: Create new scans and manage scan metadata
• Fileset Operations: Create and manage collections of files associated with scans
• File Handling: Upload and manage individual files within filesets
• Metadata Management: Comprehensive CRUD operations for scan, fileset, and file metadata
• RESTful Interface: Implements standard HTTP methods for API communication

Usage Examples

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Create a new scan
>>> scan_id = client.create_scan(
...     name="Plant Sample 001",
...     description="Arabidopsis specimen under controlled conditions"
... )
>>> # Create a fileset for the scan
>>> fileset_id = client.create_fileset(
...     scan_id=scan_id,
...     fileset_id="RGB Images",
...     description="Top view RGB images"
... )

PlantDBClient

PlantDBClient(base_url, prefix=None)

Client for interacting with the PlantDB REST API.

This class provides methods to interact with a PlantDB REST API, allowing operations on scans, filesets, and files. It handles authentication, error processing, and provides a consistent interface for all API endpoints.

Parameters:

Name	Type	Description	Default
base_url	str	The base URL of the PlantDB REST API.	required
prefix	str	The URL prefix used by the PlantDB REST API.	None

Attributes:

Name	Type	Description
base_url	str	The base URL of the PlantDB REST API.
session	Session	HTTP session that maintains cookies and connection pooling.
jwt_token	str	The JWT token to authenticate with the PlantDB REST API.
username	str	The login username.
logger	Logger	The logger to use.

Notes

This client automatically handles HTTP errors and extracts meaningful error messages from the API responses. All methods will raise appropriate exceptions with descriptive messages when API requests fail.

Examples:

>>> from plantdb.server.test_rest_api import TestRestApiServer
>>> # Start a test PlantDB REST API server first:
>>> server = TestRestApiServer(test=True)
>>> server.start()
>>> # Use the client against the server
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> client.login('admin', 'admin')
>>> print(client.jwt_token)
>>> print(client.plantdb_url)
>>> scans = client.list_scans()
>>> print(scans)
['virtual_plant', 'real_plant_analyzed', 'real_plant', 'virtual_plant_analyzed', 'arabidopsis000']
>>> # Finally, stop the server
>>> server.stop()

Initialize the PlantDBClient with a base URL.

Source code in plantdb/client/plantdb_client.py

def __init__(self, base_url, prefix=None):
    """Initialize the PlantDBClient with a base URL."""
    if prefix is None:
        prefix = api_prefix()
    self.base_url = f"{base_url}{prefix}"
    self.session = requests.Session()
    self.jwt_token = None
    self.username = None
    self.logger = get_logger(__class__.__name__)

create_file

create_file(file_data, file_id, ext, scan_id, fileset_id, metadata=None)

Create a new file in a fileset and upload its data.

Parameters:

Name	Type	Description	Default
file_data	str, pathlib.Path, or BytesIO	Path to the file to upload or BytesIO object containing file data	required
file_id	str	The ID of the file in the database	required
ext	str	File extension (must be one of the valid extensions)	required
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset to create the file in	required
metadata	dict	Additional metadata for the file	None

Returns:

Type	Description
dict	Server response containing creation confirmation message

Raises:

Type	Description
RequestException	If the request fails
ValueError	If required parameters are missing or invalid

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> import tempfile
>>> import yaml
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Example 1 - Existing YAML file path as string
>>> metadata = {'description': 'Test document', 'author': 'John Doe'}
>>> dummy_data = {'name': 'Test Plant', 'species': 'Arabidopsis thaliana'}
>>> with tempfile.NamedTemporaryFile(suffix='.yaml', mode='w', delete=False) as f: temp_file_name = f.name; yaml.dump(dummy_data, f)
>>> response = client.create_file(temp_file_name, file_id='new_file',ext='yaml',scan_id='real_plant',fileset_id='images',metadata=metadata)
>>> print(response)
{'message': "File 'new_file.yaml' created and written successfully in fileset 'images'.", 'id': 'new_file'}
>>> # Example 2 - RGB Image with BytesIO
>>> import numpy as np
>>> from PIL import Image
>>> from io import BytesIO
>>> # Generate random RGB data (values from 0-255)
>>> rgb_data = np.random.randint(0, 256, (200, 150, 3), dtype=np.uint8)
>>> # Create PIL Image from NumPy array
>>> img = Image.fromarray(rgb_data, 'RGB')
>>> # Save image to BytesIO object
>>> image_data = BytesIO()
>>> img.save(image_data, format='PNG')
>>> image_data.seek(0)  # Move to the beginning of the BytesIO object
>>> metadata = {'description': 'Random RGB test image', 'author': 'John Doe'}
>>> response = client.create_file(image_data, file_id='random_image', ext='png', scan_id='real_plant', fileset_id='images', metadata=metadata)
>>> print(response)

Source code in plantdb/client/plantdb_client.py

def create_file(self, file_data, file_id, ext, scan_id, fileset_id, metadata=None):
    """Create a new file in a fileset and upload its data.

    Parameters
    ----------
    file_data : str, pathlib.Path, or BytesIO
        Path to the file to upload or BytesIO object containing file data
    file_id : str
        The ID of the file in the database
    ext : str
        File extension (must be one of the valid extensions)
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset to create the file in
    metadata : dict, optional
        Additional metadata for the file

    Returns
    -------
    dict
        Server response containing creation confirmation message

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails
    ValueError
        If required parameters are missing or invalid

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> import tempfile
    >>> import yaml
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Example 1 - Existing YAML file path as string
    >>> metadata = {'description': 'Test document', 'author': 'John Doe'}
    >>> dummy_data = {'name': 'Test Plant', 'species': 'Arabidopsis thaliana'}
    >>> with tempfile.NamedTemporaryFile(suffix='.yaml', mode='w', delete=False) as f: temp_file_name = f.name; yaml.dump(dummy_data, f)
    >>> response = client.create_file(temp_file_name, file_id='new_file',ext='yaml',scan_id='real_plant',fileset_id='images',metadata=metadata)
    >>> print(response)
    {'message': "File 'new_file.yaml' created and written successfully in fileset 'images'.", 'id': 'new_file'}
    >>> # Example 2 - RGB Image with BytesIO
    >>> import numpy as np
    >>> from PIL import Image
    >>> from io import BytesIO
    >>> # Generate random RGB data (values from 0-255)
    >>> rgb_data = np.random.randint(0, 256, (200, 150, 3), dtype=np.uint8)
    >>> # Create PIL Image from NumPy array
    >>> img = Image.fromarray(rgb_data, 'RGB')
    >>> # Save image to BytesIO object
    >>> image_data = BytesIO()
    >>> img.save(image_data, format='PNG')
    >>> image_data.seek(0)  # Move to the beginning of the BytesIO object
    >>> metadata = {'description': 'Random RGB test image', 'author': 'John Doe'}
    >>> response = client.create_file(image_data, file_id='random_image', ext='png', scan_id='real_plant', fileset_id='images', metadata=metadata)
    >>> print(response)

    """
    import os
    import json
    from io import BytesIO
    from pathlib import Path

    url = f"{self.base_url}/api/file"

    ext = ext.lstrip('.').lower()  # Remove leading dot if present
    # Prepare form data
    data = {
        'file_id': file_id,
        'ext': ext,
        'scan_id': scan_id,
        'fileset_id': fileset_id
    }

    # Add metadata if provided
    if metadata:
        if isinstance(metadata, dict):
            data['metadata'] = json.dumps(metadata)
        elif isinstance(metadata, str):
            data['metadata'] = metadata
        else:
            raise TypeError("Invalid metadata type. Must be a dictionary or string.")

    # Prepare file data based on the type of file_data
    if isinstance(file_data, BytesIO):
        # If it's already a BytesIO object, use it directly
        filename = f"{file_id}.{ext}"
        files = {
            'file': (filename, file_data, get_mime_type(ext))
        }
        response = self.session.post(url, files=files, data=data)
    else:
        # Convert to Path object if it's a string
        file_path = Path(file_data) if isinstance(file_data, str) else file_data

        # Handle file from path
        with open(file_path, 'rb') as file_handle:
            filename = os.path.basename(str(file_path))
            files = {
                'file': (filename, file_handle, 'application/octet-stream')
            }
            response = self.session.post(url, files=files, data=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

create_fileset

create_fileset(fileset_id, scan_id, metadata=None)

Create a new fileset associated with a scan.

Parameters:

Name	Type	Description	Default
fileset_id	str	The ID of the fileset to create	required
scan_id	str	The ID of the scan to associate the fileset with	required
metadata	dict	Additional metadata for the fileset	None

Returns:

Type	Description
dict	Server response containing creation confirmation message

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> metadata = {'description': 'This is a test fileset'}
>>> response = client.create_fileset('my_fileset', 'real_plant', metadata=metadata)
>>> print(response)
{'message': "Fileset 'my_fileset' created successfully in 'real_plant'."}

Source code in plantdb/client/plantdb_client.py

def create_fileset(self, fileset_id, scan_id, metadata=None):
    """Create a new fileset associated with a scan.

    Parameters
    ----------
    fileset_id : str
        The ID of the fileset to create
    scan_id : str
        The ID of the scan to associate the fileset with
    metadata : dict, optional
        Additional metadata for the fileset

    Returns
    -------
    dict
        Server response containing creation confirmation message

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> metadata = {'description': 'This is a test fileset'}
    >>> response = client.create_fileset('my_fileset', 'real_plant', metadata=metadata)
    >>> print(response)
    {'message': "Fileset 'my_fileset' created successfully in 'real_plant'."}
    """
    url = f"{self.base_url}/api/fileset"
    data = {
        'fileset_id': fileset_id,
        'scan_id': scan_id
    }
    if metadata:
        data['metadata'] = metadata
    response = self.session.post(url, json=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

create_scan

create_scan(name, metadata=None)

Create a new scan in the database.

Parameters:

Name	Type	Description	Default
name	str	Name of the scan to create	required
metadata	dict	Additional metadata for the scan	None

Returns:

Type	Description
dict	Server response containing creation confirmation message

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> metadata = {'description': 'Test plant scan'}
>>> response = client.create_scan('test_plant', metadata=metadata)
>>> print(response)
{'message': "Scan 'test_plant' created successfully."}

Source code in plantdb/client/plantdb_client.py

def create_scan(self, name, metadata=None):
    """Create a new scan in the database.

    Parameters
    ----------
    name : str
        Name of the scan to create
    metadata : dict, optional
        Additional metadata for the scan

    Returns
    -------
    dict
        Server response containing creation confirmation message

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> metadata = {'description': 'Test plant scan'}
    >>> response = client.create_scan('test_plant', metadata=metadata)
    >>> print(response)
    {'message': "Scan 'test_plant' created successfully."}
    """
    url = f"{self.base_url}/api/scan"
    data = {'name': name}
    if metadata:
        data['metadata'] = metadata
    response = self.session.post(url, json=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

get_file_metadata

get_file_metadata(scan_id, fileset_id, file_id, key=None)

Retrieve metadata for a specified file.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset containing the file	required
file_id	str	The ID of the file	required
key	str	If provided, returns only the value for this specific metadata key	None

Returns:

Type	Description
dict	Server response containing the metadata or specific key value

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Get all metadata
>>> metadata = client.get_file_metadata('test_plant', 'images', 'image_001')
>>> print(metadata)
{'metadata': {'description': 'Test file'}}
>>> # Get specific metadata key
>>> value = client.get_file_metadata('test_plant', 'images', 'image_001', key='description')
>>> print(value)
{'metadata': 'Test file'}

Source code in plantdb/client/plantdb_client.py

def get_file_metadata(self, scan_id, fileset_id, file_id, key=None):
    """Retrieve metadata for a specified file.

    Parameters
    ----------
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset containing the file
    file_id : str
        The ID of the file
    key : str, optional
        If provided, returns only the value for this specific metadata key

    Returns
    -------
    dict
        Server response containing the metadata or specific key value

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Get all metadata
    >>> metadata = client.get_file_metadata('test_plant', 'images', 'image_001')
    >>> print(metadata)
    {'metadata': {'description': 'Test file'}}
    >>> # Get specific metadata key
    >>> value = client.get_file_metadata('test_plant', 'images', 'image_001', key='description')
    >>> print(value)
    {'metadata': 'Test file'}
    """
    url = f"{self.base_url}/api/file/{scan_id}/{fileset_id}/{file_id}/metadata"
    params = {'key': key} if key else None
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

get_fileset_metadata

get_fileset_metadata(scan_id, fileset_id, key=None)

Retrieve metadata for a specified fileset.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset	required
key	str	If provided, returns only the value for this specific metadata key	None

Returns:

Type	Description
dict	Server response containing the metadata or specific key value

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Get all metadata
>>> metadata = client.get_fileset_metadata('real_plant', 'my_fileset')
>>> print(metadata)
{'metadata': {'description': 'This is a test fileset'}}
>>> # Get specific metadata key
>>> value = client.get_fileset_metadata('real_plant', 'my_fileset', key='description')
>>> print(value)
{'metadata': 'This is a test fileset'}

Source code in plantdb/client/plantdb_client.py

def get_fileset_metadata(self, scan_id, fileset_id, key=None):
    """Retrieve metadata for a specified fileset.

    Parameters
    ----------
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset
    key : str, optional
        If provided, returns only the value for this specific metadata key

    Returns
    -------
    dict
        Server response containing the metadata or specific key value

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Get all metadata
    >>> metadata = client.get_fileset_metadata('real_plant', 'my_fileset')
    >>> print(metadata)
    {'metadata': {'description': 'This is a test fileset'}}
    >>> # Get specific metadata key
    >>> value = client.get_fileset_metadata('real_plant', 'my_fileset', key='description')
    >>> print(value)
    {'metadata': 'This is a test fileset'}
    """
    url = f"{self.base_url}/api/fileset/{scan_id}/{fileset_id}/metadata"
    params = {'key': key} if key else None
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

get_scan_metadata

get_scan_metadata(scan_id, key=None)

Retrieve metadata for a specified scan.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan	required
key	str	If provided, returns only the value for this specific metadata key	None

Returns:

Type	Description
dict	Server response containing the metadata or specific key value

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Get all metadata
>>> metadata = client.get_scan_metadata('test_plant')
>>> print(metadata)
{'metadata': {'owner': 'anonymous', 'description': 'Test plant scan'}}
>>> # Get specific metadata key
>>> value = client.get_scan_metadata('test_plant', key='description')
>>> print(value)
{'metadata': 'Test plant scan'}

Source code in plantdb/client/plantdb_client.py

def get_scan_metadata(self, scan_id, key=None):
    """Retrieve metadata for a specified scan.

    Parameters
    ----------
    scan_id : str
        The ID of the scan
    key : str, optional
        If provided, returns only the value for this specific metadata key

    Returns
    -------
    dict
        Server response containing the metadata or specific key value

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Get all metadata
    >>> metadata = client.get_scan_metadata('test_plant')
    >>> print(metadata)
    {'metadata': {'owner': 'anonymous', 'description': 'Test plant scan'}}
    >>> # Get specific metadata key
    >>> value = client.get_scan_metadata('test_plant', key='description')
    >>> print(value)
    {'metadata': 'Test plant scan'}
    """
    url = f"{self.base_url}/api/scan/{scan_id}/metadata"
    params = {'key': key} if key else None
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

list_fileset_files

list_fileset_files(scan_id, fileset_id, query=None, fuzzy=False)

List all files in a specified fileset.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset	required
query	str	Query string to filter files	None
fuzzy	bool	Whether to use fuzzy matching for the query	False

Returns:

Type	Description
dict	Server response containing the list of files

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> response = client.list_fileset_files('real_plant', 'images')
>>> print(response)
{'files': ['00000_rgb', '00001_rgb', '00002_rgb', ...]}

Source code in plantdb/client/plantdb_client.py

def list_fileset_files(self, scan_id, fileset_id, query=None, fuzzy=False):
    """List all files in a specified fileset.

    Parameters
    ----------
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset
    query : str, optional
        Query string to filter files
    fuzzy : bool, optional
        Whether to use fuzzy matching for the query

    Returns
    -------
    dict
        Server response containing the list of files

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> response = client.list_fileset_files('real_plant', 'images')
    >>> print(response)
    {'files': ['00000_rgb', '00001_rgb', '00002_rgb', ...]}
    """
    url = f"{self.base_url}/api/fileset/{scan_id}/{fileset_id}/files"
    params = {}
    if query is not None:
        params['query'] = query
    if fuzzy:
        params['fuzzy'] = fuzzy
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

list_scan_filesets

list_scan_filesets(scan_id, query=None, fuzzy=False)

List all filesets in a specified scan.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan	required
query	str	Query string to filter filesets	None
fuzzy	bool	Whether to use fuzzy matching for the query	False

Returns:

Type	Description
dict	Server response containing the list of fileset IDs

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> response = client.list_scan_filesets('real_plant')
>>> print(response)
{'filesets': ['images']}

Source code in plantdb/client/plantdb_client.py

def list_scan_filesets(self, scan_id, query=None, fuzzy=False):
    """List all filesets in a specified scan.

    Parameters
    ----------
    scan_id : str
        The ID of the scan
    query : str, optional
        Query string to filter filesets
    fuzzy : bool, optional
        Whether to use fuzzy matching for the query

    Returns
    -------
    dict
        Server response containing the list of fileset IDs

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> response = client.list_scan_filesets('real_plant')
    >>> print(response)
    {'filesets': ['images']}
    """
    url = f"{self.base_url}/api/scan/{scan_id}/filesets"
    params = {}
    if query is not None:
        params['query'] = query
    if fuzzy:
        params['fuzzy'] = fuzzy
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

list_scans

list_scans(query=None, fuzzy=False)

List all scans in the database.

Parameters:

Name	Type	Description	Default
query	str	Query string to filter scans	None
fuzzy	bool	Whether to use fuzzy matching for the query (default: False)	False

Returns:

Type	Description
dict	Server response containing the list of scan IDs

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> response = client.list_scans()
>>> print(response)
['virtual_plant', 'real_plant_analyzed', 'real_plant', 'virtual_plant_analyzed', 'arabidopsis000']

Source code in plantdb/client/plantdb_client.py

def list_scans(self, query=None, fuzzy=False):
    """List all scans in the database.

    Parameters
    ----------
    query : str, optional
        Query string to filter scans
    fuzzy : bool, optional
        Whether to use fuzzy matching for the query (default: False)

    Returns
    -------
    dict
        Server response containing the list of scan IDs

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> response = client.list_scans()
    >>> print(response)
    ['virtual_plant', 'real_plant_analyzed', 'real_plant', 'virtual_plant_analyzed', 'arabidopsis000']
    """
    url = f"{self.base_url}/scans"
    params = {}
    if query is not None:
        params['query'] = query
    if fuzzy:
        params['fuzzy'] = fuzzy
    response = self.session.get(url, params=params)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

login

login(username, password)

Authenticate the user with the PlantDB API.

Parameters:

Name	Type	Description	Default
username	str	Username for authentication	required
password	str	Password for authentication	required

Returns:

Type	Description
bool	True if login successful, False otherwise

Source code in plantdb/client/plantdb_client.py

def login(self, username: str, password: str) -> bool:
    """
    Authenticate the user with the PlantDB API.

    Parameters
    ----------
    username : str
        Username for authentication
    password : str
        Password for authentication

    Returns
    -------
    bool
        ``True`` if login successful, ``False`` otherwise
    """
    url = f"{self.base_url}/login"
    data = {
        'username': username,
        'password': password
    }

    try:
        response = self.session.post(url, json=data)
        if response.status_code == 200:
            result = response.json()
            self.jwt_token = result.get('access_token')
            self.username = username
            return True
        else:
            error_msg = response.json().get('message', 'Login failed')
            self.logger.error(f"Login failed: {error_msg}")
            return False

    except RequestException as e:
        self.logger.error(f"Login request failed: {e}")
        return False

logout

logout()

Logout user from the PlantDB API.

Returns:

Type	Description
bool	True if logout successful

Source code in plantdb/client/plantdb_client.py

def logout(self) -> bool:
    """
    Logout user from the PlantDB API.

    Returns
    -------
    bool
        True if logout successful
    """
    url = f"{self.base_url}/logout"
    try:
        response = self.session.post(url)
        if response.status_code == 200:
            self.username = None
            # Remove the Authorization with the JWT from the header
            self.session.headers.pop('Authorization')
            return True
        return False
    except Exception:
        return False

refresh

refresh()

Refresh the database.

Source code in plantdb/client/plantdb_client.py

def refresh(self) -> bool:
    """Refresh the database."""
    url = f"{self.base_url}/refresh"
    try:
        response = self.session.get(url)
        if response.status_code == 200:
            return True
        return False
    except Exception:
        return False

refresh_token

refresh_token()

Refresh the JWT token.

Source code in plantdb/client/plantdb_client.py

def refresh_token(self) -> bool:
    """Refresh the JWT token."""
    url = f"{self.base_url}/token-refresh"
    try:
        response = self.session.post(url)
        if response.status_code == 200:
            result = response.json()
            self.jwt_token = result.get('access_token')
            self.username = result.get('username')
            return True
        return False
    except Exception:
        return False

update_file_metadata

update_file_metadata(scan_id, fileset_id, file_id, metadata, replace=False)

Update metadata for a specified file.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset containing the file	required
file_id	str	The ID of the file	required
metadata	dict	The metadata to update/set	required
replace	bool	If True, replaces entire metadata. If False (default), updates only specified keys.	False

Returns:

Type	Description
dict	Server response containing the updated metadata

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Update metadata
>>> new_metadata = {'description': 'Updated description'}
>>> response = client.update_file_metadata(
...     'test_plant',
...     'images',
...     'image_001',
...     new_metadata
... )
>>> print(response)
{'metadata': {'description': 'Updated description'}}

Source code in plantdb/client/plantdb_client.py

def update_file_metadata(self, scan_id, fileset_id, file_id, metadata, replace=False):
    """Update metadata for a specified file.

    Parameters
    ----------
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset containing the file
    file_id : str
        The ID of the file
    metadata : dict
        The metadata to update/set
    replace : bool, optional
        If ``True``, replaces entire metadata. If ``False`` (default),
        updates only specified keys.

    Returns
    -------
    dict
        Server response containing the updated metadata

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Update metadata
    >>> new_metadata = {'description': 'Updated description'}
    >>> response = client.update_file_metadata(
    ...     'test_plant',
    ...     'images',
    ...     'image_001',
    ...     new_metadata
    ... )
    >>> print(response)
    {'metadata': {'description': 'Updated description'}}
    """
    url = f"{self.base_url}/api/file/{scan_id}/{fileset_id}/{file_id}/metadata"
    data = {
        'metadata': metadata,
        'replace': replace
    }
    response = self.session.post(url, json=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

update_fileset_metadata

update_fileset_metadata(scan_id, fileset_id, metadata, replace=False)

Update metadata for a specified fileset.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan containing the fileset	required
fileset_id	str	The ID of the fileset	required
metadata	dict	The metadata to update/set	required
replace	bool	If True, replaces entire metadata. If False (default), updates only specified keys.	False

Returns:

Type	Description
dict	Server response containing the updated metadata

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> # Update metadata
>>> new_metadata = {'description': 'Updated fileset description', 'author': 'John Doe'}
>>> response = client.update_fileset_metadata('real_plant', 'my_fileset', new_metadata)
>>> print(response)
{'metadata': {'description': 'Updated fileset description', 'author': 'John Doe'}}

Source code in plantdb/client/plantdb_client.py

def update_fileset_metadata(self, scan_id, fileset_id, metadata, replace=False):
    """Update metadata for a specified fileset.

    Parameters
    ----------
    scan_id : str
        The ID of the scan containing the fileset
    fileset_id : str
        The ID of the fileset
    metadata : dict
        The metadata to update/set
    replace : bool, optional
        If ``True``, replaces entire metadata. If ``False`` (default),
        updates only specified keys.

    Returns
    -------
    dict
        Server response containing the updated metadata

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> # Update metadata
    >>> new_metadata = {'description': 'Updated fileset description', 'author': 'John Doe'}
    >>> response = client.update_fileset_metadata('real_plant', 'my_fileset', new_metadata)
    >>> print(response)
    {'metadata': {'description': 'Updated fileset description', 'author': 'John Doe'}}
    """
    url = f"{self.base_url}/api/fileset/{scan_id}/{fileset_id}/metadata"
    data = {
        'metadata': metadata,
        'replace': replace
    }
    response = self.session.post(url, json=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

update_scan_metadata

update_scan_metadata(scan_id, metadata, replace=False)

Update metadata for a specified scan.

Parameters:

Name	Type	Description	Default
scan_id	str	The ID of the scan to update metadata for	required
metadata	dict	The metadata to update/set	required
replace	bool	If True, replaces entire metadata. If False (default), updates only specified keys.	False

Returns:

Type	Description
dict	Server response containing the updated metadata

Raises:

Type	Description
RequestException	If the request fails

Examples:

>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.plantdb_client import PlantDBClient
>>> from plantdb.client.rest_api import plantdb_url
>>> client = PlantDBClient(plantdb_url())
>>> new_metadata = {'description': 'Updated scan description'}
>>> response = client.update_scan_metadata('test_plant', new_metadata)
>>> print(response)
{'metadata': {'owner': 'anonymous', 'description': 'Updated scan description'}}

Source code in plantdb/client/plantdb_client.py

def update_scan_metadata(self, scan_id, metadata, replace=False):
    """Update metadata for a specified scan.

    Parameters
    ----------
    scan_id : str
        The ID of the scan to update metadata for
    metadata : dict
        The metadata to update/set
    replace : bool, optional
        If ``True``, replaces entire metadata. If ``False`` (default),
        updates only specified keys.

    Returns
    -------
    dict
        Server response containing the updated metadata

    Raises
    ------
    requests.exceptions.RequestException
        If the request fails

    Examples
    --------
    >>> # Start a test REST API server first:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.plantdb_client import PlantDBClient
    >>> from plantdb.client.rest_api import plantdb_url
    >>> client = PlantDBClient(plantdb_url())
    >>> new_metadata = {'description': 'Updated scan description'}
    >>> response = client.update_scan_metadata('test_plant', new_metadata)
    >>> print(response)
    {'metadata': {'owner': 'anonymous', 'description': 'Updated scan description'}}
    """
    url = f"{self.base_url}/api/scan/{scan_id}/metadata"
    data = {
        'metadata': metadata,
        'replace': replace
    }
    response = self.session.post(url, json=data)

    # Handle HTTP errors with explicit messages
    self._handle_http_errors(response)
    return response.json()

validate_session_token

validate_session_token(token)

Sets the JWT token for the HTTP session and updates the Authorization header.

Parameters:

Name	Type	Description	Default
token	str	The JWT token to be used for authentication.	required

Source code in plantdb/client/plantdb_client.py

def validate_session_token(self, token):
    """
    Sets the JWT token for the HTTP session and updates the Authorization header.

    Parameters
    ----------
    token : str
        The JWT token to be used for authentication.
    """
    url = f"{self.base_url}/token-validation"
    response = self.session.post(url, headers={"Authorization": f"Bearer {token}"})
    if response.status_code == 200:
        self.jwt_token = token
        self.username = response.json().get('username')
        # Add the JWT to the header
        self.session.headers.update({'Authorization': f'Bearer {self.jwt_token}'})
    else:
        self.logger.error(f"Token validation failed!")
        self.logger.error(response.json())
    return

api_prefix

api_prefix(prefix='')

Set the API prefix for all URL generation functions.

Parameters:

Name	Type	Description	Default
prefix	str	The prefix to add to all API URLs, e.g., '/plantdb'. Defaults to empty string.	''

Examples:

>>> import os
>>> from plantdb.client.plantdb_client import api_prefix
>>> api_prefix()
''
>>> os.environ['PLANTDB_API_PREFIX'] = "/plantdb"
>>> api_prefix()
'/plantdb'

Source code in plantdb/client/plantdb_client.py

def api_prefix(prefix=""):
    """Set the API prefix for all URL generation functions.

    Parameters
    ----------
    prefix : str, optional
        The prefix to add to all API URLs, e.g., '/plantdb'. Defaults to empty string.

    Examples
    --------
    >>> import os
    >>> from plantdb.client.plantdb_client import api_prefix
    >>> api_prefix()
    ''
    >>> os.environ['PLANTDB_API_PREFIX'] = "/plantdb"
    >>> api_prefix()
    '/plantdb'
    """
    if prefix is None or prefix == "":
        prefix = os.environ.get("PLANTDB_API_PREFIX", "")  # Default to no prefix

    prefix = prefix.rstrip('/')  # Remove the trailing slash if present
    os.environ['PLANTDB_API_PREFIX'] = prefix
    return prefix

get_mime_type

get_mime_type(extension)

Determine the MIME type from a file extension.

Parameters:

Name	Type	Description	Default
extension	str	File extension (with or without a leading dot)	required

Returns:

Type	Description
str	The MIME type string or 'application/octet-stream' if not found

Source code in plantdb/client/plantdb_client.py

def get_mime_type(extension):
    """Determine the MIME type from a file extension.

    Parameters
    ----------
    extension : str
        File extension (with or without a leading dot)

    Returns
    -------
    str
        The MIME type string or 'application/octet-stream' if not found
    """
    # Ensure the extension starts with a dot
    if not extension.startswith('.'):
        extension = f'.{extension}'

    mime_type, _ = mimetypes.guess_type(f'file{extension}')

    # Return a default for unknown types
    if mime_type is None:
        return 'application/octet-stream'

    return mime_type