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plantdb_client

plantdb.client.plantdb_client Link

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:Link

$ fsdb_rest_api --testLink

from plantdb.client.plantdb_client import PlantDBClient from plantdb.client.rest_api import base_url client = PlantDBClient(base_url())

Create a new scanLink

scan_id = client.create_scan( ... name="Plant Sample 001", ... description="Arabidopsis specimen under controlled conditions" ... )

Create a fileset for the scanLink

fileset_id = client.create_fileset( ... scan_id=scan_id, ... fileset_id="RGB Images", ... description="Top view RGB images" ... )

PlantDBClient Link

PlantDBClient(base_url)

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

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.

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:

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

Initialize the PlantDBClient with a base URL.

Source code in plantdb/client/plantdb_client.py
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def __init__(self, base_url):
    """Initialize the PlantDBClient with a base URL."""
    self.base_url = base_url
    self.session = requests.Session()

create_file Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_url())
>>> response = client.list_scan_filesets('real_plant')
>>> print(response)
{'filesets': ['images']}
Source code in plantdb/client/plantdb_client.py
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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()

update_file_metadata Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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 Link

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 base_url
>>> client = PlantDBClient(base_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
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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 base_url
    >>> client = PlantDBClient(base_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()

get_mime_type Link

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
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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