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rest_api

plantdb.client.rest_api Link

This module regroup the client-side methods of the REST API.

archive_url Link

archive_url(dataset_name, **kwargs)

Generates a formatted URL for accessing the archive of a specific dataset.

Parameters:

Name Type Description Default
dataset_name str

Name of the dataset to access in the archive.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

Fully constructed URL for accessing the specified dataset archive.

Examples:

>>> from plantdb.client.rest_api import archive_url
>>> archive_url('arabidopsis000')
'http://127.0.0.1:5000/archive/arabidopsis000'
>>> archive_url('../arabidopsis000')
'http://127.0.0.1:5000/archive/arabidopsis000'
>>> archive_url('arabidopsis+000')
ValueError: Invalid dataset name: 'arabidopsis+000'. Dataset names must be alphanumeric and can include underscores or dashes.
>>> archive_url('arabidopsis000', prefix='/plantdb')
'http://127.0.0.1/plantdb/archive/arabidopsis000'
Source code in plantdb/client/rest_api.py 
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def archive_url(dataset_name, **kwargs):
    """Generates a formatted URL for accessing the archive of a specific dataset.

    Parameters
    ----------
    dataset_name : str
        Name of the dataset to access in the archive.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        Fully constructed URL for accessing the specified dataset archive.

    Examples
    --------
    >>> from plantdb.client.rest_api import archive_url
    >>> archive_url('arabidopsis000')
    'http://127.0.0.1:5000/archive/arabidopsis000'
    >>> archive_url('../arabidopsis000')
    'http://127.0.0.1:5000/archive/arabidopsis000'
    >>> archive_url('arabidopsis+000')
    ValueError: Invalid dataset name: 'arabidopsis+000'. Dataset names must be alphanumeric and can include underscores or dashes.
    >>> archive_url('arabidopsis000', prefix='/plantdb')
    'http://127.0.0.1/plantdb/archive/arabidopsis000'
    """
    dataset_name = sanitize_name(dataset_name)
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    url = urljoin(url, f"archive/{dataset_name}"
                  )
    return url

base_url Link

base_url(host=REST_API_URL, port=REST_API_PORT, prefix=None, ssl=False)

Generates the URL for the PlantDB REST API using the specified host and port.

This function constructs a URL by combining the provided host, port, prefix, and SSL settings. The default values are used if no arguments are supplied.

Parameters:

Name Type Description Default
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.

 REST_API_URL
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.

 REST_API_PORT
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. If provided, it will be added to the end of the URL, excluding the port number. Defaults to None.

 None
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

 False

Returns:

Type Description
str

A properly formatted URL for the PlantDB REST API.
Notes
  • The function ensures that the prefix is correctly formatted by stripping leading and trailing slashes.
  • The SSL flag determines whether 'http' or 'https' is used in the URL scheme.

Examples:

>>> from plantdb.client.rest_api import base_url
>>> base_url()
'http://127.0.0.1:5000'
>>> base_url(host='api.example.com', port=8443, ssl=True)
'https://api.example.com:8443'
>>> base_url(port=5000, prefix='/plantdb', ssl=True)
'https://127.0.0.1/plantdb/'
Source code in plantdb/client/rest_api.py 
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def base_url(host=REST_API_URL, port=REST_API_PORT, prefix=None, ssl=False) -> str:
    """
    Generates the URL for the PlantDB REST API using the specified host and port.

    This function constructs a URL by combining the provided host, port, prefix, and SSL settings.
    The default values are used if no arguments are supplied.

    Parameters
    ----------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        If provided, it will be added to the end of the URL, excluding the port number.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        A properly formatted URL for the PlantDB REST API.

    Notes
    -----
    - The function ensures that the prefix is correctly formatted by stripping leading and trailing slashes.
    - The SSL flag determines whether 'http' or 'https' is used in the URL scheme.

    Examples
    --------
    >>> from plantdb.client.rest_api import base_url
    >>> base_url()
    'http://127.0.0.1:5000'
    >>> base_url(host='api.example.com', port=8443, ssl=True)
    'https://api.example.com:8443'
    >>> base_url(port=5000, prefix='/plantdb', ssl=True)
    'https://127.0.0.1/plantdb/'
    """
    # Attempt to split the host to check for an existing scheme (http/https)
    try:
        scheme, host = host.split('://')
    except ValueError:
        pass  # If no scheme is found, proceed with the default
    else:
        # If 's' is in the scheme, it indicates HTTPS
        if 's' in scheme:
            ssl = True

    # Format the prefix by stripping leading and trailing slashes and adding a leading slash
    if prefix:
        prefix = '/' + prefix.lstrip('/').rstrip('/') + '/'

    # Ensure port is converted to string and has no leading colon
    if port:
        if isinstance(port, int):
            port = str(port)
        port = ':' + port.lstrip(':')

    # Construct the final URL using f-string for clarity and formatting
    return f"http{'s' if ssl else ''}://{host}{prefix if prefix else port}"

configure_requests_with_certificate Link

configure_requests_with_certificate(cert_path, logger=None)

Configure the Requests library to use a specific SSL certificate.

This function sets up the Requests library to use a given SSL certificate by modifying the environment variable REQUESTS_CA_BUNDLE. It also ensures that the specified certificate file exists. If the file does not exist, it raises a FileNotFoundError.

Parameters:

Name Type Description Default
cert_path str

The path to the SSL certificate file.

 required
logger Logger

A logger instance to use. Defaults to None.

 None

Raises:

Type Description
FileNotFoundError

If cert_path does not point to a valid certificate file.
Source code in plantdb/client/rest_api.py 
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def configure_requests_with_certificate(cert_path, logger=None):
    """
    Configure the Requests library to use a specific SSL certificate.

    This function sets up the Requests library to use a given SSL certificate by
    modifying the environment variable `REQUESTS_CA_BUNDLE`. It also ensures that
    the specified certificate file exists. If the file does not exist, it raises
    a FileNotFoundError.

    Parameters
    ----------
    cert_path : str
        The path to the SSL certificate file.
    logger : logging.Logger, optional
        A logger instance to use. Defaults to ``None``.

    Raises
    ------
    FileNotFoundError
        If `cert_path` does not point to a valid certificate file.
    """
    if not os.path.exists(cert_path):
        raise FileNotFoundError(f"Certificate file not found: {cert_path}")

    os.environ['REQUESTS_CA_BUNDLE'] = cert_path
    if logger is not None and isinstance(logger, logging.Logger):
        logger.debug(f"Requests configured to use certificate: {cert_path}")

download_scan_archive Link

download_scan_archive(dataset_name, out_dir=None, **kwargs)

Downloads a scan archive file from a defined dataset based on the specified API parameters.

This function fetches a scan archive in stream mode from a remote API. The archive is expected to be in the form of a binary content stream. The success of the operation is determined by the HTTP response received from the API.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset from which the scan archive file is to be downloaded.

 required
out_dir str or Path

A path to the directory where to save the archive.

 None

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.
timeout int

A timeout, in seconds, to succeed the download request. Defaults to 10.

Returns:

Type Description
BytesIO or str

A BytesIO object containing the binary content of the downloaded scan archive. A path to the downloaded file, if a directory path is specified.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import download_scan_archive
>>> download_scan_archive("arabidopsis000", out_dir='/tmp')
('/tmp/arabidopsis000.zip', 'Download completed in 0.05 seconds.')
Source code in plantdb/client/rest_api.py 
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def download_scan_archive(dataset_name, out_dir=None, **kwargs):
    """Downloads a scan archive file from a defined dataset based on the specified API parameters.

    This function fetches a scan archive in stream mode from a remote API. The archive
    is expected to be in the form of a binary content stream. The success of the
    operation is determined by the HTTP response received from the API.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset from which the scan archive file is to be downloaded.
    out_dir : str or pathlib.Path, optional
        A path to the directory where to save the archive.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.
    timeout : int, optional
        A timeout, in seconds, to succeed the download request. Defaults to ``10``.

    Returns
    -------
    BytesIO or str
        A `BytesIO` object containing the binary content of the downloaded scan archive.
        A path to the downloaded file, if a directory path is specified.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import download_scan_archive
    >>> download_scan_archive("arabidopsis000", out_dir='/tmp')
    ('/tmp/arabidopsis000.zip', 'Download completed in 0.05 seconds.')
    """
    import time
    url = archive_url(dataset_name, **kwargs)

    start_time = time.time()  # Start timing
    response = make_api_request(url, stream=True,
                                timeout=kwargs.get("timeout", 10),
                                cert_path=kwargs.get('cert_path', None))
    end_time = time.time()  # End timing
    duration = end_time - start_time
    msg = f"Download completed in {duration:.2f} seconds."

    if response.ok:
        if out_dir is not None:
            out_dir = Path(out_dir) / f"{dataset_name}.zip"
            with open(out_dir, "wb") as archive_file:
                archive_file.write(response.content)
            return f"{out_dir}", msg
        else:
            return BytesIO(response.content), msg
    else:
        response.raise_for_status()  # Raise an error if the request failed

get_angles_and_internodes_data Link

get_angles_and_internodes_data(dataset_name, **kwargs)

Return a dictionary with 'angles' and 'internodes' data for selected dataset, if it exists.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

A dictionary with 'angles' and 'internodes' data.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_angles_and_internodes_data
>>> data = get_angles_and_internodes_data('real_plant_analyzed')
>>> print(list(data.keys()))
['angles', 'internodes']
>>> print(len(data['angles']))
33
Source code in plantdb/client/rest_api.py 
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def get_angles_and_internodes_data(dataset_name, **kwargs):
    """Return a dictionary with 'angles' and 'internodes' data for selected dataset, if it exists.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        A dictionary with 'angles' and 'internodes' data.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_angles_and_internodes_data
    >>> data = get_angles_and_internodes_data('real_plant_analyzed')
    >>> print(list(data.keys()))
    ['angles', 'internodes']
    >>> print(len(data['angles']))
    33
    """
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    response = make_api_request(urljoin(url, f"sequence/{dataset_name}"), cert_path=kwargs.get('cert_path', None))
    if response.ok:
        data = json.loads(response.content.decode('utf-8'))
        return {seq: data[seq] for seq in ['angles', 'internodes']}
    else:
        return None

get_file_uri Link

get_file_uri(scan, fileset, file)

Return the URI for the corresponding scan/fileset/file tree.

Parameters:

Name Type Description Default
scan Scan or str

A Scan instance or the name of the scan dataset.

 required
fileset Fileset or str

A Fileset instance or the name of the fileset.

 required
file File or str

A File instance or the name of the file.

 required

Returns:

Type Description
str

The URI for the corresponding scan/fileset/file tree.

Examples:

>>> from plantdb.client.rest_api import get_file_uri
>>> get_file_uri('real_plant', 'images', '00000_rgb')
'files/real_plant/images/00000_rgb'
Source code in plantdb/client/rest_api.py 
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def get_file_uri(scan, fileset, file):
    """Return the URI for the corresponding `scan/fileset/file` tree.

    Parameters
    ----------
    scan : plantdb.commons.fsdb.Scan or str
        A ``Scan`` instance or the name of the scan dataset.
    fileset : plantdb.commons.fsdb.Fileset or str
        A ``Fileset`` instance or the name of the fileset.
    file : plantdb.commons.fsdb.File or str
        A ``File`` instance or the name of the file.

    Returns
    -------
    str
        The URI for the corresponding `scan/fileset/file` tree.

    Examples
    --------
    >>> from plantdb.client.rest_api import get_file_uri
    >>> get_file_uri('real_plant', 'images', '00000_rgb')
    'files/real_plant/images/00000_rgb'
    """
    from plantdb.commons.fsdb import Scan
    from plantdb.commons.fsdb import Fileset
    from plantdb.commons.fsdb import File
    scan_id = scan.id if isinstance(scan, Scan) else scan
    fileset_id = fileset.id if isinstance(fileset, Fileset) else fileset
    file_id = file.path().name if isinstance(file, File) else file
    return f"files/{scan_id}/{fileset_id}/{file_id}"

get_images_from_task Link

get_images_from_task(dataset_name, task_name='images', size='orig', **kwargs)

Get the list of images data for a given dataset and task name.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset to retrieve the images for.

 required
task_name str

The name of the task to retrieve the images from. Defaults to 'images'.

 'images'
size (orig, large, thumb)

If an integer, use it as the size of the cached image to create and return. Else, should be a string, defaulting to 'orig', and it works as follows: * 'thumb': image max width and height to 150. * 'large': image max width and height to 1500; * 'orig': original image, no chache;

 'orig'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
list of PIL.Image

The list of PIL.Image from the PlantDB REST API.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_images_from_task
>>> images = get_images_from_task('real_plant')
>>> print(len(images))
60
>>> img1 = images[0]
>>> print(img1.size)
(1440, 1080)
Source code in plantdb/client/rest_api.py 
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def get_images_from_task(dataset_name, task_name='images', size='orig', **kwargs):
    """Get the list of images data for a given dataset and task name.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset to retrieve the images for.
    task_name : str, optional
        The name of the task to retrieve the images from. Defaults to 'images'.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use  it as the size of the cached image to create and return.
        Else, should be a string, defaulting to `'orig'`, and it works as follows:
           * `'thumb'`: image max width and height to `150`.
           * `'large'`: image max width and height to `1500`;
           * `'orig'`: original image, no chache;

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    list of PIL.Image
        The list of PIL.Image from the PlantDB REST API.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_images_from_task
    >>> images = get_images_from_task('real_plant')
    >>> print(len(images))
    60
    >>> img1 = images[0]
    >>> print(img1.size)
    (1440, 1080)
    """
    images = []
    for img_uri in list_task_images_uri(dataset_name, task_name, size, **kwargs):
        images.append(Image.open(BytesIO(make_api_request(url=img_uri, cert_path=kwargs.get('cert_path', None)).content)))
    return images

get_reconstruction_config Link

get_reconstruction_config(dataset_name, cfg_fname='pipeline.toml', **kwargs)

Return the reconstruction configuration for selected dataset, if it exists.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
cfg_fname str

The name of the configuration file.

 'pipeline.toml'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The configuration dictionary.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_reconstruction_config
>>> cfg = get_reconstruction_config('real_plant_analyzed')
>>> cfg['PointCloud']['upstream_task']
'Voxels'
Source code in plantdb/client/rest_api.py 
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def get_reconstruction_config(dataset_name, cfg_fname='pipeline.toml', **kwargs):
    """Return the reconstruction configuration for selected dataset, if it exists.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    cfg_fname : str, optional
        The name of the configuration file.
    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The configuration dictionary.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_reconstruction_config
    >>> cfg = get_reconstruction_config('real_plant_analyzed')
    >>> cfg['PointCloud']['upstream_task']
    'Voxels'

    """
    return get_toml_file(dataset_name, cfg_fname, **kwargs)

get_scan_config Link

get_scan_config(dataset_name, cfg_fname='scan.toml', **kwargs)

Return the scan configuration for selected dataset, if it exists.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
cfg_fname str

The name of the configuration file.

 'scan.toml'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The configuration dictionary.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_scan_config
>>> cfg = get_scan_config('real_plant')
>>> cfg['ScanPath']['class_name']
'Circle'
Source code in plantdb/client/rest_api.py 
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def get_scan_config(dataset_name, cfg_fname='scan.toml', **kwargs):
    """Return the scan configuration for selected dataset, if it exists.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    cfg_fname : str, optional
        The name of the configuration file.
    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The configuration dictionary.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_scan_config
    >>> cfg = get_scan_config('real_plant')
    >>> cfg['ScanPath']['class_name']
    'Circle'

    """
    return get_toml_file(dataset_name, cfg_fname, **kwargs)

get_scan_data Link

get_scan_data(scan_id, **kwargs)

Retrieve the data dictionary for a given scan dataset from the PlantDB REST API.

Parameters:

Name Type Description Default
scan_id str

The name of the scan dataset to be retrieved.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The data dictionary for the given scan dataset.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_scan_data
>>> scan_data = get_scan_data('real_plant')
>>> print(scan_data['id'])
real_plant
>>> print(scan_data['hasColmap'])
False
Source code in plantdb/client/rest_api.py 
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def get_scan_data(scan_id, **kwargs):
    """Retrieve the data dictionary for a given scan dataset from the PlantDB REST API.

    Parameters
    ----------
    scan_id : str
        The name of the scan dataset to be retrieved.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The data dictionary for the given scan dataset.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_scan_data
    >>> scan_data = get_scan_data('real_plant')
    >>> print(scan_data['id'])
    real_plant
    >>> print(scan_data['hasColmap'])
    False
    """
    scan_id = sanitize_name(scan_id)
    scan_names = list_scan_names(**kwargs)
    if scan_id in scan_names:
        url = scan_url(scan_id, **kwargs)
        return make_api_request(url=url, cert_path=kwargs.get('cert_path', None)).json()
    else:
        return {}

get_scan_image Link

get_scan_image(scan_id, fileset_id, file_id, size='orig', **kwargs)

Get the image for a scan dataset and task fileset served by the PlantDB REST API.

Parameters:

Name Type Description Default
scan_id str

The name of the scan dataset to be retrieved.

 required
fileset_id str

The name of the fileset containing the image to be retrieved.

 required
file_id str

The name of the image file to be retrieved.

 required
size (orig, large, thumb)

If an integer, use it as the size of the cached image to create and return. Else, should be a string, defaulting to 'orig', and it works as follows: * 'thumb': image max width and height to 150. * 'large': image max width and height to 1500; * 'orig': original image, no cache;

 'orig'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
Response

The URL to an image of a scan dataset and task fileset.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_scan_image
>>> response = get_scan_image('real_plant', 'images', '00000_rgb')  # download the image
>>> print(response.status_code)
200
>>> # Display the image
>>> from PIL import Image
>>> from io import BytesIO
>>> image = Image.open(BytesIO(response.content))  # Open the image from the bytes data
>>> image.show()  # Display the image
Source code in plantdb/client/rest_api.py 
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def get_scan_image(scan_id, fileset_id, file_id, size='orig', **kwargs):
    """Get the image for a scan dataset and task fileset served by the PlantDB REST API.

    Parameters
    ----------
    scan_id : str
        The name of the scan dataset to be retrieved.
    fileset_id : str
        The name of the fileset containing the image to be retrieved.
    file_id : str
        The name of the image file to be retrieved.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use  it as the size of the cached image to create and return.
        Else, should be a string, defaulting to ``'orig'``, and it works as follows:
           * ``'thumb'``: image max width and height to `150`.
           * ``'large'``: image max width and height to `1500`;
           * ``'orig'``: original image, no cache;

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    requests.Response
        The URL to an image of a scan dataset and task fileset.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_scan_image
    >>> response = get_scan_image('real_plant', 'images', '00000_rgb')  # download the image
    >>> print(response.status_code)
    200
    >>> # Display the image
    >>> from PIL import Image
    >>> from io import BytesIO
    >>> image = Image.open(BytesIO(response.content))  # Open the image from the bytes data
    >>> image.show()  # Display the image
    """
    url = scan_image_url(scan_id, fileset_id, file_id, size, **kwargs)
    return make_api_request(url=url, cert_path=kwargs.get('cert_path', None))

get_scans_info Link

get_scans_info(**kwargs)

Retrieve the information dictionary for all scans from the PlantDB REST API.

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The scans information dictionary.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_scans_info
>>> get_scans_info()
Source code in plantdb/client/rest_api.py 
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def get_scans_info(**kwargs):
    """Retrieve the information dictionary for all scans from the PlantDB REST API.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The scans information dictionary.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_scans_info
    >>> get_scans_info()
    """
    scan_list = list_scan_names(**kwargs)
    return [make_api_request(url=scan_url(scan, **kwargs), cert_path=kwargs.get('cert_path', None)).json() for scan in
            scan_list]

get_task_data Link

get_task_data(dataset_name, task, filename=None, api_data=None, **kwargs)

Get the data corresponding to a dataset/task/filename.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
task str

The name of the task.

 required
filename str

The name of the file to load. If not specified defaults to the main file returned by the task as defined in filesUri_task_mapping.

 None
api_data dict

The dictionary of information for the dataset as returned by the REST API. If not specified, fetch it from the REST API.

 None

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
any

The parsed data.
See Also

plantdb.server.rest_api.filesUri_task_mapping plantdb.client.rest_api.parse_task_requests_data

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> import numpy as np
>>> from plantdb.client.rest_api import get_task_data
>>> pcd = get_task_data('real_plant_analyzed', 'PointCloud')
>>> np.array(pcd).shape
(3, 57890)
Source code in plantdb/client/rest_api.py 
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def get_task_data(dataset_name, task, filename=None, api_data=None, **kwargs):
    """Get the data corresponding to a `dataset/task/filename`.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    task : str
        The name of the task.
    filename : str, optional
        The name of the file to load.
        If not specified defaults to the main file returned by the task as defined in `filesUri_task_mapping`.
    api_data : dict, optional
        The dictionary of information for the dataset as returned by the REST API.
        If not specified, fetch it from the REST API.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    any
        The parsed data.

    See Also
    --------
    plantdb.server.rest_api.filesUri_task_mapping
    plantdb.client.rest_api.parse_task_requests_data

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> import numpy as np
    >>> from plantdb.client.rest_api import get_task_data
    >>> pcd = get_task_data('real_plant_analyzed', 'PointCloud')
    >>> np.array(pcd).shape
    (3, 57890)
    """
    if api_data is None:
        api_data = get_scan_data(dataset_name, **kwargs)
    # Get data from `File` resource of REST API:
    ext = None
    if filename is None:
        file_uri = api_data["filesUri"][task_filesUri_mapping[task]]
    else:
        _, ext = Path(filename).suffix.split('.')
        file_uri = get_file_uri(dataset_name, api_data["tasks_fileset"][task], filename)

    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    data = make_api_request(url + file_uri, cert_path=kwargs.get('cert_path', None)).content
    return parse_task_requests_data(task, data, ext)

get_tasks_fileset_from_api Link

get_tasks_fileset_from_api(dataset_name, **kwargs)

Get the task name to fileset name mapping dictionary from the REST API.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset to retrieve the mapping for.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The mapping of the task name to fileset name.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_tasks_fileset_from_api
>>> get_tasks_fileset_from_api('real_plant')
{'images': 'images'}
Source code in plantdb/client/rest_api.py 
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def get_tasks_fileset_from_api(dataset_name, **kwargs):
    """Get the task name to fileset name mapping dictionary from the REST API.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset to retrieve the mapping for.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The mapping of the task name to fileset name.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_tasks_fileset_from_api
    >>> get_tasks_fileset_from_api('real_plant')
    {'images': 'images'}
    """
    return get_scan_data(dataset_name, **kwargs).get('tasks_fileset', dict())

get_toml_file Link

get_toml_file(dataset_name, file_path, **kwargs)

Return a loaded TOML file for selected dataset, if it exists.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
file_path str

The path to the TOML file.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The configuration dictionary.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import get_toml_file
>>> cfg = get_toml_file('real_plant_analyzed', 'pipeline.toml')
>>> cfg['PointCloud']
{'upstream_task': 'Voxels', 'level_set_value': 1.0}
Source code in plantdb/client/rest_api.py 
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def get_toml_file(dataset_name, file_path, **kwargs):
    """Return a loaded TOML file for selected dataset, if it exists.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    file_path : str
        The path to the TOML file.
    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The configuration dictionary.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import get_toml_file
    >>> cfg = get_toml_file('real_plant_analyzed', 'pipeline.toml')
    >>> cfg['PointCloud']
    {'upstream_task': 'Voxels', 'level_set_value': 1.0}
    """
    url = scan_file_url(dataset_name, file_path, **kwargs)
    return _load_toml_from_url(url, **kwargs)

list_scan_names Link

list_scan_names(**kwargs)

List the names of the scan datasets served by the PlantDB REST API.

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
list

The list of scan dataset names served by the PlantDB REST API.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import list_scan_names
>>> print(list_scan_names())
['arabidopsis000', 'real_plant', 'real_plant_analyzed', 'virtual_plant', 'virtual_plant_analyzed']
>>> print(list_scan_names(host='mellitus.biologie.ens-lyon.fr', port=433, prefix='/plantdb/', ssl=True))
Source code in plantdb/client/rest_api.py 
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def list_scan_names(**kwargs):
    """List the names of the scan datasets served by the PlantDB REST API.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    list
        The list of scan dataset names served by the PlantDB REST API.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import list_scan_names
    >>> print(list_scan_names())
    ['arabidopsis000', 'real_plant', 'real_plant_analyzed', 'virtual_plant', 'virtual_plant_analyzed']
    >>> print(list_scan_names(host='mellitus.biologie.ens-lyon.fr', port=433, prefix='/plantdb/', ssl=True))
    """
    url = scans_url(**kwargs)
    response = make_api_request(url=url, cert_path=kwargs.get('cert_path', None))
    return sorted(response.json())

list_task_images_uri Link

list_task_images_uri(dataset_name, task_name='images', size='orig', **kwargs)

Get the list of images URI for a given dataset and task name.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset to retrieve the images for.

 required
task_name str

The name of the task to retrieve the images from. Defaults to 'images'.

 'images'
size (orig, large, thumb)

If an integer, use it as the size of the cached image to create and return. Else, should be a string, defaulting to 'orig', and it works as follows: * 'thumb': image max width and height to 150. * 'large': image max width and height to 1500; * 'orig': original image, no cache;

 'orig'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
list of str

The list of image URI strings for the PlantDB REST API.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import list_task_images_uri
>>> print(list_task_images_uri('real_plant')[2])
http://127.0.0.1:5000/image/real_plant/images/00002_rgb?size=orig
>>> print(list_task_images_uri('real_plant', size=100)[2])
http://127.0.0.1:5000/image/real_plant/images/00002_rgb?size=100
Source code in plantdb/client/rest_api.py 
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def list_task_images_uri(dataset_name, task_name='images', size='orig', **kwargs):
    """Get the list of images URI for a given dataset and task name.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset to retrieve the images for.
    task_name : str, optional
        The name of the task to retrieve the images from. Defaults to 'images'.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use  it as the size of the cached image to create and return.
        Else, should be a string, defaulting to `'orig'`, and it works as follows:
           * `'thumb'`: image max width and height to `150`.
           * `'large'`: image max width and height to `1500`;
           * `'orig'`: original image, no cache;

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    list of str
        The list of image URI strings for the PlantDB REST API.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import list_task_images_uri
    >>> print(list_task_images_uri('real_plant')[2])
    http://127.0.0.1:5000/image/real_plant/images/00002_rgb?size=orig
    >>> print(list_task_images_uri('real_plant', size=100)[2])
    http://127.0.0.1:5000/image/real_plant/images/00002_rgb?size=100
    """
    dataset_name = sanitize_name(dataset_name)
    task_name = sanitize_name(task_name)
    scan_info = get_scan_data(dataset_name, **kwargs)
    tasks_fileset = scan_info["tasks_fileset"]
    images = scan_info["images"]
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    return [urljoin(url, f"image/{dataset_name}/{tasks_fileset[task_name]}/{Path(img).stem}?size={size}") for img in
            images]

make_api_request Link

make_api_request(url, method='GET', params=None, json_data=None, cert_path=None, allow_redirects=True, **kwargs)

Function to make an API request with various HTTP methods and options.

Parameters:

Name Type Description Default
url str

The URL for the API endpoint.

 required
method (GET, POST, PUT, DELETE)

The HTTP method to use. Default is 'GET'.

 'GET'
params dict

Dictionary of query parameters to append to the URL.

 None
json_data dict

JSON payload to send in the body of the request for 'POST' and 'PUT' methods.

 None
cert_path str or None

Path to a certificate file for SSL verification. If None, default SSL verification is used.

 None
allow_redirects bool

Whether to allow redirects. Default is True.

 True

Other Parameters:

Name Type Description
header dict

The HTTP headers to send in the request. Default is None.
files dict

Additional files to send in the request. Default is None.
data dict, list, or bytes

The data to send in the request. Default is None.
timeout int

Timeout to use for the request. Default is 5 seconds.
stream bool

Flag indicating whether to stream the request. Default is False.

Returns:

Name Type Description
response Response

The response object from the API request.

Raises:

Type Description
ValueError

If an unsupported HTTP method is provided.
SSLError

If there's an SSL error during the request.
RequestException

For any other exception raised by the underlying requests library.
Notes

This function is designed to handle various HTTP methods (GET, POST, PUT, DELETE) and provides a unified interface for making API requests. It supports SSL verification and allows for custom parameters and JSON data to be sent with the request. It passes keyword arguments to the underlying requests library.

Source code in plantdb/client/rest_api.py 
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def make_api_request(url, method="GET", params=None, json_data=None,
                     cert_path=None, allow_redirects=True, **kwargs):
    """
    Function to make an API request with various HTTP methods and options.

    Parameters
    ----------
    url : str
        The URL for the API endpoint.
    method : {'GET', 'POST', 'PUT', 'DELETE'}, optional
        The HTTP method to use. Default is 'GET'.
    params : dict, optional
        Dictionary of query parameters to append to the URL.
    json_data : dict, optional
        JSON payload to send in the body of the request for 'POST' and 'PUT' methods.
    cert_path : str or None, optional
        Path to a certificate file for SSL verification. If None, default SSL verification is used.
    allow_redirects : bool, optional
        Whether to allow redirects. Default is True.

    Other Parameters
    ----------------
    header : dict, optional
        The HTTP headers to send in the request. Default is None.
    files : dict, optional
        Additional files to send in the request. Default is None.
    data : dict, list, or bytes, optional
        The data to send in the request. Default is None.
    timeout : int, optional
        Timeout to use for the request. Default is 5 seconds.
    stream : bool, optional
        Flag indicating whether to stream the request. Default is False.

    Returns
    -------
    response : requests.Response
        The response object from the API request.

    Raises
    ------
    ValueError
        If an unsupported HTTP method is provided.
    requests.exceptions.SSLError
        If there's an SSL error during the request.
    requests.exceptions.RequestException
        For any other exception raised by the underlying `requests` library.

    Notes
    -----
    This function is designed to handle various HTTP methods (GET, POST, PUT, DELETE) and provides a unified interface for making API requests. It supports SSL verification and allows for custom parameters and JSON data to be sent with the request.
    It passes keyword arguments to the underlying `requests` library.
    """
    # Add a default timeout of 5 seconds if not provided
    if 'timeout' not in kwargs:
        kwargs['timeout'] = 5.0

    try:
        verify = cert_path if cert_path else True

        if method.upper() == "GET":
            response = requests.get(url, params=params, verify=verify, allow_redirects=allow_redirects, **kwargs)
        elif method.upper() == "POST":
            response = requests.post(url, params=params, json=json_data, verify=verify, allow_redirects=allow_redirects, **kwargs)
        elif method.upper() == "PUT":
            response = requests.put(url, params=params, json=json_data, verify=verify, allow_redirects=allow_redirects, **kwargs)
        elif method.upper() == "DELETE":
            response = requests.delete(url, params=params, verify=verify, allow_redirects=allow_redirects, **kwargs)
        else:
            raise ValueError(f"Unsupported HTTP method: {method}")

        response.raise_for_status()  # Raise exception for 4XX/5XX responses
        return response
    except requests.exceptions.SSLError as e:
        print(f"SSL Error: {e}")
        print("Try providing the specific certificate path with cert_path parameter")
        raise
    except requests.exceptions.RequestException as e:
        print(f"Request Error: {e}")
        raise

parse_requests_json Link

parse_requests_json(data)

Parse a requests content, should be from a AnglesAndInternodes task source.

Parameters:

Name Type Description Default
data buffer

The data source from a requests content.

 required

Returns:

Type Description
dict

The full angles and internodes dictionary with 'angles', 'internodes', '' & '' entries.
Source code in plantdb/client/rest_api.py 
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def parse_requests_json(data):
    """Parse a requests content, should be from a AnglesAndInternodes task source.

    Parameters
    ----------
    data : buffer
        The data source from a requests content.

    Returns
    -------
    dict
        The full angles and internodes dictionary with 'angles', 'internodes', '' & '' entries.
    """
    return json.loads(data)

parse_requests_mesh Link

parse_requests_mesh(data)

Parse a requests content, should be from a TriangleMesh task source.

Parameters:

Name Type Description Default
data buffer

The data source from a requests content.

 required

Returns:

Type Description
dict

The parsed triangular mesh with two entries: 'vertices' for vertex coordinates and 'triangles' for triangle coordinates.
Source code in plantdb/client/rest_api.py 
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def parse_requests_mesh(data):
    """Parse a requests content, should be from a TriangleMesh task source.

    Parameters
    ----------
    data : buffer
        The data source from a requests content.

    Returns
    -------
    dict
        The parsed triangular mesh with two entries: 'vertices' for vertex coordinates and 'triangles' for triangle coordinates.
    """
    ## Read the PLY as a `PlyData`:
    mesh_data = PlyData.read(BytesIO(data))
    ## Convert the `PlyData`:
    return {"vertices": _ply_vertex_to_array(mesh_data),
            "triangles": _ply_face_to_array(mesh_data)}

parse_requests_pcd Link

parse_requests_pcd(data)

Parse a requests content, should be from a PointCloud task source.

Parameters:

Name Type Description Default
data buffer

The data source from a requests content.

 required

Returns:

Type Description
ndarray

The parsed pointcloud with vertex coordinates sorted as XYZ.
Source code in plantdb/client/rest_api.py 
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def parse_requests_pcd(data):
    """Parse a requests content, should be from a PointCloud task source.

    Parameters
    ----------
    data : buffer
        The data source from a requests content.

    Returns
    -------
    numpy.ndarray
        The parsed pointcloud with vertex coordinates sorted as XYZ.
    """
    ## Read the pointcloud PLY as a `PlyData`:
    ply_pcd = PlyData.read(BytesIO(data))
    ## Convert the `PlyData`:
    return _ply_vertex_to_array(ply_pcd)

parse_requests_skeleton Link

parse_requests_skeleton(data)

Parse a requests content, should be from a CurveSkeleton task source.

Parameters:

Name Type Description Default
data buffer

The data source from a requests content.

 required

Returns:

Type Description
dict

The parsed skeleton with two entries: 'points' for points coordinates and 'lines' joining them.
Source code in plantdb/client/rest_api.py 
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def parse_requests_skeleton(data):
    """Parse a requests content, should be from a CurveSkeleton task source.

    Parameters
    ----------
    data : buffer
        The data source from a requests content.

    Returns
    -------
    dict
        The parsed skeleton with two entries: 'points' for points coordinates and 'lines' joining them.
    """
    return json.loads(data)

parse_requests_tree Link

parse_requests_tree(data)

Parse a requests content, should be from a TreeGraph task source.

Parameters:

Name Type Description Default
data buffer

The data source from a requests content.

 required

Returns:

Type Description
Graph

The loaded (tree) graph object.
Source code in plantdb/client/rest_api.py 
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def parse_requests_tree(data):
    """Parse a requests content, should be from a TreeGraph task source.

    Parameters
    ----------
    data : buffer
        The data source from a requests content.

    Returns
    -------
    networkx.Graph
        The loaded (tree) graph object.
    """
    import pickle
    tree = pickle.load(BytesIO(data))
    # FIXME: it would be better to return something that is JSON serializable...
    #  but the tree is not directed, so the `json_graph.tree_data` fails!
    # from networkx.readwrite import json_graph
    # data = json_graph.tree_data(tree, root=0)
    # return json.dumps(data)
    return tree

parse_scans_info Link

parse_scans_info(**kwargs)

Parse the information dictionary for all scans served by the PlantDB REST API.

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

The scan-id (dataset name) indexed information dictionary.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import parse_scans_info
>>> scan_dict = parse_scans_info()
>>> print(sorted(scan_dict.keys()))
['arabidopsis000', 'real_plant', 'real_plant_analyzed', 'virtual_plant', 'virtual_plant_analyzed']
Source code in plantdb/client/rest_api.py 
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def parse_scans_info(**kwargs):
    """Parse the information dictionary for all scans served by the PlantDB REST API.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        The scan-id (dataset name) indexed information dictionary.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import parse_scans_info
    >>> scan_dict = parse_scans_info()
    >>> print(sorted(scan_dict.keys()))
    ['arabidopsis000', 'real_plant', 'real_plant_analyzed', 'virtual_plant', 'virtual_plant_analyzed']
    """
    scan_json = get_scans_info(**kwargs)
    scan_dict = {}
    for scan in scan_json:
        name = scan.pop('id')
        scan_dict[name] = scan
    return scan_dict

parse_task_requests_data Link

parse_task_requests_data(task, data, extension=None)

The task data parser, behave according to the source and default to JSON parser.

Source code in plantdb/client/rest_api.py 
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def parse_task_requests_data(task, data, extension=None):
    """The task data parser, behave according to the source and default to JSON parser."""
    if extension is not None:
        data_parser = EXT_PARSER_DICT[extension]
    else:
        data_parser = PARSER_DICT.get(task, parse_requests_json)
    return data_parser(data)

refresh Link

refresh(dataset_name=None, **kwargs)

Refreshes the database, potentialy only for a specified dataset.

Parameters:

Name Type Description Default
dataset_name str or None

The name of the dataset to trigger a refresh. If None, the entire database is refreshed.

 None

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.
timeout int

A timeout, in seconds, to succeed the refresh request. Defaults to 5.

Returns:

Type Description
dict

Parsed JSON response from the refresh API if the request is successful.

Raises:

Type Description
HTTPError

If the request fails or the response status is not successful.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import refresh
>>> refresh("arabidopsis000")
{'message': "Successfully reloaded scan 'arabidopsis000'."}
Source code in plantdb/client/rest_api.py 
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def refresh(dataset_name=None, **kwargs):
    """Refreshes the database, potentialy only for a specified dataset.

    Parameters
    ----------
    dataset_name : str or None
        The name of the dataset to trigger a refresh.
        If ``None``, the entire database is refreshed.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.
    timeout : int, optional
        A timeout, in seconds, to succeed the refresh request. Defaults to ``5``.

    Returns
    -------
    dict
        Parsed JSON response from the refresh API if the request is successful.

    Raises
    ------
    HTTPError
        If the request fails or the response status is not successful.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import refresh
    >>> refresh("arabidopsis000")
    {'message': "Successfully reloaded scan 'arabidopsis000'."}
    """
    url = refresh_url(dataset_name, **kwargs)
    response = make_api_request(url, cert_path=kwargs.get('cert_path', None))
    if response.ok:
        return response.json()
    else:
        response.raise_for_status()  # Raise an error if the request failed

refresh_url Link

refresh_url(dataset_name=None, **kwargs)

Generates a formatted URL for refreshing a specific dataset or the entire database.

Parameters:

Name Type Description Default
dataset_name str or None

The name of the dataset for which the refresh URL needs to be generated. If not provided, the refresh URL for the entire server is returned instead. Defaults to None.

 None

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

A correctly formatted URL for refreshing the specified dataset or the entire PlantDB REST API server.

Examples:

>>> from plantdb.client.rest_api import refresh_url
>>> refresh_url("real_plant")
'http://127.0.0.1:5000/refresh?scan_id=real_plant'
>>> refresh_url("real_plant", prefix='/plantdb')
'http://127.0.0.1/plantdb/refresh?scan_id=real_plant'
Source code in plantdb/client/rest_api.py 
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def refresh_url(dataset_name=None, **kwargs):
    """Generates a formatted URL for refreshing a specific dataset or the entire database.

    Parameters
    ----------
    dataset_name : str or None, optional
        The name of the dataset for which the refresh URL needs to be generated.
        If not provided, the refresh URL for the entire server is returned instead.
        Defaults to ``None``.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        A correctly formatted URL for refreshing the specified dataset or the entire PlantDB REST API server.

    Examples
    --------
    >>> from plantdb.client.rest_api import refresh_url
    >>> refresh_url("real_plant")
    'http://127.0.0.1:5000/refresh?scan_id=real_plant'
    >>> refresh_url("real_plant", prefix='/plantdb')
    'http://127.0.0.1/plantdb/refresh?scan_id=real_plant'
    """
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    url = urljoin(url, "refresh")
    if dataset_name is None:
        return url
    else:
        dataset_name = sanitize_name(dataset_name)
        return f"{url}?scan_id={dataset_name}"

sanitize_name Link

sanitize_name(name)

Sanitizes and validates the provided name.

The function ensures that the input string adheres to predefined naming rules by:

  • stripping leading/trailing spaces,
  • isolating the last segment after splitting by slashes,
  • validating the name against an alphanumeric pattern with optional underscores (_), dashes (-), or periods (.).

Parameters:

Name Type Description Default
name str

The name to sanitize and validate.

 required

Returns:

Type Description
str

Sanitized name that conforms to the rules.

Raises:

Type Description
ValueError

If the provided name contains invalid characters or does not meet the naming rules.
Source code in plantdb/client/rest_api.py 
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def sanitize_name(name):
    """Sanitizes and validates the provided name.

    The function ensures that the input string adheres to predefined naming rules by:

    - stripping leading/trailing spaces,
    - isolating the last segment after splitting by slashes,
    - validating the name against an alphanumeric pattern
      with optional underscores (`_`), dashes (`-`), or periods (`.`).

    Parameters
    ----------
    name : str
        The name to sanitize and validate.

    Returns
    -------
    str
        Sanitized name that conforms to the rules.

    Raises
    ------
    ValueError
        If the provided name contains invalid characters or does not meet the naming rules.
    """
    import re
    sanitized_name = name.strip()  # Remove leading/trailing spaces
    sanitized_name = sanitized_name.split('/')[-1]  # isolate the last segment after splitting by slashes
    # Validate against an alphanumeric pattern with optional underscores, dashes, or periods
    if not re.match(r"^[a-zA-Z0-9_.-]+$", sanitized_name):
        raise ValueError(
            f"Invalid name: '{name}'. Names must be alphanumeric and can include underscores, dashes, or periods.")
    return sanitized_name

scan_config_url Link

scan_config_url(dataset_name, cfg_fname='scan.toml', **kwargs)

Return the scan URL to access the scanning configuration file.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
cfg_fname str

The name of the TOML scan file, defaults to 'scan.toml'.

 'scan.toml'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

The URL to the scanning configuration file.

Examples:

>>> from plantdb.client.rest_api import scan_config_url
>>> scan_config_url('real_plant')
'http://127.0.0.1:5000/files/real_plant/scan.toml'
>>> scan_config_url('real_plant', prefix='/plantdb')
'http://127.0.0.1/plantdb/files/real_plant/scan.toml'
Source code in plantdb/client/rest_api.py 
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def scan_config_url(dataset_name, cfg_fname='scan.toml', **kwargs):
    """Return the scan URL to access the scanning configuration file.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    cfg_fname : str, optional
        The name of the TOML scan file, defaults to ``'scan.toml'``.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        The URL to the scanning configuration file.

    Examples
    --------
    >>> from plantdb.client.rest_api import scan_config_url
    >>> scan_config_url('real_plant')
    'http://127.0.0.1:5000/files/real_plant/scan.toml'
    >>> scan_config_url('real_plant', prefix='/plantdb')
    'http://127.0.0.1/plantdb/files/real_plant/scan.toml'
    """
    return scan_file_url(dataset_name, cfg_fname, **kwargs)

scan_file_url Link

scan_file_url(dataset_name, file_path, **kwargs)

Build the URL for accessing a dataset file.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
file_path str

The path to the file.

 required
**kwargs

Keyword arguments passed to base_url().

 {}

Returns:

Type Description
str

The complete URL for the dataset file.
Source code in plantdb/client/rest_api.py 
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def scan_file_url(dataset_name, file_path, **kwargs):
    """Build the URL for accessing a dataset file.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    file_path : str
        The path to the file.
    **kwargs
        Keyword arguments passed to base_url().

    Returns
    -------
    str
        The complete URL for the dataset file.
    """
    url = base_url(
        host=kwargs.get("host", REST_API_URL),
        port=kwargs.get("port", REST_API_PORT),
        prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
        ssl=kwargs.get("ssl", False)
    )
    return urljoin(url, f"files/{dataset_name}/{file_path}")

scan_image_url Link

scan_image_url(scan_id, fileset_id, file_id, size='orig', **kwargs)

Get the URL to the image for a scan dataset and task fileset served by the PlantDB REST API.

Parameters:

Name Type Description Default
scan_id str

The name of the scan dataset to be retrieved.

 required
fileset_id str

The name of the fileset containing the image to be retrieved.

 required
file_id str

The name of the image file to be retrieved.

 required
size (orig, large, thumb)

If an integer, use it as the size of the cached image to create and return. Else, should be a string, defaulting to 'orig', and it works as follows: * 'thumb': image max width and height to 150. * 'large': image max width and height to 1500; * 'orig': original image, no cache;

 'orig'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

The URL to an image of a scan dataset and task fileset.

Examples:

>>> from plantdb.client.rest_api import scan_image_url
>>> scan_image_url("real_plant", "images", "00000_rgb")
'http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=orig'
>>> scan_image_url("real_plant", "images", "00000_rgb", prefix='/plantdb')
'http://127.0.0.1/plantdb/image/real_plant/images/00000_rgb?size=orig'
Source code in plantdb/client/rest_api.py 
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def scan_image_url(scan_id, fileset_id, file_id, size='orig', **kwargs):
    """Get the URL to the image for a scan dataset and task fileset served by the PlantDB REST API.

    Parameters
    ----------
    scan_id : str
        The name of the scan dataset to be retrieved.
    fileset_id : str
        The name of the fileset containing the image to be retrieved.
    file_id : str
        The name of the image file to be retrieved.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use  it as the size of the cached image to create and return.
        Else, should be a string, defaulting to ``'orig'``, and it works as follows:
           * ``'thumb'``: image max width and height to `150`.
           * ``'large'``: image max width and height to `1500`;
           * ``'orig'``: original image, no cache;

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        The URL to an image of a scan dataset and task fileset.

    Examples
    --------
    >>> from plantdb.client.rest_api import scan_image_url
    >>> scan_image_url("real_plant", "images", "00000_rgb")
    'http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=orig'
    >>> scan_image_url("real_plant", "images", "00000_rgb", prefix='/plantdb')
    'http://127.0.0.1/plantdb/image/real_plant/images/00000_rgb?size=orig'
    """
    scan_id = sanitize_name(scan_id)
    fileset_id = sanitize_name(fileset_id)
    file_id = sanitize_name(file_id)
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    return urljoin(url, f"image/{scan_id}/{fileset_id}/{file_id}?size={size}")

scan_preview_image_url Link

scan_preview_image_url(scan_id, size='thumb', **kwargs)

Get the URL to the preview image for a scan dataset served by the PlantDB REST API.

Parameters:

Name Type Description Default
scan_id str

The name of the scan dataset to be retrieved.

 required
size (orig, large, thumb)

If an integer, use it as the size of the cached image to create and return. Else, should be a string, defaulting to 'thumb', and it works as follows: * 'thumb': image max width and height to 150. * 'large': image max width and height to 1500; * 'orig': original image, no cache;

 'orig'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

The URL to the preview image for a scan dataset.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import scan_preview_image_url
>>> img_url = scan_preview_image_url('real_plant')
>>> print(img_url)
http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=thumb
>>> img_url = scan_preview_image_url('real_plant', size=100)
>>> print(img_url)
http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=100
>>> # Download and display the image
>>> import requests
>>> from PIL import Image
>>> from io import BytesIO
>>> response = requests.get(img_url)  # Send a GET request to the URL
>>> image = Image.open(BytesIO(response.content))  # Open the image from the bytes data
>>> image.show()  # Display the image
Source code in plantdb/client/rest_api.py 
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def scan_preview_image_url(scan_id, size="thumb", **kwargs):
    """Get the URL to the preview image for a scan dataset served by the PlantDB REST API.

    Parameters
    ----------
    scan_id : str
        The name of the scan dataset to be retrieved.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use  it as the size of the cached image to create and return.
        Else, should be a string, defaulting to ``'thumb'``, and it works as follows:
           * ``'thumb'``: image max width and height to `150`.
           * ``'large'``: image max width and height to `1500`;
           * ``'orig'``: original image, no cache;

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        The URL to the preview image for a scan dataset.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import scan_preview_image_url
    >>> img_url = scan_preview_image_url('real_plant')
    >>> print(img_url)
    http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=thumb
    >>> img_url = scan_preview_image_url('real_plant', size=100)
    >>> print(img_url)
    http://127.0.0.1:5000/image/real_plant/images/00000_rgb?size=100
    >>> # Download and display the image
    >>> import requests
    >>> from PIL import Image
    >>> from io import BytesIO
    >>> response = requests.get(img_url)  # Send a GET request to the URL
    >>> image = Image.open(BytesIO(response.content))  # Open the image from the bytes data
    >>> image.show()  # Display the image
    """
    scan_id = sanitize_name(scan_id)
    scan_names = list_scan_names(**kwargs)
    if scan_id not in scan_names:
        return None

    thumb_uri = get_scan_data(scan_id)["thumbnailUri"]
    if size != "thumb":
        thumb_uri = thumb_uri.replace("size=thumb", f"size={size}")
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    return urljoin(url, thumb_uri.lstrip("/"))

scan_reconstruction_url Link

scan_reconstruction_url(dataset_name, cfg_fname='pipeline.toml', **kwargs)

Return the scan URL to access the reconstruction configuration file.

Parameters:

Name Type Description Default
dataset_name str

The name of the dataset.

 required
cfg_fname str

The name of the TOML scan file, defaults to 'pipeline.toml'.

 'pipeline.toml'

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

The URL to the reconstruction configuration file.

Examples:

>>> from plantdb.client.rest_api import scan_reconstruction_url
>>> scan_reconstruction_url('real_plant')
'http://127.0.0.1:5000/files/real_plant/pipeline.toml'
>>> scan_reconstruction_url('real_plant', prefix='/plantdb')
'http://127.0.0.1/plantdb/files/real_plant/pipeline.toml'
Source code in plantdb/client/rest_api.py 
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def scan_reconstruction_url(dataset_name, cfg_fname='pipeline.toml', **kwargs):
    """Return the scan URL to access the reconstruction configuration file.

    Parameters
    ----------
    dataset_name : str
        The name of the dataset.
    cfg_fname : str, optional
        The name of the TOML scan file, defaults to ``'pipeline.toml'``.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        The URL to the reconstruction configuration file.

    Examples
    --------
    >>> from plantdb.client.rest_api import scan_reconstruction_url
    >>> scan_reconstruction_url('real_plant')
    'http://127.0.0.1:5000/files/real_plant/pipeline.toml'
    >>> scan_reconstruction_url('real_plant', prefix='/plantdb')
    'http://127.0.0.1/plantdb/files/real_plant/pipeline.toml'
    """
    return scan_file_url(dataset_name, cfg_fname, **kwargs)

scan_url Link

scan_url(scan_id, **kwargs)

Generates the URL pointing to the scan JSON from the PlantDB REST API.

Parameters:

Name Type Description Default
scan_id str

The name of the scan dataset to retrieve the JSON from.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

A properly formatted URL of the PlantDB REST API pointing to the scans list.

Examples:

>>> from plantdb.client.rest_api import scan_url
>>> scan_url("real_plant")
'http://127.0.0.1:5000/scans/real_plant'
>>> scan_url("real_plant", prefix='/plantdb')
'http://127.0.0.1/plantdb/scans/real_plant'
Source code in plantdb/client/rest_api.py 
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def scan_url(scan_id, **kwargs):
    """Generates the URL pointing to the scan JSON from the PlantDB REST API.

    Parameters
    ----------
    scan_id : str
        The name of the scan dataset to retrieve the JSON from.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        A properly formatted URL of the PlantDB REST API pointing to the scans list.

    Examples
    --------
    >>> from plantdb.client.rest_api import scan_url
    >>> scan_url("real_plant")
    'http://127.0.0.1:5000/scans/real_plant'
    >>> scan_url("real_plant", prefix='/plantdb')
    'http://127.0.0.1/plantdb/scans/real_plant'
    """
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    return urljoin(url, f"scans/{sanitize_name(scan_id)}")

scans_url Link

scans_url(**kwargs)

Generates the URL listing the scans from the PlantDB REST API.

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
str

A properly formatted URL of the PlantDB REST API pointing to the scans list.

Examples:

>>> from plantdb.client.rest_api import scans_url
>>> scans_url()
'http://127.0.0.1:5000/scans'
>>> scans_url(prefix='/plantdb')
'http://127.0.0.1/plantdb/scans'
>>> scans_url(host='mellitus.biologie.ens-lyon.fr', port=433, prefix='/plantdb/', ssl=True)
Source code in plantdb/client/rest_api.py 
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def scans_url(**kwargs):
    """Generates the URL listing the scans from the PlantDB REST API.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    str
        A properly formatted URL of the PlantDB REST API pointing to the scans list.

    Examples
    --------
    >>> from plantdb.client.rest_api import scans_url
    >>> scans_url()
    'http://127.0.0.1:5000/scans'
    >>> scans_url(prefix='/plantdb')
    'http://127.0.0.1/plantdb/scans'
    >>> scans_url(host='mellitus.biologie.ens-lyon.fr', port=433, prefix='/plantdb/', ssl=True)
    """
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    return urljoin(url, "scans")

test_availability Link

test_availability(url)

Verifies the connectivity to a given host and port from a URL-like string. This function parses a URL string into host and port components, attempts to establish a socket connection to check its availability, and raises appropriate exceptions on failure.

Parameters:

Name Type Description Default
url str

A URL string in various formats like 'http://host:port', 'https://host/path/', etc.

 required

Raises:

Type Description
ValueError

If the input URL is not a valid URL format.
ConnectionError

If the specified host cannot be connected, indicating that the server might be unavailable.
RuntimeError

If an unexpected error occurs during the verification process.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import test_availability
>>> test_availability('http://127.0.0.1:5000')
>>> test_availability('https://127.0.0.1/plantdb/')
>>> test_availability('https://mellitus.biologie.ens-lyon.fr/plantdb/')
Source code in plantdb/client/rest_api.py 
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def test_availability(url):
    """Verifies the connectivity to a given host and port from a URL-like string.
    This function parses a URL string into host and port components, attempts to establish a
    socket connection to check its availability, and raises appropriate exceptions on failure.
    Parameters
    ----------
    url : str
        A URL string in various formats like 'http://host:port', 'https://host/path/', etc.
    Raises
    ------
    ValueError
        If the input URL is not a valid URL format.
    ConnectionError
        If the specified host cannot be connected, indicating that the server might
        be unavailable.
    RuntimeError
        If an unexpected error occurs during the verification process.
    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import test_availability
    >>> test_availability('http://127.0.0.1:5000')
    >>> test_availability('https://127.0.0.1/plantdb/')
    >>> test_availability('https://mellitus.biologie.ens-lyon.fr/plantdb/')
    """
    import socket
    try:
        parsed_url = urlparse(url)

        # Validate URL has at least a scheme and hostname
        if not parsed_url.scheme or not parsed_url.netloc:
            raise ValueError(f"Invalid URL format: '{url}'. Must include scheme (http/https) and hostname.")

        host = parsed_url.hostname
        # Use default port based on scheme if not specified
        port = parsed_url.port
        if port is None:
            port = 443 if parsed_url.scheme == 'https' else 80

        socket.setdefaulttimeout(2)  # Set a timeout for the connection check
        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
            if s.connect_ex((host, port)) != 0:
                raise ConnectionError(f"Cannot connect to {host}:{port}. Server might be unavailable.")
    except ValueError as e:
        raise ValueError(f"{e}")
    except ConnectionError as e:
        raise e
    except Exception as e:
        raise RuntimeError(f"Unexpected error during connection check: {e}")

upload_dataset_file Link

upload_dataset_file(scan_id, file_path, chunk_size=0, **kwargs)

Uploads a file to the server using the DatasetFile POST endpoint.

Parameters:

Name Type Description Default
server_url str

The base URL of the server hosting the REST API.

 required
scan_id str

The unique identifier of the scan associated with the file upload.

 required
file_path str

The path to the file to be uploaded.

 required
chunk_size int

The size of chunks (in bytes) to read and send, by default 0 (no chunking).

 0

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.

Returns:

Type Description
dict

A dictionary containing the server's response.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import upload_dataset_file
>>> upload_dataset_file('arabidopsis000', '/path/to/local/file.txt')
Source code in plantdb/client/rest_api.py 
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def upload_dataset_file(scan_id, file_path, chunk_size=0, **kwargs):
    """Uploads a file to the server using the DatasetFile POST endpoint.

    Parameters
    ----------
    server_url : str
        The base URL of the server hosting the REST API.
    scan_id : str
        The unique identifier of the scan associated with the file upload.
    file_path : str
        The path to the file to be uploaded.
    chunk_size : int, optional
        The size of chunks (in bytes) to read and send, by default 0 (no chunking).

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.

    Returns
    -------
    dict
        A dictionary containing the server's response.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import upload_dataset_file
    >>> upload_dataset_file('arabidopsis000', '/path/to/local/file.txt')
    """
    from os.path import basename
    from os.path import getsize
    # Prepare the URL and headers
    scan_id = sanitize_name(scan_id)
    url = base_url(host=kwargs.get("host", REST_API_URL),
                   port=kwargs.get("port", REST_API_PORT),
                   prefix=kwargs.get('prefix', os.environ.get('PLANTDB_API_PREFIX', None)),
                   ssl=kwargs.get("ssl", False))
    url = urljoin(url, f"files/{scan_id}")

    filename = basename(file_path)
    file_size = getsize(file_path)
    # Create the request header
    headers = {
        "Content-Disposition": f"attachment; filename={filename}",
        "Content-Length": str(file_size),
        "X-File-Path": filename,
    }

    try:
        # Open the file for reading
        with open(file_path, 'rb') as f:
            if chunk_size > 0:
                # Upload in chunks
                headers["X-Chunk-Size"] = str(chunk_size)
                bytes_sent = 0
                while bytes_sent < file_size:
                    chunk = f.read(chunk_size)
                    response = make_api_request(
                        url,
                        method="POST",
                        headers=headers,
                        data=chunk,
                        cert_path=kwargs.get('cert_path', None)
                    )
                    bytes_sent += len(chunk)
                    # Check if the request was successful
                    if response.status_code not in (200, 201):
                        return {"error": "File upload failed", "status_code": response.status_code,
                                "response": response.json()}
            else:
                # Upload the entire file
                response = make_api_request(url, method='POST', headers=headers, data=f, cert_path=kwargs.get('cert_path', None))

        # Return the server's response
        if response.status_code in (200, 201):
            return response.json()
        else:
            return {"error": "File upload failed", "status_code": response.status_code, "response": response.json()}
    except Exception as e:
        return {"error": str(e)}

upload_scan_archive Link

upload_scan_archive(dataset_name, path, **kwargs)

Upload a scan archive file to a specified dataset on a server.

This function sends a POST request to upload a scan archive file to a particular dataset, utilizing the archive URL and optionally specified additional API-related request parameters. Ensures proper handling of file opening/closing procedures and response status checks.

Parameters:

Name Type Description Default
dataset_name str

The name of the target dataset for the archive upload.

 required
path str

The local file system path to the archive to be uploaded.

 required

Other Parameters:

Name Type Description
host str

The hostname or IP address of the PlantDB REST API server. Defaults to REST_API_URL.
port int or str

The port number of the PlantDB REST API server. Defaults to REST_API_PORT.
prefix str

The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes. Defaults to None.
ssl bool

Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to False.
timeout int

A timeout, in seconds, to succeed the upload request. Defaults to 120.

Returns:

Type Description
str

The time it took to upload the archive.

Raises:

Type Description
RequestException

If the HTTP request fails for any reason.
HTTPError

If the request returns an unsuccessful HTTP status code.

Examples:

>>> # Start a test PlantDB REST API server first, in a terminal:
>>> # $ fsdb_rest_api --test
>>> from plantdb.client.rest_api import upload_scan_archive
>>> upload_scan_archive("arabidopsis000", path='/tmp/arabidopsis000.zip')
'Upload completed in 0.10 seconds.'
Source code in plantdb/client/rest_api.py 
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def upload_scan_archive(dataset_name, path, **kwargs):
    """Upload a scan archive file to a specified dataset on a server.

    This function sends a POST request to upload a scan archive file to a
    particular dataset, utilizing the archive URL and optionally specified
    additional API-related request parameters. Ensures proper handling of
    file opening/closing procedures and response status checks.

    Parameters
    ----------
    dataset_name : str
        The name of the target dataset for the archive upload.
    path : str
        The local file system path to the archive to be uploaded.

    Other Parameters
    ----------------
    host : str, optional
        The hostname or IP address of the PlantDB REST API server. Defaults to ``REST_API_URL``.
    port : int or str, optional
        The port number of the PlantDB REST API server. Defaults to ``REST_API_PORT``.
    prefix : str, optional
        The prefix to be prepended to the URL. If provided, it will be stripped of leading and trailing slashes.
        Defaults to ``None``.
    ssl : bool, optional
        Flag indicating whether to use HTTPS (True) or HTTP (False). Defaults to ``False``.
    timeout : int, optional
        A timeout, in seconds, to succeed the upload request. Defaults to ``120``.

    Returns
    -------
    str
        The time it took to upload the archive.

    Raises
    ------
    requests.exceptions.RequestException
        If the HTTP request fails for any reason.
    requests.exceptions.HTTPError
        If the request returns an unsuccessful HTTP status code.

    Examples
    --------
    >>> # Start a test PlantDB REST API server first, in a terminal:
    >>> # $ fsdb_rest_api --test
    >>> from plantdb.client.rest_api import upload_scan_archive
    >>> upload_scan_archive("arabidopsis000", path='/tmp/arabidopsis000.zip')
    'Upload completed in 0.10 seconds.'
    """
    import time
    from zipfile import ZipFile

    path = Path(path)
    # Verify path existence
    if not path.is_file():
        raise FileNotFoundError(f"The file at path '{path}' does not exist!")
    # Verify the integrity of the ZIP file
    try:
        with ZipFile(path, 'r') as zip_file:
            zip_file.testzip()
    except Exception as e:
        print(e)
        raise IOError(f"Invalid ZIP file '{path}!'")

    # Construct the URL for the archive upload:
    url = archive_url(dataset_name, **kwargs)

    start_time = time.time()  # Start timing
    with open(path, "rb") as f:
        try:
            res = make_api_request(url,
                                   method="POST",
                                   files={"zip_file": (path.name, f, "application/zip")},
                                   stream=True,
                                   timeout=kwargs.get("timeout", 120),
                                   cert_path=kwargs.get("cert_path", None))
        except requests.exceptions.Timeout:
            timeout = kwargs.get("timeout", 120)
            raise RuntimeError(f"The upload request timed out after {timeout} seconds.")
        except requests.exceptions.RequestException as e:
            raise RuntimeError(f"An error occurred during the upload: {e}")
    end_time = time.time()  # End timing

    if res.ok:
        duration = end_time - start_time
        return f"Upload completed in {duration:.2f} seconds."
    else:
        res.raise_for_status()  # Raise an error if the request failed