testing

Testing Utilities for PlantDB

Provides a collection of helper classes and unittest mix‑ins that simplify writing tests for PlantDB databases. By offering temporary database clones and ready‑made test cases, it enables developers to create isolated, repeatable test environments without affecting the original data.

Key Features

• TemporaryCloneDB: Creates a temporary copy of an existing PlantDB on disk, ensuring tests run against an isolated sandbox that is automatically cleaned up.
• DummyDBTestCase: A unittest.TestCase subclass that builds a lightweight dummy database containing a sample scan, fileset, and file, with convenience methods to retrieve them.
• FSDBTestCase: A unittest.TestCase subclass for real‑world datasets; it handles connecting, authenticating, and cleaning up a temporary FSDB instance.
• Helper methods (get_test_db, get_test_scan, get_test_fileset, get_test_image_file, get_task_fileset, etc.) to quickly access common test objects and locate task‑specific filesets.

Usage Examples

>>> from plantdb.commons.testing import DummyDBTestCase
>>> class MyTest(DummyDBTestCase):
>>>     def test_scan_properties(self):
>>>         db = self.get_test_db()
>>>         scan = self.get_test_scan()
>>>         # Perform assertions on the scan object
>>>         self.assertEqual(scan.name, "myscan_001")

DummyDBTestCase

Bases: TestCase

A dummy test database.

Attributes:

Name	Type	Description
db	FSDB	The temporary directory.
tmpclone	TemporaryCloneDB	A local temporary copy of a dummy test database.

get_test_db

get_test_db(db_path=None)

Return the test FSDB database.

Parameters:

Name	Type	Description	Default
db_path	str	If None (default), return the dummy database. Else, should be the location of the source database to clone in the temporary folder.	None

Returns:

Type	Description
FSDB	The database to test.

Source code in plantdb/commons/testing.py

def get_test_db(self, db_path=None):
    """Return the test ``FSDB`` database.

    Parameters
    ----------
    db_path : str, optional
        If `None` (default), return the dummy database.
        Else, should be the location of the source database to clone in the temporary folder.

    Returns
    -------
    plantdb.commons.FSDB
        The database to test.
    """
    if db_path is not None:
        self.tmpclone = TemporaryCloneDB(db_path)
        self.db = FSDB(self.tmpclone.tmpdir.name)

    return self.db

get_test_fileset

get_test_fileset()

Return the default test Fileset object named 'fileset_001'.

Returns:

Type	Description
Scan	The default fileset instance to test.

Source code in plantdb/commons/testing.py

def get_test_fileset(self):
    """Return the default test ``Fileset`` object named 'fileset_001'.

    Returns
    -------
    plantdb.commons.Scan
        The default fileset instance to test.
    """
    scan = self.get_test_scan()
    fileset = scan.get_fileset("fileset_001")
    return fileset

get_test_image_file

get_test_image_file()

Return the default test File object named 'test_image'.

Returns:

Type	Description
File	The default image file instance to test.

Source code in plantdb/commons/testing.py

def get_test_image_file(self):
    """Return the default test ``File`` object named 'test_image'.

    Returns
    -------
    plantdb.commons.File
        The default image file instance to test.
    """
    fileset = self.get_test_fileset()
    file = fileset.get_file("test_image")
    return file

get_test_scan

get_test_scan()

Return the default test Scan object named 'myscan_001'.

Returns:

Type	Description
Scan	The default scan instance to test.

Source code in plantdb/commons/testing.py

def get_test_scan(self):
    """Return the default test ``Scan`` object named 'myscan_001'.

    Returns
    -------
    plantdb.commons.Scan
        The default scan instance to test.
    """
    db = self.get_test_db()
    scan = db.get_scan("myscan_001")
    return scan

setUp

setUp()

Set up a dummy database with fake scan, fileset & files.

Source code in plantdb/commons/testing.py

def setUp(self):
    """Set up a dummy database with fake scan, fileset & files."""
    self.db = dummy_db(with_scan=True, with_fileset=True, with_file=True)
    self.tmpclone = None

tearDown

tearDown()

Clean up after test.

Source code in plantdb/commons/testing.py

def tearDown(self):
    """Clean up after test."""
    try:
        self.db.disconnect()
    except:
        return
    from shutil import rmtree
    rmtree(self.db.path(), ignore_errors=True)

FSDBTestCase

Bases: TestCase

A local FSDB test database.

Attributes:

Name	Type	Description
db	FSDB	The temporary test database with the 'real_plant_analyzed' dataset.

get_task_fileset

get_task_fileset(task_name)

Return the fileset for the corresponding task.

Parameters:

Name	Type	Description	Default
task_name	str	The name of the task to get the fileset for.	required

Returns:

Type	Description
Fileset	The Fileset corresponding to the given task.

Source code in plantdb/commons/testing.py

def get_task_fileset(self, task_name):
    """Return the fileset for the corresponding task.

    Parameters
    ----------
    task_name : str
        The name of the task to get the fileset for.

    Returns
    -------
    plantdb.commons.fsdb.core.Fileset
        The ``Fileset`` corresponding to the given task.
    """
    scan = self.get_test_scan()
    return scan.get_fileset(self.get_task_fileset_id(task_name))

get_task_fileset_id

get_task_fileset_id(task_name)

Return the fileset id for the corresponding task.

Parameters:

Name	Type	Description	Default
task_name	str	The name of the task to get the fileset for.	required

Returns:

Type	Description
str	The Fileset name corresponding to the given task.

Source code in plantdb/commons/testing.py

def get_task_fileset_id(self, task_name):
    """Return the fileset id for the corresponding task.

    Parameters
    ----------
    task_name : str
        The name of the task to get the fileset for.

    Returns
    -------
    str
        The ``Fileset`` name corresponding to the given task.
    """
    scan = self.get_test_scan()
    return locate_task_filesets(scan, [task_name])[task_name]

get_test_db

get_test_db()

Return the test FSDB database.

Source code in plantdb/commons/testing.py

def get_test_db(self) -> FSDB:
    """Return the test ``FSDB`` database."""
    self.db.connect()
    self.db.login('guest', 'guest')
    return self.db

get_test_fileset

get_test_fileset(fs_id)

Return the default test Fileset object named 'fileset_001'.

Returns:

Type	Description
Scan	The default fileset instance to test.

Source code in plantdb/commons/testing.py

def get_test_fileset(self, fs_id):
    """Return the default test ``Fileset`` object named 'fileset_001'.

    Returns
    -------
    plantdb.commons.Scan
        The default fileset instance to test.
    """
    scan = self.get_test_scan()
    fileset = scan.get_fileset(fs_id)
    return fileset

get_test_scan

get_test_scan()

Return the default test Scan object named 'real_plant_analyzed'.

Returns:

Type	Description
Scan	The default Scan instance to test.

Source code in plantdb/commons/testing.py

def get_test_scan(self):
    """Return the default test ``Scan`` object named 'real_plant_analyzed'.

    Returns
    -------
    plantdb.commons.fsdb.core.Scan
        The default ``Scan`` instance to test.
    """
    db = self.get_test_db()
    scan = db.get_scan("real_plant_analyzed")
    return scan

setUp

setUp()

Set up a test database with the 'real_plant_analyzed' dataset.

Source code in plantdb/commons/testing.py

def setUp(self):
    """Set up a test database with the 'real_plant_analyzed' dataset."""
    self.db = test_database('real_plant_analyzed')

tearDown

tearDown()

Clean up after test.

Source code in plantdb/commons/testing.py

def tearDown(self):
    """Clean up after test."""
    try:
        self.db.disconnect()
    except:
        pass
    from shutil import rmtree
    rmtree(self.db.path(), ignore_errors=True)

TemporaryCloneDB

TemporaryCloneDB(db_location)

Bases: object

Class for doing tests on a copy of a local DB.

Parameters:

Name	Type	Description	Default
db_location	str	Location of the source database to clone in the temporary folder.	required

Attributes:

Name	Type	Description
tmpdir	TemporaryDirectory	The temporary directory.

Source code in plantdb/commons/testing.py

def __init__(self, db_location):
    self.tmpdir = tempfile.TemporaryDirectory()
    shutil.copytree(db_location, self.tmpdir.name)