utils.py

QuietStdOut

Context for quieting standard output, and setting datajoint loglevel to warning

Used in pytest functions to render clear output showing only pass/fail

Example

with QuietStdOut(): table.delete(safemode=False)

Source code in element_interface/utils.py

class QuietStdOut:
    """Context for quieting standard output, and setting datajoint loglevel to warning

    Used in pytest functions to render clear output showing only pass/fail

    Example:
        with QuietStdOut():
            table.delete(safemode=False)
    """

    def __enter__(self):
        self.prev_log_level = logger.level
        logger.setLevel(30)  # set DataJoint logger to warning
        self._original_stdout = sys.stdout
        sys.stdout = open(os.devnull, "w")

    def __exit__(self, *args):
        logger.setLevel(self.prev_log_level)
        sys.stdout.close()
        sys.stdout = self._original_stdout

dict_to_uuid(key)

Given a dictionary key, returns a hash string as UUID

Parameters:

Name	Type	Description	Default
key	dict	Any python dictionary	required

Source code in element_interface/utils.py

def dict_to_uuid(key: dict):
    """Given a dictionary `key`, returns a hash string as UUID

    Args:
        key (dict): Any python dictionary"""
    hashed = hashlib.md5()
    for k, v in sorted(key.items()):
        hashed.update(str(k).encode())
        hashed.update(str(v).encode())
    return uuid.UUID(hex=hashed.hexdigest())

find_full_path(root_directories, relative_path)

Given a list of roots and a relative path, search and return the full-path

Root directories are searched in the provided order

Parameters:

Name	Type	Description	Default
root_directories	list	potential root directories	required
relative_path	str	the relative path to find the valid root directory	required

Returns:

Type	Description
pathlib.PosixPath	full-path (pathlib.Path object)

Raises:

Type	Description
FileNotFoundError	No valid full path

Source code in element_interface/utils.py

def find_full_path(root_directories: list, relative_path: str) -> pathlib.PosixPath:
    """Given a list of roots and a relative path, search and return the full-path

    Root directories are searched in the provided order

    Args:
        root_directories (list): potential root directories
        relative_path (str): the relative path to find the valid root directory

    Returns:
        full-path (pathlib.Path object)

    Raises:
        FileNotFoundError: No valid full path
    """
    relative_path = _to_Path(relative_path)

    if relative_path.exists():
        return relative_path

    # Turn to list if only a single root directory is provided
    if isinstance(root_directories, (str, pathlib.Path)):
        root_directories = [_to_Path(root_directories)]

    for root_dir in root_directories:
        if (_to_Path(root_dir) / relative_path).exists():
            return _to_Path(root_dir) / relative_path

    raise FileNotFoundError(
        "No valid full-path found (from {})"
        " for {}".format(root_directories, relative_path)
    )

find_root_directory(root_directories, full_path)

Given multiple potential root directories and a full-path, return parent root.

Search and return one directory that is the parent of the given path.

Parameters:

Name	Type	Description	Default
root_directories	list	potential root directories	required
full_path	str	the full path to search the root directory	required

Returns:

Type	Description
pathlib.PosixPath	root_directory (pathlib.Path object)

Raises:

Type	Description
FileNotFoundError	Full path does not exist
FileNotFoundError	No valid root directory

Source code in element_interface/utils.py

def find_root_directory(root_directories: list, full_path: str) -> pathlib.PosixPath:
    """Given multiple potential root directories and a full-path, return parent root.

    Search and return one directory that is the parent of the given path.

    Args:
        root_directories (list): potential root directories
        full_path (str): the full path to search the root directory

    Returns:
        root_directory (pathlib.Path object)

    Raises:
        FileNotFoundError: Full path does not exist
        FileNotFoundError: No valid root directory
    """
    full_path = _to_Path(full_path)

    if not full_path.exists():
        raise FileNotFoundError(f"{full_path} does not exist!")

    # Turn to list if only a single root directory is provided
    if isinstance(root_directories, (str, pathlib.Path)):
        root_directories = [_to_Path(root_directories)]

    try:
        return next(
            _to_Path(root_dir)
            for root_dir in root_directories
            if _to_Path(root_dir) in set(full_path.parents)
        )

    except StopIteration:
        raise FileNotFoundError(
            "No valid root directory found (from {})"
            " for {}".format(root_directories, full_path)
        )

ingest_csv_to_table(csvs, tables, verbose=True, skip_duplicates=True, ignore_extra_fields=True, allow_direct_insert=False)

Inserts data from a series of csvs into their corresponding table:

Example

ingest_csv_to_table(['./lab_data.csv', './proj_data.csv'], [lab.Lab(),lab.Project()]

Parameters:

Name	Type	Description	Default
csvs	list	list of paths to CSV files relative to current directory. CSV are delimited by commas.	required
tables	list	list of datajoint tables with terminal ()	required
verbose	bool	print number inserted (i.e., table length change)	True
skip_duplicates	bool	skip duplicate entries. See DataJoint's insert	True
ignore_extra_fields	bool	if a csv feeds multiple tables, the subset of columns not applicable to a table will be ignored. See DataJoint's insert	True
allow_direct_insert	bool	permit insertion into Imported and Computed tables See DataJoint's insert.	False

Source code in element_interface/utils.py

def ingest_csv_to_table(
    csvs: list,
    tables: list,
    verbose: bool = True,
    skip_duplicates: bool = True,
    ignore_extra_fields: bool = True,
    allow_direct_insert: bool = False,
):
    """Inserts data from a series of csvs into their corresponding table:

    Example:
        > ingest_csv_to_table(['./lab_data.csv', './proj_data.csv'],
                                 [lab.Lab(),lab.Project()]

    Args:
        csvs (list): list of paths to CSV files relative to current directory.
            CSV are delimited by commas.
        tables (list): list of datajoint tables with terminal `()`
        verbose (bool): print number inserted (i.e., table length change)
        skip_duplicates (bool): skip duplicate entries. See DataJoint's `insert`
        ignore_extra_fields (bool): if a csv feeds multiple tables, the subset of
            columns not applicable to a table will be ignored. See DataJoint's `insert`
        allow_direct_insert (bool): permit insertion into Imported and Computed tables
            See DataJoint's `insert`.
    """
    for csv_filepath, table in zip(csvs, tables):
        with open(csv_filepath, newline="") as f:
            data = list(csv.DictReader(f, delimiter=","))
        if verbose:
            prev_len = len(table)
        table.insert(
            data,
            skip_duplicates=skip_duplicates,
            # Ignore extra fields because some CSVs feed multiple tables
            ignore_extra_fields=ignore_extra_fields,
            # Allow direct bc element-event uses dj.Imported w/o `make` funcs
            allow_direct_insert=allow_direct_insert,
        )
        if verbose:
            insert_len = len(table) - prev_len
            logger.info(
                f"\n---- Inserting {insert_len} entry(s) "
                + f"into {to_camel_case(table.table_name)} ----"
            )

value_to_bool(value)

Return whether the provided value represents true. Otherwise false.

Parameters:

Name	Type	Description	Default
value	(str, bool, int)	Any input	required

Returns:

Name	Type	Description
bool	bool	True if value in ("y", "yes", "t", "true", "on", "1")

Source code in element_interface/utils.py

def value_to_bool(value) -> bool:
    """Return whether the provided value represents true. Otherwise false.

    Args:
        value (str, bool, int): Any input

    Returns:
        bool (bool): True if value in ("y", "yes", "t", "true", "on", "1")
    """
    if not value:
        return False
    return str(value).lower() in ("y", "yes", "t", "true", "on", "1")