phenopacket_mapper.utils package

This submodule contains utility functions that are used throughout the package.

class phenopacket_mapper.utils.NotebookBuilder

Bases: object

A class to build a Jupyter notebook programmatically.

add_markdown_cell(text)

Adds a Markdown cell to the notebook.

Parameters:

text – The Markdown content to be added to the cell.

add_code_cell(code)

Adds a code cell to the notebook.

Parameters:

code – The Python code to be added to the cell.

write_to_file(path: Path)

Writes the notebook content to a file.

Parameters:

path – The name of the file where the notebook will be saved.

phenopacket_mapper.utils.loc_default(df: DataFrame, row_index: int, column_name: str, default: Any = '') → Any

Safely performs loc on a pd.DataFrame, returns default value if something goes wrong

Parameters:

• df – the dataframe

• row_index – index of the row

• column_name – name of the column

• default – default value to return if some error occurs

Returns:

Value at the row and column specified

phenopacket_mapper.utils.str_to_valid_id(s: str) → str

Converts a string to a valid id

This function converts a string to a valid id by replacing spaces with underscores and removing all other non-alphanumeric characters.

Parameters:

s – The string to convert to a valid id

Returns:

The valid id

phenopacket_mapper.utils.recursive_dict_call(d: Dict, keys: List, default=None)

Subpackages

• phenopacket_mapper.utils.parsing package
  • parse_data_type()
  • parse_single_data_type()
  • parse_ordinal()
  • parse_primitive_data_value()
  • parse_int()
  • parse_float()
  • parse_bool()
  • parse_date()
  • parse_coding()
  • parse_value()
  • get_codesystem_by_namespace_prefx()
  • parse_value_set()
  • Submodules

Submodules

• phenopacket_mapper.utils.create_ipynb_in_code module
  • NotebookBuilder
• phenopacket_mapper.utils.get_field_name module
  • get_field_name()
• phenopacket_mapper.utils.pandas_utils module
  • loc_default()