syndirella.check_inputs
=======================

.. py:module:: syndirella.check_inputs

.. autoapi-nested-parse::

   syndirella.check_inputs.py

   This module contains the functions used to check the inputs for running the pipeline.



Attributes
----------

.. autoapisummary::

   syndirella.check_inputs.logger


Functions
---------

.. autoapisummary::

   syndirella.check_inputs.check_csv
   syndirella.check_inputs.metadata_dict
   syndirella.check_inputs.check_template_paths
   syndirella.check_inputs.fill_in_product
   syndirella.check_inputs.check_route
   syndirella.check_inputs.check_manual
   syndirella.check_inputs.check_hit_names
   syndirella.check_inputs.check_apo_template
   syndirella.check_inputs.format_additional_info
   syndirella.check_inputs.get_exact_hit_names
   syndirella.check_inputs.get_template_path
   syndirella.check_inputs.check_additional_columns
   syndirella.check_inputs.format_manual_route
   syndirella.check_inputs.check_pipeline_inputs


Module Contents
---------------

.. py:data:: logger

.. py:function:: check_csv(csv_path: str) -> None

   Make sure that the csv path exists, can be read, and contains the required columns.


.. py:function:: metadata_dict(metadata_path: str, long_code_column: str = 'Long code') -> Dict

   Get the metadata dictionary from the metadata file, checking that it contains the required columns.


.. py:function:: check_template_paths(template_dir: str, csv_path: str, metadata_path: str) -> Set[str]

   Get the exact template paths, checking that they exist in the template directory.


.. py:function:: fill_in_product(row: pandas.Series, step: int) -> None

   Fill in the scaffold for the given step.


.. py:function:: check_route(i: int, row: pandas.Series) -> None

   Checks that the route is in the correct format and fills in missing products if needed.


.. py:function:: check_manual(csv_path: str) -> None

   Check that the manual dataframe is in the correct format, otherwise raise errors.


.. py:function:: check_hit_names(csv_path: str, hits_path: str, metadata_path: str, long_code_column: str) -> None

   Check that the hit names are found within SDF.


.. py:function:: check_apo_template(template_path: str) -> None

   Check that the template is actually apo (containing no LIG).


.. py:function:: format_additional_info(row: pandas.Series, additional_columns: List[str]) -> Dict[str, Any]

   This function is used to format the additional info from the dataframe into a dictionary.


.. py:function:: get_exact_hit_names(row: pandas.Series, metadata_path: str, hits_path: str) -> List[str]

   Get the exact hit name to use for placement.


.. py:function:: get_template_path(template_dir: str, template: str, metadata_path: str) -> str

   Get the exact template path to use for placement.


.. py:function:: check_additional_columns(csv_path: str, additional_columns: List[str]) -> None

   Check that the additional columns are in the csv.


.. py:function:: format_manual_route(row: pandas.Series) -> Tuple[List[Tuple[Any, Any]], List[Any], int]

   Format route to output reactants, reaction names, and products.


.. py:function:: check_pipeline_inputs(*, csv_path: str, template_dir: str, hits_path: str, metadata_path: str, additional_columns: List[str], manual_routes: bool, long_code_column: str) -> None

   Check the inputs for the pipeline.