:py:mod:`peptidedigest.article_db`
==================================

.. py:module:: peptidedigest.article_db

.. autoapi-nested-parse::

   Functions for creating and managing a SQLite database for storing articles and their model responses.



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


Functions
~~~~~~~~~

.. autoapisummary::

   peptidedigest.article_db.create_database
   peptidedigest.article_db.insert_article
   peptidedigest.article_db.get_article
   peptidedigest.article_db.get_articles
   peptidedigest.article_db.update_article
   peptidedigest.article_db.check_article_exists
   peptidedigest.article_db.delete_article



.. py:function:: create_database(name)

   Create a SQLite database with the given name.

   :Parameters: **name** (*str*) -- The name of the database to create.

   :returns: The database is created in the current working directory.
   :rtype: None


.. py:function:: insert_article(database, article_info, model_responses=None)

   Insert an article and its model responses into the database.

   :Parameters: * **database** (*str*) -- The name of the database to insert the article into.
                * **article_info** (*dict*) -- A dictionary containing the article information.
                * **model_responses** (*dict*) -- A dictionary containing the model responses for the article.

   :returns: The article and model responses are inserted into the database.
   :rtype: None


.. py:function:: get_article(database, doi=None, pmc_id=None)

   Get the article information and model responses for a given DOI.

   :Parameters: * **database** (*str*) -- The name of the database to retrieve the article from.
                * **doi** (*str*) -- The DOI of the article to retrieve.
                * **pmc_id** (*str*) -- The PMC ID of the article to retrieve.

   :returns: A dictionary containing the article information and model responses.
   :rtype: dict


.. py:function:: get_articles(database)

   Get all articles from the database.

   :Parameters: **database** (*str*) -- The name of the database to retrieve the articles from.

   :returns: A list of dictionaries containing the article information and model responses.
   :rtype: list


.. py:function:: update_article(database, doi, model_responses)

   Update the model responses for an article in the database.

   :Parameters: * **database** (*str*) -- The name of the database to update the article in.
                * **doi** (*str*) -- The DOI of the article to update.
                * **model_responses** (*dict*) -- A dictionary containing the updated model responses.

   :returns: The model responses for the article are updated in the database.
   :rtype: None


.. py:function:: check_article_exists(database, value, column)

   Check if an article with the given value in the specified column exists in the database.

   :Parameters: * **database** (*str*) -- The name of the database to check for the article.
                * **value** (*str*) -- The value to check for in the specified column.
                * **column** (*str*) -- The column to check for the value.

   :returns: True if the article exists, False otherwise.
   :rtype: bool


.. py:function:: delete_article(database, doi=None, pmc_id=None)

   Delete an article and its model responses from the database.

   :Parameters: * **database** (*str*) -- The name of the database to delete the article from.
                * **doi** (*str*) -- The DOI of the article to delete.
                * **pmc_id** (*str*) -- The PMC ID of the article to delete.

   :returns: The article and model responses are deleted from the database.
   :rtype: None