aoptk.literature.databases.ncbi
===============================

.. py:module:: aoptk.literature.databases.ncbi


Classes
-------

.. autoapisummary::

   aoptk.literature.databases.ncbi.NCBI


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

.. py:class:: NCBI(database: Literal['pmc', 'pubmed'])

   Bases: :py:obj:`aoptk.literature.get_id.GetID`


   Helper class to retrieve data from NCBI databases - PubMed and PMC.


   .. py:attribute:: max_ncbi_results
      :value: 9998



   .. py:attribute:: max_concurrency
      :value: 2



   .. py:attribute:: max_requests_per_second
      :value: 2



   .. py:attribute:: minimal_year_publication
      :value: 1940



   .. py:attribute:: datetype
      :value: 'pdat'



   .. py:attribute:: batch_size
      :value: 200



   .. py:attribute:: async_retries
      :value: 10



   .. py:attribute:: database


   .. py:attribute:: semaphore


   .. py:attribute:: limiter


   .. py:method:: get_ids(search_term: str) -> list[aoptk.literature.id.ID]

      Retrieve a list of publication IDs based on the search term.



   .. py:method:: get_abstract_records(ids: list[aoptk.literature.id.ID]) -> list[dict]

      Retrieve abstract records based on the list of IDs. Note: There is still the 10 000 records limit.

      :param ids: A list of publication IDs for which to retrieve abstracts.
      :type ids: list[ID]



   .. py:method:: get_publications_metadata_records(ids: list[aoptk.literature.id.ID]) -> list[Any]

      Retrieve publication metadata records based on the list of IDs.



   .. py:method:: _batch_requests(ids: list[aoptk.literature.id.ID], func: collections.abc.Callable[Ellipsis, Any]) -> list[Any]

      Helper function to batch requests to NCBI.



   .. py:method:: _async_get_ids(search_term: str) -> list[aoptk.literature.id.ID]
      :async:


      Asynchronously retrieve a list of publication IDs based on the search term.



   .. py:method:: _get_publication_count_and_ids(search_term: str, mindate: str | None = None, maxdate: str | None = None) -> tuple[int, list[str]]

      Helper function to retrieve the count of publications and their IDs.

      Retrieves IDs and total count based on the given search term and an
      optional date range.



   .. py:method:: _async_get_publication_count_and_ids(search_term: str, mindate: str | None = None, maxdate: str | None = None) -> tuple[int, list[str]]
      :async:


      Asynchronously retrieve the count of publications and their IDs based on the search term and date range.



   .. py:method:: _collect_ids_for_year(search_term: str, year: int) -> list[str]
      :async:


      Collect publication IDs for a specific year, splitting by months and days if the count exceeds the limit.



   .. py:method:: _collect_ids_split_by_months_days(search_term: str, year: int) -> list[str]
      :async:


      Collect publication IDs for a specific year.

      Split the search into months and days to avoid exceeding the result
      limit.