aoptk.literature.databases.pubmed
=================================

.. py:module:: aoptk.literature.databases.pubmed


Exceptions
----------

.. autoapisummary::

   aoptk.literature.databases.pubmed.QueryTooLargeError


Classes
-------

.. autoapisummary::

   aoptk.literature.databases.pubmed.PubMed


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

.. py:exception:: QueryTooLargeError(count: int, maximum: int)

   Bases: :py:obj:`Exception`


   Exception raised when query returns more than maximum_results.


   .. py:attribute:: count


   .. py:attribute:: maximum


.. py:class:: PubMed(query: str)

   Bases: :py:obj:`aoptk.literature.get_abstract.GetAbstract`, :py:obj:`aoptk.literature.get_id.GetID`, :py:obj:`aoptk.literature.get_publication_metadata.GetPublicationMetadata`


   Class to get data from PubMed based on a query.


   .. py:attribute:: maximum_results
      :value: 10000



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



   .. py:attribute:: max_retries
      :value: 5



   .. py:attribute:: _query


   .. py:attribute:: id_list


   .. py:attribute:: publication_count


   .. py:method:: get_abstracts() -> list[aoptk.literature.abstract.Abstract]

      Retrieve Abstracts based on the query.



   .. py:method:: get_publications_metadata() -> list[aoptk.literature.publication_metadata.PublicationMetadata]

      Retrieve Publication metadata based on the query.



   .. py:method:: get_publication_count() -> int

      Return the number of publications matching the query in PubMed.



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

      Get a list of PubMed IDs from PubMed based on the query.



   .. py:method:: _get_abstract(pmid: str) -> aoptk.literature.abstract.Abstract

      Get the abstract for a given PubMed ID.



   .. py:method:: _get_publication_metadata(pmid: str) -> aoptk.literature.publication_metadata.PublicationMetadata

      Get the publication metadata for a given PubMed ID.