aoptk.literature.databases.pmc
==============================

.. py:module:: aoptk.literature.databases.pmc


Classes
-------

.. autoapisummary::

   aoptk.literature.databases.pmc.PMC


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

.. py:class:: PMC(storage: pathlib.Path, figure_storage: pathlib.Path, query: aoptk.literature.query.Query | None = None)

   Bases: :py:obj:`aoptk.literature.get_publication.GetPublication`, :py:obj:`aoptk.literature.get_pdf.GetPDF`, :py:obj:`aoptk.literature.get_id.GetID`, :py:obj:`aoptk.literature.get_abstract.GetAbstract`, :py:obj:`aoptk.literature.get_metadata.GetMetadata`


   Class to get data from PMC based on a query.


   .. py:attribute:: aws_region
      :value: 'us-east-1'



   .. py:attribute:: s3


   .. py:attribute:: bucket
      :value: 'pmc-oa-opendata'



   .. py:attribute:: paginator


   .. py:attribute:: image_extensions
      :value: ('.jpg', '.jpeg', '.png', '.gif', '.bmp', '.tiff', '.tif')



   .. py:attribute:: unified_image_format
      :value: 'png'



   .. py:attribute:: search_term


   .. py:attribute:: _ncbi


   .. py:attribute:: storage


   .. py:attribute:: figure_storage


   .. py:method:: build_search_term(query: aoptk.literature.query.Query) -> str

      Convert Query to PMC search syntax.



   .. py:method:: _get_license_filter(licensing: str) -> str

      Get the license filter string for a given licensing type.

      :param licensing: The licensing type.
      :type licensing: str

      :returns: The license filter string for PMC search.
      :rtype: str



   .. py:method:: get_pdfs(ids: list[aoptk.literature.id.ID]) -> list[aoptk.literature.pdf.PDF]

      Retrieve PDFs.

      :returns: A list of PDF objects.
      :rtype: list[PDF]



   .. py:method:: get_publications(ids: list[aoptk.literature.id.ID], download_figures_enabled: bool = True) -> list[aoptk.literature.publication.Publication]

      Get a list of publications.

      :param ids: A list of publication IDs to retrieve.
      :type ids: list[ID]
      :param download_figures_enabled: Whether to download figures
      :type download_figures_enabled: bool
      :param and include their paths in the Publication objects.:

      :returns: A list of Publication objects.
      :rtype: list[Publication]



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

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



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

      Retrieve Abstracts based on the list of IDs.



   .. py:method:: _parse_pmc_abstract_records(records: list[Any]) -> list[aoptk.literature.abstract.Abstract]

      Parse PMC abstract handles and return a list of Abstract objects.

      :param records: A list of PMC Entrez fetch handles.
      :type records: list[Any]



   .. py:method:: get_publications_metadata(ids: list[aoptk.literature.id.ID]) -> list[aoptk.literature.metadata.Metadata]

      Retrieve Publication metadata.

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



   .. py:method:: _parse_pmc_metadata_records(records: list[str]) -> list[aoptk.literature.metadata.Metadata]

      Parse PMC metadata records and return a list of PublicationMetadata objects.

      :param records: A list of PMC XML summary payloads.
      :type records: list



   .. py:method:: _get_publication(publication_id: aoptk.literature.id.ID, download_figures_enabled: bool = True) -> aoptk.literature.publication.Publication | None

      Parse a single PDF and return a Publication object.

      :param publication_id: The publication ID to retrieve and parse.
      :type publication_id: str
      :param download_figures_enabled: Whether to download figures
      :type download_figures_enabled: bool
      :param and include their paths in the Publication object.:



   .. py:method:: _get_full_text(publication_id: aoptk.literature.id.ID) -> str | None

      Retrieve the full text for a given publication ID.

      :param publication_id: The publication ID to retrieve the full text for.
      :type publication_id: str



   .. py:method:: _get_file(publication_id: aoptk.literature.id.ID, file_format: str) -> pathlib.Path | None

      Retrieve the file for a given publication ID and format.

      :param publication_id: The publication ID to retrieve the file for.
      :type publication_id: str
      :param file_format: The format of the file to retrieve (pdf, xml, json, or txt).
      :type file_format: str
      :param Formats txt:
      :param xml:
      :param pdf contain full-text:
      :param while json contains metadata.:



   .. py:method:: _get_figures(publication_id: aoptk.literature.id.ID) -> list[pathlib.Path]

      Retrieve the figure files for a given publication ID.

      :param publication_id: The publication ID to retrieve the figure files for.
      :type publication_id: ID



   .. py:method:: _extract_figures_from_supplements(publication_id: aoptk.literature.id.ID, supplementary_files: list[str]) -> list[pathlib.Path]

      Extract figure files from the supplementary files.

      :param publication_id: The publication ID to retrieve the figure files for.
      :type publication_id: ID
      :param supplementary_files: A list of supplementary file URLs to extract figures from.
      :type supplementary_files: list[str]



   .. py:method:: _get_json(publication_id: aoptk.literature.id.ID) -> dict[str, Any] | None

      Retrieve the json for a given publication ID.

      :param publication_id: The publication ID to retrieve the json for.
      :type publication_id: str



   .. py:method:: _get_pdf(publication_id: aoptk.literature.id.ID) -> aoptk.literature.pdf.PDF | None

      Retrieve the PDF for a given publication ID.

      :param publication_id: The publication ID to retrieve the PDF for.
      :type publication_id: str