aoptk.literature.databases.pmc

Classes

PMC	Class to get data from PMC based on a query.

Module Contents

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

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

Class to get data from PMC based on a query.

aws_region = 'us-east-1'

s3

bucket = 'pmc-oa-opendata'

paginator

image_extensions = ('.jpg', '.jpeg', '.png', '.gif', '.bmp', '.tiff', '.tif')

unified_image_format = 'png'

search_term

_ncbi

storage

figure_storage

build_search_term(query: aoptk.literature.query.Query) → str

Convert Query to PMC search syntax.

_get_license_filter(licensing: str) → str

Get the license filter string for a given licensing type.

Parameters:

licensing (str) – The licensing type.

Returns:

The license filter string for PMC search.

Return type:

str

get_pdfs(ids: list[aoptk.literature.id.ID]) → list[aoptk.literature.pdf.PDF]

Retrieve PDFs.

Returns:

A list of PDF objects.

Return type:

list[PDF]

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

Get a list of publications.

Parameters:

• ids (list[ID]) – A list of publication IDs to retrieve.

• download_figures_enabled (bool) – Whether to download figures

• objects. (and include their paths in the Publication)

Returns:

A list of Publication objects.

Return type:

list[Publication]

get_ids() → list[aoptk.literature.id.ID]

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

get_abstracts(ids: list[aoptk.literature.id.ID]) → list[aoptk.literature.abstract.Abstract]

Retrieve Abstracts based on the list of IDs.

_parse_pmc_abstract_records(records: list[Any]) → list[aoptk.literature.abstract.Abstract]

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

Parameters:

records (list[Any]) – A list of PMC Entrez fetch handles.

get_publications_metadata(ids: list[aoptk.literature.id.ID]) → list[aoptk.literature.metadata.Metadata]

Retrieve Publication metadata.

Parameters:

ids (list[ID]) – A list of publication IDs for which to retrieve metadata.

_parse_pmc_metadata_records(records: list[str]) → list[aoptk.literature.metadata.Metadata]

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

Parameters:

records (list) – A list of PMC XML summary payloads.

_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.

Parameters:

• publication_id (str) – The publication ID to retrieve and parse.

• download_figures_enabled (bool) – Whether to download figures

• object. (and include their paths in the Publication)

_get_full_text(publication_id: aoptk.literature.id.ID) → str | None

Retrieve the full text for a given publication ID.

Parameters:

publication_id (str) – The publication ID to retrieve the full text for.

_get_file(publication_id: aoptk.literature.id.ID, file_format: str) → pathlib.Path | None

Retrieve the file for a given publication ID and format.

Parameters:

• publication_id (str) – The publication ID to retrieve the file for.

• file_format (str) – The format of the file to retrieve (pdf, xml, json, or txt).

• txt (Formats)

• xml

• full-text (pdf contain)

• metadata. (while json contains)

_get_figures(publication_id: aoptk.literature.id.ID) → list[pathlib.Path]

Retrieve the figure files for a given publication ID.

Parameters:

publication_id (ID) – The publication ID to retrieve the figure files for.

_extract_figures_from_supplements(publication_id: aoptk.literature.id.ID, supplementary_files: list[str]) → list[pathlib.Path]

Extract figure files from the supplementary files.

Parameters:

• publication_id (ID) – The publication ID to retrieve the figure files for.

• supplementary_files (list[str]) – A list of supplementary file URLs to extract figures from.

_get_json(publication_id: aoptk.literature.id.ID) → dict[str, Any] | None

Retrieve the json for a given publication ID.

Parameters:

publication_id (str) – The publication ID to retrieve the json for.

_get_pdf(publication_id: aoptk.literature.id.ID) → aoptk.literature.pdf.PDF | None

Retrieve the PDF for a given publication ID.

Parameters:

publication_id (str) – The publication ID to retrieve the PDF for.