Usage

Downloading and processing functions for PubMed.

class AbstractText(*, text: str, label: str | None = None, category: str | None = None)

Represents an abstract text object.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Article(*, pubmed: int, title: str, date_completed: date | None = None, date_revised: date | None = None, type_mesh_ids: list[str] = <factory>, headings: list[Heading] = <factory>, journal: Journal, journal_issue: JournalIssue, abstract: list[AbstractText] = <factory>, authors: list[Author | Collective] = <factory>, cites_pubmed_ids: list[str] = <factory>, xrefs: list[Reference] = <factory>, history: list[History] = <factory>, grants: list[Grant] = <factory>)

Represents an article.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

property year: int | None

The year the article was published.

property date_published: date | None

Get the date published from the journal issue.

get_abstract() → str

Get the full abstract.

is_retracted() → bool

Check if the article is retracted.

is_review() → bool

Check if the article is a review.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Journal(*, issn: str | None = None, nlm_catalog_id: str, issns: list[ISSN] = <factory>)

Represents a reference to a journal.

Note, full information about a journal can be loaded elsewhere.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

ensure_baselines(*, force: bool, source: Literal['remote', 'local'] | None = None) → list[Path]

Ensure all the baseline files are downloaded.

ensure_updates(*, force: bool, source: Literal['remote', 'local'] | None = None) → list[Path]

Ensure all the baseline files are downloaded.

iterate_ensure_articles(*, force: bool = False, source: Literal['remote', 'local'] | None = None) → Iterable[Path]

Ensure articles from baseline, then updates.

iterate_ensure_baselines(*, source: Literal['remote', 'local'] | None = None, force: bool = False) → Iterable[Path]

Ensure all the baseline files are downloaded.

iterate_ensure_updates(*, force: bool = False, source: Literal['remote', 'local'] | None = None) → Iterable[Path]

Ensure all the baseline files are downloaded.

iterate_process_articles(*, force_process: bool = False, ror_grounder: Grounder | None = None, mesh_grounder: Grounder | None = None, author_grounder: Grounder | None = None, multiprocessing: bool = False, force_listing: bool = False, source: Literal['remote', 'local'] | None = None, ground: bool = True) → Iterable[Article]

Ensure and process articles from baseline, then updates.

iterate_process_baselines(*, force_process: bool = False, multiprocessing: bool = False, ror_grounder: Grounder | None = None, mesh_grounder: Grounder | None = None, author_grounder: Grounder | None = None, force_listing: bool = False, source: Literal['remote', 'local'] | None = None) → Iterable[Article]

Ensure and process all baseline files.

iterate_process_updates(*, force_process: bool = False, multiprocessing: bool = False, ror_grounder: Grounder | None = None, mesh_grounder: Grounder | None = None, author_grounder: Grounder | None = None, force_listing: bool = False, source: Literal['remote', 'local'] | None = None) → Iterable[Article]

Ensure and process updates.

process_articles(*, force_process: bool = False, multiprocessing: bool = False, force_listing: bool = False, source: Literal['remote', 'local'] | None = None) → list[Article]

Ensure and process articles from baseline, then updates.

process_baselines(*, force_process: bool = False, source: Literal['remote', 'local'] | None = None) → list[Article]

Ensure and process all baseline files.

process_updates(*, force_process: bool = False) → list[Article]

Ensure and process updates.