langchain_community.utilities.pubmed
.PubMedAPIWrapper¶
- class langchain_community.utilities.pubmed.PubMedAPIWrapper[source]¶
Bases:
BaseModel
Wrapper around PubMed API.
This wrapper will use the PubMed API to conduct searches and fetch document summaries. By default, it will return the document summaries of the top-k results of an input search.
- Parameters
top_k_results – number of the top-scored document used for the PubMed tool
MAX_QUERY_LENGTH – maximum length of the query. Default is 300 characters.
doc_content_chars_max – maximum length of the document content. Content will be truncated if it exceeds this length. Default is 2000 characters.
max_retry – maximum number of retries for a request. Default is 5.
sleep_time – time to wait between retries. Default is 0.2 seconds.
email – email address to be used for the PubMed API.
Create a new model by parsing and validating input data from keyword arguments.
Raises ValidationError if the input data cannot be parsed to form a valid model.
- param MAX_QUERY_LENGTH: int = 300¶
- param base_url_efetch: str = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'¶
- param base_url_esearch: str = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?'¶
- param doc_content_chars_max: int = 2000¶
- param email: str = 'your_email@example.com'¶
- param max_retry: int = 5¶
- param sleep_time: float = 0.2¶
- param top_k_results: int = 3¶
- classmethod construct(_fields_set: Optional[SetStr] = None, **values: Any) Model ¶
Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values
- Parameters
_fields_set (Optional[SetStr]) –
values (Any) –
- Return type
Model
- copy(*, include: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, exclude: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, update: Optional[DictStrAny] = None, deep: bool = False) Model ¶
Duplicate a model, optionally choose which fields to include, exclude and change.
- Parameters
include (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) – fields to include in new model
exclude (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) – fields to exclude from new model, as with values this takes precedence over include
update (Optional[DictStrAny]) – values to change/add in the new model. Note: the data is not validated before creating the new model: you should trust this data
deep (bool) – set to True to make a deep copy of the model
self (Model) –
- Returns
new model instance
- Return type
Model
- dict(*, include: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, exclude: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, by_alias: bool = False, skip_defaults: Optional[bool] = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) DictStrAny ¶
Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.
- Parameters
include (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) –
exclude (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) –
by_alias (bool) –
skip_defaults (Optional[bool]) –
exclude_unset (bool) –
exclude_defaults (bool) –
exclude_none (bool) –
- Return type
DictStrAny
- classmethod from_orm(obj: Any) Model ¶
- Parameters
obj (Any) –
- Return type
Model
- json(*, include: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, exclude: Optional[Union[AbstractSetIntStr, MappingIntStrAny]] = None, by_alias: bool = False, skip_defaults: Optional[bool] = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Optional[Callable[[Any], Any]] = None, models_as_dict: bool = True, **dumps_kwargs: Any) unicode ¶
Generate a JSON representation of the model, include and exclude arguments as per dict().
encoder is an optional function to supply as default to json.dumps(), other arguments as per json.dumps().
- Parameters
include (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) –
exclude (Optional[Union[AbstractSetIntStr, MappingIntStrAny]]) –
by_alias (bool) –
skip_defaults (Optional[bool]) –
exclude_unset (bool) –
exclude_defaults (bool) –
exclude_none (bool) –
encoder (Optional[Callable[[Any], Any]]) –
models_as_dict (bool) –
dumps_kwargs (Any) –
- Return type
unicode
- lazy_load(query: str) Iterator[dict] [source]¶
Search PubMed for documents matching the query. Return an iterator of dictionaries containing the document metadata.
- Parameters
query (str) –
- Return type
Iterator[dict]
- lazy_load_docs(query: str) Iterator[Document] [source]¶
- Parameters
query (str) –
- Return type
Iterator[Document]
- load(query: str) List[dict] [source]¶
Search PubMed for documents matching the query. Return a list of dictionaries containing the document metadata.
- Parameters
query (str) –
- Return type
List[dict]
- load_docs(query: str) List[Document] [source]¶
- Parameters
query (str) –
- Return type
List[Document]
- classmethod parse_file(path: Union[str, Path], *, content_type: unicode = None, encoding: unicode = 'utf8', proto: Protocol = None, allow_pickle: bool = False) Model ¶
- Parameters
path (Union[str, Path]) –
content_type (unicode) –
encoding (unicode) –
proto (Protocol) –
allow_pickle (bool) –
- Return type
Model
- classmethod parse_obj(obj: Any) Model ¶
- Parameters
obj (Any) –
- Return type
Model
- classmethod parse_raw(b: Union[str, bytes], *, content_type: unicode = None, encoding: unicode = 'utf8', proto: Protocol = None, allow_pickle: bool = False) Model ¶
- Parameters
b (Union[str, bytes]) –
content_type (unicode) –
encoding (unicode) –
proto (Protocol) –
allow_pickle (bool) –
- Return type
Model
- retrieve_article(uid: str, webenv: str) dict [source]¶
- Parameters
uid (str) –
webenv (str) –
- Return type
dict
- run(query: str) str [source]¶
Run PubMed search and get the article meta information. See https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch It uses only the most informative fields of article meta information.
- Parameters
query (str) –
- Return type
str
- classmethod schema(by_alias: bool = True, ref_template: unicode = '#/definitions/{model}') DictStrAny ¶
- Parameters
by_alias (bool) –
ref_template (unicode) –
- Return type
DictStrAny
- classmethod schema_json(*, by_alias: bool = True, ref_template: unicode = '#/definitions/{model}', **dumps_kwargs: Any) unicode ¶
- Parameters
by_alias (bool) –
ref_template (unicode) –
dumps_kwargs (Any) –
- Return type
unicode
- classmethod update_forward_refs(**localns: Any) None ¶
Try to update ForwardRefs on fields based on this Model, globalns and localns.
- Parameters
localns (Any) –
- Return type
None
- classmethod validate(value: Any) Model ¶
- Parameters
value (Any) –
- Return type
Model