owmeta.document module

exception owmeta.document.PubmedRetrievalException

Bases: Exception

exception owmeta.document.WormbaseRetrievalException

Bases: Exception

class owmeta.document.BaseDocument(*args, no_type_decl=False, **kwargs)

Bases: DataObject

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci")

class owmeta.document.Document(*args, no_type_decl=False, **kwargs)

Bases: BaseDocument

A representation of some document.

Possible keys include:

pmid, pubmed: a pubmed id or url (e.g., 24098140)
wbid, wormbase: a wormbase id or url (e.g., WBPaper00044287)
doi: a Digitial Object id or url (e.g., s00454-010-9273-0)
uri: a URI specific to the document, preferably usable for accessing
     the document

Parameters

bibtexstr

A string containing a single BibTeX entry. Parsed during initialization, but not saved thereafter. optional

doistr

A Digital Object Identifier (DOI). optional

pubmedstr

A PubMed ID (PMID) or URL that points to a paper. Ignored if ‘pmid’ is provided. optional

wormbasestr

An ID or URL from WormBase that points to a record. Ignored if wbid or wormbaseid are provided. optional

defined_augment()

This fuction must return False if identifier_augment() would raise an IdentifierMissingException. Override it when defining a non-standard identifier for subclasses of DataObjects.

identifier_augment()

Override this method to define an identifier in lieu of one explicity set.

One must also override defined_augment() to return True whenever this method could return a valid identifier. IdentifierMissingException should be raised if an identifier cannot be generated by this method.

Raises

IdentifierMissingException

update_from_pubmed(read_size=65536, **kwargs)

Update the document attributes from NCBI Entrez API using the pubmed attribute

Parameters

chunk_sizeint

The number of bytes to pass to requests.Response.iter_content. This may reduce runtime memory requirements for the request.

**kwargs

Passed on as arguments to requests.Session.get

update_from_wormbase(replace_existing=False, **kwargs)

Queries WormBase.org for additional data to fill in the Document.

If replace_existing is set to True, then existing values will be cleared.

Parameters

replace_existingbool

Whether to replace values that are already set for a given property

**kwargs

Passed on as arguments to requests.Session.get

property author

An author of the document

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci")

property date

Alias to year

property doi

A Digital Object Identifier (DOI), optional

property pmid

A PubMed ID (PMID) that points to a paper

property title

The title of the document

property uri

A non-standard URI for the document

property wbid

An ID from WormBase.org that points to a record, optional

property wormbaseid

An alias to wbid

property year

The year (e.g., publication year) of the document

class owmeta.document.SourcedFrom(*args, **kwargs)

Bases: ObjectProperty

Indicates which document provided the source for an object

owner_type

alias of BaseDataObject

value_type

alias of BaseDocument

lazy = True

If True, then the property is not attached to an instance until the property is set or queried.

multiple = False

If True, then the property will only maintain a single staged value at a time. No effort is made to check how many values are stored in the RDF graph.

rdf_type_class = None