PyOpenWorm.evidence module

exception PyOpenWorm.evidence.EvidenceError

Bases: Exception

class PyOpenWorm.evidence.Evidence(**kwargs)

Bases: PyOpenWorm.dataObject.DataObject

A representation which provides evidence, for a group of statements.

Attaching evidence to an set of statements is done like this:

>>> from PyOpenWorm.connection import Connection
>>> from PyOpenWorm.evidence import Evidence
>>> from PyOpenWorm.context import Context

Declare contexts:

>>> ACTX = Context(ident="http://example.org/data/some_statements")
>>> BCTX = Context(ident="http://example.org/data/some_other_statements")
>>> EVCTX = Context(ident="http://example.org/data/some_statements#evidence")

Make statements in ACTX and BCTX contexts:

>>> ACTX(Connection)(pre_cell="VA11", post_cell="VD12", number=3)
>>> BCTX(Connection)(pre_cell="VA11", post_cell="VD12", number=2)

In EVCTX, state that a that a certain document supports the set of statements in ACTX, but refutes the set of statements in BCTX:

>>> doc = EVCTX(Document)(author='White et al.', date='1986')
>>> EVCTX(Evidence)(reference=doc, supports=ACTX.rdf_object)
>>> EVCTX(Evidence)(reference=doc, refutes=BCTX.rdf_object)

Finally, save the contexts:

>>> ACTX.save_context()
>>> BCTX.save_context()
>>> EVCTX.save_context()

One note about the reference predicate: the reference should, ideally, be an unambiguous link to a peer-reviewed piece of scientific literature detailing methods and data analysis that supports the set of statements. However, in gather data from pre-existing sources, going to that level of specificity may be difficult due to deficient query capability at the data source. In such cases, a broader reference, such as a Website with information which guides readers to a peer-reviewed article supporting the statement is sufficient.

defined_augment(self)

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(self)

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

reference

The resource providing evidence supporting/refuting the attached context

refutes

A context naming a set of statements which are refuted by the attached reference

supports

A context naming a set of statements which are supported by the attached reference

PyOpenWorm.evidence.evidence_for(qctx, ctx, evctx=None)

Returns an iterable of Evidence

Parameters:

qctx : object

an object supported by evidence. If the object is a Context with no identifier, then the query considers statements ‘staged’ (rather than stored) in the context

ctx : Context

Context that bounds where we look for statements about qctx. The contexts for statements found in this context are the actual targets of Evidence.supports statements.

evctx : Context

if the Evidence.supports statements should be looked for somewhere other than ctx, that can be specified in evctx. optional

PyOpenWorm.evidence.query_context(graph, qctx)

graph : rdflib.graph.Graph

Graph where we can find the contexts for statements in qctx

qctx : PyOpenWorm.context.Context

Container for statements