indivo.rdf package¶
Subpackages¶
Submodules¶
indivo.rdf.rdf module¶
Utilities for generating RDF graphs.
Adapted from the Smart Sample Data generator.
- class indivo.rdf.rdf.PatientGraph(record)¶
Bases: object
Represents a patient’s RDF graph
- _getCodeFromField(model, field_prefix, classes=None)¶
Build up a dictionary representing a sp:code
- _getCodedValueFromField(model, field_prefix, classes=None)¶
Build up a dictionary representing a sp:CodedValue
- _getProvenanceFromField(model, field_prefix)¶
Build up a dictionary representing a sp:provenance
- _obj_fields_by_name(obj, prefix, suffixes)¶
Given an object, returns a dictionary of its attributes based on prefix and suffixes.
Specifically, the dictionary is of the form:
{ 'suffix': getattr(obj, prefix + '_' + suffix) }
for each suffix in suffixes.
- addAllergyExclusions(exclusions)¶
Add allergy exclusions to the patient graph.
- addAllergyList(allergies)¶
Add a list of allergies to the patient graph.
- addClinicalNoteList(notes, order_results=False)¶
Add clinical notes to a patient’s graph
- addCombinedAllergyList(combinedAllergies, order_results=False)¶
Add a list of AllergyExclusions and Allergies to the patient graph
- addCombinedResponseSummary(query, result_order=None)¶
Add SMART ResponseSummary to the graph based off queries with merged results
- addDemographics(record)¶
Adds patient Demographics info to the graph.
- addEncounterList(encounters, order_results=False)¶
Add encounters to a patient’s graph
- addFill(fill, medNode=None, med_uri_only=True)¶
Build a Fill and add it to the patient graph, optionally linking it with a medication node.
- addFillList(fills, order_results=False)¶
Adds a FillList to a patient’s graph.
- addImmunizationList(immunizations, order_results=False)¶
Add immunizations to a patient’s graph
- addLabPanelList(lab_panels, order_results=False)¶
Adds Lab Panels to the patient’s graph
- addLabResultList(labs, order_results=False)¶
Adds Lab Results to the patient’s graph
- addMedList(meds, order_results=False)¶
Adds a MedList to a patient’s graph
- addProblemList(problems, order_results=None)¶
Add problems to a patient’s graph
- addProcedureList(procedures, order_results=False)¶
Add procedures to a patient’s graph
- addResponseSummary(query, result_order=None)¶
Add SMART ResponseSummary to the graph
- addSocialHistoryList(histories, order_results=False)¶
Add social histories to a patient’s graph
- addStatement(s)¶
- addVitalsList(vitals, order_results=False)¶
Add vitals to a patient’s graph
- address(obj, prefix)¶
- allergy(allergy)¶
Build an Allergy
- allergy_exclusion(exclusion)¶
Build an AllergyExclusion
- bloodPressure(obj, prefix)¶
- code(title, system, identifier, blank=False, classes=[])¶
Adds a Code to the graph and returns node
- codeProvenance(provenance)¶
Adds a CodeProvenance to the graph and returns node
- codedValue(codeclass, uri, title, system, identifier)¶
Adds a CodedValue to the graph and returns node
- encounter(encounter)¶
Build an Encounter, but don’t link it to a patient graph
- lab_result(lab)¶
Build a Medication, but don’t add fills and don’t link it to the patient. Returns the med node.
- medication(m)¶
Build a Medication, but don’t add fills and don’t link it to the patient. Returns the med node.
- name(obj, prefix)¶
- newCodedValue(coded_value)¶
Adds a CodedValue to the graph and returns a node
- new_code(code, blank=False)¶
Adds a Code to the graph and returns node
- organization(obj, prefix)¶
- pharmacy(obj, prefix)¶
- provider(obj, prefix)¶
- quantitativeResult(obj, prefix)¶
Adds a QuantitativeResult node to a graph; returns the node
- telephone(obj, prefix)¶
- toRDF(format='xml')¶
- valueAndUnit(value, units)¶
Adds a ValueAndUnit node to a graph; returns the node
- valueAndUnitFromObj(obj, prefix)¶
- valueRange(obj, prefix)¶
Adds a ValueRange node to a graph; returns the node
- vital(obj, prefix)¶