Switch to SMART clinical note

- fixes chb#42

indivo/accesscontrol/__init__.py

@@ -257,7 +257,6 @@ def carenet_doc_access(principal, carenet, **unused_args):
   views = [carenet_measurement_list,
            carenet_procedure_list,
            carenet_equipment_list,
-           carenet_simple_clinical_notes_list,
            carenet_generic_list,
            carenet_document_list,
            carenet_document,
@@ -283,7 +282,6 @@ def record_doc_access(principal, record, **unused_args):
            smart_generic_instance,
            equipment_list,
            generic_list,
-           simple_clinical_notes_list,
            report_ccr,
            record_document_list,
            record_document_meta,

indivo/data_models/core/clinical_note/example.py

@@ -0,0 +1,10 @@
+from indivo.models import ClinicalNote
+
+social_history_fact = ClinicalNote(
+    date="2012-05-17",
+    title="Telephone note",
+    format="http://purl.org/NET/mediatypes/text/plain",
+    value="Patient's mother telephoned to say that he no longer needs documentation of a sports physical for school",
+    provider_name_given="Josuha",
+    provider_name_family="Mandel",
+    )

indivo/data_models/core/clinical_note/example.sdmj

@@ -0,0 +1,9 @@
+{
+    "__modelname__": "ClinicalNote",
+    "date": "2012-05-17",
+    "title": "Telephone note",
+    "format": "http://purl.org/NET/mediatypes/text/plain",
+    "value": "Patient's mother telephoned to say that he no longer needs documentation of a sports physical for school",
+    "provider_name_given": "Josuha",
+    "provider_name_family": "Mandel",
+}

indivo/data_models/core/clinical_note/example.sdmx

@@ -0,0 +1,10 @@
+<Models xmlns="http://indivo.org/vocab/xml/documents#">
+  <Model name="ClinicalNote">
+    <Field name="date">2012-05-17</Field>
+    <Field name="title">Telephone note</Field>
+    <Field name="format">http://purl.org/NET/mediatypes/text/plain</Field>
+    <Field name="value">Patient's mother telephoned to say that he no longer needs documentation of a sports physical for school</Field>
+    <Field name="provider_name_given">Josuha</Field>
+    <Field name="provider_name_family">Mandel</Field>
+  </Model>
+</Models>

indivo/data_models/core/clinical_note/extra.py

@@ -0,0 +1,23 @@
+from indivo.serializers import DataModelSerializers
+from indivo.data_models.options import DataModelOptions
+from indivo.lib.rdf import PatientGraph
+from indivo.validators import ValueInSetValidator, ExactValueValidator, NonNullValidator
+
+SNOMED_URI = 'http://purl.bioontology.org/ontology/SNOMEDCT/'
+
+class ClinicalNoteSerializers(DataModelSerializers):
+
+    def to_rdf(queryset, result_count, record=None, carenet=None):
+        if not record:
+            record = carenet.record
+
+        graph = PatientGraph(record)
+        graph.addClinicalNoteList(queryset.iterator())
+        return graph.toRDF()        
+
+class ClinicalNoteOptions(DataModelOptions):
+    model_class_name = 'ClinicalNote'
+    serializers = ClinicalNoteSerializers
+    field_validators = {
+        'format': [NonNullValidator()],
+        }

indivo/data_models/core/clinical_note/model.py

@@ -0,0 +1,10 @@
+from indivo.models import Fact
+from indivo.fields import ProviderField
+from django.db import models
+
+class ClinicalNote(Fact):
+    date = models.DateTimeField()
+    title = models.CharField(max_length=255, null=True)
+    format = models.CharField(max_length=255, null=True)
+    value = models.CharField(max_length=255, null=True)
+    provider = ProviderField()

indivo/lib/rdf.py

@@ -388,15 +388,45 @@ def addSocialHistoryList(self, histories):
         g = self.g
 
         for history in histories:
-            pnode = URIRef(history.uri())
-            g.add((pnode, RDF.type, SP['SocialHistory']))
+            hnode = URIRef(history.uri())
+            g.add((hnode, RDF.type, SP['SocialHistory']))
 
             # optional
             smoking_status = self._getCodedValueFromField(history, 'smoking_status', [SPCODE['SmokingStatus']])
             if smoking_status:    
-                g.add((pnode, SP['smokingStatus'], self.newCodedValue(smoking_status)))
+                g.add((hnode, SP['smokingStatus'], self.newCodedValue(smoking_status)))
 
-            self.addStatement(pnode)
+            self.addStatement(hnode)
+
+    def addClinicalNoteList(self, notes):
+        """Add clinical notes to a patient's graph"""
+
+        g = self.g
+
+        for note in notes:
+            nnode = URIRef(note.uri())
+            g.add((nnode, RDF.type, SP['ClinicalNote']))
+
+            # required
+            document_with_format = BNode();
+            g.add((document_with_format, RDF.type, SP['DocumentWithFormat']))
+            g.add((document_with_format, DCTERMS['format'], Literal(note.format)))
+            if note.value:
+                g.add((document_with_format, DCTERMS['value'], Literal(note.value)))
+
+            g.add((nnode, DCTERMS['hasFormat'], document_with_format))
+
+            # optional
+            if note.date:
+                g.add((nnode, DCTERMS['date'], Literal(note.date)))
+            if note.title:
+                g.add((nnode, DCTERMS['title'], Literal(note.title))) 
+
+            note_provider = self.provider(note, 'provider')
+            if note_provider:
+                g.add((nnode, SP['provider'], note_provider))
+
+            self.addStatement(nnode)
 
     #####################################################
     ### Helper Methods for reusable low-level objects ###