Add SMART LabPanel

- fixes chb#44
jgkim · Dec 31, 2012 · 1e6b8eb · 1e6b8eb
1 parent 0288bba
commit 1e6b8eb
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diff --git a/indivo/data_models/core/lab_panel/example.sdmx b/indivo/data_models/core/lab_panel/example.sdmx
@@ -0,0 +1,41 @@
+<Models xmlns="http://indivo.org/vocab/xml/documents#">
+	<Model name="LabPanel">
+		<Field name="lab_results">
+			<Models>
+				<Model name="LabResult">
+					<Field name="date">2009-05-16T12:00:00Z</Field>
+
+					<Field name="abnormal_interpretation_code_title">Normal</Field>
+					<Field name="abnormal_interpretation_code_system">http://smartplatforms.org/terms/codes/LabResultInterpretation#</Field>
+					<Field name="abnormal_interpretation_code_identifier">normal</Field>
+
+					<Field name="accession_number">AC09205823577</Field>
+
+					<Field name="name_title">Serum Sodium</Field>
+					<Field name="name_code_title">Serum Sodium</Field>
+					<Field name="name_code_system">http://purl.bioontology.org/ontology/LNC/</Field>
+					<Field name="name_code_identifier">2951-2</Field>
+
+					<Field name="status_code_title">Final results: complete and verified</Field>
+					<Field name="status_code_system">http://smartplatforms.org/terms/codes/LabStatus#</Field>
+					<Field name="status_code_identifier">final</Field>
+
+					<Field name="notes">Blood sample appears to have hemolyzed</Field>
+
+					<Field name="quantitative_result_non_critical_range_max_value">155</Field>
+					<Field name="quantitative_result_non_critical_range_max_unit">mEq/L</Field>
+					<Field name="quantitative_result_non_critical_range_min_value">120</Field>
+					<Field name="quantitative_result_non_critical_range_min_unit">mEq/L</Field>
+
+					<Field name="quantitative_result_normal_range_max_value">145</Field>
+					<Field name="quantitative_result_normal_range_max_unit">mEq/L</Field>
+					<Field name="quantitative_result_normal_range_min_value">135</Field>
+					<Field name="quantitative_result_normal_range_min_unit">mEq/L</Field>
+
+					<Field name="quantitative_result_value_value">140</Field> 
+					<Field name="quantitative_result_value_unit">mEq/L</Field>
+				</Model>
+			</Models>
+		</Field>
+	</Model>
+</Models>
diff --git a/indivo/data_models/core/lab_panel/extra.py b/indivo/data_models/core/lab_panel/extra.py
@@ -0,0 +1,19 @@
+from indivo.serializers import DataModelSerializers
+from indivo.validators import ValueInSetValidator, ExactValueValidator, NonNullValidator
+from indivo.data_models.options import DataModelOptions
+from indivo.lib.rdf import PatientGraph
+
+LOINC_URI="http://purl.bioontology.org/ontology/LNC/"
+
+class LabPanelSerializers(DataModelSerializers):
+    def to_rdf(query, record=None, carenet=None):
+        if not record:
+            record = carenet.record
+        graph = PatientGraph(record)
+        resultOrder = graph.addLabPanelList(query.results.iterator(), True if query.limit else False)
+        graph.addResponseSummary(query, resultOrder)
+        return graph.toRDF()
+
+class LabPanelOptions(DataModelOptions):
+    model_class_name = 'LabPanel'
+    serializers = LabPanelSerializers
diff --git a/indivo/data_models/core/lab_panel/model.py b/indivo/data_models/core/lab_panel/model.py
@@ -0,0 +1,7 @@
+from indivo.models import Fact
+from django.db import models
+from indivo.fields import CodedValueField
+
+class LabPanel(Fact):
+    name = CodedValueField()
+
diff --git a/indivo/data_models/core/lab/example.py → ...vo/data_models/core/lab_result/example.py b/indivo/data_models/core/lab/example.py → ...vo/data_models/core/lab_result/example.py
diff --git a/indivo/data_models/core/lab/example.sdmj → .../data_models/core/lab_result/example.sdmj b/indivo/data_models/core/lab/example.sdmj → .../data_models/core/lab_result/example.sdmj
diff --git a/indivo/data_models/core/lab/example.sdmx → .../data_models/core/lab_result/example.sdmx b/indivo/data_models/core/lab/example.sdmx → .../data_models/core/lab_result/example.sdmx
diff --git a/indivo/data_models/core/lab/extra.py → indivo/data_models/core/lab_result/extra.py b/indivo/data_models/core/lab/extra.py → indivo/data_models/core/lab_result/extra.py
@@ -19,18 +19,18 @@
     'final',
 ]
 
-class LabSerializers(DataModelSerializers):
+class LabResultSerializers(DataModelSerializers):
     def to_rdf(query, record=None, carenet=None):
         if not record:
             record = carenet.record
         graph = PatientGraph(record)
-        resultOrder = graph.addLabList(query.results.iterator(), True if query.limit else False)
+        resultOrder = graph.addLabResultList(query.results.iterator(), True if query.limit else False)
         graph.addResponseSummary(query, resultOrder)
         return graph.toRDF()
 
-class LabOptions(DataModelOptions):
+class LabResultOptions(DataModelOptions):
     model_class_name = 'LabResult'
-    serializers = LabSerializers
+    serializers = LabResultSerializers
     field_validators = {
         'abnormal_interpretation_code_system': [ExactValueValidator(LAB_INTERP_URI, nullable=True)],
         'abnormal_interpretation_code_identifier': [ValueInSetValidator(VALID_INTERPS, nullable=True)],

diff --git a/indivo/data_models/core/lab/model.py → indivo/data_models/core/lab_result/model.py b/indivo/data_models/core/lab/model.py → indivo/data_models/core/lab_result/model.py
@@ -10,4 +10,5 @@ class LabResult(Fact):
     status = CodedValueField()
     narrative_result = models.CharField(max_length=255, null=True)
     notes = models.CharField(max_length=600, null=True)
-    quantitative_result = QuantitativeResultField()
+    quantitative_result = QuantitativeResultField()
+    lab_panel = models.ForeignKey('LabPanel', null=True, related_name='lab_results')
diff --git a/indivo/data_models/core/lab/model.sdml → ...vo/data_models/core/lab_result/model.sdml b/indivo/data_models/core/lab/model.sdml → ...vo/data_models/core/lab_result/model.sdml
diff --git a/indivo/lib/rdf.py b/indivo/lib/rdf.py
@@ -382,7 +382,35 @@ def addImmunizationList(self, immunizations, order_results=False):
 
         return immunization_list_node
 
-    def addLabList(self, labs, order_results=False):
+    def addLabPanelList(self, lab_panels, order_results=False):
+        """Adds Lab Panels to the patient's graph"""
+
+        g = self.g
+        panel_list_node = None
+
+        if order_results:
+            # build an ordered list if requested
+            panel_list_node = BNode()
+            panel_collection = Collection(g, panel_list_node, [])
+
+        for panel in lab_panels:
+            panel_node = URIRef(panel.uri('lab_panels'))
+            g.add((panel_node, RDF.type, SP['LabPanel']))
+            if order_results:
+                panel_collection.append(panel_node)
+
+            lab_name = self._getCodedValueFromField(panel, 'name', [SPCODE['LOINC']])
+            if lab_name:
+                g.add((panel_node , SP['labName'], self.newCodedValue(lab_name)))
+
+            for lab_result in panel.lab_results.all().iterator():
+                result_node = self.lab_result(lab_result)
+                g.add((panel_node, SP['labResult'], result_node))
+                self.addStatement(result_node)
+
+        return panel_list_node
+
+    def addLabResultList(self, labs, order_results=False):
         """Adds Lab Results to the patient's graph"""
         g = self.g
         lab_list_node = None
@@ -393,42 +421,11 @@ def addLabList(self, labs, order_results=False):
             lab_collection = Collection(g, lab_list_node, [])
 
         for lab in labs:
-            lNode = URIRef(lab.uri('lab_results'))
-            g.add((lNode, RDF.type, SP['LabResult']))
+            lNode = self.lab_result(lab)
+            self.addStatement(lNode)
             if order_results:
                 lab_collection.append(lNode)
 
-            lab_name = self._getCodedValueFromField(lab, 'name', [SPCODE['LOINC']])
-            g.add((lNode , SP['labName'], self.newCodedValue(lab_name)))
-
-            g.add((lNode, DCTERMS['date'], Literal(lab.date)))
-
-            abnormal_interpretation = self._getCodedValueFromField(lab, 'abnormal_interpretation', [SPCODE['LabResultInterpretation']])
-            if abnormal_interpretation:
-                g.add((lNode, SP['abnormalInterpretation'], self.newCodedValue(abnormal_interpretation)))
-
-            if lab.accession_number:
-                g.add((lNode, SP['accessionNumber'], Literal(lab.accession_number)))
-
-            lab_status = self._getCodedValueFromField(lab, 'status', [SPCODE['LabResultStatus']])
-            if lab_status:
-                g.add((lNode, SP['labStatus'], self.newCodedValue(lab_status)))
-
-            if lab.narrative_result:
-                nrNode = BNode()
-                g.add((nrNode, RDF.type, SP['NarrativeResult']))
-                g.add((nrNode, SP['value'], Literal(lab.narrative_result)))
-                g.add((lNode, SP['narrativeResult'], nrNode))
-
-            if lab.notes:
-                g.add((lNode, SP['notes'], Literal(lab.notes)))
-
-            qrNode = self.quantitativeResult(lab, 'quantitative_result')
-            if qrNode:
-                g.add((lNode, SP['quantitativeResult'], qrNode))
-
-            self.addStatement(lNode)
-
         return lab_list_node
 
     def addCombinedAllergyList(self, combinedAllergies, order_results=False):
@@ -644,6 +641,45 @@ def encounter(self, encounter):
             g.add((eNode, SP['encounterType'], self.newCodedValue(encounter_type)))
         return eNode
 
+    def lab_result(self, lab):
+        """ Build a Medication, but don't add fills and don't link it to the patient. Returns the med node. """
+        g = self.g
+        if not lab: return 
+
+        lNode = URIRef(lab.uri('lab_results'))
+        g.add((lNode, RDF.type, SP['LabResult']))
+
+        lab_name = self._getCodedValueFromField(lab, 'name', [SPCODE['LOINC']])
+        g.add((lNode , SP['labName'], self.newCodedValue(lab_name)))
+
+        g.add((lNode, DCTERMS['date'], Literal(lab.date)))
+
+        abnormal_interpretation = self._getCodedValueFromField(lab, 'abnormal_interpretation', [SPCODE['LabResultInterpretation']])
+        if abnormal_interpretation:
+            g.add((lNode, SP['abnormalInterpretation'], self.newCodedValue(abnormal_interpretation)))
+
+        if lab.accession_number:
+            g.add((lNode, SP['accessionNumber'], Literal(lab.accession_number)))
+
+        lab_status = self._getCodedValueFromField(lab, 'status', [SPCODE['LabResultStatus']])
+        if lab_status:
+            g.add((lNode, SP['labStatus'], self.newCodedValue(lab_status)))
+
+        if lab.narrative_result:
+            nrNode = BNode()
+            g.add((nrNode, RDF.type, SP['NarrativeResult']))
+            g.add((nrNode, SP['value'], Literal(lab.narrative_result)))
+            g.add((lNode, SP['narrativeResult'], nrNode))
+
+        if lab.notes:
+            g.add((lNode, SP['notes'], Literal(lab.notes)))
+
+        qrNode = self.quantitativeResult(lab, 'quantitative_result')
+        if qrNode:
+            g.add((lNode, SP['quantitativeResult'], qrNode))
+
+        return lNode
+
     def medication(self, m):
         """ Build a Medication, but don't add fills and don't link it to the patient. Returns the med node. """
         g = self.g

diff --git a/indivo/lib/view_decorators.py b/indivo/lib/view_decorators.py
@@ -58,6 +58,9 @@ def parse_date_group(value):
           field, time_incr = value.split('*')
           return {'field':field, 'time_incr':time_incr}
 
+      def parse_date(value):
+          return iso8601.parse_utc_date(value)
+
       check_safety()
 
       parse_map = {
@@ -69,8 +72,8 @@ def parse_date_group(value):
         'aggregate_by': parse_aggregate_by,  
         'date_range': parse_date_range,   
         'date_group': parse_date_group,
-        'date_from': parse_string,  # SMART v0.5, transformed to date_range in smart views
-        'date_to': parse_string,    # SMART v0.5, transformed to date_range in smart views
+        'date_from': parse_date,  # SMART v0.5, transformed to date_range in smart views
+        'date_to': parse_date,    # SMART v0.5, transformed to date_range in smart views
       }
 
       ignore_map = {