inital changes for SMART v0.5

- Update CodedValue - Move Procedure to SMART data model, fixes chb#24 - Update LabResult, fixes chb#28 - Update Vital Signs, fixes chb#29 - Update Allergy, fixes chb#30 -
jgkim · Dec 31, 2012 · 0817432 · 0817432
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diff --git a/indivo/data_models/core/allergy/example.py b/indivo/data_models/core/allergy/example.py
@@ -1,22 +1,23 @@
 from indivo.models import Allergy
 
 allergy_fact = Allergy(
-    allergic_reaction_title="Anaphylaxis",
-    allergic_reaction_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
-    allergic_reaction_identifier="39579001",
-    category_title="Drug allergy",
-    category_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
-    category_identifier="416098002",
-    drug_class_allergen_title="Sulfonamide Antibacterial",
-    drug_class_allergen_system="http://purl.bioontology.org/ontology/NDFRT/",
-    drug_class_allergen_identifier="N0000175503",
-    severity_title="Severe",
-    severity_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
-    severity_identifier="24484000",
+    allergic_reaction_code_title="Anaphylaxis",
+    allergic_reaction_code_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
+    allergic_reaction_code_identifier="39579001",
+    category_code_title="Drug allergy",
+    category_code_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
+    category_code_identifier="416098002",
+    drug_class_allergen_code_title="Sulfonamide Antibacterial",
+    drug_class_allergen_code_system="http://purl.bioontology.org/ontology/NDFRT/",
+    drug_class_allergen_code_identifier="N0000175503",
+    severity_code_title="Severe",
+    severity_code_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
+    severity_code_identifier="24484000",
     )
 
 allergy_exclusion = AllergyExclusion(
     name_title="No known allergies",
-    name_identifier="160244002",
-    name_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
+    name_code_title="No known allergies",
+    name_code_identifier="160244002",
+    name_code_system="http://purl.bioontology.org/ontology/SNOMEDCT/",
 )
diff --git a/indivo/data_models/core/allergy/example.sdmj b/indivo/data_models/core/allergy/example.sdmj
@@ -1,21 +1,22 @@
 [{
     "__modelname__": "Allergy",
-    "allergic_reaction_title": "Anaphylaxis",
-    "allergic_reaction_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
-    "allergic_reaction_identifier": "39579001",
-    "category_title": "Drug allergy",
-    "category_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
-    "category_identifier": "416098002",
-    "drug_class_allergen_title": "Sulfonamide Antibacterial",
-    "drug_class_allergen_system": "http://purl.bioontology.org/ontology/NDFRT/",
-    "drug_class_allergen_identifier": "N0000175503",
-    "severity_title": "Severe",
-    "severity_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
-    "severity_identifier": "24484000"
+    "allergic_reaction_code_title": "Anaphylaxis",
+    "allergic_reaction_code_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
+    "allergic_reaction_code_identifier": "39579001",
+    "category_code_title": "Drug allergy",
+    "category_code_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
+    "category_code_identifier": "416098002",
+    "drug_class_allergen_code_title": "Sulfonamide Antibacterial",
+    "drug_class_allergen_code_system": "http://purl.bioontology.org/ontology/NDFRT/",
+    "drug_class_allergen_code_identifier": "N0000175503",
+    "severity_code_title": "Severe",
+    "severity_code_system": "http://purl.bioontology.org/ontology/SNOMEDCT/",
+    "severity_code_identifier": "24484000"
 },
 {
     "__modelname__": "AllergyExclusion",
     "name_title": "No known allergies",
-    "name_identifier":"160244002",
-    "name_system": "http://purl.bioontology.org/ontology/SNOMEDCT"
+    "name_code_title": "No known allergies",
+    "name_code_identifier":"160244002",
+    "name_code_system": "http://purl.bioontology.org/ontology/SNOMEDCT"
 }]
diff --git a/indivo/data_models/core/allergy/example.sdmx b/indivo/data_models/core/allergy/example.sdmx
@@ -1,21 +1,22 @@
-<Models>
+<Models xmlns="http://indivo.org/vocab/xml/documents#">
   <Model name="Allergy">
-    <Field name="allergic_reaction_title">Anaphylaxis</Field>
-    <Field name="allergic_reaction_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
-    <Field name="allergic_reaction_identifier">39579001</Field>
-    <Field name="category_title">Drug allergy</Field>
-    <Field name="category_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
-    <Field name="category_identifier">416098002</Field>
-    <Field name="drug_class_allergen_title">Sulfonamide Antibacterial</Field>
-    <Field name="drug_class_allergen_system">http://purl.bioontology.org/ontology/NDFRT/</Field>
-    <Field name="drug_class_allergen_identifier">N0000175503</Field>
-    <Field name="severity_title">Severe</Field>
-    <Field name="severity_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
-    <Field name="severity_identifier">24484000</Field>
+    <Field name="allergic_reaction_code_title">Anaphylaxis</Field>
+    <Field name="allergic_reaction_code_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
+    <Field name="allergic_reaction_code_identifier">39579001</Field>
+    <Field name="category_code_title">Drug allergy</Field>
+    <Field name="category_code_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
+    <Field name="category_code_identifier">416098002</Field>
+    <Field name="drug_class_allergen_code_title">Sulfonamide Antibacterial</Field>
+    <Field name="drug_class_allergen_code_system">http://purl.bioontology.org/ontology/NDFRT/</Field>
+    <Field name="drug_class_allergen_code_identifier">N0000175503</Field>
+    <Field name="severity_code_title">Severe</Field>
+    <Field name="severity_code_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
+    <Field name="severity_code_identifier">24484000</Field>
   </Model>
   <Model name="AllergyExclusion">
-    <Field name="name_title">No known allergies</Field>
-    <Field name="name_identifier">160244002</Field>
-    <Field name = "name_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
+  	<Field name="name_title">No known allergies</Field>
+    <Field name="name_code_title">No known allergies</Field>
+    <Field name="name_code_identifier">160244002</Field>
+    <Field name = "name_code_system">http://purl.bioontology.org/ontology/SNOMEDCT/</Field>
   </Model>
 </Models>
diff --git a/indivo/data_models/core/allergy/extra.py b/indivo/data_models/core/allergy/extra.py
@@ -44,18 +44,18 @@ class AllergyOptions(DataModelOptions):
     model_class_name = 'Allergy'
     serializers = AllergySerializers
     field_validators = {
-        'allergic_reaction_system': [ExactValueValidator(SNOMED)],
-        'allergic_reaction_identifier': [NonNullValidator()],
-        'allergic_reaction_title': [NonNullValidator()],
-        'category_system': [ExactValueValidator(SNOMED)],
-        'category_identifier': [ValueInSetValidator(VALID_CATEGORY_IDS)],
-        'category_title': [NonNullValidator()],
-        'drug_allergen_system': [ExactValueValidator(RXNORM, nullable=True)],
-        'drug_class_allergen_system': [ExactValueValidator(NUI, nullable=True)],
-        'food_allergen_system': [ExactValueValidator(UNII, nullable=True)],
-        'severity_system': [ExactValueValidator(SNOMED)],
-        'severity_identifier': [ValueInSetValidator(VALID_SEVERITY_IDS)],
-        'severity_title': [NonNullValidator()],
+        'allergic_reaction_code_system': [ExactValueValidator(SNOMED)],
+        'allergic_reaction_code_identifier': [NonNullValidator()],
+        'allergic_reaction_code_title': [NonNullValidator()],
+        'category_code_system': [ExactValueValidator(SNOMED)],
+        'category_code_identifier': [ValueInSetValidator(VALID_CATEGORY_IDS)],
+        'category_code_title': [NonNullValidator()],
+        'drug_allergen_code_system': [ExactValueValidator(RXNORM, nullable=True)],
+        'drug_class_allergen_code_system': [ExactValueValidator(NUI, nullable=True)],
+        'other_allergen_code_system': [ExactValueValidator(UNII, nullable=True)],
+        'severity_code_system': [ExactValueValidator(SNOMED)],
+        'severity_code_identifier': [ValueInSetValidator(VALID_SEVERITY_IDS)],
+        'severity_code_title': [NonNullValidator()],
         }
 
 class AllergyExclusionSerializers(DataModelSerializers):
@@ -71,7 +71,7 @@ class AllergyExclusionOptions(DataModelOptions):
     model_class_name = 'AllergyExclusion'
     serializers = AllergyExclusionSerializers
     field_validators = {
-        'name_system': [ExactValueValidator(SNOMED)],
-        'name_identifier': [ValueInSetValidator(VALID_EXCLUSION_IDS)],
-        'name_title': [NonNullValidator()],
+        'name_code_system': [ExactValueValidator(SNOMED)],
+        'name_code_identifier': [ValueInSetValidator(VALID_EXCLUSION_IDS)],
+        'name_code_title': [NonNullValidator()],
         }
diff --git a/indivo/data_models/core/allergy/model.py b/indivo/data_models/core/allergy/model.py
@@ -6,7 +6,7 @@ class Allergy(Fact):
     category = CodedValueField()
     drug_allergen = CodedValueField()
     drug_class_allergen = CodedValueField()
-    food_allergen = CodedValueField()
+    other_allergen = CodedValueField()
     severity = CodedValueField()
 
 class AllergyExclusion(Fact):

diff --git a/indivo/data_models/core/equipment/example.sdmx b/indivo/data_models/core/equipment/example.sdmx
@@ -1,4 +1,4 @@
-<Models>
+<Models xmlns="http://indivo.org/vocab/xml/documents#">
   <Model name="Equipment">
     <Field name="date_started">2009-02-05</Field>
     <Field name="date_stopped">2009-06-12</Field>

diff --git a/indivo/data_models/core/immunization/example.py b/indivo/data_models/core/immunization/example.py
@@ -3,17 +3,17 @@
 
 immunization_fact = Immunization(
     date=date("2009-05-16T12:00:00Z"),
-    administration_status_title="Not Administered",
-    administration_status_system="http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#",
-    administration_status_identifier="notAdministered", 
-    product_class_title="TYPHOID",
-    product_class_system="http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#",
-    product_class_identifier="TYPHOID",
-    product_name_title="typhoid, oral",
-    product_name_system="http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#",
-    product_name_identifier="25",
-    refusal_reason_title="Allergy to vaccine/vaccine components, or allergy to eggs",
-    refusal_reason_system="http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#",
-    refusal_reason_identifier="allergy",
+    administration_status_code_title="Not Administered",
+    administration_status_code_system="http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#",
+    administration_status_code_identifier="notAdministered", 
+    product_class_code_title="TYPHOID",
+    product_class_code_system="http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#",
+    product_class_code_identifier="TYPHOID",
+    product_name_code_title="typhoid, oral",
+    product_name_code_system="http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#",
+    product_name_code_identifier="25",
+    refusal_reason_code_title="Allergy to vaccine/vaccine components, or allergy to eggs",
+    refusal_reason_code_system="http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#",
+    refusal_reason_code_identifier="allergy",
   )
 
diff --git a/indivo/data_models/core/immunization/example.sdmj b/indivo/data_models/core/immunization/example.sdmj
@@ -1,17 +1,17 @@
 {
     "__modelname__": "Immunization",
     "date": "2009-05-16T12:00:00Z",
-    "administration_status_title": "Not Administered",
-    "administration_status_system": "http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#",
-    "administration_status_identifier": "notAdministered", 
-    "product_class_title": "TYPHOID",
-    "product_class_system": "http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#",
-    "product_class_identifier": "TYPHOID",
-    "product_name_title": "typhoid, oral",
-    "product_name_system": "http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#",
-    "product_name_identifier": "25",
-    "refusal_reason_title": "Allergy to vaccine/vaccine components, or allergy to eggs",
-    "refusal_reason_system": "http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#",
-    "refusal_reason_identifier": "allergy"
+    "administration_status_code_title": "Not Administered",
+    "administration_status_code_system": "http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#",
+    "administration_status_code_identifier": "notAdministered", 
+    "product_class_code_title": "TYPHOID",
+    "product_class_code_system": "http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#",
+    "product_class_code_identifier": "TYPHOID",
+    "product_name_code_title": "typhoid, oral",
+    "product_name_code_system": "http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#",
+    "product_name_code_identifier": "25",
+    "refusal_reason_code_title": "Allergy to vaccine/vaccine components, or allergy to eggs",
+    "refusal_reason_code_system": "http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#",
+    "refusal_reason_code_identifier": "allergy"
 }
 
diff --git a/indivo/data_models/core/immunization/example.sdmx b/indivo/data_models/core/immunization/example.sdmx
@@ -1,18 +1,18 @@
-<Models>
+<Models xmlns="http://indivo.org/vocab/xml/documents#">
   <Model name="Immunization">
     <Field name="date">2009-05-16T12:00:00Z</Field>
-    <Field name="administration_status_title">Not Administered</Field>
-    <Field name="administration_status_system">http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#</Field>
-    <Field name="administration_status_identifier">notAdministered</Field> 
-    <Field name="product_class_title">TYPHOID</Field>
-    <Field name="product_class_system">http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#</Field>
-    <Field name="product_class_identifier">TYPHOID</Field>
-    <Field name="product_name_title">typhoid, oral</Field>
-    <Field name="product_name_system">http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#</Field>
-    <Field name="product_name_identifier">25</Field>
-    <Field name="refusal_reason_title">Allergy to vaccine/vaccine components, or allergy to eggs</Field>
-    <Field name="refusal_reason_system">http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#</Field>
-    <Field name="refusal_reason_identifier">allergy</Field>
+    <Field name="administration_status_code_title">Not Administered</Field>
+    <Field name="administration_status_code_system">http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#</Field>
+    <Field name="administration_status_code_identifier">notAdministered</Field> 
+    <Field name="product_class_code_title">TYPHOID</Field>
+    <Field name="product_class_code_system">http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=vg#</Field>
+    <Field name="product_class_code_identifier">TYPHOID</Field>
+    <Field name="product_name_code_title">typhoid, oral</Field>
+    <Field name="product_name_code_system">http://www2a.cdc.gov/nip/IIS/IISStandards/vaccines.asp?rpt=cvx#</Field>
+    <Field name="product_name_code_identifier">25</Field>
+    <Field name="refusal_reason_code_title">Allergy to vaccine/vaccine components, or allergy to eggs</Field>
+    <Field name="refusal_reason_code_system">http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#</Field>
+    <Field name="refusal_reason_code_identifier">allergy</Field>
   </Model>
 </Models>
 
diff --git a/indivo/data_models/core/immunization/extra.py b/indivo/data_models/core/immunization/extra.py
@@ -44,14 +44,14 @@ class ImmunizationOptions(DataModelOptions):
     serializers = ImmunizationSerializers
     field_validators = {
         'date': [NonNullValidator()],
-        'administration_status_system': [ExactValueValidator(IMM_STATUS_URI)],
-        'administration_status_identifier': [ValueInSetValidator(VALID_IMM_STATUSES)],
-        'administration_status_title': [NonNullValidator()],
-        'product_class_system': [ExactValueValidator(IMM_CLASS_URI, nullable=True)],
-        'product_class_2_system': [ExactValueValidator(IMM_CLASS_URI, nullable=True)],
-        'product_name_system': [ExactValueValidator(IMM_PROD_URI)],
-        'product_name_identifier': [NonNullValidator()],
-        'product_name_title': [NonNullValidator()],
-        'refusal_reason_system': [ExactValueValidator(IMM_REFUSE_URI, nullable=True)],
-        'refusal_reason_identifier': [ValueInSetValidator(VALID_REFUSALS, nullable=True)],
+        'administration_status_code_system': [ExactValueValidator(IMM_STATUS_URI)],
+        'administration_status_code_identifier': [ValueInSetValidator(VALID_IMM_STATUSES)],
+        'administration_status_code_title': [NonNullValidator()],
+        'product_class_code_system': [ExactValueValidator(IMM_CLASS_URI, nullable=True)],
+        'product_class_2_code_system': [ExactValueValidator(IMM_CLASS_URI, nullable=True)],
+        'product_name_code_system': [ExactValueValidator(IMM_PROD_URI)],
+        'product_name_code_identifier': [NonNullValidator()],
+        'product_name_code_title': [NonNullValidator()],
+        'refusal_reason_code_system': [ExactValueValidator(IMM_REFUSE_URI, nullable=True)],
+        'refusal_reason_code_identifier': [ValueInSetValidator(VALID_REFUSALS, nullable=True)],
         }
diff --git a/indivo/data_models/core/lab/example.py b/indivo/data_models/core/lab/example.py
@@ -2,19 +2,21 @@
 from indivo.lib.iso8601 import parse_utc_date as date
 
 lab_fact = LabResult(
-    abnormal_interpretation_title="Normal",
-    abnormal_interpretation_system="http://smartplatforms.org/terms/codes/LabResultInterpretation#",
-    abnormal_interpretation_identifier="normal",
+    date=date("2009-05-16T12:00:00Z"),
+
+    abnormal_interpretation_code_title="Normal",
+    abnormal_interpretation_code_system="http://smartplatforms.org/terms/codes/LabResultInterpretation#",
+    abnormal_interpretation_code_identifier="normal",
 
     accession_number="AC09205823577",
 
-    test_name_title="Serum Sodium",
-    test_name_system="http://purl.bioontology.org/ontology/LNC/",
-    test_name_identifier="2951-2",
+    name_code_title="Serum Sodium",
+    name_code_system="http://purl.bioontology.org/ontology/LNC/",
+    name_code_identifier="2951-2",
 
-    status_title="Final results: complete and verified",
-    status_system="http://smartplatforms.org/terms/codes/LabStatus#",
-    status_identifier="final",
+    status_code_title="Final results: complete and verified",
+    status_code_system="http://smartplatforms.org/terms/codes/LabStatus#",
+    status_code_identifier="final",
 
     notes="Blood sample appears to have hemolyzed",
 
@@ -29,20 +31,6 @@
     quantitative_result_normal_range_min_unit="mEq/L",
 
     quantitative_result_value_value="140", 
-    quantitative_result_value_unit="mEq/L",
-
-    collected_at=date("2010-12-27T17:00:00Z"), 
-
-    collected_by_org_name="City Lab",
-    collected_by_org_adr_country="USA",
-    collected_by_org_adr_city="Springfield",
-    collected_by_org_adr_postalcode="11111",
-    collected_by_org_adr_region="MA",
-    collected_by_org_adr_street="20 Elm St",
-
-    collected_by_name_family="Finnialispi",
-    collected_by_name_given="Tad",
-
-    collected_by_role="Lab Specialist",
+    quantitative_result_value_unit="mEq/L"
     )
 
diff --git a/indivo/data_models/core/lab/example.sdmj b/indivo/data_models/core/lab/example.sdmj
@@ -1,18 +1,20 @@
 {
     "__modelname__": "LabResult",
+    "date": "2009-05-16T12:00:00Z",
+
     "abnormal_interpretation_title": "Normal",
     "abnormal_interpretation_system": "http"://smartplatforms.org/terms/codes/LabResultInterpretation#",
     "abnormal_interpretation_identifier": "normal",
 
     "accession_number": "AC09205823577",
 
-    "test_name_title": "Serum Sodium",
-    "test_name_system": "http"://purl.bioontology.org/ontology/LNC/",
-    "test_name_identifier": "2951-2",
+    "name_code_title": "Serum Sodium",
+    "name_code_system": "http"://purl.bioontology.org/ontology/LNC/",
+    "name_code_identifier": "2951-2",
 
-    "status_title": "Final results": complete and verified",
-    "status_system": "http"://smartplatforms.org/terms/codes/LabStatus#",
-    "status_identifier": "final",
+    "status_code_title": "Final results": complete and verified",
+    "status_code_system": "http"://smartplatforms.org/terms/codes/LabStatus#",
+    "status_code_identifier": "final",
 
     "notes": "Blood sample appears to have hemolyzed",
 
@@ -27,20 +29,6 @@
     "quantitative_result_normal_range_min_unit": "mEq/L",
 
     "quantitative_result_value_value": "140", 
-    "quantitative_result_value_unit": "mEq/L",
-
-    "collected_at": "2010-12-27T17":00":00Z", 
-
-    "collected_by_org_name": "City Lab",
-    "collected_by_org_adr_country": "USA",
-    "collected_by_org_adr_city": "Springfield",
-    "collected_by_org_adr_postalcode": "11111",
-    "collected_by_org_adr_region": "MA",
-    "collected_by_org_adr_street": "20 Elm St",
-
-    "collected_by_name_family": "Finnialispi",
-    "collected_by_name_given": "Tad",
-
-    "collected_by_role": "Lab Specialist"
+    "quantitative_result_value_unit": "mEq/L"
 }