From d92b14ef4e09330ced27eec9fd57a3fadb0f7102 Mon Sep 17 00:00:00 2001
From: caufieldjh <j.harry.caufield@gmail.com>
Date: Fri, 13 Dec 2024 14:51:50 -0500
Subject: [PATCH] Tweaks to RadiationTherapy

---
 src/ontogpt/templates/phenopackets.py   |  8 ++++----
 src/ontogpt/templates/phenopackets.yaml | 18 ++++++++++--------
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/ontogpt/templates/phenopackets.py b/src/ontogpt/templates/phenopackets.py
index fa24d53a0..364858557 100644
--- a/src/ontogpt/templates/phenopackets.py
+++ b/src/ontogpt/templates/phenopackets.py
@@ -1944,16 +1944,16 @@ class RadiationTherapy(ConfiguredBaseModel):
     """
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/phenopackets'})
 
-    bodySite: OntologyClass = Field(..., description="""The anatomical site where radiation therapy was administered. REQUIRED. ARGO mapping radiation::anatomical_site_irradiated""", json_schema_extra = { "linkml_meta": {'alias': 'bodySite',
+    bodySite: str = Field(..., description="""The anatomical site where radiation therapy was administered. REQUIRED. ARGO mapping radiation::anatomical_site_irradiated""", json_schema_extra = { "linkml_meta": {'alias': 'bodySite',
          'domain_of': ['RadiationTherapy'],
          'exact_mappings': ['ARGO:radiation.anatomical_site_irradiated']} })
-    dosage: int = Field(..., description="""The total dose given in units of Gray (Gy). REQUIRED. ARGO mapping radiation::radiation_therapy_dosage""", json_schema_extra = { "linkml_meta": {'alias': 'dosage',
+    dosage: Optional[str] = Field(None, description="""The total dose given in units of Gray (Gy). REQUIRED. ARGO mapping radiation::radiation_therapy_dosage""", json_schema_extra = { "linkml_meta": {'alias': 'dosage',
          'domain_of': ['RadiationTherapy'],
          'exact_mappings': ['ARGO:radiation.radiation_therapy_dosage']} })
-    fractions: int = Field(..., description="""The total number of fractions delivered as part of treatment. REQUIRED. ARGO mapping radiation::radiation_therapy_fractions""", json_schema_extra = { "linkml_meta": {'alias': 'fractions',
+    fractions: Optional[str] = Field(None, description="""The total number of fractions delivered as part of treatment. REQUIRED. ARGO mapping radiation::radiation_therapy_fractions""", json_schema_extra = { "linkml_meta": {'alias': 'fractions',
          'domain_of': ['RadiationTherapy'],
          'exact_mappings': ['ARGO:radiation.radiation_therapy_fractions']} })
-    modality: OntologyClass = Field(..., description="""The modality of radiation therapy (e.g., electron, photon,…). REQUIRED. ARGO mapping radiation::radiation_therapy_modality""", json_schema_extra = { "linkml_meta": {'alias': 'modality',
+    modality: Optional[str] = Field(None, description="""The modality of radiation therapy (e.g., electron, photon,…). REQUIRED. ARGO mapping radiation::radiation_therapy_modality""", json_schema_extra = { "linkml_meta": {'alias': 'modality',
          'domain_of': ['RadiationTherapy'],
          'exact_mappings': ['ARGO:radiation.radiation_therapy_modality']} })
 
diff --git a/src/ontogpt/templates/phenopackets.yaml b/src/ontogpt/templates/phenopackets.yaml
index 3e716c107..43592e2a2 100644
--- a/src/ontogpt/templates/phenopackets.yaml
+++ b/src/ontogpt/templates/phenopackets.yaml
@@ -1767,8 +1767,7 @@ classes:
           REQUIRED. ARGO mapping radiation::anatomical_site_irradiated
         exact_mappings:
           - ARGO:radiation.anatomical_site_irradiated
-        inlined: true
-        range: OntologyClass
+        range: AnatomyClass
         required: true
       dosage:
         description: >-
@@ -1776,16 +1775,18 @@ classes:
           REQUIRED. ARGO mapping radiation::radiation_therapy_dosage
         exact_mappings:
           - ARGO:radiation.radiation_therapy_dosage
-        range: integer
-        required: true
+        # range: integer
+        range: string
+        # required: true
       fractions:
         description: >-
           The total number of fractions delivered as part of treatment.
           REQUIRED. ARGO mapping radiation::radiation_therapy_fractions
         exact_mappings:
           - ARGO:radiation.radiation_therapy_fractions
-        range: integer
-        required: true
+        # range: integer
+        range: string
+        # required: true
       modality:
         description: >-
           The modality of radiation therapy (e.g., electron, photon,…).
@@ -1793,8 +1794,9 @@ classes:
         exact_mappings:
           - ARGO:radiation.radiation_therapy_modality
         inlined: true
-        range: OntologyClass
-        required: true
+        # range: OntologyClass
+        range: string
+        # required: true
 
   TherapeuticRegimen:
     description: ARGO mapping radiation::radiation_therapy_type (missing)