Merge pull request #53 from monarch-initiative/get_stage_info

Get stage info

pyproject.toml

@@ -41,7 +41,7 @@ dependencies = [
     "tqdm"
 ]
 [project.optional-dependencies]
-test = ["pytest"]
+test = ["pytest", "parameterized"]
 
 
 

src/oncoexporter/cda/cda_disease_factory.py

@@ -1,3 +1,5 @@
+from typing import List
+
 import phenopackets as PPkt
 import pandas as pd
 
@@ -61,13 +63,18 @@ def to_ga4gh(self, row):
         if not isinstance(row, pd.core.series.Series):
             raise ValueError(f"Invalid argument. Expected pandas series but got {type(row)}")
 
-        disease_term  = self._parse_diagnosis_into_ontology_term(
+        disease_term = self._parse_diagnosis_into_ontology_term(
             primary_diagnosis=row["primary_diagnosis"],
             primary_diagnosis_condition=row["primary_diagnosis_condition"],
             primary_diagnosis_site=row["primary_diagnosis_site"]
         )
-        ## Collect other piences of data to add to the constructor on the next line
-        diseaseModel = OpDisease(disease_term=disease_term)
+        ## Collect other pieces of data to add to the constructor on the next line
+
+        # Deal with stage
+        stage_term_list = self._parse_stage_into_ontology_terms(row['stage'])
+
+        diseaseModel = OpDisease(disease_term=disease_term,
+                                 disease_stage_term_list=stage_term_list)
         return diseaseModel.to_ga4gh()
 
     def _parse_diagnosis_into_ontology_term(self,
@@ -113,3 +120,40 @@ def _parse_diagnosis_into_ontology_term(self,
             ontology_term.id = 'NCIT:C9133'
             ontology_term.label = 'Lung Adenosquamous Carcinoma'
         return ontology_term
+
+    def _parse_stage_into_ontology_terms(self, stage_str: str) -> List[PPkt.OntologyClass]:
+        ontology_term = PPkt.OntologyClass()
+        ontology_term.id ='NCIT:C92207'  # Stage unknown
+        ontology_term.label = 'Stage Unknown'
+
+        if stage_str in ['Stage I', 'Stage 1', 'stage 1', 'stage I']:
+            ontology_term.id = 'NCIT:C27966'
+            ontology_term.label = 'Stage I'
+        elif stage_str in ['IA', 'Stage IA', 'stage IA']:
+            ontology_term.id = 'NCIT:C27975'
+            ontology_term.label = 'Stage IA'
+        elif stage_str in ['IB', 'Stage IB', 'stage IB']:
+            ontology_term.id = 'NCIT:C27976'
+            ontology_term.label = 'Stage IB'
+        elif stage_str in ['Stage II', 'Stage 2', 'stage 2', 'stage II']:
+            ontology_term.id = 'NCIT:C28054'
+            ontology_term.label = 'Stage II'
+        elif stage_str in ['IIA', 'Stage IIA', 'stage IIA']:
+            ontology_term.id = 'NCIT:C27967'
+            ontology_term.label = 'Stage IIA'
+        elif stage_str in ['IIB', 'Stage IIB', 'stage IIB']:
+            ontology_term.id = 'NCIT:C27968'
+            ontology_term.label = 'Stage IIB'
+        elif stage_str in ['Stage 3', 'stage 3']:
+            ontology_term.id = 'NCIT:C27970'
+            ontology_term.label = 'Stage III'
+        elif stage_str in ['IIIA', 'Stage IIIA', 'Stage 3A', 'stage 3A']:
+            ontology_term.id = 'NCIT:C27977'
+            ontology_term.label = 'Stage IIIA'
+        elif stage_str in ['IIIB', 'Stage IIIB', 'Stage 3B', 'stage 3B']:
+            ontology_term.id = 'NCIT:C27978'
+            ontology_term.label = 'Stage IIIB'
+        elif stage_str in ['IV', 'Stage 4']:
+            ontology_term.id = 'NCIT:C27971'
+            ontology_term.label = 'Stage IV'
+        return [ontology_term]

src/oncoexporter/model/op_disease.py

@@ -22,8 +22,7 @@ def __init__(self, disease_term:PPKt.OntologyClass,
                 excluded:bool=None,
                 iso8601duration_onset_age:str=None,
                 iso8601duration_resolution_age: str = None,
-                disease_stage_term_list:List[str]=None,
-                disease_stage_term_label:str=None,
+                disease_stage_term_list:List[PPKt.OntologyClass]=None,
                 clinical_tnm_finding_list:list=None,
                 primary_site_id:str=None,
                 primary_site_label: str = None,
@@ -42,13 +41,9 @@ def __init__(self, disease_term:PPKt.OntologyClass,
                 raise ValueError(f"If passed, argument \"disease_stage_term_list\" must be a list but was {type(disease_stage_term_list)}")
             if len(disease_stage_term_list) == 0:
                 raise ValueError(f"If passed, argument \"disease_stage_term_list\" cannot be an empty list")
-
-
+            for term in disease_stage_term_list:
+                disease_obj.disease_stage.append(term)
         self._disease = disease_obj
 
-
-
-
-
     def to_ga4gh(self):
         return self._disease