Use PatientNode for patients

MOZI-AI · Nov 27, 2020 · 1229a55 · 1229a55
1 parent be7458c
commit 1229a55
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/atomwrappers.py b/atomwrappers.py
@@ -151,6 +151,9 @@ class ChebiOntology(CNode):
 class NcbiTaxonomy(CNode):
     atom_type = 'NcbiTaxonomyNode'
 
+class CPatientNode(CNode):
+    atom_type = 'PatientNode'
+
 class Entrez(CNode):
     atom_type = 'EntrezNode'
 

diff --git a/cancer/patient_gene_expression.py b/cancer/patient_gene_expression.py
@@ -59,7 +59,7 @@ def import_gene_expr(patient_df, overexpr_fp, underexpr_fp):
         mean_dict[str(col)] = df[col].median()
 
     for i in range(df.shape[0]):
-        patient = CConceptNode(str(int(df.iloc[i]["patient_ID"])))
+        patient = CPatientNode(str(int(df.iloc[i]["patient_ID"])))
         for k in mean_dict:
             create_member_ln(k, overexpr_fp)
             create_member_ln(k, underexpr_fp)

diff --git a/cancer/patient_outcome.py b/cancer/patient_outcome.py
@@ -66,7 +66,6 @@ def create_treatment_ln(patient, treatment, value, drugs_df, fp):
     """
     if not pd.isna(value) and value != 0:
         if treatment == "surgery_type":
-            eval_ln = CEvaluationLink(CPredicateNode("surgery"), CListLink(patient, CConceptNode(treatment)), stv=CStv(1.0, 1.0))
             surgery_type_ln = CEvaluationLink(CPredicateNode("surgery_type"), CListLink(patient, CConceptNode(value)), stv=CStv(1.0, 1.0))
             fp.write(surgery_type_ln.recursive_print() + "\n")
         else:
@@ -103,7 +102,7 @@ def import_info(df, drugs_df, fp):
     treatment_cols.append('surgery_type')
 
     for i in range(df.shape[0]):
-        patient = CConceptNode(str(df.iloc[i]["patient_ID"]))
+        patient = CPatientNode(str(df.iloc[i]["patient_ID"]))
         for marker in bool_vals:
             create_state_ln(patient, marker, df.iloc[i][marker], fp)