fix int method, more details in warning (#58)

src/clinical_etl/mappings.py

@@ -336,9 +336,9 @@ def integer(data_values):
     if cell is None or cell.lower() == "nan":
         return None
     try:
-        return int(cell)
+        return int(float(cell))
     except ValueError as e:
-        _warn(e)
+        _warn(e, data_values)
         return None
 
 
@@ -360,7 +360,7 @@ def floating(data_values):
     try:
         return float(cell)
     except ValueError as e:
-        _warn(e)
+        _warn(e, data_values)
         return None
 
 
@@ -445,13 +445,15 @@ def moh_indexed_on_donor_if_others_absent(data_values):
     }
 
 
-def _warn(message):
+def _warn(message, input_values=None):
     """Warns a user when a mapping is unsuccessful with the IDENTIFIER and FIELD."""
     global IDENTIFIER
-    if IDENTIFIER is not None:
-        print(f"WARNING for {IDENTIFIER_FIELD}={IDENTIFIER}: {message}")
+    if IDENTIFIER is not None and input_values is not None:
+        print(f"WARNING for {IDENTIFIER_FIELD}={IDENTIFIER}: {message}. Input data: {input_values}")
     else:
         print(f"WARNING: {message}")
+        if input_values is not None:
+            print(f"WARNING: {message}. Input data: {input_values}")
 
 
 def _push_to_stack(sheet, id, rownum):

tests/raw_data/PrimaryDiagnosis.csv

@@ -1,9 +1,9 @@
 submitter_donor_id, submitter_primary_diagnosis_id, date_of_diagnosis, cancer_type_code, basis_of_diagnosis, lymph_nodes_examined_status, lymph_nodes_examined_method, number_lymph_nodes_positive, clinical_tumour_staging_system, clinical_t_category, clinical_n_category, clinical_m_category, clinical_stage_group, laterality
-DONOR_1,PD_1,1_2018,C43.1,Cytology,No lymph nodes found in resected specimen,Lymph node dissection/pathological exam,5,International Neuroblastoma Staging System,,,,Stage 1,Left
+DONOR_1,PD_1,1_2018,C43.1,Cytology,No lymph nodes found in resected specimen,Lymph node dissection/pathological exam,5.0,International Neuroblastoma Staging System,,,,Stage 1,Left
 DONOR_2,PD_2,3/2020,C04.9,Specific tumour markers,Not applicable,Physical palpation of patient,4,Rai staging system,,,,Stage 1A,Bilateral
 DONOR_3,PD_3,5/2018,C43.9,Unknown,Yes,Imaging,5,AJCC 7th edition,T0,N0,M1a,,Left
 DONOR_3,DUPLICATE_ID,5/2018,C43.9,Unknown,Yes,Imaging,5,AJCC 7th edition,T0,N0,M1a,,Left
 DONOR_4,PD_4,1_2018,C64.9,Death certificate only,Not applicable,Physical palpation of patient,67,Revised International staging system (RISS),,,,Stage 1B,"Unilateral, side not specified"
-DONOR_5,PD_5,3/2020,C64.9,Death certificate only,Yes,Lymph node dissection/pathological exam,5,Revised International staging system (RISS),T1,N0a,M0,,Left
+DONOR_5,PD_5,3/2020,C64.9,Death certificate only,Yes,Lymph node dissection/pathological exam,5.0,Revised International staging system (RISS),T1,N0a,M0,,Left
 DONOR_6,PD_6,5/2018,C02.2,Specific tumour markers,No,Physical palpation of patient,2,International Neuroblastoma Staging System,,,,Stage C,"Unilateral, side not specified"
-DONOR_2,PD_2_1,6/3/2018,C43.9,Histology of a primary tumour,No lymph nodes found in resected specimen,Physical palpation of patient,1,Binet staging system,,,,Stage B,Bilateral
+DONOR_2,PD_2_1,6/3/2018,C43.9,Histology of a primary tumour,No lymph nodes found in resected specimen,Physical palpation of patient,1.0,Binet staging system,,,,Stage B,Bilateral