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Develop issue97: bug fix #98

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Develop issue97: bug fix #98

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8715ddd
Verify the content of patient gender before import into files.
xiaoliz0 Jan 13, 2026
66cef77
Codes optimization.
xiaoliz0 Jan 13, 2026
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22 changes: 11 additions & 11 deletions Script/PRONTO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,7 +333,9 @@ def get_patient_info_from_MTF_2023(ipd_material_file,ipd_no,DNA_sampleID,RNA_sam
except:
ipd_birth_year = "-"
if(sheet_material.cell_value(r,c) == columns['gender'] and ipd_gender == ""):
ipd_gender = str(sheet_material.cell_value(r+2,c))
gender = str(sheet_material.cell_value(r+2,c))
if(gender != "" and gender != "X"):
ipd_gender = gender[0]
Comment on lines +336 to +338
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@marrip marrip Feb 6, 2026

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what exactly is happening here, we check if the column is Gender and then we extract the value from 2 rows down. We check if the value is not empty string and not Xand only then we assign it to ipd_gender. But I don't get why gender at index 0 (is gender a list?). Also it seems that ipd_gender is already empty string why check if gender is empty string if this would actually not change anything?

if(sheet_material.cell_value(r,c) == columns['age']):
ipd_age = str(sheet_material.cell_value(r+2,c))
if(sheet_material.cell_value(r,c) == columns['consent'] and ipd_consent == ""):
Expand Down Expand Up @@ -465,7 +467,9 @@ def get_patient_info_from_MTF_new(ipd_material_file,ipd_no,DNA_sampleID,RNA_samp
except:
ipd_birth_year = "-"
if(sheet_material.cell_value(r,c) == columns['gender'] and ipd_gender == ""):
ipd_gender = str(sheet_material.cell_value(r+2,c))
gender = str(sheet_material.cell_value(r+2,c))
if(gender != "" and gender != "X"):
ipd_gender = gender[0]
if(sheet_material.cell_value(r,c) == columns['age']):
ipd_age = str(sheet_material.cell_value(r+2,c))
if(sheet_material.cell_value(r,c) == columns['Histopathological_diagnosis'] and sheet_material.cell_value(r+1,c) != ""):
Expand Down Expand Up @@ -563,10 +567,6 @@ def get_RNA_material_id(InPreD_clinical_data_file,RNA_sampleID,encoding_sys):


def update_ppt_template_data(inpred_node,ipd_no,ipd_gender,ipd_age,ipd_diagnosis_year,DNA_material_id,RNA_material_id,ipd_consent,requisition_hospital,pathology_comment,ipd_clinical_diagnosis,tumor_type,sample_type,sample_material,sample_info_comment,pipline,tumor_content,ppt_template,output_ppt_file):
if(ipd_gender != "" and ipd_gender != "X"):
gender = ipd_gender[0]
else:
gender = ""
if(ipd_age != "" and ipd_age != "-" and ipd_age != "XX" and ipd_age != "<1"):
age = str(int(float(ipd_age)))
else:
Expand Down Expand Up @@ -673,7 +673,7 @@ def update_ppt_template_data(inpred_node,ipd_no,ipd_gender,ipd_age,ipd_diagnosis
tf11.paragraphs[0].text = pathology_comment + "\n\n" + sample_info_comment.replace("|","\n")
tf11.paragraphs[0].font.size = Pt(10)
tf11.paragraphs[0].alignment = PP_ALIGN.LEFT
gender_age = gender + '/' + age + 'y'
gender_age = ipd_gender + '/' + age + 'y'
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@marrip marrip Feb 6, 2026

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Suggested change
gender_age = ipd_gender + '/' + age + 'y'
gender_age = "{}/{}y'.format(ipd_gender, age)

if(RNA_material_id != ""):
ipd_material_id_index = "DNA:" + DNA_material_id + "\nRNA:" + RNA_material_id
else:
Expand Down Expand Up @@ -1060,7 +1060,7 @@ def update_clinical_master_file(InPreD_clinical_data_file,sample_id,if_generate_
for ln in fr:
if(ln.split('\t')[0] == sample_id):
if_exist = True
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender[0], ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, pathology_comment, sample_info_comment + '\n'])
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender, ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, pathology_comment, sample_info_comment + '\n'])
new_line = ln.replace(ln,line)
new_content = new_content + new_line
else:
Expand All @@ -1071,7 +1071,7 @@ def update_clinical_master_file(InPreD_clinical_data_file,sample_id,if_generate_
else:
fa = open(InPreD_clinical_data_file, 'a')
if(if_exist == False):
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender[0], ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, pathology_comment, sample_info_comment + '\n'])
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender, ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, pathology_comment, sample_info_comment + '\n'])
if(encoding_sys != ""):
fa = open(InPreD_clinical_data_file, 'a', encoding=encoding_sys)
else:
Expand Down Expand Up @@ -1109,14 +1109,14 @@ def update_clinical_tsoppi_file(InPreD_clinical_tsoppi_data_file,sample_id,if_ge
for ln in fr:
if(ln.split('\t')[0] == sample_id):
if_exist = True
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender[0], ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, sample_material, sample_type, tumor_type, str(TMB_DRUP), TMB_TSO500, MSI_TSO500, pipline, pathology_comment, sample_info_comment + '\n'])
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender, ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, sample_material, sample_type, tumor_type, str(TMB_DRUP), TMB_TSO500, MSI_TSO500, pipline, pathology_comment, sample_info_comment + '\n'])
new_line = ln.replace(ln,line)
new_content = new_content + new_line
else:
new_content = new_content + ln
fr.close()
if(if_exist == False):
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender[0], ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, sample_material, sample_type, tumor_type, str(TMB_DRUP), TMB_TSO500, MSI_TSO500, pipline, pathology_comment, sample_info_comment + '\n'])
line = '\t'.join([sample_id, runID, if_generate_report, ipd_birth_year, ipd_diagnosis_year, clinical_diagnosis, ipd_gender, ipd_consent, material_id, ipd_collection_year, requisition_hospital, extraction_hospital, str(tumor_content_nr), batch_nr, sample_material, sample_type, tumor_type, str(TMB_DRUP), TMB_TSO500, MSI_TSO500, pipline, pathology_comment, sample_info_comment + '\n'])
with open(InPreD_clinical_tsoppi_data_file, 'a') as fa:
fa.write(line)
fa.close()
Expand Down