[fix] ignore journal entry based invoice in payment tool and payment reconciliation tool

erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py

@@ -79,6 +79,7 @@ class PaymentReconciliation(Document):
 				`tabGL Entry`
 			where
 				party_type = %(party_type)s and party = %(party)s
+				and voucher_type != "Journal Entry"
 				and account = %(account)s and {dr_or_cr} > 0 {cond}
 			group by voucher_type, voucher_no
 		""".format(**{

erpnext/accounts/doctype/payment_tool/payment_tool.py

@@ -71,7 +71,7 @@ def get_outstanding_vouchers(args):
 
 	# Get all outstanding sales /purchase invoices
 	outstanding_invoices = get_outstanding_invoices(amount_query, args.get("party_account"),
-		args.get("party_type"), args.get("party"))
+		args.get("party_type"), args.get("party"), with_journal_entry=False)
 
 	# Get all SO / PO which are not fully billed or aginst which full advance not paid
 	orders_to_be_billed = get_orders_to_be_billed(args.get("party_type"), args.get("party"),

erpnext/accounts/utils.py

@@ -392,7 +392,7 @@ def get_stock_rbnb_difference(posting_date, company):
 	# Amount should be credited
 	return flt(stock_rbnb) + flt(sys_bal)
 
-def get_outstanding_invoices(amount_query, account, party_type, party):
+def get_outstanding_invoices(amount_query, account, party_type, party, with_journal_entry=True):
 	all_outstanding_vouchers = []
 	outstanding_voucher_list = frappe.db.sql("""
 		select
@@ -420,6 +420,9 @@ def get_outstanding_invoices(amount_query, account, party_type, party):
 		payment_amount = -1*payment_amount[0][0] if payment_amount else 0
 		precision = frappe.get_precision("Sales Invoice", "outstanding_amount")
 
+		if not with_journal_entry and d.voucher_type=="Journal Entry":
+			continue
+
 		if d.invoice_amount > payment_amount:
 
 			all_outstanding_vouchers.append({