From 0e85c667cd761eb0ff2c759aae72f6adadfabe98 Mon Sep 17 00:00:00 2001
From: Aaron Petkau <aaron.petkau@gmail.com>
Date: Mon, 3 Jun 2024 16:10:23 -0500
Subject: [PATCH] Fixed up structure of returned empty tables

---
 modules/local/report.nf        |  7 ++++---
 tests/functions/report.nf.test | 23 +++++++++++++++++++++++
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/modules/local/report.nf b/modules/local/report.nf
index d61ae712..adf1fe77 100644
--- a/modules/local/report.nf
+++ b/modules/local/report.nf
@@ -813,8 +813,8 @@ def table_values(file_path, header_p, seperator, headers=null){
     } else if (!header_p) {
         if (file_lines.size() == 0) {
             // headers were not in the file, and file size is 0, so return missing data based
-            // on passed headers
-            rows_list = headers.collectEntries { [(it): null] }
+            // on passed headers (i.e., single row of empty values)
+            rows_list = [headers.collectEntries { [(it): null] }]
         } else {
             // verify that passed headers and rows have same number
             def row_line = file_lines[0].replaceAll('(\n|\r\n)$', '')
@@ -846,7 +846,8 @@ def table_values(file_path, header_p, seperator, headers=null){
 
         if (file_lines.size() == 1) {
             // There is no row lines, only headers, so return missing data
-            rows_list = headers_from_file.collectEntries { [(it): null] }
+            // (single row of empty values)
+            rows_list = [headers_from_file.collectEntries { [(it): null] }]
         } else {
             // If there exists a row line, then make sure rows + headers match
 
diff --git a/tests/functions/report.nf.test b/tests/functions/report.nf.test
index baae3b66..2218c7d1 100644
--- a/tests/functions/report.nf.test
+++ b/tests/functions/report.nf.test
@@ -207,6 +207,7 @@ nextflow_function {
     }
 
     test("Test empty file"){
+        tag "test_empty"
 
         when {
             function {
@@ -223,9 +224,31 @@ nextflow_function {
         }
         then{
             assert function.failed
+            assert function.stdout.any { it.contains("ERROR ~ Attempting to parse empty file") }
         }
     }
 
+    test("Test empty file pass header"){
+        tag "test_empty_pass_header"
+
+        when {
+            function {
+                """
+                input[0] = file("$baseDir/tests/data/tables/empty.csv")
+                input[1] = false
+                input[2] = ','
+                input[3] = ['header1', 'header2']
+                """
+            }
+            params {
+                outdir = "results"
+            }
+        }
+        then{
+            assert function.success
+            assert function.result == ['0':['header1':'NoData', 'header2':'NoData']]
+        }
+    }
 
     test("Test more values than columns"){