From 74e3080e6752cdb316d0c5d460e584b9da081de0 Mon Sep 17 00:00:00 2001
From: "Tristan F." <LeoDog896@hotmail.com>
Date: Thu, 21 Aug 2025 19:55:58 +0000
Subject: [PATCH] fix: never parse index_col from node data

---
 spras/dataset.py                              |  2 +-
 .../fixtures/toy-372/input-interactome.txt    |  2 ++
 test/dataset/fixtures/toy-372/input-nodes.txt |  3 +++
 test/dataset/test_dataset.py                  | 22 +++++++++++++++++++
 4 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 test/dataset/fixtures/toy-372/input-interactome.txt
 create mode 100644 test/dataset/fixtures/toy-372/input-nodes.txt

diff --git a/spras/dataset.py b/spras/dataset.py
index 891f4d6f9..c2271235c 100644
--- a/spras/dataset.py
+++ b/spras/dataset.py
@@ -121,7 +121,7 @@ def load_files_from_dict(self, dataset_dict: DatasetDict):
         # Load generic node tables
         self.node_table = pd.DataFrame(node_set, columns=[self.NODE_ID])
         for node_file in node_data_files:
-            single_node_table = pd.read_table(os.path.join(data_loc, node_file))
+            single_node_table = pd.read_table(os.path.join(data_loc, node_file), index_col=False)
             # If we have only 1 column, assume this is an indicator variable
             if len(single_node_table.columns) == 1:
                 single_node_table = pd.read_table(
diff --git a/test/dataset/fixtures/toy-372/input-interactome.txt b/test/dataset/fixtures/toy-372/input-interactome.txt
new file mode 100644
index 000000000..f252ca4ca
--- /dev/null
+++ b/test/dataset/fixtures/toy-372/input-interactome.txt
@@ -0,0 +1,2 @@
+C	D	0.77	U
+N	O	0.66	U
\ No newline at end of file
diff --git a/test/dataset/fixtures/toy-372/input-nodes.txt b/test/dataset/fixtures/toy-372/input-nodes.txt
new file mode 100644
index 000000000..2efa6f320
--- /dev/null
+++ b/test/dataset/fixtures/toy-372/input-nodes.txt
@@ -0,0 +1,3 @@
+NODEID	prize	active	dummy	sources	targets
+N											
+C	5.7	True			True
diff --git a/test/dataset/test_dataset.py b/test/dataset/test_dataset.py
index 4cb988632..52333ca91 100644
--- a/test/dataset/test_dataset.py
+++ b/test/dataset/test_dataset.py
@@ -2,6 +2,7 @@
 
 import pandas
 import pytest
+import numpy as np
 
 from spras.dataset import Dataset
 
@@ -58,3 +59,24 @@ def test_standard(self):
         })
 
         assert len(dataset.get_interactome()) == 2
+    
+    # 372 is a PR, but for the relevant comment, see
+    # https://github.com/Reed-CompBio/spras/pull/372/files#r2291953612.
+    # Note that the input-nodes file has more tabs than the original fixture.
+    def test_372(self):
+        dataset = Dataset({
+            'label': 'toy-372',
+            'edge_files': ['input-interactome.txt'],
+            'node_files': ['input-nodes.txt'],
+            'data_dir': FIXTURES_PATH / 'toy-372',
+            'other_files': []
+        })
+
+        node_table = dataset.node_table
+        assert node_table is not None
+
+        assert node_table[node_table[Dataset.NODE_ID] == 'C'].iloc[0]['prize'] == 5.7
+        assert node_table[node_table[Dataset.NODE_ID] == 'C'].iloc[0]['active'] == True
+
+        assert np.isnan(node_table[node_table[Dataset.NODE_ID] == 'C'].iloc[0]['sources'])
+        assert node_table[node_table[Dataset.NODE_ID] == 'C'].iloc[0]['targets'] == True