fix: never parse index_col from node data

spras/dataset.py

@@ -1,6 +1,7 @@
 import os
 import pickle as pkl
 import warnings
+from typing import TypedDict
 
 import pandas as pd
 
@@ -11,13 +12,23 @@
 Methods and intermediate state for loading data and putting it into pandas tables for use by pathway reconstruction algorithms.
 """
 
+class DatasetDict(TypedDict):
+    """
+    Type class containing a collection of information pertaining to creating a Dataset
+    object. This layout is replicated directly in SPRAS configuration files.
+    """
+    label: str
+    node_files: list[str | os.PathLike]
+    edge_files: list[str | os.PathLike]
+    other_files: list[str | os.PathLike]
+    data_dir: str | os.PathLike
 
 class Dataset:
 
     NODE_ID = "NODEID"
     warning_threshold = 0.05  # Threshold for scarcity of columns to warn user
 
-    def __init__(self, dataset_dict):
+    def __init__(self, dataset_dict: DatasetDict):
         self.label = None
         self.interactome = None
         self.node_table = None
@@ -47,7 +58,7 @@ def from_file(cls, file_name: str):
         with open(file_name, "rb") as f:
             return pkl.load(f)
 
-    def load_files_from_dict(self, dataset_dict):
+    def load_files_from_dict(self, dataset_dict: DatasetDict):
         """
         Loads data files from dataset_dict, which is one dataset dictionary from the list
         in the config file with the fields in the config file.
@@ -110,14 +121,14 @@ def load_files_from_dict(self, dataset_dict):
         # 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(
                     os.path.join(data_loc, node_file), header=None
                 )
                 single_node_table.columns = [self.NODE_ID]
-                new_col_name = node_file.split(".")[0]
+                new_col_name = str(node_file).split(".")[0]
                 single_node_table[new_col_name] = True
 
             # Use only keys from the existing node table so that nodes that are not in the interactome are ignored

test/dataset/fixtures/dataless/network.txt

@@ -0,0 +1,2 @@
+A	B	1	U
+B	C	0.5	U

test/dataset/fixtures/dataless/node-prizes.txt

@@ -0,0 +1 @@
+NODEID	prize	active	dummy

test/dataset/fixtures/empty-headers/network.txt

@@ -0,0 +1,2 @@
+A	B	1	U
+B	C	0.5	U

test/dataset/fixtures/empty-headers/node-prizes.txt

@@ -0,0 +1 @@
+NODEID	prize	active	dummy

test/dataset/fixtures/empty-network/node-prizes.txt

@@ -0,0 +1,3 @@
+NODEID	prize	active	dummy
+A	2	true	true
+C	5.7	true

test/dataset/fixtures/empty-network/sources.txt

@@ -0,0 +1 @@
+A

test/dataset/fixtures/empty-network/targets.txt

@@ -0,0 +1 @@
+B

test/dataset/fixtures/standard/network.txt

@@ -0,0 +1,2 @@
+A	B	1	U
+B	C	0.5	U

test/dataset/fixtures/standard/node-prizes.txt

@@ -0,0 +1,3 @@
+NODEID	prize	active	dummy
+A	2	true	true
+C	5.7	true

test/dataset/fixtures/standard/sources.txt

@@ -0,0 +1 @@
+A

test/dataset/fixtures/standard/targets.txt

@@ -0,0 +1 @@
+C

test/dataset/fixtures/toy-372/input-interactome.txt

@@ -0,0 +1,2 @@
+C	D	0.77	U
+N	O	0.66	U

test/dataset/fixtures/toy-372/input-nodes.txt

@@ -0,0 +1,3 @@
+NODEID	prize	active	dummy	sources	targets
+N											
+C	5.7	True			True

test/dataset/test_dataset.py

@@ -0,0 +1,82 @@
+from pathlib import Path
+
+import pandas
+import pytest
+import numpy as np
+
+from spras.dataset import Dataset
+
+FIXTURES_PATH = Path('test', 'dataset', 'fixtures')
+
+class TestDataset:
+    def test_not_allow_no_cols(self):
+        with pytest.raises(pandas.errors.EmptyDataError):
+            Dataset({
+                'label': 'empty',
+                'edge_files': ['network.txt'],
+                'node_files': ['sources.txt', 'node-prizes.txt'],
+                'other_files': [],
+                'data_dir': FIXTURES_PATH / 'empty'
+            })
+
+    def test_not_allow_no_cols_headers(self):
+        with pytest.raises(pandas.errors.EmptyDataError):
+            Dataset({
+                'label': 'empty-headers',
+                'edge_files': ['network.txt'],
+                'node_files': ['sources.txt', 'node-prizes.txt'],
+                'other_files': [],
+                'data_dir': FIXTURES_PATH / 'empty-headers'
+            })
+
+    def test_dataless(self):
+        with pytest.raises(pandas.errors.EmptyDataError):
+            Dataset({
+                'label': 'dataless',
+                'edge_files': ['network.txt'],
+                'node_files': ['sources.txt', 'node-prizes.txt'],
+                'other_files': [],
+                'data_dir': FIXTURES_PATH / 'dataless'
+            })
+
+    def test_empty_network(self):
+        with pytest.raises(pandas.errors.EmptyDataError):
+            Dataset({
+                'label': 'empty-network',
+                'edge_files': ['network.txt'],
+                'node_files': ['sources.txt', 'node-prizes.txt'],
+                'other_files': [],
+                'data_dir': FIXTURES_PATH / 'empty-network'
+            })
+
+    def test_standard(self):
+        dataset = Dataset({
+            'label': 'empty',
+            'edge_files': ['network.txt'],
+            'node_files': ['node-prizes.txt', 'sources.txt', 'targets.txt'],
+            'other_files': [],
+            'data_dir': FIXTURES_PATH / 'standard'
+        })
+
+        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