From 4965dd473be87150a05eefe6da70da984bf79341 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 20 May 2024 11:37:25 -0400
Subject: [PATCH] fix for #459

---
 peppy/project.py                                      |  4 ++++
 tests/conftest.py                                     |  5 +++++
 .../example_custom_index/project_config.yaml          |  2 +-
 .../example_custom_index/sample_table.csv             |  2 +-
 tests/test_Project.py                                 | 11 +++++++++++
 5 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/peppy/project.py b/peppy/project.py
index 1e0ebb68..5c4524bd 100644
--- a/peppy/project.py
+++ b/peppy/project.py
@@ -659,6 +659,10 @@ def _assert_samples_have_names(self):
                     )
                 else:
                     raise InvalidSampleTableFileException(message)
+            else:
+                if self.st_index != SAMPLE_NAME_ATTR:
+                    sample[SAMPLE_NAME_ATTR] = self.st_index
+                    _LOGGER.warning(f"Setting sample.sample_name: {self.st_index}")
 
     def _auto_merge_duplicated_names(self):
         """
diff --git a/tests/conftest.py b/tests/conftest.py
index 50c7ffd5..a689ffc1 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -51,6 +51,11 @@ def example_pep_cfg_noname_path(request):
     return get_path_to_example_file(EPB, "noname", request.param)
 
 
+@pytest.fixture
+def example_pep_cfg_custom_index(request):
+    return get_path_to_example_file(EPB, "custom_index", request.param)
+
+
 @pytest.fixture
 def example_peps_cfg_paths(request):
     """
diff --git a/tests/data/example_peps-master/example_custom_index/project_config.yaml b/tests/data/example_peps-master/example_custom_index/project_config.yaml
index 83f85a88..a9a777be 100644
--- a/tests/data/example_peps-master/example_custom_index/project_config.yaml
+++ b/tests/data/example_peps-master/example_custom_index/project_config.yaml
@@ -1,3 +1,3 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
-sample_table_index: sample_id
+sample_table_index: NOT_SAMPLE_NAME
diff --git a/tests/data/example_peps-master/example_custom_index/sample_table.csv b/tests/data/example_peps-master/example_custom_index/sample_table.csv
index 30228147..c9965421 100644
--- a/tests/data/example_peps-master/example_custom_index/sample_table.csv
+++ b/tests/data/example_peps-master/example_custom_index/sample_table.csv
@@ -1,3 +1,3 @@
-sample_id,protocol,file
+NOT_SAMPLE_NAME,protocol,file
 frog_1,anySampleType,data/frog1_data.txt
 frog_2,anySampleType,data/frog2_data.txt
diff --git a/tests/test_Project.py b/tests/test_Project.py
index c77439ec..3c3c975f 100644
--- a/tests/test_Project.py
+++ b/tests/test_Project.py
@@ -322,6 +322,17 @@ def test_missing_sample_name_custom_index(self, example_pep_cfg_noname_path):
         p = Project(cfg=example_pep_cfg_noname_path, sample_table_index="id")
         assert p.sample_name_colname == "id"
 
+    @pytest.mark.parametrize(
+        "example_pep_cfg_custom_index", ["project_config.yaml"], indirect=True
+    )
+    def test_sample_name_custom_index(self, example_pep_cfg_custom_index):
+        """
+        Verify that sample_name attribute becomes st_index from cfg
+        """
+        p = Project(cfg=example_pep_cfg_custom_index)
+        assert p.sample_name_colname == "NOT_SAMPLE_NAME"
+        assert p.samples[0].sample_name == "NOT_SAMPLE_NAME"
+
     @pytest.mark.parametrize(
         "example_pep_cfg_path",
         ["basic"],