From 30a6fe93e35b9a591551a236c1bdf924eb183c5d Mon Sep 17 00:00:00 2001
From: Matt Garber <matthew.garber@childrens.harvard.edu>
Date: Tue, 27 Feb 2024 15:12:50 -0500
Subject: [PATCH] markdown generation test

---
 cumulus_library/study_parser.py               |  3 +-
 tests/test_cli.py                             | 48 +++++++++++++++++++
 .../test_data/study_python_valid_generated.md | 15 ++++++
 3 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_data/study_python_valid_generated.md

diff --git a/cumulus_library/study_parser.py b/cumulus_library/study_parser.py
index 4b60e0f5..46407310 100644
--- a/cumulus_library/study_parser.py
+++ b/cumulus_library/study_parser.py
@@ -575,11 +575,12 @@ def run_generate_markdown(
 
         tables = [x[0] for x in cursor.execute(query).fetchall()]
         query = base_templates.get_column_datatype_query(
-            schema_name=schema, table_name=tables, include_table_names=True
+            schema_name=schema, table_names=tables, include_table_names=True
         )
         study_df = pandas.DataFrame(
             cursor.execute(query).fetchall(), columns=["Table", "Column", "Type"]
         )
+        print(self._study_path)
         with open(
             self._study_path / f"{self.get_study_prefix()}_generated.md", "w"
         ) as f:
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 37356982..3045cb2d 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,6 +1,7 @@
 """ tests for the cli interface to studies """
 
 import builtins
+import filecmp
 import glob
 import io
 import os
@@ -193,6 +194,53 @@ def test_generate_sql(mock_path, tmp_path):
         assert "CREATE TABLE IF NOT EXISTS study_python_valid__table" in query
 
 
+@mock.patch.dict(
+    os.environ,
+    clear=True,
+)
+@mock.patch("sysconfig.get_path")
+def test_generate_md(mock_path, tmp_path):
+    mock_path.return_value = f"{tmp_path}/study_python_valid/"
+    with does_not_raise():
+        shutil.copytree(
+            f"{Path(__file__).resolve().parents[0]}/test_data/study_python_valid",
+            f"{tmp_path}/study_python_valid/",
+        )
+        args = duckdb_args(
+            [
+                "build",
+                "-t",
+                "study_python_valid",
+                "-s",
+                f"{tmp_path}",
+                "--database",
+                "test",
+            ],
+            tmp_path,
+        )
+
+        cli.main(cli_args=args)
+        args = duckdb_args(
+            [
+                "generate-md",
+                "-t",
+                "study_python_valid",
+                "-s",
+                f"{tmp_path}",
+                "--database",
+                "test",
+            ],
+            tmp_path,
+        )
+        cli.main(cli_args=args)
+        test_file = f"{tmp_path}/study_python_valid/study_python_valid_generated.md"
+        ref_file = (
+            pathlib.Path(__file__).resolve().parent
+            / "test_data/study_python_valid_generated.md"
+        )
+        assert filecmp.cmp(test_file, ref_file, shallow=True)
+
+
 @mock.patch.dict(
     os.environ,
     clear=True,
diff --git a/tests/test_data/study_python_valid_generated.md b/tests/test_data/study_python_valid_generated.md
new file mode 100644
index 00000000..33dd60d7
--- /dev/null
+++ b/tests/test_data/study_python_valid_generated.md
@@ -0,0 +1,15 @@
+## study_python_valid base tables
+
+### study_python_valid__lib_transactions
+|    Column     |  Type   |Description|
+|---------------|---------|-----------|
+|study_name     |VARCHAR  |           |
+|library_version|VARCHAR  |           |
+|status         |VARCHAR  |           |
+|event_time     |TIMESTAMP|           |
+
+### study_python_valid__table
+|Column| Type  |Description|
+|------|-------|-----------|
+|test  |INTEGER|           |
+