From 8ccace1fddf2610cefea93aa75a314e24ba40160 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 21 Mar 2024 18:04:53 -0400
Subject: [PATCH] add test for yaml variable

---
 ...ocker_yaml_conversion_specification_cli.py | 55 ++++++++++++++++++-
 1 file changed, 53 insertions(+), 2 deletions(-)

diff --git a/tests/docker_yaml_conversion_specification_cli.py b/tests/docker_yaml_conversion_specification_cli.py
index 4145a6888..fb2405758 100644
--- a/tests/docker_yaml_conversion_specification_cli.py
+++ b/tests/docker_yaml_conversion_specification_cli.py
@@ -28,7 +28,7 @@ def test_run_conversion_from_yaml_cli(self):
         yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification.yml"
         deploy_process(
             command=(
-                "docker run -it "
+                "docker run -t "
                 f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:{self.tag}"
                 f"neuroconv /neuroconv/tests/test_on_data/conversion_specifications/{yaml_file_path} "
                 f"--data-folder-path /neuroconv/{DATA_PATH} --output-folder-path {self.test_folder} --overwrite"
@@ -74,7 +74,7 @@ def test_run_conversion_from_yaml_default_nwbfile_name(self):
         yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification_missing_nwbfile_names.yml"
         deploy_process(
             command=(
-                "docker run -it "
+                "docker run -t "
                 f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:{self.tag}"
                 f"neuroconv {yaml_file_path} "
                 f"--data-folder-path {DATA_PATH} --output-folder-path {self.test_folder} --overwrite"
@@ -123,3 +123,54 @@ def test_run_conversion_from_yaml_default_nwbfile_name(self):
             assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-11T21:19:09+00:00")
             assert nwbfile.subject.subject_id == "Subject Name"
             assert "spike_times" in nwbfile.units
+
+def test_run_conversion_from_yaml_variable(self):
+        path_to_test_yml_files = Path(__file__).parent / "conversion_specifications"
+        yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification.yml"
+
+        with open(file=yaml_file_path, mode="r") as io:
+            yaml_lines = io.readlines()
+
+        yaml_string = "".join(yaml_lines)
+        os.environ["NEUROCONV_YAML"] = yaml_string
+        os.environ["NEUROCONV_DATA_PATH"] = DATA_PATH
+        os.environ["NEUROCONV_OUTPUT_PATH"] = OUTPUT_PATH
+    
+        deploy_process(
+            command=(
+                "docker run -t "
+                f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:yaml_variable"
+            )
+        )
+
+        nwbfile_path = self.test_folder / "example_converter_spec_1.nwb"
+        assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! "
+        with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+            nwbfile = io.read()
+            assert nwbfile.session_description == "Subject navigating a Y-shaped maze."
+            assert nwbfile.lab == "My Lab"
+            assert nwbfile.institution == "My Institution"
+            assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-09T21:19:09+00:00")
+            assert nwbfile.subject.subject_id == "1"
+            assert "ElectricalSeriesAP" in nwbfile.acquisition
+
+        nwbfile_path = self.test_folder / "example_converter_spec_2.nwb"
+        assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! "
+        with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+            nwbfile = io.read()
+            assert nwbfile.session_description == "Subject navigating a Y-shaped maze."
+            assert nwbfile.lab == "My Lab"
+            assert nwbfile.institution == "My Institution"
+            assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-10T21:19:09+00:00")
+            assert nwbfile.subject.subject_id == "002"
+
+        nwbfile_path = self.test_folder / "example_converter_spec_3.nwb"
+        assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! "
+        with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+            nwbfile = io.read()
+            assert nwbfile.session_description == "Auto-generated by neuroconv"
+            assert nwbfile.lab == "My Lab"
+            assert nwbfile.institution == "My Institution"
+            assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-11T21:19:09+00:00")
+            assert nwbfile.subject.subject_id == "Subject Name"
+            assert "spike_times" in nwbfile.units