Tests page 3

alphastats/gui/utils/overview_helper.py

@@ -43,8 +43,8 @@ def display_matrix():
     st.markdown("**DataFrame used for analysis** *preview*")
     st.markdown(text)
 
-    df = get_display_matrix(st.session_state.user_session_id)
-    csv = convert_df(st.session_state.dataset.mat, st.session_state.user_session_id)
+    df = get_display_matrix()
+    csv = convert_df(st.session_state.dataset.mat)
 
     st.dataframe(df)
 

alphastats/load_data.py

@@ -4,6 +4,7 @@
 from alphastats.loader.MaxQuantLoader import *
 
 
+# TODO: Currenlty only used by tests, but should maybe be used more widely
 def load_data(file, type, **kwargs):
     type = type.lower()
     if type == "maxquant":

tests/gui/conftest.py

@@ -0,0 +1,53 @@
+from streamlit.testing.v1 import AppTest
+from alphastats.load_data import load_data
+from pathlib import Path
+from alphastats import DataSet
+from io import BytesIO
+
+# TODO: Turn the helpers into fixtures
+
+APP_FOLDER = Path(__file__).parent / "../../alphastats/gui/"
+TEST_INPUT_FILES_PATH = APP_FOLDER / "../../testfiles"
+
+
+def print_session_state(apptest: AppTest):
+    """Prints the session state of the AppTest object.
+    Not used productively, but for debugging purposes."""
+    for k, v in apptest.session_state.filtered_state.items():
+        print(
+            f"{k}:    {str(type(v))}   {str(v)[:20] if type(v) not in [int, list, str] else v}"
+        )
+
+
+def create_dataset_alphapept():
+    """Creates a dataset object from the alphapept testfiles."""
+    loader = load_data(
+        file=str(TEST_INPUT_FILES_PATH / "alphapept/results_proteins.csv"),
+        type="alphapept",
+    )
+    metadata_path = TEST_INPUT_FILES_PATH / "alphapept/metadata.csv"
+    return DataSet(
+        loader=loader,
+        metadata_path=str(metadata_path),
+        sample_column="sample",
+    )
+
+
+def data_buf(file_path: str):
+    """Helper function to open a data file from the testfiles folder and return a BytesIO object.
+
+    Additionally add filename as attribute."""
+    with open(TEST_INPUT_FILES_PATH / file_path, "rb") as f:
+        buf = BytesIO(f.read())
+        buf.name = file_path.split("/")[-1]
+        return buf
+
+
+def metadata_buf(file_path: str):
+    """Helper function to open a metadata file from the testfiles folder and return a BytesIO object.
+
+    Additionally add filename as attribute and set the metadatafile in the session state."""
+    with open(TEST_INPUT_FILES_PATH / file_path, "rb") as f:
+        buf = BytesIO(f.read())
+        buf.name = file_path.split("/")[-1]
+        return buf

tests/gui/test_02_import_data.py

@@ -1,19 +1,10 @@
 from streamlit.testing.v1 import AppTest
 from pathlib import Path
 from unittest.mock import MagicMock, patch
-from io import BytesIO
+from .conftest import APP_FOLDER, data_buf, metadata_buf
 
 
-def print_session_state(apptest: AppTest):
-    for k, v in apptest.session_state.filtered_state.items():
-        print(
-            f"{k}:    {str(type(v))}   {str(v)[:20] if type(v) not in [int, list, str] else v}"
-        )
-
-
-APP_FOLDER = Path(__file__).parent / Path("../../alphastats/gui/")
 TESTED_PAGE = f"{APP_FOLDER}/pages/02_Import Data.py"
-TEST_INPUT_FILES_PATH = APP_FOLDER / "../../testfiles"
 
 
 def test_page_02_loads_without_input():
@@ -69,26 +60,6 @@ def test_page_02_loads_example_data(mock_page_link: MagicMock):
     assert "statistic_options" in at.session_state
 
 
-def _data_buf(file_path: str):
-    """Helper function to open a data file from the testfiles folder and return a BytesIO object.
-
-    Additionally add filename as attribute."""
-    with open(TEST_INPUT_FILES_PATH / file_path, "rb") as f:
-        buf = BytesIO(f.read())
-        buf.name = file_path.split("/")[-1]
-        return buf
-
-
-def _metadata_buf(file_path: str, at: AppTest):
-    """Helper function to open a metadata file from the testfiles folder and return a BytesIO object.
-
-    Additionally add filename as attribute and set the metadatafile in the session state."""
-    with open(TEST_INPUT_FILES_PATH / file_path, "rb") as f:
-        buf = BytesIO(f.read())
-        buf.name = file_path.split("/")[-1]
-        return buf
-
-
 @patch("streamlit.file_uploader")
 @patch(
     "streamlit.page_link"
@@ -114,22 +85,22 @@ def test_page_02_loads_maxquant_testfiles(
     at.run()
 
     # User uploads the data file
-    mock_file_uploader.side_effect = [_data_buf(DATA_FILE), None]
+    mock_file_uploader.side_effect = [data_buf(DATA_FILE), None]
     at.run()
 
     # User uploads the metadata file
     mock_file_uploader.side_effect = [
-        _data_buf(DATA_FILE),
-        _metadata_buf(METADATA_FILE, at),
+        data_buf(DATA_FILE),
+        metadata_buf(METADATA_FILE),
     ]
     at.run()
 
     assert not at.exception
 
     # User clicks the Load Data button
     mock_file_uploader.side_effect = [
-        _data_buf(DATA_FILE),
-        _metadata_buf(METADATA_FILE, at),
+        data_buf(DATA_FILE),
+        metadata_buf(METADATA_FILE),
     ]
     at.button(key="_create_dataset").click()
     at.run()

tests/gui/test_03_data_overview.py

@@ -1,25 +1,25 @@
 from streamlit.testing.v1 import AppTest
 from pathlib import Path
 from unittest.mock import MagicMock, patch
-import pandas as pd
-from io import BytesIO
+from .conftest import create_dataset_alphapept, APP_FOLDER
 
+TESTED_PAGE = f"{APP_FOLDER}/pages/03_Data Overview.py"
 
-def print_session_state(apptest: AppTest):
-    for k, v in apptest.session_state.filtered_state.items():
-        print(
-            f"{k}:    {str(type(v))}   {str(v)[:20] if type(v) not in [int, list, str] else v}"
-        )
 
+def test_page_03_loads_without_input():
+    """Test if the page loads without any input and inititalizes the session state with the correct values."""
+    at = AppTest(TESTED_PAGE, default_timeout=200)
+    at.run()
+
+    assert not at.exception
 
-APP_FOLDER = Path(__file__).parent / Path("../../alphastats/gui/")
-APP_FILE = f"{APP_FOLDER}/pages/03_Data Overview.py"
-TEST_INPUT_FILES = f"{APP_FOLDER}/../../testfiles"
 
+def test_page_03_loads_with_input():
+    """Test if the page loads with input and inititalizes the session state with the correct values."""
+    at = AppTest(TESTED_PAGE, default_timeout=200)
+    at.run()
 
-def test_page_03_loads_without_input():
-    """Test if the page loads without any input and inititalizes the session state with the correct values."""
-    at = AppTest(APP_FILE, default_timeout=200)
+    at.session_state["dataset"] = create_dataset_alphapept()
     at.run()
 
     assert not at.exception

tests/gui/test_04_preprocessing.py

@@ -1,47 +1,23 @@
-from alphastats import DataSet
-from alphastats.load_data import load_data
 from streamlit.testing.v1 import AppTest
 from pathlib import Path
 from unittest.mock import MagicMock, patch
-import pandas as pd
-from io import BytesIO
+from .conftest import create_dataset_alphapept, APP_FOLDER
 
 
-APP_FOLDER = Path(__file__).parent / Path("../../alphastats/gui/")
-APP_FILE = f"{APP_FOLDER}/pages/03_Preprocessing.py"
-TEST_INPUT_FILES = f"{APP_FOLDER}/../../testfiles"
-
-
-def print_session_state(apptest: AppTest):
-    for k, v in apptest.session_state.filtered_state.items():
-        print(
-            f"{k}:    {str(type(v))}   {str(v)[:20] if type(v) not in [int, list, str] else v}"
-        )
-
-
-def create_dataset_alphapept():
-    loader = load_data(
-        file=TEST_INPUT_FILES + "/alphapept/results_proteins.csv", type="alphapept"
-    )
-    metadata_path = TEST_INPUT_FILES + "/alphapept/metadata.csv"
-    return DataSet(
-        loader=loader,
-        metadata_path=metadata_path,
-        sample_column="sample",
-    )
+TESTED_PAGE = f"{APP_FOLDER}/pages/03_Preprocessing.py"
 
 
 def test_page_04_loads_without_input():
     """Test if the page loads without any input and inititalizes the session state with the correct values."""
-    at = AppTest(APP_FILE, default_timeout=200)
+    at = AppTest(TESTED_PAGE, default_timeout=200)
     at.run()
 
     assert not at.exception
 
 
 def test_page_04_loads_with_input():
-    """Test if the page loads with input and inititalizes the session state with the correct values."""
-    at = AppTest(APP_FILE, default_timeout=200)
+    """Test if the page loads with input and serves the processing interface correctly."""
+    at = AppTest(TESTED_PAGE, default_timeout=200)
     at.run()
 
     at.session_state["dataset"] = create_dataset_alphapept()
@@ -54,7 +30,7 @@ def test_page_04_loads_with_input():
 
 def test_page_04_runs_preprocessreset_alphapept():
     """Test if the page preprocesses and resets preprocessing without exceptions."""
-    at = AppTest(APP_FILE, default_timeout=200)
+    at = AppTest(TESTED_PAGE, default_timeout=200)
     at.run()
 
     at.session_state["dataset"] = create_dataset_alphapept()