Fixing Test Failures In GEDIDB: A Deep Dive

by SLV Team 44 views

Hey guys! So, we've got a bit of a pickle – two tests in our GEDIDB project are failing, and it's time to roll up our sleeves and figure out what's going on. This article will walk you through the issue, the code, the error messages, and the versions of Python and gedidb we're using. We'll also dive into the context surrounding the problem. Let's get started!

The Issue: Two Tests Down

First things first: Two tests are currently failing. This is a serious problem, guys! Tests are essential because they ensure our code functions correctly and that any changes we make don't break existing features. When tests fail, it means something isn't working as expected. This could be due to a bug in the code, an incorrect configuration, or maybe the data used for the tests has changed. Understanding why the tests are failing is the first step towards getting everything back on track. We need to identify which specific tests are failing and then analyze the code within those tests to pinpoint the root cause of the problem.

Failing tests can lead to more serious issues if left unaddressed. They can make it difficult to introduce new features, since you can’t be sure whether new changes break existing functionalities. They can also create confusion among the developers, because they won’t be sure if the program is working properly. Addressing the test failures quickly will make sure the project remains healthy and manageable in the long run. Let's dive into the code and see what might be happening.

Reproducing the Code Example and Error Messages

To understand the problem better, we need to look closely at the code examples. Here's the code that’s causing the issues:

# SPDX-License-Identifier: EUPL-1.2
# Contact: besnard@gfz.de, felix.dombrowski@uni-potsdam.de and ah2174@cam.ac.uk
# SPDX-FileCopyrightText: 2025 Amelia Holcomb
# SPDX-FileCopyrightText: 2025 Felix Dombrowski
# SPDX-FileCopyrightText: 2025 Simon Besnard
# SPDX-FileCopyrightText: 2025 Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences
#

import tempfile
import unittest
from pathlib import Path

import numpy as np
import pandas as pd
import tiledb
import yaml

from gedidb.core.gedidatabase import GEDIDatabase


class TestGEDIDatabase(unittest.TestCase):
    @classmethod
    def setUpClass(cls):
        # Dynamically resolve the path to the `data` folder
        cls.data_dir = Path(__file__).parent / "data"
        cls.yaml_file_path = cls.data_dir / "data_config.yml"

        if not cls.yaml_file_path.exists():
            raise FileNotFoundError(f"Config file not found: {cls.yaml_file_path}")

        with open(cls.yaml_file_path, "r") as file:
            cls.config = yaml.safe_load(file)

        # Override local TileDB path with a temporary directory
        cls.temp_dir = tempfile.TemporaryDirectory()
        cls.config["tiledb"]["local_path"] = cls.temp_dir.name

        # Initialize GEDIDatabase instance
        cls.gedi_db = GEDIDatabase(cls.config)
        cls.gedi_db._create_arrays()  # Create the TileDB array for testing

    @classmethod
    def tearDownClass(cls):
        """Cleanup temporary directory."""
        cls.temp_dir.cleanup()

    def test_tiledb_dimensions(self):
        """Test that TileDB dimensions are configured correctly."""
        with tiledb.open(
            self.gedi_db.array_uri, mode="r", ctx=self.gedi_db.ctx
        ) as array:
            schema = array.schema
            dims = schema.domain

            # Check dimensions
            lat_dim = dims.dim("latitude")
            lon_dim = dims.dim("longitude")
            time_dim = dims.dim("time")

            self.assertIn(
                "latitude",
                lat_dim.name,
                "The 'latitude' dimension is missing from the TileDB schema.",
            )
            self.assertIn(
                "longitude",
                lon_dim.name,
                "The 'longitude' dimension is missing from the TileDB schema.",
            )
            self.assertIn(
                "time",
                time_dim.name,
                "The 'time' dimension is missing from the TileDB schema.",
            )

            self.assertEqual(lat_dim.domain, (-56.0, 56.0), "Latitude range mismatch")
            self.assertEqual(
                lon_dim.domain, (-180.0, 180.0), "Longitude range mismatch"
            )
            # Check chunk size
            self.assertEqual(lat_dim.tile, 0.5, "Latitude chunk size mismatch")
            self.assertEqual(lon_dim.tile, 0.5, "Longitude chunk size mismatch")

    def test_tiledb_attributes(self):
        """Test that TileDB attributes are correctly set."""
        with tiledb.open(
            self.gedi_db.array_uri, mode="r", ctx=self.gedi_db.ctx
        ) as array:
            schema = array.schema

            # Check for expected attributes
            expected_attributes = [
                "shot_number",
                "beam_type",
                "degrade_flag",
            ]  # Example attributes in the array

            for attr in expected_attributes:
                self.assertIn(
                    attr, schema.attr(attr).name, f"Missing attribute: {attr}"
                )

    def test_overwrite_behavior(self):
        """Ensure overwrite behavior works correctly."""
        self.assertTrue(
            self.config["tiledb"]["overwrite"],
            "Overwrite setting should be True",
        )

        # Check if array exists after creation
        self.assertTrue(
            tiledb.array_exists(self.gedi_db.array_uri),
            "TileDB array should exist after creation",
        )

        # Re-create the array and confirm it overwrites
        self.gedi_db._create_arrays()  # Overwrite
        self.assertTrue(
            tiledb.array_exists(self.gedi_db.array_uri),
            "TileDB array should still exist after overwrite",
        )

    def test_write_granule(self):
        """Test the `write_granule` function to write data to TileDB."""
        granule_file = self.data_dir / "example_data.csv"

        if not granule_file.exists():
            raise FileNotFoundError(f"Granule file not found: {granule_file}")

        granule_data = pd.read_csv(granule_file)
        self.gedi_db.write_granule(granule_data)

        with tiledb.open(
            self.gedi_db.array_uri, mode="r", ctx=self.gedi_db.ctx
        ) as array:
            shot_number = array.query(attrs=("shot_number",)).multi_index[:, :, :]
            beam_type = array.query(attrs=("beam_type",)).multi_index[:, :, :]
            beam_name = array.query(attrs=("beam_name",)).multi_index[:, :, :]

            print((shot_number["shot_number"]))

            self.assertTrue(
                np.array_equal(
                    shot_number["shot_number"],
                    [
                        84480000200057734,
                        84480000200057402,
                        84480000200057755,
                        84480000200057754,
                        84480000200057753,
                    ],
                ),
                "Shot number mismatch",
            )
            self.assertTrue(
                np.array_equal(
                    beam_type["beam_type"],
                    [
                        "coverage",
                        "coverage",
                        "coverage",
                        "coverage",
                        "coverage",
                    ],
                ),
                "Beam type mismatch",
            )
            self.assertTrue(
                np.array_equal(
                    beam_name["beam_name"],
                    [
                        "/BEAM0000",
                        "/BEAM0000",
                        "/BEAM0000",
                        "/BEAM0000",
                        "/BEAM0000",
                    ],
                ),
                "Beam name mismatch",
            )


suite = unittest.TestLoader().loadTestsFromTestCase(TestGEDIDatabase)

This Python code defines a set of unit tests for the GEDIDatabase class. The tests cover various aspects of the database, including the configuration of TileDB dimensions, attributes, overwrite behavior, and data writing. The TestGEDIDatabase class inherits from unittest.TestCase, providing the structure for running the tests. The setUpClass method initializes the test environment by setting up the data directory and configuration, and the tearDownClass method cleans up the temporary directory after the tests are completed. Individual test methods, such as test_tiledb_dimensions, test_tiledb_attributes, test_overwrite_behavior, and test_write_granule, perform specific checks on the database functionality. These tests verify the correct configuration of TileDB dimensions and attributes, ensure the overwrite behavior works as expected, and validate the functionality of writing data to the database using the write_granule function. If any of these checks fail, the corresponding test will report an error.

The error messages and how to reproduce are not provided; this is key to solving the issue. However, you can use the code provided to reproduce the error and see the error messages to solve the problem!

Python and gedidb Versions: Understanding the Versions

Here’s the version information:

3.11.14 | packaged by conda-forge | (main, Oct 13 2025, 14:09:32) [GCC 14.3.0]

Knowing the exact versions of Python and the gedidb library is crucial for debugging. Version compatibility issues are a common reason for tests to fail. If the code was written for one version of a library and you're running it with a different version, you might encounter unexpected behavior. Always make sure that the versions used in the test environment are compatible with the code. If the versions don’t match, you may need to upgrade or downgrade the library. You must first analyze the code thoroughly to identify potential causes of the problem.

Context for the Issue: Unveiling the Details

Without additional context, it's a bit harder to understand the full scope of the problem. However, we have a starting point and the code. We can check the dimensions and attributes to see what the actual problem is.

Troubleshooting Steps and Possible Solutions

Let’s go through a few troubleshooting steps and possible solutions:

  1. Examine the Error Messages: The first thing to do is get the error messages. They give us vital clues. They usually tell us what went wrong, and where. Are there AssertionError exceptions? If so, why? Are there any unexpected exceptions? Reading the error messages carefully is super important.
  2. Code Review: Carefully review the code of the failing tests. Check for common issues like incorrect data types, incorrect comparisons, and incorrect array indexing. Pay attention to the expected values and how they are compared with the actual values. Are you using the correct methods to check your data?
  3. Data Inspection: Verify that the data used in the tests matches the expectations. Data mismatches are another frequent cause of test failures. Sometimes, the data might not be in the format that the test expects. Check the example_data.csv to ensure it has the correct data.
  4. Configuration Check: Ensure the configuration file (data_config.yml) is set up correctly. Incorrect configurations can make your tests fail. Ensure that the paths are correctly set and all dependencies are included.
  5. Environment Check: Make sure your testing environment is properly set up. Ensure that all the dependencies are installed and accessible, and that the environment variables are correctly configured. A misconfigured environment is often the source of test failures.
  6. Version Compatibility: Double-check the compatibility of the gedidb library with Python 3.11.14. Upgrade to the latest compatible version or revert to an older version if necessary.
  7. Debugging Tools: Use debugging tools like pdb (Python Debugger) or logging statements to step through the code and inspect the variables. These tools can help pinpoint the exact point where the tests fail and understand the state of the variables at that time.
  8. Simplify and Isolate: Try simplifying the tests or isolating the problematic parts to narrow down the issue. Comment out sections of the test code to see if the tests pass. If the test passes after commenting out a specific part, the problem is likely in that section.
  9. Test Granule File: Make sure the test is running with a correct granule file, otherwise, it might produce an error.

Conclusion: Getting the Tests Green Again

Alright guys, we've covered a lot. We've looked at the failing tests, the code, the versions, and some of the possible causes and solutions. Now, the real work begins: we need to get into the code, reproduce the errors, and debug our way to success! Remember that fixing failing tests is essential for the health of our project. By carefully examining the code, understanding the error messages, and checking the data, we can resolve these issues and make sure our GEDIDB project is in great shape. Keep up the great work, and let's get those tests passing!