test: adding unit tests to separate branch #15

Karanjot786 · 2024-07-16T07:35:47Z

Description:

This PR separates the unit tests from the main implementation and moves them to a dedicated branch. This is done to ensure focused testing and validation of individual components without merging the tests prematurely.

Files Included:

tests/unit/test_tes_converter.py
tests/unit/test_wes_converter.py

Details:

Unit Tests for TES Converter:

Tests the conversion from TES to WRROC.
Tests the conversion from WRROC to TES.

Unit Tests for WES Converter:

Tests the conversion from WES to WRROC.
Tests the conversion from WRROC to WES.

Instructions for Running the Tests:

Ensure all dependencies are installed:
```
poetry install
```
Run the unit tests:
```
poetry run pytest tests/unit
```

Sample TES Input (`tes_example.json`):

{
    "id": "task-id",
    "name": "test-task",
    "description": "test-description",
    "executors": [{"image": "executor-image"}],
    "inputs": [{"url": "input-url", "path": "input-path"}],
    "outputs": [{"url": "output-url", "path": "output-path"}],
    "creation_time": "2023-07-10T14:30:00Z",
    "end_time": "2023-07-10T15:30:00Z"
}

Sample WES Input (`wes_example.json`):

{
    "run_id": "run-id",
    "run_log": {
        "name": "test-run",
        "start_time": "2023-07-10T14:30:00Z",
        "end_time": "2023-07-10T15:30:00Z"
    },
    "state": "COMPLETED",
    "outputs": [{"location": "output-location", "name": "output-name"}]
}

Summary by Sourcery

This pull request introduces new conversion functionalities for TES and WES formats to WRROC and vice versa. It also includes a CLI for performing these conversions, updates the project name to 'CrateGen', and adjusts the CI configuration accordingly. Additionally, unit tests for the new conversion functionalities have been added.

New Features:
- Introduced TES to WRROC and WRROC to TES conversion functionality.
- Introduced WES to WRROC and WRROC to WES conversion functionality.
- Added a CLI for converting TES/WES to WRROC.
Enhancements:
- Renamed project from 'WRROC <> GA4GH API Conversion Tool' to 'CrateGen'.
CI:
- Updated CI configuration to reflect the new project structure and naming.
Tests:
- Added unit tests for TES to WRROC and WRROC to TES conversion.
- Added unit tests for WES to WRROC and WRROC to WES conversion.

…oc-ga4gh-cloud-converter into repository-setup

…c-ga4gh-cloud-converter into initial-version

sourcery-ai · 2024-07-16T07:35:53Z

Reviewer's Guide by Sourcery

This pull request introduces unit tests for the TES and WES converters, moving them to a dedicated branch to ensure focused testing. Additionally, it updates the CI workflow and README to reflect the new project structure and naming conventions.

File-Level Changes

Files	Changes
`tests/unit/test_tes_converter.py` `tests/unit/test_wes_converter.py`	Added unit tests for TES and WES converters.
`crategen/converters/tes_converter.py` `crategen/converters/wes_converter.py`	Implemented conversion logic for TES and WES to WRROC and vice versa.
`tests/data/output/tes_to_wrroc_output.json` `tests/data/output/wes_to_wrroc_output.json` `tests/data/input/tes_example.json` `tests/data/input/wes_example.json`	Added sample input and output JSON files for TES and WES conversions.

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sourcery-ai

Hey @Karanjot786 - I've reviewed your changes and they look great!

Here's what I looked at during the review

🟡 General issues: 6 issues found
🟢 Security: all looks good
🟡 Testing: 9 issues found
🟢 Complexity: all looks good
🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

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sourcery-ai · 2024-07-16T07:37:52Z

.github/workflows/ci.yml

@@ -25,24 +25,20 @@ jobs:

    - name: Lint with Ruff
      run: |
-        poetry run ruff check src/ tests/
+        poetry run ruff check crategen/ tests/


suggestion (testing): Consider adding a specific file path for tests.

To ensure that only the relevant test files are checked, consider specifying the exact path to the test files instead of using a general 'tests/' directory.

Suggested change

poetry run ruff check crategen/ tests/

poetry run ruff check crategen/ tests/specific_test_file.py

sourcery-ai · 2024-07-16T07:37:52Z

crategen/converters/tes_converter.py

+        inputs = tes_data.get("inputs", [])
+        outputs = tes_data.get("outputs", [])
+        creation_time = tes_data.get("creation_time", "")
+        end_time = tes_data.get("logs", [{}])[0].get("end_time", "")  # Corrected to fetch from logs


issue (bug_risk): Check for potential IndexError.

If 'logs' is an empty list, this line will raise an IndexError. Consider adding a check to ensure 'logs' is not empty before accessing the first element.

sourcery-ai · 2024-07-16T07:37:52Z

crategen/converters/tes_converter.py

+            "@id": id,
+            "name": name,
+            "description": description,
+            "instrument": executors[0].get("image", None) if executors else None,


issue (bug_risk): Check for potential IndexError.

If 'executors' is an empty list, this line will raise an IndexError. Consider adding a check to ensure 'executors' is not empty before accessing the first element.

sourcery-ai · 2024-07-16T07:37:52Z

crategen/converters/wes_converter.py

+            "status": state,
+            "startTime": convert_to_iso8601(start_time),
+            "endTime": convert_to_iso8601(end_time),
+            "result": [{"@id": output.get("location", ""), "name": output.get("name", "")} for output in outputs],


issue (bug_risk): Check for potential KeyError.

Ensure that 'outputs' is a list of dictionaries and that each dictionary contains the keys 'location' and 'name'. If not, this line may raise a KeyError.

sourcery-ai · 2024-07-16T07:37:52Z

crategen/converters/utils.py

+            except ValueError:
+                continue
+        # Handle incorrect format or other issues
+        return None


suggestion: Consider logging incorrect timestamp formats.

Instead of silently returning None for incorrect timestamp formats, consider logging a warning or error message to help with debugging.

Suggested change

return None

import logging

logging.basicConfig(level=logging.WARNING)

# Handle incorrect format or other issues

logging.warning("Incorrect timestamp format encountered.")

return None

sourcery-ai · 2024-07-16T07:37:53Z

tests/unit/test_wes_converter.py

+        result = self.converter.convert_to_wrroc(wes_data)
+        self.assertEqual(result, expected_wrroc_data)
+
+    def test_convert_from_wrroc(self):


suggestion (testing): Add tests for invalid data formats

It would be beneficial to add tests that check how the converter handles invalid data formats, such as incorrect date formats or unexpected data types.

Suggested change

def test_convert_from_wrroc(self):

def test_convert_from_wrroc_invalid_data(self):

invalid_wrroc_data = {

"@id": 123, # Invalid type, should be a string

"date": "invalid-date-format" # Invalid date format

}

with self.assertRaises(ValueError):

self.converter.convert_from_wrroc(invalid_wrroc_data)

sourcery-ai · 2024-07-16T07:37:53Z

tests/unit/test_tes_converter.py

@@ -0,0 +1,62 @@
+import unittest


suggestion (testing): Consider using pytest for more concise tests

Using pytest can make the tests more concise and easier to read. For example, you can use fixtures for setup and teardown, and avoid boilerplate code.

Suggested change

import unittest

import pytest

sourcery-ai · 2024-07-16T07:37:53Z

tests/unit/test_wes_converter.py

@@ -0,0 +1,58 @@
+import unittest


suggestion (testing): Consider using pytest for more concise tests

Using pytest can make the tests more concise and easier to read. For example, you can use fixtures for setup and teardown, and avoid boilerplate code.

Suggested change

import unittest

import pytest

sourcery-ai · 2024-07-16T07:37:53Z

tests/unit/test_tes_converter.py

+        }
+
+        result = self.converter.convert_to_wrroc(tes_data)
+        self.assertEqual(result, expected_wrroc_data)


suggestion (testing): Add assertion messages for better debugging

Adding custom messages to assertions can help with debugging when a test fails. For example: self.assertEqual(result, expected_wrroc_data, 'Conversion to WRROC failed').

Suggested change

self.assertEqual(result, expected_wrroc_data)

self.assertEqual(result, expected_wrroc_data, 'Conversion to WRROC failed')

sourcery-ai · 2024-07-16T07:37:53Z

tests/unit/test_wes_converter.py

+        }
+
+        result = self.converter.convert_to_wrroc(wes_data)
+        self.assertEqual(result, expected_wrroc_data)


suggestion (testing): Add assertion messages for better debugging

Adding custom messages to assertions can help with debugging when a test fails. For example: self.assertEqual(result, expected_wrroc_data, 'Conversion to WRROC failed').

Suggested change

self.assertEqual(result, expected_wrroc_data)

self.assertEqual(result, expected_wrroc_data, 'Conversion to WRROC failed')

Karanjot786 and others added 30 commits June 21, 2024 09:56

chore(setup): add pyproject.toml and poetry.lock for project setup

94d8a10

chore: Set up CI pipeline

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chore: Set up CI pipeline

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chore: Set up CI pipeline

d925593

Merge branch 'repository-setup' of https://github.com/Karanjot786/wrr…

5d34282

…oc-ga4gh-cloud-converter into repository-setup

fix: resolve merge conflicts and update CI pipeline

60a5dd1

feat: initial project structure and implementation

f3a0695

Merge branch 'elixir-cloud-aai:main' into initial-version

ecf3347

feat: initial project structure and implementation

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Merge branch 'initial-version' of https://github.com/Karanjot786/wrro…

de41acb

…c-ga4gh-cloud-converter into initial-version

feat: initial project structure and implementation

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Karanjot786 closed this Jul 16, 2024

Karanjot786 deleted the add-tests branch July 16, 2024 07:36

sourcery-ai bot reviewed Jul 16, 2024

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test: adding unit tests to separate branch #15

test: adding unit tests to separate branch #15

Karanjot786 commented Jul 16, 2024 •

edited by sourcery-ai bot

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	poetry run ruff check crategen/ tests/
	poetry run ruff check crategen/ tests/specific_test_file.py

-    def test_convert_from_wrroc(self):
+    def test_convert_from_wrroc_invalid_data(self):
+        invalid_wrroc_data = {
+            "@id": 123,  # Invalid type, should be a string
+            "date": "invalid-date-format"  # Invalid date format
+        }
+        with self.assertRaises(ValueError):
+            self.converter.convert_from_wrroc(invalid_wrroc_data)

	self.assertEqual(result, expected_wrroc_data)
	self.assertEqual(result, expected_wrroc_data, 'Conversion to WRROC failed')

test: adding unit tests to separate branch #15

test: adding unit tests to separate branch #15

Conversation

Karanjot786 commented Jul 16, 2024 • edited by sourcery-ai bot Loading

Description:

Files Included:

Details:

Unit Tests for TES Converter:

Unit Tests for WES Converter:

Instructions for Running the Tests:

Sample TES Input (tes_example.json):

Sample WES Input (wes_example.json):

Summary by Sourcery

sourcery-ai bot commented Jul 16, 2024 • edited Loading

Reviewer's Guide by Sourcery

File-Level Changes

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Karanjot786 commented Jul 16, 2024 •

edited by sourcery-ai bot

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Sample TES Input (`tes_example.json`):

Sample WES Input (`wes_example.json`):

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