tests all functioning, now to fix imports and lint

src/cyto_ml/pipeline/pipeline_decollage.py

@@ -119,7 +119,7 @@ def requires(self):
 
     def output(self):
         date = datetime.today().date()
-        return luigi.LocalTarget(f'./decollage_complete_{date}.txt')
+        return luigi.LocalTarget(f'{self.directory}/decollage_complete_{date}.txt')
 
     def run(self):
         metadata = pd.read_csv(self.input()[0].path)
@@ -166,7 +166,7 @@ def requires(self):
 
     def output(self):
         date = datetime.today().date()
-        return luigi.LocalTarget(f'./s3_upload_complete_{date}.txt')
+        return luigi.LocalTarget(f'{self.directory}/s3_upload_complete_{date}.txt')
 
     def run(self):
         # Collect the list of decollaged image files from the output of DecollageImages

tests/test_pipeline.py

@@ -64,21 +64,30 @@ def test_decollage_images(temp_dir):
     output_image = os.path.join(temp_dir, "test_experiment_0.tif")
     assert os.path.exists(output_image), "Decollaged image should be created."
 
-
+class MockTask(luigi.Task):
+    directory = luigi.Parameter()
+    check_unfulfilled_deps = False
+    def output(self) -> luigi.Target:
+        # "The output() method returns one or more Target objects.""
+        return luigi.LocalTarget(f'{self.directory}/out.txt') 
+
 def test_upload_to_api(temp_dir, mocker):
-    # Mock the DecollageImages output using pytest-mock
-    mock_output = mocker.patch('pipeline.pipeline_decollage.DecollageImages.output')
-    mock_output.return_value = [os.path.join(temp_dir, "test_experiment_0.tif")]
-
+    # Write a tmp file to serve as our upstream task's output
+    with open(os.path.join(temp_dir, 'out.txt'), 'w') as out:
+        out.write("blah")
+    # The task `requires` DecollageImages, but that requires other tasks, which run first
+    # Rather than mock its output, or the whole chain, require a mock task that replaces it 
+    mock_output = mocker.patch(f'cyto_ml.pipeline.pipeline_decollage.UploadDecollagedImagesToS3.requires')
+    mock_output.return_value = MockTask(directory=temp_dir)
+
     # Mock the requests.post to simulate the API response
-    mock_post = mocker.patch('pipeline.pipeline_decollage.requests.post')
+    mock_post = mocker.patch('cyto_ml.pipeline.pipeline_decollage.requests.post')
     mock_post.return_value.status_code = 200
 
     task = UploadDecollagedImagesToS3(
         directory=str(temp_dir),
         output_directory=str(temp_dir),
         s3_bucket="mock_bucket",
-        s3_folder="mock_folder"
     )
 
     luigi.build([task], local_scheduler=True)