Merge pull request #7 from fmi-faim/improve-api

Improve API and tests

src/mobiedantic/__init__.py

@@ -54,6 +54,26 @@ def initialize_with_paths(
         data_format: str = 'ome.zarr',
     ) -> None:
         sources = {}
+        self._update_sources(
+            sources=sources,
+            path_dict=path_dict,
+            channel_index=channel_index,
+            data_format=data_format,
+        )
+        views_dict = {'default': {'uiSelectionGroup': 'view', 'isExclusive': True}}
+        self.model = DatasetSchema(
+            is2D=is2d,
+            sources=sources,
+            views=views_dict,
+        )
+
+    def _update_sources(
+        self,
+        sources: dict[str, Source],
+        path_dict: dict[str, Path],
+        channel_index: int = 0,
+        data_format: str = 'ome.zarr',
+    ):
         for name in path_dict:
             try:
                 source_path = {
@@ -77,11 +97,19 @@ def initialize_with_paths(
                 }
             }
             sources[name] = Source(**data)
-        views_dict = {'default': {'uiSelectionGroup': 'view', 'isExclusive': True}}
-        self.model = DatasetSchema(
-            is2D=is2d,
-            sources=sources,
-            views=views_dict,
+
+    def add_sources(
+        self,
+        path_dict: dict[str, Path],
+        *,
+        channel_index: int = 0,
+        data_format: str = 'ome.zarr',
+    ):
+        self._update_sources(
+            sources=self.model.sources,
+            path_dict=path_dict,
+            channel_index=channel_index,
+            data_format=data_format,
         )
 
     def add_merged_grid(
@@ -151,6 +179,15 @@ def new_dataset(
             self.model.defaultDataset = name
         return Dataset(path=dataset_folder)
 
+    def load(self):
+        project_path = self.path / 'project.json'
+        if not project_path.exists():
+            message = f'Project file not found: {project_path}'
+            raise ValueError(message)
+        with open(project_path) as project_file:
+            data = json.loads(project_file.read())
+            self.model = ProjectSchema(**data)
+
     def save(self, *, create_directory: bool = True):
         if self.model is None:
             message = 'Project not initialized.'

tests/test_api.py

@@ -1,6 +1,8 @@
 from pathlib import Path
 
-from mobiedantic import Project
+import pytest
+
+from mobiedantic import Dataset, Project
 
 
 def test_project(tmp_path):
@@ -15,7 +17,7 @@ def test_project(tmp_path):
 def test_dataset(tmp_path):
     project = Project(tmp_path)
     project.initialize_model(description='Testing datasets')
-    dataset1 = project.new_dataset('Dataset_1')
+    dataset1: Dataset = project.new_dataset('Dataset_1')
     sources1 = {
         'A01': Path('../../non-existent.zarr/A/01/0'),
         'A02': Path('../../non-existent.zarr/A/02/0'),
@@ -44,14 +46,100 @@ def test_dataset(tmp_path):
     assert (
         len(dataset1.model.views['default'].sourceTransforms[0].mergedGrid.sources) == 2
     )
-
-    dataset2 = project.new_dataset('Dataset_2')
     sources2 = {
         'C01': Path('../../non-existent.zarr/C/01/0'),
         'C02': Path('../../non-existent.zarr/C/02/0'),
     }
-    dataset2.initialize_with_paths(
+    dataset1.add_sources(
         path_dict=sources2,
-        is2d=False,
         channel_index=0,
+        data_format='ome.zarr',
+    )
+    dataset1.add_merged_grid(
+        name='Merged_grid_view_2',
+        sources=list(sources2),
+    )
+    assert len(dataset1.model.sources) == 4
+    assert len(dataset1.model.views['default'].sourceDisplays) == 2
+    assert (
+        dataset1.model.views['default'].sourceDisplays[1].imageDisplay.name.root
+        == 'Merged_grid_view_2'
+    )
+    assert len(dataset1.model.views['default'].sourceTransforms) == 2
+    assert (
+        dataset1.model.views['default']
+        .sourceTransforms[1]
+        .mergedGrid.mergedGridSourceName.root
+        == 'Merged_grid_view_2'
+    )
+    assert (
+        len(dataset1.model.views['default'].sourceTransforms[1].mergedGrid.sources) == 2
+    )
+    project.new_dataset('Dataset_2')
+    assert len(project.model.datasets) == 2
+
+
+def test_save_and_load(tmp_path):
+    project = Project(tmp_path)
+    project.initialize_model(description='Testing saving and loading')
+    dataset_name = 'dataset1'
+    dataset = project.new_dataset(dataset_name)
+    sources = {
+        'A01': '/path/to/source',
+    }
+    dataset.initialize_with_paths(
+        path_dict=sources,
+        is2d=True,
     )
+    dataset.save()
+    project.save()
+
+    project_loaded = Project(tmp_path)
+    project_loaded.load()
+
+    assert project.model == project_loaded.model
+
+    dataset_loaded = Dataset(tmp_path / dataset_name)
+    dataset_loaded.load()
+
+    assert dataset.model == dataset_loaded.model
+
+
+def test_dataset_errors(tmp_path):
+    filename = 'dataset.json'
+    with open(tmp_path / filename, 'w'):
+        pass
+    with pytest.raises(ValueError, match="'path' needs to point to a directory"):
+        Dataset(path=(tmp_path / filename))
+    dataset_dir = tmp_path / 'dataset'
+    dataset = Dataset(path=dataset_dir)
+    with pytest.raises(ValueError, match='Dataset not initialized.'):
+        dataset.save()
+    sources = {
+        'A01': '/path/to/source',
+    }
+    dataset.initialize_with_paths(
+        path_dict=sources,
+        is2d=True,
+    )
+    with pytest.raises(
+        ValueError, match="Dataset folder doesn't exist yet and may not be created."
+    ):
+        dataset.save(create_directory=False)
+    with pytest.raises(ValueError, match='Dataset file not found'):
+        dataset.load()
+
+
+def test_project_errors(tmp_path):
+    project = Project(tmp_path / 'non-existent_subfolder')
+    with pytest.raises(ValueError, match='Project not initialized'):
+        project.save()
+    with pytest.raises(ValueError, match='Project file not found'):
+        project.load()
+    with pytest.raises(ValueError, match='Project not initialized'):
+        project.new_dataset('dataset1')
+    project.initialize_model(description='Test raising errors.')
+    with pytest.raises(
+        ValueError, match="Project folder doesn't exist yet and may not be created."
+    ):
+        project.save(create_directory=False)