Allow passing artifacts as data in addition to paths, urls, and zarr …

…stores (#371)

* Register artifacts in wrapper constructors

* Docs

* Add test

* Update

* Version bump

* Lint

* Update is_remote logic

* Update

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "vitessce"
-version = "3.3.5"
+version = "3.4.0"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

tests/test_config.py

@@ -20,6 +20,20 @@
 )
 
 
+class MockArtifactPath:
+    def __init__(self, url):
+        self.url = url
+
+    def to_url(self):
+        return self.url
+
+
+class MockArtifact:
+    def __init__(self, name, url):
+        self.name = name
+        self.path = MockArtifactPath(url)
+
+
 def test_config_creation():
     vc = VitessceConfig(schema_version="1.0.15")
     vc_dict = vc.to_dict()
@@ -107,6 +121,55 @@ def test_config_add_anndata_url():
     }
 
 
+def test_config_add_anndata_artifact():
+    vc = VitessceConfig(schema_version="1.0.15")
+    vc.add_dataset(name='My Dataset').add_object(
+        AnnDataWrapper(
+            adata_artifact=MockArtifact("My anndata artifact", "http://example.com/adata.h5ad.zarr"),
+            obs_set_paths=["obs/louvain"],
+        )
+    )
+
+    vc_dict = vc.to_dict()
+
+    assert vc_dict == {
+        "version": "1.0.15",
+        "name": "",
+        "description": "",
+        "datasets": [
+            {
+                'uid': 'A',
+                'name': 'My Dataset',
+                'files': [
+                    {
+                        "fileType": "anndata.zarr",
+                        "url": "http://example.com/adata.h5ad.zarr",
+                        "options": {
+                            "obsSets": [
+                                {
+                                    "name": "louvain",
+                                    "path": "obs/louvain",
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        ],
+        'coordinationSpace': {
+            'dataset': {
+                'A': 'A'
+            },
+        },
+        "layout": [],
+        "initStrategy": "auto"
+    }
+
+    vc_artifacts = vc.get_artifacts()
+    assert list(vc_artifacts.keys()) == ["http://example.com/adata.h5ad.zarr"]
+    assert vc_artifacts["http://example.com/adata.h5ad.zarr"].name == "My anndata artifact"
+
+
 def test_config_add_dataset_add_files():
     vc = VitessceConfig(schema_version="1.0.15")
     vc.add_dataset(name='My Chained Dataset').add_file(

vitessce/config.py

@@ -235,6 +235,13 @@ def get_routes(self):
 
         return routes
 
+    def get_artifacts(self):
+        artifacts = {}
+        for obj in self.objs:
+            artifacts.update(obj.get_artifacts())
+
+        return artifacts
+
     def get_stores(self, base_url=None):
         stores = {}
         for obj in self.objs:
@@ -1590,6 +1597,18 @@ def get_routes(self):
             routes += d.get_routes()
         return routes
 
+    def get_artifacts(self):
+        """
+        Get all artifacts for this view config from the datasets.
+
+        :returns: A dict mapping artifact URLs to corresponding artifact objects.
+        :rtype: dict[str, lamindb.Artifact]
+        """
+        artifacts = {}
+        for d in self.config["datasets"]:
+            artifacts.update(d.get_artifacts())
+        return artifacts
+
     def get_stores(self, base_url=None):
         """
         Convert the routes for this view config from the datasets.