Test new type metadata

silx-kit · Jan 25, 2024 · de5ceee · de5ceee
1 parent 0f21787
commit de5ceee
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Showing 4 changed files with 135 additions and 11 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -6,7 +6,7 @@
 pip install -e .[dev]
 ```
 
-will install `h5grove` in editable mode with all the linting/formating/testing packages. This will also install the [flask](https://flask.palletsprojects.com/en/) and [tornado](https://www.tornadoweb.org/en/stable/) packages as they are needed to build the documentation.
+will install `h5grove` in editable mode with all the linting/formating/testing packages. This will also install the [fastapi](https://fastapi.tiangolo.com/), [flask](https://flask.palletsprojects.com/en/) and [tornado](https://www.tornadoweb.org/en/stable/) packages as they are needed to build the documentation and test the project.
 
 ## Linting
 

diff --git a/setup.cfg b/setup.cfg
@@ -26,7 +26,7 @@ install_requires =
 
 [options.extras_require]
 fastapi = 
-    fastapi
+	fastapi
 	pydantic > 2
 	pydantic-settings
 	uvicorn
@@ -35,14 +35,15 @@ flask =
 	Flask-Compress
 	Flask-Cors
 tornado =
-    tornado
+	tornado
 dev = 
 	black
 	bump2version
 	check-manifest
 	flake8
 	h5grove[fastapi]
 	h5grove[flask]
+	h5grove[tornado]
 	invoke
 	mypy
 	myst-parser

diff --git a/tasks.py b/tasks.py
@@ -32,9 +32,14 @@ def lint(c):
 
 
 @task
-def test(c):
+def test(c, verbose=False, keyword="", cov_lines=False):
     """Test without benchmark"""
-    c.run("pytest --benchmark-skip")
+    c.run(
+        "pytest --benchmark-skip"
+        + (" -vv" if verbose else "")
+        + ((" -k" + keyword) if keyword else "")
+        + (" --cov-report term-missing" if cov_lines else "")
+    )
 
 
 @task

diff --git a/test/base_test.py b/test/base_test.py
@@ -85,7 +85,7 @@ def test_data_on_array_with_dtype(self, server, format_arg, dtype_arg):
             h5file[tested_h5entity_path] = data
 
         response = server.get(
-            f"/data/?{urlencode({ 'file': filename, 'path': tested_h5entity_path, 'format': format_arg, 'dtype': dtype_arg })}"
+            f"/data/?{urlencode({'file': filename, 'path': tested_h5entity_path, 'format': format_arg, 'dtype': dtype_arg})}"
         )
 
         retrieved_data = decode_array_response(
@@ -134,11 +134,11 @@ def test_meta_on_chunked_compressed_dataset(self, server):
         assert content == {
             "attributes": [],
             "chunks": [5, 5],
-            "dtype": "<f8",
             "filters": [{"id": 2, "name": "shuffle"}, {"id": 1, "name": "deflate"}],
             "kind": "dataset",
             "name": "data",
             "shape": [10, 10],
+            "type": {"class": 1, "dtype": "<f8", "size": 8, "order": 0},
         }
 
     def test_meta_on_compound_dataset(self, server):
@@ -161,11 +161,129 @@ def test_meta_on_compound_dataset(self, server):
         assert content == {
             "attributes": [],
             "chunks": None,
-            "dtype": {"name": "|S10", "age": "<i4", "weight": "<f4"},
             "filters": None,
+            "kind": "dataset",
             "name": "dogs",
             "shape": [2],
-            "type": "dataset",
+            "type": {
+                "class": 6,
+                "dtype": {"age": "<i4", "name": "|S10", "weight": "<f4"},
+                "size": 18,
+                "members": {
+                    "age": {
+                        "class": 0,
+                        "dtype": "<i4",
+                        "size": 4,
+                        "order": 0,
+                        "sign": 1,
+                    },
+                    "name": {
+                        "class": 3,
+                        "dtype": "|S10",
+                        "size": 10,
+                        "cset": 0,
+                        "vlen": False,
+                    },
+                    "weight": {"class": 1, "dtype": "<f4", "size": 4, "order": 0},
+                },
+            },
+        }
+
+    def test_meta_on_compound_dataset_with_advanced_types(self, server):
+        """Test /meta/ endpoint on compound dataset with advanced types"""
+        filename = "test.h5"
+        tested_h5entity_path = "/foo"
+
+        with h5py.File(server.served_directory / filename, mode="w") as h5file:
+            opaque = np.void(b"\x00\x11\x22")
+
+            for_ref = h5file.create_dataset("/bar", data=0)
+
+            h5file.create_dataset(
+                tested_h5entity_path,
+                data=np.array(
+                    [
+                        (
+                            opaque,
+                            42,
+                            np.array(["bar"], h5py.string_dtype()),
+                            np.array([0], np.uint64),
+                            for_ref.ref,
+                        )
+                    ],
+                    dtype=[
+                        ("opaque", opaque.dtype),
+                        ("enum", h5py.enum_dtype({"H2G2": 42})),
+                        ("arr", h5py.string_dtype(), (1,)),
+                        ("vlen", h5py.vlen_dtype(np.uint64)),
+                        ("ref", h5py.ref_dtype),
+                    ],
+                ),
+            )
+
+        response = server.get(f"/meta/?file={filename}&path={tested_h5entity_path}")
+        content = decode_response(response)
+
+        assert content == {
+            "attributes": [],
+            "chunks": None,
+            "filters": None,
+            "kind": "dataset",
+            "name": "foo",
+            "shape": [1],
+            "type": {
+                "class": 6,
+                "dtype": {
+                    "opaque": "|V3",
+                    "enum": "|u1",
+                    "arr": "|V8",
+                    "vlen": "|O",
+                    "ref": "|O",
+                },
+                "size": 36,
+                "members": {
+                    "opaque": {"class": 5, "dtype": "|V3", "size": 3, "tag": ""},
+                    "enum": {
+                        "class": 8,
+                        "dtype": "|u1",
+                        "size": 1,
+                        "members": {"H2G2": 42},
+                        "base": {
+                            "class": 0,
+                            "dtype": "|u1",
+                            "size": 1,
+                            "order": 0,
+                            "sign": 0,
+                        },
+                    },
+                    "arr": {
+                        "class": 10,
+                        "dtype": "|V8",
+                        "size": 8,
+                        "dims": [1],
+                        "base": {
+                            "class": 3,
+                            "dtype": "|O",
+                            "size": 8,
+                            "cset": 1,
+                            "vlen": True,
+                        },
+                    },
+                    "vlen": {
+                        "class": 9,
+                        "dtype": "|O",
+                        "size": 16,
+                        "base": {
+                            "class": 0,
+                            "dtype": "<u8",
+                            "order": 0,
+                            "sign": 0,
+                            "size": 8,
+                        },
+                    },
+                    "ref": {"class": 7, "dtype": "|O", "size": 8},
+                },
+            },
         }
 
     def test_meta_on_group(self, server):
@@ -221,11 +339,11 @@ def test_meta_on_valid_ext_link(self, server, resolve_links):
             assert content == {
                 "attributes": [],
                 "chunks": None,
-                "dtype": "<f8",
                 "filters": None,
                 "kind": "dataset",
                 "name": "ext_link",
                 "shape": [10],
+                "type": {"class": 1, "dtype": "<f8", "order": 0, "size": 8},
             }
 
     def test_stats_on_negative_scalar(self, server):
@@ -358,9 +476,9 @@ def test_meta_on_broken_soft_link(self, server, resolve_links):
             response = server.get(url)
             content = decode_response(response)
             assert content == {
+                "kind": "soft_link",
                 "name": "link",
                 "target_path": "not_an_entity",
-                "type": "soft_link",
             }
 
     def test_403_on_file_without_read_permission(self, server):