Merge pull request #44 from silx-kit/binary

Added bin format to encoders

docs/low_level.md

@@ -44,7 +44,7 @@ These methods are directly plugged to the endpoints from the example implementat
 
 ## `encoders` module
 
-The [encoders](https://silx-kit.github.io/h5grove/reference.html#encoders-module) module contain functions that encode data and provide the appropriate headers to build request responses. The module provides a JSON encoder using `orjson` and a binary encoder for NumPy arrays.
+The [encoders](https://silx-kit.github.io/h5grove/reference.html#encoders-module) module contain functions that encode data and provide the appropriate headers to build request responses. The module provides a JSON encoder using `orjson` and binary encoders for NumPy arrays.
 
 ### General
 
@@ -61,8 +61,9 @@ The [encoders](https://silx-kit.github.io/h5grove/reference.html#encoders-module
 .. autofunction:: h5grove.encoders.orjson_encode
 ```
 
-### npy
+### binary
 
 ```{eval-rst}
+.. autofunction:: h5grove.encoders.bin_encode
 .. autofunction:: h5grove.encoders.npy_stream
 ```

h5grove/encoders.py

@@ -7,6 +7,16 @@
 from .utils import sanitize_array
 
 
+def bin_encode(array: Sequence[Number]) -> bytes:
+    """Sanitize an array and convert it to bytes.
+
+    :param array: Data to convert
+    """
+    sanitized_array = sanitize_array(array)
+
+    return sanitized_array.tobytes()
+
+
 def orjson_default(o) -> Union[list, str, None]:
     """Converts Python objects to JSON-serializable objects.
 
@@ -66,7 +76,7 @@ def npy_stream(array: Sequence[Number]) -> Generator[bytes, None, None]:
 
 
 class Response(NamedTuple):
-    content: Generator[bytes, None, None]
+    content: Union[Generator[bytes, None, None], bytes]
     """ Encoded `content` as a generator of bytes """
     headers: Dict[str, str]
     """ Associated headers """
@@ -86,16 +96,25 @@ def encode(content, encoding: Optional[str] = "json") -> Response:
     """
     if encoding in ("json", None):
         return Response(
-            (chunk for chunk in (orjson_encode(content),)),  # generator
+            orjson_encode(content),
             headers={"Content-Type": "application/json"},
         )
-    elif encoding == "npy":
+
+    if encoding == "npy":
         return Response(
             npy_stream(content),
             headers={
                 "Content-Type": "application/octet-stream",
                 "Content-Disposition": 'attachment; filename="data.npy"',
             },
         )
-    else:
-        raise ValueError(f"Unsupported encoding {encoding}")
+
+    if encoding == "bin":
+        return Response(
+            bin_encode(content),
+            headers={
+                "Content-Type": "application/octet-stream",
+            },
+        )
+
+    raise ValueError(f"Unsupported encoding {encoding}")

h5grove/flaskutils.py

@@ -19,9 +19,9 @@
 ]
 
 
-def make_encoded_response(content, format: Optional[str]) -> Response:
+def make_encoded_response(content, format_arg: Optional[str]) -> Response:
     """Prepare flask Response according to format"""
-    encoded_content, headers = encode(content, format)
+    encoded_content, headers = encode(content, format_arg)
     response = Response(encoded_content)
     response.headers.update(headers)
     return response
@@ -35,8 +35,8 @@ def get_content(h5file: h5py.File, path: Optional[str], resolve_links: bool = Tr
         abort(404, str(e))
 
 
-def get_filename(request: Request) -> str:
-    file_path = request.args.get("file")
+def get_filename(a_request: Request) -> str:
+    file_path = a_request.args.get("file")
     if file_path is None:
         raise KeyError("File argument is required")
 
@@ -51,53 +51,53 @@ def attr_route():
     """`/attr/` endpoint handler"""
     filename = get_filename(request)
     path = request.args.get("path")
-    format = request.args.get("format")
+    format_arg = request.args.get("format")
 
     with h5py.File(filename, mode="r") as h5file:
         content = get_content(h5file, path)
         assert isinstance(content, ResolvedEntityContent)
-        return make_encoded_response(content.attributes(), format)
+        return make_encoded_response(content.attributes(), format_arg)
 
 
 def data_route():
     """`/data/` endpoint handler"""
     filename = get_filename(request)
     path = request.args.get("path")
     selection = request.args.get("selection")
-    format = request.args.get("format")
+    format_arg = request.args.get("format")
 
     with h5py.File(filename, mode="r") as h5file:
         content = get_content(h5file, path)
         assert isinstance(content, DatasetContent)
-        return make_encoded_response(content.data(selection), format)
+        return make_encoded_response(content.data(selection), format_arg)
 
 
 def meta_route():
     """`/meta/` endpoint handler"""
     filename = get_filename(request)
     path = request.args.get("path")
-    format = request.args.get("format")
+    format_arg = request.args.get("format")
     resolve_links_arg = request.args.get("resolve_links")
     resolve_links = (
         resolve_links_arg.lower() != "false" if resolve_links_arg is not None else True
     )
 
     with h5py.File(filename, mode="r") as h5file:
         content = get_content(h5file, path, resolve_links)
-        return make_encoded_response(content.metadata(), format)
+        return make_encoded_response(content.metadata(), format_arg)
 
 
 def stats_route():
     """`/stats/` endpoint handler"""
     filename = get_filename(request)
     path = request.args.get("path")
     selection = request.args.get("selection")
-    format = request.args.get("format")
+    format_arg = request.args.get("format")
 
     with h5py.File(filename, mode="r") as h5file:
         content = get_content(h5file, path)
         assert isinstance(content, DatasetContent)
-        return make_encoded_response(content.data_stats(selection), format)
+        return make_encoded_response(content.data_stats(selection), format_arg)
 
 
 URL_RULES = {

h5grove/tornadoutils.py

@@ -1,7 +1,7 @@
 """Helpers for usage with `Tornado <https://www.tornadoweb.org>`_"""
 from h5grove.utils import NotFoundError
 import os
-from typing import Any, Optional
+from typing import Any, Generator, Optional
 import h5py
 from tornado.web import RequestHandler, MissingArgumentError, HTTPError
 from .content import DatasetContent, ResolvedEntityContent, create_content
@@ -31,7 +31,7 @@ def get(self):
             raise MissingArgumentError("file")
 
         path = self.get_query_argument("path", None)
-        format = self.get_query_argument("format", None)
+        format_arg = self.get_query_argument("format", None)
 
         full_file_path = os.path.join(self.base_dir, file_path)
         if not os.path.isfile(full_file_path):
@@ -43,12 +43,16 @@ def get(self):
             except NotFoundError as e:
                 raise HTTPError(status_code=404, reason=str(e))
 
-        encoded_content_chunks, headers = encode(content, format)
+        chunks, headers = encode(content, format_arg)
 
         for key, value in headers.items():
             self.set_header(key, value)
-        for chunk in encoded_content_chunks:
-            self.write(chunk)
+
+        if isinstance(chunks, Generator):
+            for chunk in chunks:
+                self.write(chunk)
+        else:
+            self.write(chunks)
         self.finish()
 
     def get_content(self, h5file, path):

test/test_benchmark_data.py

@@ -7,7 +7,7 @@
 import pytest
 
 # Benchmark conditions
-BENCHMARK_FORMAT = "json", "npy"
+BENCHMARK_FORMAT = "json", "npy", "bin"
 BENCHMARKS = dict(
     (f"/{size}square_{dtype}", (size, dtype))
     for dtype in ("float32",)