Merge pull request #98 from sbesson/json_snippets

Extract specification snippets as standalone JSON files
ome · Mar 18, 2022 · 8dec691 · 8dec691
2 parents 047bc0b + 51ccdd9
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diff --git a/0.4/examples/valid_strict/multiscales_example.json b/0.4/examples/valid_strict/multiscales_example.json
@@ -0,0 +1,54 @@
+{
+    "multiscales": [
+        {
+            "version": "0.4",
+            "name": "example",
+            "axes": [
+                {"name": "t", "type": "time", "unit": "millisecond"},
+                {"name": "c", "type": "channel"},
+                {"name": "z", "type": "space", "unit": "micrometer"},
+                {"name": "y", "type": "space", "unit": "micrometer"},
+                {"name": "x", "type": "space", "unit": "micrometer"}
+            ],
+            "datasets": [
+                {
+                    "path": "0",
+                    "coordinateTransformations": [{
+                        // the voxel size for the first scale level (0.5 micrometer)
+                        "type": "scale",
+                        "scale": [1.0, 1.0, 0.5, 0.5, 0.5]
+                    }]
+                },
+                {
+                    "path": "1",
+                    "coordinateTransformations": [{
+                        // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
+                        "type": "scale",
+                        "scale": [1.0, 1.0, 1.0, 1.0, 1.0]
+                    }]
+                },
+                {
+                    "path": "2",
+                    "coordinateTransformations": [{
+                        // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
+                        "type": "scale",
+                        "scale": [1.0, 1.0, 2.0, 2.0, 2.0]
+                    }]
+                }
+            ],
+            "coordinateTransformations": [{
+                // the time unit (0.1 milliseconds), which is the same for each scale level
+                "type": "scale",
+                "scale": [0.1, 1.0, 1.0, 1.0, 1.0]
+            }],
+            "type": "gaussian",
+            "metadata": {
+                "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
+                "method": "skimage.transform.pyramid_gaussian",
+                "version": "0.16.1",
+                "args": "[true]",
+                "kwargs": {"multichannel": true}
+            }
+        }
+    ]
+}
diff --git a/0.4/index.bs b/0.4/index.bs
@@ -92,6 +92,16 @@ of bioimaging data, whether during acquisition or sharing in the cloud.
 Note: The following text makes use of OME-Zarr [[ome-zarr-py]], the current prototype implementation,
 for all examples.
 
+Document conventions
+--------------------
+
+The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”,
+“RECOMMENDED”, “MAY”, and “OPTIONAL” are to be interpreted as described in
+[RFC 2119](https://tools.ietf.org/html/rfc2119).
+
+Some of the JSON examples in this document include commments. However, these are only for
+clarity purposes and comments MUST NOT be included in JSON objects.
+
 On-disk (or in-cloud) layout {#on-disk}
 =======================================
 
@@ -285,45 +295,11 @@ Each "multiscales" dictionary SHOULD contain the field "name". It SHOULD contain
 Each "multiscales" dictionary SHOULD contain the field "type", which gives the type of downscaling method used to generate the multiscale image pyramid.
 It SHOULD contain the field "metadata", which contains a dictionary with additional information about the downscaling method.
 
-```
-{
-    "multiscales": [
-        {
-            "version": "0.4",
-            "name": "example",
-            "axes": [
-                {"name": "t", "type": "time", "unit": "millisecond"},
-                {"name": "c", "type": "channel"},
-                {"name": "z", "type": "space", "unit": "micrometer"},
-                {"name": "y", "type": "space", "unit": "micrometer"},
-                {"name": "x", "type": "space", "unit": "micrometer"}
-            ],
-            "datasets": [
-                {
-                    "path": "0",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 0.5, 0.5, 0.5]}]  # the voxel size for the first scale level (0.5 micrometer)
-                }
-                {
-                    "path": "1",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 1.0, 1.0, 1.0]}]  # the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
-                },
-                {
-                    "path": "2",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 2.0, 2.0, 2.0]}]  # the voxel size for the second scale level (downscaled by a factor of 4 -> 2 micrometer)
-                }
-            ],
-            "coordinateTransformations": [{"type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0]],  # the time unit (0.1 milliseconds), which is the same for each scale level
-            "type": "gaussian",
-            "metadata": {                                       # the fields in metadata depend on the downscaling implementation
-                "method": "skimage.transform.pyramid_gaussian", # here, the paramters passed to the skimage function are given
-                "version": "0.16.1",
-                "args": "[true]",
-                "kwargs": {"multichannel": true}
-            }
-        }
-    ]
-}
-```
+<pre class=include-code>
+path: examples/valid_strict/multiscales_example.json
+highlight: json
+</pre>
+
 
 If only one multiscale is provided, use it. Otherwise, the user can choose by
 name, using the first multiscale as a fallback:

diff --git a/0.4/tests/test_validation.py b/0.4/tests/test_validation.py
@@ -35,9 +35,10 @@ def ids(files):
     "testfile", valid_strict_files, ids=ids(valid_strict_files))
 def test_valid_strict(testfile):
     with open(testfile) as f:
-        json_file = json.load(f)
-        validator.validate(json_file)
-        strict_validator.validate(json_file)
+        data = ''.join(line for line in f if not line.lstrip().startswith('//'))
+        jsondata = json.loads(data)
+        validator.validate(jsondata)
+        strict_validator.validate(jsondata)
 
 
 @pytest.mark.parametrize("testfile", valid_files, ids=ids(valid_files))