Add jsonschema for validating schemas

MANIFEST.in

@@ -2,3 +2,4 @@ include *.txt
 include *.rst
 prune dist
 prune build
+include src/omero_render/*.yaml

setup.py

@@ -96,8 +96,9 @@ def read(fname):
 
 setup(
     version=version,
-    packages=['', 'omero.plugins'],
+    packages=['', 'omero.plugins', 'omero_render'],
     package_dir={"": "src"},
+    include_package_data=True,
     name='omero-cli-render',
     description="Plugin for use in the OMERO CLI.",
     long_description=read('README.rst'),
@@ -120,6 +121,7 @@ def read(fname):
     install_requires=[
         'PyYAML',
         'omero-py>=5.6.0',
+        'jsonschema',
         'future'
         ],
     python_requires='>=3',

src/omero_cli_render.py

@@ -45,6 +45,8 @@
 
 from omero import UnloadedEntityException
 
+from omero_render import validate_renderdef, validate_renderdef_batch
+
 HELP = "Tools for working with rendering settings"
 
 INFO_HELP = """Show details of a rendering setting
@@ -667,6 +669,8 @@ def _load_rendering_settings(self, source, session=None):
             self.ctx.dbg(e)
             self.ctx.die(103, "Could not read %s" % source)
 
+        validate_renderdef(data)
+
         if 'channels' not in data:
             self.ctx.die(104, "ERROR: No channels found in %s" % source)
 
@@ -773,6 +777,8 @@ def batchset(self, args):
         except Exception as e:
             self.ctx.dbg(e)
             self.ctx.die(103, "Could not read %s" % args.path)
+        validate_renderdef_batch(batch_data)
+
         for key, containers in batch_data.items():
             if key.startswith('_'):
                 continue

src/omero_render/__init__.py

@@ -0,0 +1,2 @@
+from .schema import validate_renderdef, validate_renderdef_batch
+__all__ = ['validate_renderdef', 'validate_renderdef_batch']

src/omero_render/renderdef-batch-schema.yaml

@@ -0,0 +1,115 @@
+---
+
+$schema: https://json-schema.org/schema#
+$id: https://github.com/ome/omero-cli-render#renderdef-batch
+title: jsonschema for batch rendering configuration
+type: object
+additionalProperties: false
+# Top level objects beginning with _ will be ignored
+patternProperties:
+  "^_":
+      type:
+        object
+
+# Python jsonschema doesn't support $ref so use YAML anchors instead
+definitions:
+  channel: &channel
+    type: object
+    additionalProperties: false
+    properties:
+      active:
+        title: Active channel
+        type: boolean
+      color:
+        title: Channel color as HTML RGB triplet
+        type: string
+      label:
+        title: Channel name
+        type: string
+      start:
+        title: Start of rendering window, optional (needs end)
+        type: number
+      end:
+        title: End of rendering window, optional (needs start)
+        type: number
+      min:
+        title: Minimum pixel intensity, optional (needs max)
+        type: number
+      max:
+        title: Maximum pixel intensity, optional (needs min)
+        type: number
+
+  renderdef: &renderdef
+    type: object
+    additionalProperties: false
+    required:
+      - channels
+    properties:
+      channels:
+        title: Dictionary of channels
+        type: object
+        additionalProperties: false
+        patternProperties:
+          "^[0-9]+$":
+            title: Channel index, 1-based
+            type: object
+            properties: *channel
+              # $ref: "#/definitions/channel"
+      greyscale:
+        title: Greyscale rendering, optional
+        type: boolean
+      z:
+        title: Default Z plane index, 1-based, optional
+        type: integer
+      t:
+        title: Default T plane index, 1-based, optional
+        type: integer
+      version:
+        title: Version of the renderdef specification
+        type: integer
+
+  dataset: &dataset
+    type: object
+    additionalProperties: false
+    required:
+      - name
+      - renderdef
+    properties:
+      name:
+        title: Name of Dataset
+        type: string
+      renderdef: *renderdef
+        # $ref: "#/definitions/renderdef"
+
+  project: &project
+    type: object
+    additionalProperties: false
+    required:
+      - name
+    properties:
+      name:
+        title: Name of Project
+        type: string
+      datasets:
+        title: List of Datasets
+        type: array
+        minItems: 1
+        items: *dataset
+          # $ref: "#/definitions/dataset"
+      renderdef: *renderdef
+        # $ref: "#/definitions/renderdef"
+
+properties:
+  projects:
+    title: List of Projects
+    type: array
+    minItems: 1
+    items: *project
+      # $ref: "#/definitions/project"
+
+  datasets:
+    title: List of Datasets
+    type: array
+    minItems: 1
+    items: *dataset
+      # $ref: "#/definitions/dataset"

src/omero_render/renderdef-schema.yaml

@@ -0,0 +1,61 @@
+---
+
+$schema: https://json-schema.org/schema#
+$id: https://github.com/ome/omero-cli-render#renderdef
+title: jsonschema for render configuration file
+type: object
+additionalProperties: false
+required:
+  - channels
+
+# Python jsonschema doesn't support $ref so use YAML anchors instead
+definitions:
+  channel: &channel
+    type: object
+    additionalProperties: false
+    properties:
+      active:
+        title: Active channel
+        type: boolean
+      color:
+        title: Channel color as HTML RGB triplet
+        type: string
+      label:
+        title: Channel name
+        type: string
+      start:
+        title: Start of rendering window, optional (needs end)
+        type: number
+      end:
+        title: End of rendering window, optional (needs start)
+        type: number
+      min:
+        title: Minimum pixel intensity, optional (needs max)
+        type: number
+      max:
+        title: Maximum pixel intensity, optional (needs min)
+        type: number
+
+properties:
+  channels:
+    title: Dictionary of channels
+    type: object
+    additionalProperties: false
+    patternProperties:
+      "^[0-9]+$":
+        title: Channel index, 1-based
+        type: object
+        properties:
+          channel: *channel
+  greyscale:
+    title: Greyscale rendering, optional
+    type: boolean
+  z:
+    title: Default Z plane index, 1-based, optional
+    type: integer
+  t:
+    title: Default T plane index, 1-based, optional
+    type: integer
+  version:
+    title: Version of the renderdef specification
+    type: integer

src/omero_render/schema.py

@@ -0,0 +1,31 @@
+import json
+from jsonschema import Draft7Validator
+from pkgutil import get_data
+import yaml
+
+
+def _validate(schema_name, renderdef):
+    schemastr = get_data('omero_render', schema_name)
+    yml = yaml.safe_load(schemastr)
+    # Hack to expand anchors
+    # https://stackoverflow.com/a/64993515
+    schema = json.loads(json.dumps(yml))
+    v = Draft7Validator(schema)
+    # print(yaml.dump(schema))
+    # print(renderdef)
+    # Hack to ensure YAML integer keys are JSON strings
+    renderdef_json = json.loads(json.dumps(renderdef))
+
+    if not v.is_valid(renderdef_json):
+        errs = '\n\n** '.join(
+            ['Invalid definition'] +
+            ['\n\n'.join(str(e) for e in v.iter_errors(renderdef_json))])
+        raise ValueError(errs)
+
+
+def validate_renderdef(renderdef):
+    _validate('renderdef-schema.yaml', renderdef)
+
+
+def validate_renderdef_batch(renderdef):
+    _validate('renderdef-batch-schema.yaml', renderdef)