Use example values for JSON interfaces in examples

grand_challenge_forge/generation_utils.py

@@ -1,9 +1,11 @@
+import json
 import os
 import shutil
 import uuid
 from datetime import datetime, timezone
 from pathlib import Path
 
+import black
 from jinja2 import FileSystemLoader, StrictUndefined, TemplateNotFound
 from jinja2.sandbox import ImmutableSandboxedEnvironment
 
@@ -27,20 +29,36 @@ def is_file(component_interface):
     ] == "File" and not component_interface["relative_path"].endswith(".json")
 
 
+def has_example_value(component_interface):
+    return (
+        "example_value" in component_interface
+        and component_interface["example_value"] is not None
+    )
+
+
 def create_civ_stub_file(*, target_path, component_interface):
     """Creates a stub based on a component interface"""
     target_path.parent.mkdir(parents=True, exist_ok=True)
+
+    if has_example_value(component_interface):
+        target_path.write_text(
+            json.dumps(
+                component_interface["example_value"],
+                indent=4,
+            )
+        )
+        return
+
+    # Copy over an example
     if is_json(component_interface):
-        src = RESOURCES_PATH / "example.json"
+        shutil.copy(RESOURCES_PATH / "example.json", target_path)
     elif is_image(component_interface):
         target_path = target_path / f"{str(uuid.uuid4())}.mha"
         target_path.parent.mkdir(parents=True, exist_ok=True)
-        src = RESOURCES_PATH / "example.mha"
+        shutil.copy(RESOURCES_PATH / "example.mha", target_path)
     else:
         target_path.parent.mkdir(parents=True, exist_ok=True)
-        src = RESOURCES_PATH / "example.txt"
-
-    shutil.copy(src, target_path)
+        shutil.copy(RESOURCES_PATH / "example.txt", target_path)
 
 
 def ci_to_civ(component_interface):
@@ -60,7 +78,9 @@ def ci_to_civ(component_interface):
             f"{component_interface['relative_path']}"
         )
     if component_interface["super_kind"] == "Value":
-        civ["value"] = '{"some_key": "some_value"}'
+        civ["value"] = component_interface.get(
+            "example_value", {"some_key": "some_value"}
+        )
     return {
         **civ,
         "interface": component_interface,
@@ -140,10 +160,25 @@ def copy_and_render(
                 # Copy non-template files
                 shutil.copy2(source_file, output_file)
 
+    apply_black(output_path)
+
 
 def check_allowed_source(path):
     if PARTIALS_PATH.resolve() not in path.resolve().parents:
         raise PermissionError(
             f"Only files under {PARTIALS_PATH} are allowed "
             "to be copied or rendered"
         )
+
+
+def apply_black(target_path):
+    for python_file in target_path.glob("**/*.py"):
+        # Use direct black format call because black
+        # CLI entrypoint ignores files in .gitignore
+
+        black.format_file_in_place(
+            python_file,
+            fast=False,
+            mode=black.Mode(),
+            write_back=black.WriteBack.YES,
+        )

grand_challenge_forge/partials/algorithm-template/inference.py.j2

@@ -64,7 +64,8 @@ def run():
     # For now, let us make bogus predictions
     {%- for ci in algorithm.outputs %}
     output_{{ ci.slug.replace("-", "_")}} =
-        {%- if ci | is_image %} numpy.eye(4, 2)
+        {%- if ci | has_example_value %} {{ ci.example_value }}
+        {%- elif ci | is_image %} numpy.eye(4, 2)
         {%- elif ci | is_json %} {"content": "should match the required format"}
         {%- elif ci | is_file %} "content: should match the required format"
         {% endif %}

grand_challenge_forge/partials/example-algorithm/inference.py.j2

@@ -62,7 +62,8 @@ def run():
     # For now, let us make bogus predictions
     {%- for ci in phase.algorithm_outputs %}
     output_{{ ci.slug.replace("-", "_")}} =
-        {%- if ci | is_image %} numpy.eye(4, 2)
+        {%- if ci | has_example_value %} {{ ci.example_value }}
+        {%- elif ci | is_image %} numpy.eye(4, 2)
         {%- elif ci | is_json %} {"content": "should match the required format"}
         {%- elif ci | is_file %} "content: should match the required format"
         {% endif %}

grand_challenge_forge/partials/filters.py

@@ -36,3 +36,8 @@ def is_file(arg):
 @register_simple_filter
 def has_file(arg):
     return any(generation_utils.is_file(item) for item in arg)
+
+
+@register_simple_filter
+def has_example_value(arg):
+    return generation_utils.has_example_value(arg)

pyproject.toml

@@ -21,6 +21,7 @@ python = ">3.10"
 jinja2 = "*"
 click = "*"
 jsonschema = "*"
+black = "23.9.1"
 
 [tool.poetry.dev-dependencies]
 pytest = "*"

tests/utils.py

@@ -38,51 +38,59 @@
                         "slug": "input-ci-slug",
                         "kind": "Segmentation",
                         "super_kind": "Image",
-                        "relative_path": "images/input-value"
+                        "relative_path": "images/input-value",
+                        "example_value": None
                     },
                     {
                         "slug": "another-input-ci-slug",
                         "kind": "Anything",
                         "super_kind": "File",
-                        "relative_path": "another-input-value.json"
+                        "relative_path": "another-input-value.json",
+                        "example_value": {"key": "value"}
                     },
                     {
                         "slug": "yet-another-input-ci-slug",
                         "kind": "Anything",
                         "super_kind": "Value",
-                        "relative_path": "yet-another-input-value.json"
+                        "relative_path": "yet-another-input-value.json",
+                        "example_value": {"key": "value"}
                     },
                     {
                         "slug": "yet-another-non-json-input-ci-slug",
                         "kind": "Anything",
                         "super_kind": "File",
-                        "relative_path": "yet-another-non-json-input-value"
+                        "relative_path": "yet-another-non-json-input-value",
+                        "example_value": None
                     }
                 ],
                 "algorithm_outputs": [
                     {
                         "slug": "output-ci-slug",
                         "kind": "Image",
                         "super_kind": "Image",
-                        "relative_path": "images/output-value"
+                        "relative_path": "images/output-value",
+                        "example_value": None
                     },
                     {
                         "slug": "another-output-ci-slug",
                         "kind": "Anything",
                         "super_kind": "File",
-                        "relative_path": "output-value.json"
+                        "relative_path": "output-value.json",
+                        "example_value": {"key": "value"}
                     },
                     {
                         "slug": "yet-another-output-ci-slug",
                         "kind": "Anything",
                         "super_kind": "Value",
-                        "relative_path": "yet-another-output-value.json"
+                        "relative_path": "yet-another-output-value.json",
+                        "example_value": {"key": "value"}
                     },
                     {
                         "slug": "yet-another-non-json-output-ci-slug",
                         "kind": "Anything",
                         "super_kind": "File",
-                        "relative_path": "yet-another-non-json-output-value"
+                        "relative_path": "yet-another-non-json-output-value",
+                        "example_value": None
                     }
                 ]
             },
@@ -97,15 +105,17 @@
                         "slug": "input-ci-slug",
                         "kind": "Image",
                         "super_kind": "Image",
-                        "relative_path": "images/input-value"
+                        "relative_path": "images/input-value",
+                        "example_value": None
                     }
                 ],
                 "algorithm_outputs": [
                     {
                         "slug": "another-output-ci-slug",
                         "kind": "Anything",
                         "super_kind": "File",
-                        "relative_path": "output-value.json"
+                        "relative_path": "output-value.json",
+                        "example_value": {"key": "value"}
                     }
                 ]
             }
@@ -124,51 +134,59 @@
                 "slug": "input-ci-slug",
                 "kind": "Segmentation",
                 "super_kind": "Image",
-                "relative_path": "images/input-value"
+                "relative_path": "images/input-value",
+                "example_value": None
             },
             {
                 "slug": "another-input-ci-slug",
                 "kind": "Anything",
                 "super_kind": "File",
-                "relative_path": "another-input-value.json"
+                "relative_path": "another-input-value.json",
+                "example_value": {"key": "value"}
             },
             {
                 "slug": "yet-another-input-ci-slug",
                 "kind": "Anything",
                 "super_kind": "Value",
-                "relative_path": "yet-another-input-value.json"
+                "relative_path": "yet-another-input-value.json",
+                "example_value": {"key": "value"}
             },
             {
                 "slug": "yet-another-non-json-input-ci-slug",
                 "kind": "Anything",
                 "super_kind": "File",
-                "relative_path": "yet-another-non-json-input-value"
+                "relative_path": "yet-another-non-json-input-value",
+                "example_value": None
             }
         ],
         "outputs": [
             {
                 "slug": "output-ci-slug",
                 "kind": "Image",
                 "super_kind": "Image",
-                "relative_path": "images/output-value"
+                "relative_path": "images/output-value",
+                "example_value": None
             },
             {
                 "slug": "another-output-ci-slug",
                 "kind": "Anything",
                 "super_kind": "File",
-                "relative_path": "output-value.json"
+                "relative_path": "output-value.json",
+                "example_value": {"key": "value"}
             },
             {
                 "slug": "yet-another-output-ci-slug",
                 "kind": "Anything",
                 "super_kind": "Value",
-                "relative_path": "yet-another-output-value.json"
+                "relative_path": "yet-another-output-value.json",
+                "example_value": {"key": "value"}
             },
             {
                 "slug": "yet-another-non-json-output-ci-slug",
                 "kind": "Anything",
                 "super_kind": "File",
-                "relative_path": "yet-another-non-json-output-value"
+                "relative_path": "yet-another-non-json-output-value",
+                "example_value": None
             }
         ]
     }