Add tutorial notebook (#19)

* Add tutorial notebooks * Fix reference and how plugins are supplied * Update README.md * Bump version
linkml · Dec 6, 2022 · 9e9447f · 9e9447f
1 parent d11f1a3
commit 9e9447f
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Showing 9 changed files with 828 additions and 14 deletions.
diff --git a/README.md b/README.md
@@ -233,7 +233,7 @@ data_obj = {
     "name": "Object 1",
     "type": "X"
 }
-validator = Validator(schema="examples/example_schema.yaml", plugins={MyCustomPlugin})
+validator = Validator(schema="examples/example_schema.yaml", plugins=[{"plugin_class": "MyCustomPlugin", "args": {}])
 validator.validate(obj=data_obj, target_class="NamedThing")
 
 ```

diff --git a/examples/example_data1_validation_report.json b/examples/example_data1_validation_report.json
@@ -9,7 +9,7 @@
     "valid": true,
     "validation_results": [
       {
-        "plugin_name": "JsonschemaValidationPlugin",
+        "plugin_name": "JsonSchemaValidationPlugin",
         "valid": true,
         "validation_messages": []
       }
@@ -25,7 +25,7 @@
     "valid": true,
     "validation_results": [
       {
-        "plugin_name": "JsonschemaValidationPlugin",
+        "plugin_name": "JsonSchemaValidationPlugin",
         "valid": true,
         "validation_messages": []
       }

diff --git a/examples/example_data2_validation_report.json b/examples/example_data2_validation_report.json
@@ -9,7 +9,7 @@
     "valid": true,
     "validation_results": [
       {
-        "plugin_name": "JsonschemaValidationPlugin",
+        "plugin_name": "JsonSchemaValidationPlugin",
         "valid": true,
         "validation_messages": []
       }
@@ -25,7 +25,7 @@
     "valid": true,
     "validation_results": [
       {
-        "plugin_name": "JsonschemaValidationPlugin",
+        "plugin_name": "JsonSchemaValidationPlugin",
         "valid": true,
         "validation_messages": []
       }

diff --git a/linkml_validator/__init__.py b/linkml_validator/__init__.py
@@ -1 +1 @@
-__version__ = "0.4.4"
+__version__ = "0.4.5"
diff --git a/linkml_validator/cli.py b/linkml_validator/cli.py
@@ -5,7 +5,7 @@
 
 
 PLUGINS = {
-    "JsonschemaValidationPlugin": "linkml_validator.plugins.jsonschema_validation.JsonschemaValidationPlugin",
+    "JsonSchemaValidationPlugin": "linkml_validator.plugins.jsonschema_validation.JsonSchemaValidationPlugin",
     "RangeValidationPlugin": "linkml_validator.plugins.range_validation.RangeValidationPlugin",
 }
 
@@ -50,7 +50,7 @@ def cli(inputs, schema, output, target_class, plugins, strict):
     """
     Run the Validator on data from one or more files.
     """
-    plugin_class_references = set()
+    plugin_class_references = []
     if not plugins:
         plugins = DEFAULT_PLUGINS.values()
     for plugin in plugins:
@@ -59,7 +59,7 @@ def cli(inputs, schema, output, target_class, plugins, strict):
         plugin_module_name = ".".join(plugin.split(".")[:-1])
         plugin_class_name = plugin.split(".")[-1]
         plugin_class = import_plugin(plugin_module_name, plugin_class_name)
-        plugin_class_references.add(plugin_class)
+        plugin_class_references.append({'plugin_class': plugin_class})
     validator = Validator(schema=schema, plugins=plugin_class_references)
     for filename in inputs:
         reports = [x for x in validator.validate_file(filename=filename, target_class=target_class, strict=strict)]

diff --git a/linkml_validator/validator.py b/linkml_validator/validator.py
@@ -7,7 +7,7 @@
 
 
 DEFAULT_PLUGINS = {
-    "JsonschemaValidationPlugin": JsonSchemaValidationPlugin
+    "JsonSchemaValidationPlugin": JsonSchemaValidationPlugin
 }
 
 
@@ -17,13 +17,13 @@ class Validator:
 
     Args:
         schema: Path or URL to schema YAML
-        plugins: A set of plugin classes to use for validation
+        plugins: A list of plugin classes to use for validation
 
     """
 
     def __init__(self, schema: str, plugins: List[Dict] = None) -> None:
         self.schema = schema
-        self.plugins = set()
+        self.plugins = []
         if plugins:
             for plugin in plugins:
                 plugin_class = plugin["plugin_class"]
@@ -33,11 +33,11 @@ def __init__(self, schema: str, plugins: List[Dict] = None) -> None:
                 if not issubclass(plugin_class, BasePlugin):
                     raise Exception(f"{plugin_class} must be a subclass of {BasePlugin}")
                 instance = plugin_class(schema=self.schema, **plugin_args)
-                self.plugins.add(instance)
+                self.plugins.append(instance)
         else:
             for plugin_class in DEFAULT_PLUGINS.values():
                 instance = plugin_class(schema=self.schema)
-                self.plugins.add(instance)
+                self.plugins.append(instance)
 
     def validate(
         self, obj: Dict, target_class: str, strict: bool = False, **kwargs