Version two

README.md

@@ -2,27 +2,115 @@
 
 **Gen3 Validator** is a Python toolkit designed to make working with Gen3 metadata schemas and data validation straightforward for developers.
 
-With this tool, you can:
-
-- **Resolve and flatten Gen3 JSON schemas** so you can work with them programmatically.
-- **Validate JSON metadata files** against Gen3 schemas, catching schema violations early in your pipeline.
-- **Check linkage integrity** between data nodes (e.g., ensuring all sample-to-subject references are valid).
-- **Parse Excel-based metadata templates** and convert them to JSON for Gen3 ingestion.
-- **Get detailed validation results and summary stats** as Python data structures or pandas DataFrames, making it easy to integrate with your own scripts or reporting tools.
-
+## Installation
+```bash
+pip install gen3_validator
+pip show gen3_validator
+```
 
 ## Docs
-- [src docs](https://australianbiocommons.github.io/gen3_validator/)
 - [example usage](https://github.com/AustralianBioCommons/gen3_validator/blob/main/docs/usage.md)
 
-*Note: *I recommend you clone this repo, and walk through the examples in the [usage](https://github.com/AustralianBioCommons/gen3_validator/blob/main/docs/usage.md) page. The usage examples load data from the `tests/data` [directory](https://github.com/AustralianBioCommons/gen3_validator/tree/main/tests/data) so you can see how the data is structured.*
 
+## Quickstart
+```python
+import gen3_validator
 
-## Installation
-```bash
-pip install gen3_validator
-pip show gen3_validator
+resolver = gen3_validator.ResolveSchema(schema_path = "../tests/schema/gen3_test_schema.json")
+resolver.resolve_schema()
+schema = resolver.schema_resolved
+
+data = [
+    {
+        "baseline_timepoint": True, # variable not in data dictionary
+        "freeze_thaw_cycles": "10", # should be an integer
+        "sample_collection_method": "2fddbe7d09",
+        "sample_id": "d4f31f7bb6",
+        "sample_in_preservation": "snap Frozen",
+        "sample_in_storage": "yes",
+        "sample_provider": "USYD",
+        "sample_source": "UBERON:3781554",
+        "sample_storage_method": "not stored",
+        "sample_type": "59a8fd8005",
+        "storage_location": "UMELB",
+        "subjects": {
+            "submitter_id": "subject_e5616257f8"
+        },
+        "submitter_id": "sample_efdbe56d20",
+        "type": "sample"
+    },
+    {
+        "baseline_timepoint": True, 
+        "freeze_thaw_cycles": 76,
+        "sample_collection_method": "e2a6403b51",
+        "sample_id": 3324635, # should be a string
+        "sample_in_preservation": "not allowed to collect",
+        "sample_in_storage": "unknown",
+        "sample_provider": "USYD",
+        "sample_source": "UBERON:9332357",
+        "sample_storage_method": "frozen, liquid nitrogen",
+        "sample_type": "8fd28ec2f3",
+        "storage_location": "Baker",
+        "subjects": {
+            "submitter_id": "subject_071bc3e81a"
+        },
+        "submitter_id": "sample_f7645c1221",
+        "type": "sample"
+    }
+]
+results = gen3_validator.validate.validate_list_dict(data, schema)
+
+print(results)
 ```
+
+Example output:
+
+```python
+[
+    {
+        'node': 'sample',
+        'index': 0,
+        'validation_result': 'FAIL',
+        'invalid_key': 'freeze_thaw_cycles',
+        'schema_path': 'properties.freeze_thaw_cycles.type',
+        'validator': 'type',
+        'validator_value': 'integer',
+        'validation_error': "'10' is not of type 'integer'"
+    },
+    {
+        'node': 'sample',
+        'index': 0,
+        'validation_result': 'FAIL',
+        'invalid_key': 'root',
+        'schema_path': 'additionalProperties',
+        'validator': 'additionalProperties',
+        'validator_value': False,
+        'validation_error': "Additional properties are not allowed ('baseline_timepoint', 'subjects' were unexpected)"
+    },
+    {
+        'node': 'sample',
+        'index': 1,
+        'validation_result': 'FAIL',
+        'invalid_key': 'sample_id',
+        'schema_path': 'properties.sample_id.type',
+        'validator': 'type',
+        'validator_value': 'string',
+        'validation_error': "3324635 is not of type 'string'"
+    },
+    {
+        'node': 'sample',
+        'index': 1,
+        'validation_result': 'FAIL',
+        'invalid_key': 'root',
+        'schema_path': 'additionalProperties',
+        'validator': 'additionalProperties',
+        'validator_value': False,
+        'validation_error': "Additional properties are not allowed ('baseline_timepoint', 'subjects' were unexpected)"
+    }
+]
+
+```
+
 ---
 
 ## Dev Setup