handle merge conflict

Author: andrewelamb

docs/guides/extensions/curator/metadata_curation.md

@@ -18,6 +18,7 @@ By following this guide, you will:
 - Python environment with synapseclient and the `curator` extension installed (ie. `pip install --upgrade "synapseclient[curator]"`)
 - An existing Synapse project and folder where you want to manage metadata
 - A JSON Schema registered in Synapse (many schemas are already available for Sage-affiliated projects, or you can register your own by following the [JSON Schema tutorial](../../../tutorials/python/json_schema.md))
+    - If you are leveraging the [Curator CSV data model](../../../explanations/curator_data_model.md), you can create JSON schemas by following this [tutorial](../../extensions/curator/schema_operations.md)
 - (Optional) An existing Synapse team if you want multiple users to collaborate on the same Grid session. Pass the team's ID as `assignee_principal_id` when creating the curation task.
 
 ## Step 1: Authenticate and import required functions

docs/guides/extensions/curator/schema_operations.md

@@ -0,0 +1,178 @@
+# How to Generate JSONschemas from Curator CSV data models
+
+JSON Schema is a tool used to validate data. In Synapse, JSON Schemas can be used to validate the metadata applied to an entity such as project, file, folder, table, or view, including the [annotations](https://help.synapse.org/docs/Annotating-Data-With-Metadata.2667708522.html) applied to it. To learn more about JSON Schemas, check out [JSON-Schema.org](https://json-schema.org/).
+
+Synapse supports a subset of features from [json-schema-draft-07](https://json-schema.org/draft-07). To see the list of features currently supported, see the [JSON Schema object definition](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/schema/JsonSchema.html) from Synapse's REST API Documentation.
+
+In this tutorial, you will learn how to create, register, and bind JSON Schemas using an existing data model.
+
+## Tutorial Purpose
+
+You will learn the complete JSON Schema workflow:
+
+1. **Generate** JSON schemas from your data model
+2. **Register** schemas to a Synapse organization
+3. **Bind** schemas to Synapse entities for metadata validation
+
+This tutorial uses the Python client as a library. To use the CLI tool, see the [command line documentation](../command_line_client.md).
+
+## Prerequisites
+
+* You have a working [installation](../../tutorials/installation.md) of the Synapse Python Client. You must install the Curator extensions package.
+* You have a data model, see this [data model_documentation](../../explanations/curator_data_model.md).
+
+## 1. Initial set up
+
+```python
+from synapseclient import Synapse
+from synapseclient.extensions.curator import (
+    bind_jsonschema,
+    generate_jsonschema,
+    register_jsonschema,
+)
+
+# Path or URL to your data model (CSV or JSONLD format)
+# Example: "path/to/my_data_model.csv" or "https://raw.githubusercontent.com/example.csv"
+DATA_MODEL_SOURCE = "tests/unit/synapseclient/extensions/schema_files/example.model.csv"
+# List of component names/data types to create schemas for, or None for all components/data types
+# Example: ["Patient", "Biospecimen"] or None
+DATA_TYPE = ["Patient"]
+# Directory where JSON Schema files will be saved
+OUTPUT_DIRECTORY = "temp"
+# Path to a generated JSON Schema file for registration
+SCHEMA_PATH = "temp/Patient.json"
+# Your Synapse organization name for schema registration
+ORGANIZATION_NAME = "my.organization"
+# Name for the schema
+SCHEMA_NAME = "patient.schema"
+# Version number for the schema
+SCHEMA_VERSION = "0.0.1"
+# Synapse entity ID to bind the schema to (file, folder, etc.)
+ENTITY_ID = "syn12345678"
+```
+
+To create a JSON Schema you need a data model, and the data types you want to create.
+The data model must be in either CSV or JSON-LD form. The data model may be a local path or a URL.
+[Data model_documentation](../../explanations/curator_data_model.md).
+
+The data types must exist in your data model. This can be a list of data types, or `None` to create all data types in the data model.
+
+## 2. Create JSON Schemas
+
+### Create multiple JSON Schema
+
+The JSONschema looks like [this](https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/dpetest-test.schematic.Patient). By setting the `output` parameter as path to a "temp" directory, the file will be created as "temp/Patient.json". The `data_types` parameter is a list and can have multiple data types.
+
+```python
+# Create JSON Schemas for multiple data types
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    output=OUTPUT_DIRECTORY,
+    data_types=DATA_TYPE,
+    synapse_client=syn,
+)
+```
+
+### Create every JSON schema
+
+If you don't set a `data_types` parameter a JSON Schema will be created for every data type in the data model.
+
+```python
+# Create JSON Schemas for all data types
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    output=OUTPUT_DIRECTORY,
+    synapse_client=syn,
+)
+```
+
+### Create a JSON Schema with a certain path
+
+If you have only one data type and set the `output` parameter to a file path(ending in.json), the JSON Schema file will have that path.
+
+```python
+# Specify path for JSON Schema
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    data_types=DATA_TYPE,
+    output="test.json",
+    synapse_client=syn,
+)
+```
+
+### Create a JSON Schema in the current working directory
+
+If you don't set `output` parameter the JSON Schema file will be created in the current working directory.
+
+```python
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    data_types=DATA_TYPE,
+    synapse_client=syn,
+)
+```
+
+
+### Create a JSON Schema using display names
+
+You can have Curator format the property names and valid values in the JSON Schema. This will remove whitespace and special characters.
+
+```python
+# Create JSON Schema using display names for both properties names and valid values
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    data_types=DATA_TYPE,
+    data_model_labels="display_label",
+    synapse_client=syn,
+)
+```
+
+
+## 3. Register a JSON Schema to Synapse
+
+Once you've created a JSON Schema file, you can register it to a Synapse organization.
+
+The `register_jsonschema` function:
+- Takes a path to your generated JSON Schema file
+- Registers it with the specified organization in Synapse
+- Returns the schema URI and a success message
+- You can optionally specify a version (e.g., "0.0.1") or let it auto-generate
+
+```python
+# Register a JSON Schema to Synapse
+json_schema = register_jsonschema(
+    schema_path=SCHEMA_PATH,
+    organization_name=ORGANIZATION_NAME,
+    schema_name=SCHEMA_NAME,
+    schema_version=SCHEMA_VERSION,
+    synapse_client=syn,
+)
+print(f"Registered schema URI: {json_schema.uri}")
+```
+
+
+## 8. Bind a JSON Schema to a Synapse Entity
+
+After registering a schema, you can bind it to Synapse entities (files, folders, etc.) for metadata validation.
+
+The `bind_jsonschema` function:
+- Takes a Synapse entity ID (e.g., "syn12345678")
+- Binds the registered schema URI to that entity
+- Optionally enables derived annotations to auto-populate metadata
+- Returns binding details
+
+```python
+# Bind a JSON Schema to a Synapse entity
+result = bind_jsonschema(
+    entity_id=ENTITY_ID,
+    json_schema_uri=json_schema.uri,
+    enable_derived_annotations=True,
+    synapse_client=syn,
+)
+print(f"Successfully bound schema to entity: {result}")
+```
+
+## Reference
+- [JSON Schema Object Definition](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/schema/JsonSchema.html)
+- [JSON Schema Draft 7](https://json-schema.org/draft-07)
+- [JSON-Schema.org](https://json-schema.org/)