[SYNPY-1696] Add create JSON Schema CLI command

docs/tutorials/command_line_client.md

@@ -81,8 +81,7 @@ synapse [-h] [--version] [-u SYNAPSEUSER] [-p SYNAPSE_AUTH_TOKEN] [-c CONFIGPATH
 - [test-encoding](#test-encoding): test character encoding to help diagnose problems
 - [get-sts-token](#get-sts-token): Get an STS token for access to AWS S3 storage underlying Synapse
 - [migrate](#migrate): Migrate Synapse entities to a different storage location
-
-
+- [generate-json-schema](#generate-json-schema): Generate JSON Schema(s) from a data model
 
 ### `get`
 
@@ -544,3 +543,18 @@ synapse migrate [-h] [--source_storage_location_ids [SOURCE_STORAGE_LOCATION_IDS
 | `--csv_log_path`                | Named      | Path where to log a csv documenting the changes from the migration.                                                                                                                                                                            |         |
 | `--dryRun`                      | Named      | Dry run, files will be indexed by not migrated.                                                                                                                                                                                                | False   |
 | `--force`                       | Named      | Bypass interactive prompt confirming migration.                                                                                                                                                                                                | False   |
+
+### `generate-json-schema`
+
+Generate JSON Schema(s) from a data model
+
+```bash
+synapse generate-json-schema [-h] --name NAME [--parentid syn123] [--csv foo.csv] data_model_path
+```
+
+| Name                     | Type       | Description                                                         |
+|--------------------------|------------|---------------------------------------------------------------------|
+| `data_model_path`        | Positional | Data model path or URL                                              |
+| `--data-types`           | Named      | Optional list of data types to create JSON Schema for               |
+| `--output`               | Named      | Optional. Either a file path ending in '.json', or a directory path |
+| `--data-model-labels`    | Named      | Either 'class_label', or 'display_label'                            |

docs/tutorials/python/schema_operations.md

@@ -5,11 +5,13 @@ Synapse supports a subset of features from [json-schema-draft-07](https://json-s
 In this tutorial, you will learn how to create these JSON Schema using an existing data model.
 
 ## Tutorial Purpose
-You will create a JSON schema using your data model.
+
+You will create a JSON schema using your data model suing the python client as a library. To use a CLI tool see the [documentation](../command_line_client.md).
 
 ## Prerequisites
+
 * You have a working [installation](../installation.md) of the Synapse Python Client.
-* You have a data model, see this [example data model](https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.column_type_component.csv).
+* You have a data model, see this [data model_documentation](../../explanations/curator_data_model.md).
 
 ## 1. Imports
 
@@ -20,29 +22,72 @@ You will create a JSON schema using your data model.
 ## 2. Set up your variables
 
 ```python
-{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=4-10}
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=4-11}
 ```
 
 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.
-[Example data model](https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.column_type_component.csv).
+[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.
 
 ## 3. Log into Synapse
+
 ```python
-{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=12-13}
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=13-14}
 ```
 
+## 4. Create a JSON Schema
+
+Create a JSON Schema
 
-## 4. Create the JSON Schema
-Create the JSON Schema(s)
 ```python
-{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=15-23}
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=16-23}
 ```
-You should see the first JSON Schema for the datatype(s) you selected printed.
+
+You should see the first JSON Schema for the datatype you selected printed.
 It will look like [this schema](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".
+
+## 5. Create multiple JSON Schema
+
+Create multiple JSON Schema
+
+```python
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=25-30}
+```
+
+The `data_types` parameter is a list and can have multiple data types.
+
+## 6. Create every JSON Schema
+
+Create every JSON Schema
+
+```python
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=32-36}
+```
+
+If you don't set a `data_types` parameter a JSON Schema will be created for every data type in the data model.
+
+## 7. Create a JSON Schema with a certain path
+
+Create a JSON Schema
+
+```python
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=38-43}
+```
+
+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.
+
+## 8. Create a JSON Schema in the current working directory
+
+Create a JSON Schema
+
+```python
+{!docs/tutorials/python/tutorial_scripts/schema_operations.py!lines=45-48}
+```
 
+If you don't set `output` parameter the JSON Schema file will be created in the current working directory.
 
 ## Source Code for this Tutorial
 

docs/tutorials/python/tutorial_scripts/schema_operations.py

@@ -8,17 +8,42 @@
 # Example: ["Patient", "Biospecimen"] or None
 DATA_TYPE = ["Patient"]
 # Directory where JSON Schema files will be saved
-OUTPUT_DIRECTORY = "./"
+OUTPUT_DIRECTORY = "temp"
 
 syn = Synapse()
 syn.login()
 
 schemas, file_paths = generate_jsonschema(
     data_model_source=DATA_MODEL_SOURCE,
-    output_directory=OUTPUT_DIRECTORY,
-    data_type=DATA_TYPE,
-    data_model_labels="class_label",
+    output=OUTPUT_DIRECTORY,
+    data_types=DATA_TYPE,
     synapse_client=syn,
 )
 
 print(schemas[0])
+
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    output=OUTPUT_DIRECTORY,
+    data_types=["Patient", "Biospecimen"],
+    synapse_client=syn,
+)
+
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    output=OUTPUT_DIRECTORY,
+    synapse_client=syn,
+)
+
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    data_types=DATA_TYPE,
+    output="test.json",
+    synapse_client=syn,
+)
+
+schemas, file_paths = generate_jsonschema(
+    data_model_source=DATA_MODEL_SOURCE,
+    data_types=DATA_TYPE,
+    synapse_client=syn,
+)

synapseclient/__main__.py

@@ -35,6 +35,7 @@
     SynapseHTTPError,
     SynapseNoCredentialsError,
 )
+from synapseclient.extensions.curator.schema_generation import generate_jsonschema
 from synapseclient.wiki import Wiki
 
 tracer = trace.get_tracer("synapseclient")
@@ -801,6 +802,17 @@ def migrate(args, syn):
         result.as_csv(args.csv_log_path)
 
 
+def generate_json_schema(args, syn):
+    """Generate JSON schema for Synapse entity types"""
+    _, path = generate_jsonschema(
+        data_model_source=args.data_model_path,
+        output=args.output,
+        data_types=args.data_types,
+        data_model_labels=args.data_model_labels,
+        synapse_client=syn,
+    )
+
+
 def build_parser():
     """Builds the argument parser and returns the result."""
 
@@ -1793,6 +1805,45 @@ def build_parser():
         help="Bypass interactive prompt confirming migration",
     )
 
+    parser_generate_json_schema = subparsers.add_parser(
+        "generate-json-schema", help="Generates a JSON Schema file from a data model."
+    )
+    parser_generate_json_schema.add_argument(
+        "data_model_path",
+        type=str,
+        help="Required path to CSV or JSONLD data model. Must be a path to a local file, or a URL.",
+    )
+    parser_generate_json_schema.add_argument(
+        "--data-types",
+        nargs="*",
+        type=str,
+        default=None,
+        help="Optional list of data types to generate schema for. If not provided, schema will be generated for all data types in the model.",
+    )
+    parser_generate_json_schema.add_argument(
+        "--output",
+        type=str,
+        default=None,
+        help=(
+            "Optional path. "
+            "If None, output file(s) will be created in the current working directory as ./<data-type>.json. "
+            "If a directory path, output file(s) will be created in the specified directory as <data-type>.json. "
+            "If a file path, schema will be written to the specified file. "
+        ),
+    )
+    parser_generate_json_schema.add_argument(
+        "--data-model-labels",
+        type=str,
+        default="class_label",
+        choices=["class_label", "display_label"],
+        help=(
+            "Optional Label format for properties in the generated schema. "
+            "'class_label' uses standard attribute names (default). "
+            "'display_label' uses display names when valid"
+        ),
+    )
+    parser_generate_json_schema.set_defaults(func=generate_json_schema)
+
     parser_migrate.set_defaults(func=migrate)
 
     return parser