merge in master

CHANGELOG.rst

@@ -6,15 +6,24 @@ dcicutils
 Change Log
 ----------
 
-8.6.1
+
+8.7.1
 =====
+
 * Changed scripts/publish_to_pypi.py to allow untracked gitinfo.json to exist;
   this so that we can (optionally) have repos write relevant git info to this
   file (via GitHub Actions) and make it accessible to the package for inspection.
 
 
+8.7.0
+=====
+
+* Add new schema_utils module for schema parsing
+
+
 8.6.0
 =====
+
 * Minor fix to misc_utils.to_integer to handle float strings.
 * Minor fix to structured_data to accumulate unique resolved_refs across schemas.
 * Added ability to autoadd properties structured_data.StructuredDataSet;
@@ -28,12 +37,14 @@ Change Log
 
 8.5.0
 =====
+
 * Moved structured_data.py from smaht-portal to here; new portal_utils and data_readers modules.
 * Strip sheet name in data_readers.Excel; respecte (ignore) hidden sheets.
 
 
 8.4.0
 =====
+
 * More work related to SMaHT ingestion (bundle/sheet_utils, data_readers, etc).
 
 
@@ -44,6 +55,7 @@ Change Log
 
 8.2.0
 =====
+
 * 2023-11-02
 * Added ``SchemaManager.get_identifying_properties`` in ``bundle_utils``
   which implicitly adds ``identifier`` to ``identifyingProperties``.

dcicutils/schema_utils.py

@@ -0,0 +1,185 @@
+from typing import Any, Dict, List
+
+
+class JsonSchemaConstants:
+    ANY_OF = "anyOf"
+    ARRAY = "array"
+    BOOLEAN = "boolean"
+    DEFAULT = "default"
+    ENUM = "enum"
+    FORMAT = "format"
+    INTEGER = "integer"
+    ITEMS = "items"
+    NUMBER = "number"
+    OBJECT = "object"
+    ONE_OF = "oneOf"
+    PATTERN = "pattern"
+    PROPERTIES = "properties"
+    REF = "$ref"
+    REQUIRED = "required"
+    STRING = "string"
+    TYPE = "type"
+
+
+class EncodedSchemaConstants:
+    IDENTIFYING_PROPERTIES = "identifyingProperties"
+    LINK_TO = "linkTo"
+    MERGE_REF = "$merge"
+    MIXIN_PROPERTIES = "mixinProperties"
+    UNIQUE_KEY = "uniqueKey"
+
+
+class SchemaConstants(JsonSchemaConstants, EncodedSchemaConstants):
+    pass
+
+
+def get_properties(schema: Dict[str, Any]) -> Dict[str, Any]:
+    """Return the properties of a schema."""
+    return schema.get(SchemaConstants.PROPERTIES, {})
+
+
+def get_property(schema: Dict[str, Any], property_name: str) -> Dict[str, Any]:
+    """Return property in properties, if found."""
+    return get_properties(schema).get(property_name, {})
+
+
+def has_property(schema: Dict[str, Any], property_name: str) -> bool:
+    """Return True if the schema has the given property."""
+    return property_name in get_properties(schema)
+
+
+def get_required(schema: Dict[str, Any]) -> List[str]:
+    """Return the required properties of a schema."""
+    return schema.get(SchemaConstants.REQUIRED, [])
+
+
+def get_pattern(schema: Dict[str, Any]) -> str:
+    """Return the pattern property of a schema."""
+    return schema.get(SchemaConstants.PATTERN, "")
+
+
+def get_any_of(schema: Dict[str, Any]) -> List[Dict[str, Any]]:
+    """Return the anyOf properties of a schema."""
+    return schema.get(SchemaConstants.ANY_OF, [])
+
+
+def get_one_of(schema: Dict[str, Any]) -> List[Dict[str, Any]]:
+    """Return the oneOf properties of a schema."""
+    return schema.get(SchemaConstants.ONE_OF, [])
+
+
+def get_conditional_required(schema: Dict[str, Any]) -> List[str]:
+    """Get required + possibly required properties.
+
+    Using heuristics here; update as needed.
+    """
+    return sorted(
+        list(
+            set(
+                get_required(schema)
+                + get_any_of_required(schema)
+                + get_one_of_required(schema)
+            )
+        )
+    )
+
+
+def get_any_of_required(schema: Dict[str, Any]) -> List[str]:
+    """Get required properties from anyOf."""
+    return [
+        property_name
+        for any_of_schema in get_any_of(schema)
+        for property_name in get_required(any_of_schema)
+    ]
+
+
+def get_one_of_required(schema: Dict[str, Any]) -> List[str]:
+    """Get required properties from oneOf."""
+    return [
+        property_name
+        for one_of_schema in get_one_of(schema)
+        for property_name in get_required(one_of_schema)
+    ]
+
+
+def get_mixin_properties(schema: Dict[str, Any]) -> List[Dict[str, Any]]:
+    """Return the mixin properties of a schema."""
+    return schema.get(SchemaConstants.MIXIN_PROPERTIES, [])
+
+
+def get_identifying_properties(schema: Dict[str, Any]) -> List[str]:
+    """Return the identifying properties of a schema."""
+    return schema.get(SchemaConstants.IDENTIFYING_PROPERTIES, [])
+
+
+def get_schema_type(schema: Dict[str, Any]) -> str:
+    """Return the type of a schema."""
+    return schema.get(SchemaConstants.TYPE, "")
+
+
+def is_array_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is an array."""
+    return get_schema_type(schema) == SchemaConstants.ARRAY
+
+
+def is_object_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is an object."""
+    return get_schema_type(schema) == SchemaConstants.OBJECT
+
+
+def is_string_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is a string."""
+    return get_schema_type(schema) == SchemaConstants.STRING
+
+
+def is_number_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is a number."""
+    return get_schema_type(schema) == SchemaConstants.NUMBER
+
+
+def is_integer_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is an integer."""
+    return get_schema_type(schema) == SchemaConstants.INTEGER
+
+
+def is_boolean_schema(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is a boolean."""
+    return get_schema_type(schema) == SchemaConstants.BOOLEAN
+
+
+def get_items(schema: Dict[str, Any]) -> Dict[str, Any]:
+    """Return the items of a schema."""
+    return schema.get(SchemaConstants.ITEMS, {})
+
+
+def get_format(schema: Dict[str, Any]) -> str:
+    """Return the format of a schema."""
+    return schema.get(SchemaConstants.FORMAT, "")
+
+
+def get_conditional_formats(schema: Dict[str, Any]) -> List[str]:
+    """Return the format of a schema, as directly given or as listed
+    as an option via oneOf or anyOf.
+    """
+    formats = set(
+        get_any_of_formats(schema) + get_one_of_formats(schema) + [get_format(schema)]
+    )
+    return sorted(list([format_ for format_ in formats if format_]))
+
+
+def get_any_of_formats(schema: Dict[str, Any]) -> List[str]:
+    """Return the formats of a schema's anyOf properties."""
+    return [
+        get_format(any_of_schema)
+        for any_of_schema in get_any_of(schema)
+        if get_format(any_of_schema)
+    ]
+
+
+def get_one_of_formats(schema: Dict[str, Any]) -> List[str]:
+    """Return the formats of a schema's oneOf properties."""
+    return [
+        get_format(one_of_schema)
+        for one_of_schema in get_one_of(schema)
+        if get_format(one_of_schema)
+    ]

docs/source/dcicutils.rst

@@ -295,6 +295,13 @@ s3_utils
   :members:
 
 
+schema_utils
+^^^^^^^^
+
+.. automodule:: dcicutils.schema_utils
+  :members:
+
+
 secrets_utils
 ^^^^^^^^^^^^^
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.6.0.1b3"  # TODO: To become 8.6.1
+version = "8.7.0.1b1"  # TODO: To become 8.7.1
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"