Merge pull request #5 from linkml/rename

Rename

README.md

@@ -1,9 +1,7 @@
-# linkml-runtime-api
+# linkml-dataops
 
 An extension to linkml-runtime to provide an API over runtime data objects.
 
-Documentation will later be added in the main [linkml](https://linkml.io/linkml/) repo
-
 This provides data models for CRUD (Create, Read, Update, Delete) objects, i.e.
 
 * Representations of *queries* over objects that instantiate linkml classes
@@ -18,11 +16,11 @@ Current engines implemented here:
 
 Other engines may be implemented elsewhere - e.g. linkml-solr
 
-See [tests/](https://github.com/linkml/linkml-runtime-api/tree/main/tests) for examples
+See [tests/](https://github.com/linkml/linkml-dataops/tree/main/tests) for examples
 
 ## Changes Datamodel
 
-See linkml_runtime_api.changes
+See linkml_dataops.changes
 
 Change classes include:
 
@@ -67,7 +65,7 @@ In future there will be other datastores
 
 ## Query Datamodel
 
-See linkml_runtime_api.query
+See linkml_dataops.query
 
 The main query class is `FetchQuery`
 

linkml_dataops/__init__.py

@@ -0,0 +1,2 @@
+from linkml_dataops.query import *
+from linkml_dataops.changer import *

linkml_dataops/changer/__init__.py

@@ -0,0 +1,2 @@
+from linkml_dataops.changer.object_changer import ObjectChanger
+from linkml_dataops.changer.jsonpatch_changer import JsonPatchChanger

linkml_runtime_api/changer/changer.py → linkml_dataops/changer/changer.py

@@ -2,8 +2,8 @@
 
 from linkml_runtime.utils.formatutils import underscore
 
-from linkml_runtime_api.apiroot import ApiRoot, PATH_EXPRESSION
-from linkml_runtime_api.changer.changes_model import Change, AddObject, RemoveObject
+from linkml_dataops.apiroot import ApiRoot, PATH_EXPRESSION
+from linkml_dataops.changer.changes_model import Change, AddObject, RemoveObject
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
 @dataclass

linkml_runtime_api/changer/jsonpatch_changer.py → linkml_dataops/changer/jsonpatch_changer.py

@@ -17,11 +17,11 @@
 from linkml_runtime.utils.schemaview import SchemaView
 from ruamel.yaml import YAML
 
-from linkml_runtime_api.changer.changer import Changer, ChangeResult
-from linkml_runtime_api.changer.changes_model import Change, AddObject, RemoveObject, Append, Rename
+from linkml_dataops.changer.changer import Changer, ChangeResult
+from linkml_dataops.changer.changes_model import Change, AddObject, RemoveObject, Append, Rename
 from linkml_runtime.utils.formatutils import underscore, is_empty
 from linkml_runtime.utils.yamlutils import YAMLRoot, as_json_object
-from linkml_runtime_api.diffs.yaml_patch import YAMLPatch
+from linkml_dataops.diffs.yaml_patch import YAMLPatch
 
 OPDICT = Dict[str, Any]
 OPS = List[OPDICT]

linkml_runtime_api/changer/object_changer.py → linkml_dataops/changer/object_changer.py

@@ -1,7 +1,7 @@
 from copy import copy, deepcopy
 
-from linkml_runtime_api.changer.changer import Changer, ChangeResult
-from linkml_runtime_api.changer.changes_model import Change, AddObject, RemoveObject, Append, Rename
+from linkml_dataops.changer.changer import Changer, ChangeResult
+from linkml_dataops.changer.changes_model import Change, AddObject, RemoveObject, Append, Rename
 from linkml_runtime.utils.formatutils import underscore
 from linkml_runtime.utils.yamlutils import YAMLRoot
 

linkml_runtime_api/diffs/differ.py → linkml_dataops/diffs/differ.py

@@ -6,7 +6,7 @@
 
 from linkml_runtime.dumpers import json_dumper
 
-from linkml_runtime_api.apiroot import ApiRoot
+from linkml_dataops.apiroot import ApiRoot
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
 def _as_dict(obj: YAMLRoot) -> dict:

linkml_dataops/generators/__init__.py

@@ -0,0 +1,2 @@
+from linkml_dataops.generators.apigenerator import ApiGenerator
+from linkml_dataops.generators.pyapigenerator import PythonApiGenerator

linkml_runtime_api/generators/apigenerator.py → linkml_dataops/generators/apigenerator.py

@@ -9,7 +9,7 @@
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from linkml_runtime.utils.schemaview import SchemaView
 
-from linkml_runtime_api.apiroot import ApiRoot
+from linkml_dataops.apiroot import ApiRoot
 
 @dataclass
 class ApiGenerator(ApiRoot):

linkml_runtime_api/generators/fastapigenerator.py → linkml_dataops/generators/fastapigenerator.py

@@ -13,16 +13,16 @@
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from linkml_runtime.utils.schemaview import SchemaView
 
-from linkml_runtime_api.apiroot import ApiRoot
+from linkml_dataops.apiroot import ApiRoot
 
 # TODO
 jinja2_template = """
 import logging
 from dataclasses import dataclass
-from linkml_runtime_api.query.queryengine import QueryEngine
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
+from linkml_dataops.query.queryengine import QueryEngine
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
     FetchById
-from linkml_runtime_api.query.queryengine import MatchExpression
+from linkml_dataops.query.queryengine import MatchExpression
 
 from {{ datamodel_package_full}} import *
 

linkml_runtime_api/generators/pyapigenerator.py → linkml_dataops/generators/pyapigenerator.py

@@ -13,15 +13,15 @@
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from linkml_runtime.utils.schemaview import SchemaView
 
-from linkml_runtime_api.apiroot import ApiRoot
+from linkml_dataops.apiroot import ApiRoot
 
 jinja2_template = """
 import logging
 from dataclasses import dataclass
-from linkml_runtime_api.query.queryengine import QueryEngine
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
+from linkml_dataops.query.queryengine import QueryEngine
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
     FetchById
-from linkml_runtime_api.query.queryengine import MatchExpression
+from linkml_dataops.query.queryengine import MatchExpression
 
 from {{ datamodel_package_full}} import *
 

linkml_dataops/query/__init__.py

@@ -0,0 +1 @@
+from linkml_dataops.query.object_queryengine import ObjectQueryEngine

linkml_runtime_api/query/object_queryengine.py → linkml_dataops/query/object_queryengine.py

@@ -6,11 +6,11 @@
 
 from linkml_runtime.utils.formatutils import camelcase, underscore
 
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
     FetchById
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
-from linkml_runtime_api.query.queryengine import QueryEngine, create_match_constraint
+from linkml_dataops.query.queryengine import QueryEngine, create_match_constraint
 
 
 def like(x: Any, y: Any) -> bool:

linkml_runtime_api/query/queryengine.py → linkml_dataops/query/queryengine.py

@@ -5,8 +5,8 @@
 
 from linkml_runtime.utils.formatutils import camelcase, underscore
 
-from linkml_runtime_api.apiroot import ApiRoot, Database
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
+from linkml_dataops.apiroot import ApiRoot, Database
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
     FetchById
 from linkml_runtime.utils.yamlutils import YAMLRoot
 

setup.cfg

@@ -1,11 +1,11 @@
 [metadata]
-name = linkml_runtime_api
-url = https://github.com/biolink/linkml-runtime-api
-author = Harold Solbrig
-author-email = [email protected]
-summary = LinkML Runtime Environment API
-description = Runtime Environment API for the Linked Open Data Modeling Language
-home-page = http://linkml.github.io/linkml-runtime-api
+name = linkml_dataops
+url = https://github.com/biolink/linkml-dataops
+author = Chris Mungall
+author-email = [email protected]
+summary = LinkML Data Operations API
+description = Data Operations API for the Linked Open Data Modeling Language
+home-page = http://github.com/linkml/linkml-dataops
 license = CC0 1.0 Universal
 python-requires = >=3.7
 classifiers =
@@ -30,11 +30,11 @@ keywords =
 
 [files]
 packages =
-    linkml_runtime_api
+    linkml_dataops
 
 [entry_points]
 console_scripts =
-    gen-api-datamodel = linkml_runtime_api.generators.apigenerator:cli
-    gen-crud-datamodel = linkml_runtime_api.generators.apigenerator:cli
-    gen-python-api = linkml_runtime_api.generators.pyapigenerator:cli
-    linkml-apply = linkml_runtime_api.changer.jsonpatch_changer:cli
+    gen-api-datamodel = linkml_dataops.generators.apigenerator:cli
+    gen-crud-datamodel = linkml_dataops.generators.apigenerator:cli
+    gen-python-api = linkml_dataops.generators.pyapigenerator:cli
+    linkml-apply = linkml_dataops.changer.jsonpatch_changer:cli

tests/model/kitchen_sink_api_bespoke.py

@@ -1,8 +1,8 @@
 import logging
 from dataclasses import dataclass
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery, \
     FetchById
-from linkml_runtime_api.query.queryengine import MatchExpression, QueryEngine
+from linkml_dataops.query.queryengine import MatchExpression, QueryEngine
 
 from tests.model.kitchen_sink import *
 

tests/output/kitchen_sink_api_generated_test.py

@@ -1,9 +1,9 @@
 
 import logging
 from dataclasses import dataclass
-from linkml_runtime_api.query.queryengine import QueryEngine
-from linkml_runtime_api.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery,     FetchById
-from linkml_runtime_api.query.queryengine import MatchExpression
+from linkml_dataops.query.queryengine import QueryEngine
+from linkml_dataops.query.query_model import FetchQuery, Constraint, MatchConstraint, OrConstraint, AbstractQuery,     FetchById
+from linkml_dataops.query.queryengine import MatchExpression
 
 from tests.model.kitchen_sink import *
 

tests/test_apigenerator.py

@@ -3,8 +3,8 @@
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime_api.generators.apigenerator import ApiGenerator
-from linkml_runtime_api.changer.changes_model import AddObject, RemoveObject, Append, Rename
+from linkml_dataops.generators.apigenerator import ApiGenerator
+from linkml_dataops.changer.changes_model import AddObject, RemoveObject, Append, Rename
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.schemaview import SchemaView
 from tests.model.kitchen_sink import Person, Dataset, FamilialRelationship

tests/test_changer_common.py

@@ -3,8 +3,8 @@
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime_api.changer.object_changer import ObjectChanger
-from linkml_runtime_api.changer.changes_model import AddObject, RemoveObject, Append, Rename
+from linkml_dataops.changer.object_changer import ObjectChanger
+from linkml_dataops.changer.changes_model import AddObject, RemoveObject, Append, Rename
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.schemaview import SchemaView
 from tests.model.kitchen_sink import Person, Dataset, FamilialRelationship

tests/test_differ.py

@@ -2,9 +2,9 @@
 import unittest
 import logging
 
-from linkml_runtime_api.changer.object_changer import ObjectChanger
-from linkml_runtime_api.changer.changes_model import Rename
-from linkml_runtime_api.diffs.differ import DiffEngine
+from linkml_dataops.changer.object_changer import ObjectChanger
+from linkml_dataops.changer.changes_model import Rename
+from linkml_dataops.diffs.differ import DiffEngine
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.schemaview import SchemaView
 from tests.model.kitchen_sink import Dataset

tests/test_jsonpatch_changer.py

@@ -9,8 +9,8 @@
 from linkml_runtime.utils.schemaview import SchemaView
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
-from linkml_runtime_api.changer.jsonpatch_changer import JsonPatchChanger
-from linkml_runtime_api.changer.changes_model import AddObject, RemoveObject, Append, Rename
+from linkml_dataops.changer.jsonpatch_changer import JsonPatchChanger
+from linkml_dataops.changer.changes_model import AddObject, RemoveObject, Append, Rename
 
 from tests.model.kitchen_sink import Person, Dataset, FamilialRelationship
 from tests import MODEL_DIR, INPUT_DIR, OUTPUT_DIR

tests/test_object_changer.py

@@ -3,8 +3,8 @@
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime_api.changer.object_changer import ObjectChanger
-from linkml_runtime_api.changer.changes_model import AddObject, RemoveObject, Append, Rename
+from linkml_dataops.changer.object_changer import ObjectChanger
+from linkml_dataops.changer.changes_model import AddObject, RemoveObject, Append, Rename
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.schemaview import SchemaView
 from tests.model.kitchen_sink import Person, Dataset, FamilialRelationship

tests/test_objectqueryengine.py

@@ -4,9 +4,9 @@
 from typing import List
 
 from linkml_runtime.loaders import yaml_loader
-from linkml_runtime_api.query.object_queryengine import ObjectQueryEngine
-from linkml_runtime_api.query.queryengine import Database, MatchExpression
-from linkml_runtime_api.query.query_model import FetchQuery, MatchConstraint, OrConstraint, FetchById
+from linkml_dataops.query.object_queryengine import ObjectQueryEngine
+from linkml_dataops.query.queryengine import Database, MatchExpression
+from linkml_dataops.query.query_model import FetchQuery, MatchConstraint, OrConstraint, FetchById
 from linkml_runtime.utils.schemaview import SchemaView
 from tests.model.kitchen_sink import Person, Dataset
 from tests.model.kitchen_sink_api import PersonQuery, PersonFetchById

tests/test_pythonapigenerator.py

@@ -5,12 +5,12 @@
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.utils.compile_python import compile_python
 
-from linkml_runtime_api import ObjectQueryEngine
-from linkml_runtime_api.generators import PythonApiGenerator
+from linkml_dataops import ObjectQueryEngine
+from linkml_dataops.generators import PythonApiGenerator
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.schemaview import SchemaView
 
-from linkml_runtime_api.query.queryengine import Database, MatchExpression
+from linkml_dataops.query.queryengine import Database, MatchExpression
 from tests.model.kitchen_sink import Person, Dataset, FamilialRelationship
 from tests import MODEL_DIR, INPUT_DIR, OUTPUT_DIR
 

tests/test_schema_manipulation.py

@@ -3,8 +3,8 @@
 
 from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime_api.changer.object_changer import ObjectChanger
-from linkml_runtime_api.changer.changes_model import AddObject, RemoveObject, Append
+from linkml_dataops.changer.object_changer import ObjectChanger
+from linkml_dataops.changer.changes_model import AddObject, RemoveObject, Append
 
 class ObjectPatcherTestCase(unittest.TestCase):
 

tests/test_yaml_patch.py

@@ -0,0 +1,49 @@
+import os
+import sys
+import unittest
+import logging
+from ruamel.yaml import YAML
+
+from jsonpatch import JsonPatch
+
+from linkml_dataops.diffs.yaml_patch import YAMLPatch
+
+inp = """\
+# example
+name:
+  # details
+  family: Smith   # very common
+  given: Alice    # one of the siblings
+"""
+
+yaml_patch = YAMLPatch()
+
+class YamlPatchTestCase(unittest.TestCase):
+    """
+    Tests yaml patching
+    """
+
+    def test_patch(self):
+        """
+        test patch works, preserving comments
+        """
+        patch = JsonPatch([
+            {'op': 'add', 'path': '/foo', 'value': {'bar': 'baz'}},
+            {'op': 'remove', 'path': '/name/family'}
+        ])
+        nu = yaml_patch.patchs(inp, patch)
+        assert '# example' in nu
+        assert '# details' in nu
+        assert '# one of the siblings' in nu
+        yaml=YAML()
+        obj = yaml.load(nu)
+        self.assertEqual(obj, {"name": {"given": "Alice"},
+                               "foo": {"bar": "baz"}})
+
+
+
+
+
+
+if __name__ == '__main__':
+    unittest.main()