Neat 279 add write endpoint (#491)

Improved
Single NeatGraphStore instantiated via three options:
from_memory_store
from_oxi_store
from_sparql_store
Removed
Removed various superclassing of NeatGraphStore
Remove Prometheus reminisce in code base
Remove logging
Added
RdfFileExtractor graph extractor added.

Makefile

@@ -1,5 +1,5 @@
 .PHONY: run-explorer run-tests run-linters build-ui build-python build-docker run-docker compose-up
-version="0.79.0"
+version="0.80.0"
 run-explorer:
 	@echo "Running explorer API server..."
 	# open "http://localhost:8000/static/index.html" || true

cognite/neat/_version.py

@@ -1 +1 @@
-__version__ = "0.79.0"
+__version__ = "0.80.0"

cognite/neat/graph/__init__.py

@@ -1,3 +1,3 @@
-from .stores import NeatGraphStoreBase
+from .stores import NeatGraphStore
 
-__all__ = ["NeatGraphStoreBase"]
+__all__ = ["NeatGraphStore"]

cognite/neat/graph/_shared.py

@@ -0,0 +1,5 @@
+from typing import Literal, TypeAlias
+
+MIMETypes: TypeAlias = Literal[
+    "application/rdf+xml", "text/turtle", "application/n-triple", "application/n-quads", "application/trig"
+]

cognite/neat/graph/extractors/__init__.py

@@ -6,6 +6,7 @@
 from ._classic_cdf._sequences import SequencesExtractor
 from ._classic_cdf._timeseries import TimeSeriesExtractor
 from ._mock_graph_generator import MockGraphGenerator
+from ._rdf_file import RdfFileExtractor
 
 __all__ = [
     "AssetsExtractor",
@@ -16,4 +17,18 @@
     "EventsExtractor",
     "FilesExtractor",
     "LabelsExtractor",
+    "RdfFileExtractor",
 ]
+
+
+TripleExtractors = (
+    AssetsExtractor
+    | MockGraphGenerator
+    | RelationshipsExtractor
+    | TimeSeriesExtractor
+    | SequencesExtractor
+    | EventsExtractor
+    | FilesExtractor
+    | LabelsExtractor
+    | RdfFileExtractor
+)

cognite/neat/graph/extractors/_rdf_file.py

@@ -0,0 +1,18 @@
+from pathlib import Path
+
+from rdflib import URIRef
+
+from cognite.neat.graph._shared import MIMETypes
+from cognite.neat.graph.extractors._base import BaseExtractor
+
+
+class RdfFileExtractor(BaseExtractor):
+    def __init__(
+        self,
+        filepath: Path,
+        mime_type: MIMETypes = "application/rdf+xml",
+        base_uri: URIRef | None = None,
+    ):
+        self.filepath = filepath
+        self.mime_type = mime_type
+        self.base_uri = base_uri

cognite/neat/graph/loaders/_base.py

@@ -6,7 +6,7 @@
 from cognite.client import CogniteClient
 from cognite.client.data_classes.capabilities import Capability
 
-from cognite.neat.graph import NeatGraphStoreBase
+from cognite.neat.graph import NeatGraphStore
 from cognite.neat.graph.issues.loader import FailedAuthorizationError
 from cognite.neat.issues import NeatIssue, NeatIssueList
 from cognite.neat.utils.upload import UploadDiffsID, UploadResultIDs
@@ -18,7 +18,7 @@ class BaseLoader(ABC, Generic[T_Output]):
     _new_line = "\n"
     _encoding = "utf-8"
 
-    def __init__(self, graph_store: NeatGraphStoreBase):
+    def __init__(self, graph_store: NeatGraphStore):
         self.graph_store = graph_store
 
     @abstractmethod

cognite/neat/graph/loaders/_rdf2dms.py

@@ -17,7 +17,7 @@
 
 from cognite.neat.graph._tracking import LogTracker, Tracker
 from cognite.neat.graph.issues import loader as loader_issues
-from cognite.neat.graph.stores import NeatGraphStoreBase
+from cognite.neat.graph.stores import NeatGraphStore
 from cognite.neat.issues import NeatIssue, NeatIssueList
 from cognite.neat.rules.models import DMSRules
 from cognite.neat.rules.models.data_types import _DATA_TYPE_BY_DMS_TYPE
@@ -29,7 +29,7 @@
 class DMSLoader(CDFLoader[dm.InstanceApply]):
     def __init__(
         self,
-        graph_store: NeatGraphStoreBase,
+        graph_store: NeatGraphStore,
         data_model: dm.DataModel[dm.View] | None,
         instance_space: str,
         class_by_view_id: dict[ViewId, str] | None = None,
@@ -48,7 +48,7 @@ def from_data_model_id(
         cls,
         client: CogniteClient,
         data_model_id: dm.DataModelId,
-        graph_store: NeatGraphStoreBase,
+        graph_store: NeatGraphStore,
         instance_space: str,
     ) -> "DMSLoader":
         issues: list[NeatIssue] = []
@@ -61,7 +61,7 @@ def from_data_model_id(
         return cls(graph_store, data_model, instance_space, {}, issues)
 
     @classmethod
-    def from_rules(cls, rules: DMSRules, graph_store: NeatGraphStoreBase, instance_space: str) -> "DMSLoader":
+    def from_rules(cls, rules: DMSRules, graph_store: NeatGraphStore, instance_space: str) -> "DMSLoader":
         issues: list[NeatIssue] = []
         data_model: dm.DataModel[dm.View] | None = None
         try:

cognite/neat/graph/stores/__init__.py

@@ -1,13 +1,3 @@
-from ._base import NeatGraphStoreBase
-from ._graphdb_store import GraphDBStore
-from ._memory_store import MemoryStore
-from ._oxigraph_store import OxiGraphStore
+from ._base import NeatGraphStore
 
-STORE_BY_TYPE: dict[str, type[NeatGraphStoreBase]] = {}
-for store in NeatGraphStoreBase.__subclasses__():
-    STORE_BY_TYPE[store.rdf_store_type] = store  # type: ignore[type-abstract]
-
-del store  # Cleanup namespace
-AVAILABLE_STORES = set(STORE_BY_TYPE.keys())
-
-__all__ = ["NeatGraphStoreBase", "MemoryStore", "OxiGraphStore", "GraphDBStore", "STORE_BY_TYPE", "AVAILABLE_STORES"]
+__all__ = ["NeatGraphStore"]