Merge pull request #4 from MI-FraunhoferIWM/enh/sparql-update

Enh/sparql update

dsms/core/utils.py

@@ -2,16 +2,17 @@
 import re
 from typing import Any
 from urllib.parse import urljoin
+from uuid import UUID
 
 import requests
 from requests import Response
 
 
-def _kitem_id2uri(kitem_id: str) -> str:
+def _kitem_id2uri(kitem_id: UUID) -> str:
     "Convert a kitem id in the DSMS to the full resolvable URI"
     from dsms import Context
 
-    return f"{Context.dsms.config.host_url}/{kitem_id}"
+    return urljoin(str(Context.dsms.config.host_url), str(kitem_id))
 
 
 def _uri2kitem_idi(uri: str) -> str:

dsms/knowledge/kitem.py

@@ -404,7 +404,9 @@ def dsms(cls, value: "DSMS") -> None:
     @property
     def subgraph(cls) -> Optional[Graph]:
         """Getter for Subgraph"""
-        return _get_subgraph(cls.id, cls.dsms.config.kitem_repo)
+        return _get_subgraph(
+            cls.id, cls.dsms.config.kitem_repo, is_kitem_id=True
+        )
 
     @property
     def context(cls) -> "Context":

dsms/knowledge/sparql_interface/sparql_interface.py

@@ -2,14 +2,15 @@
 
 from typing import TYPE_CHECKING
 
+from dsms.knowledge.sparql_interface.subgraph import Subgraph
 from dsms.knowledge.sparql_interface.utils import (
     _add_rdf,
     _sparql_query,
     _sparql_update,
 )
 
 if TYPE_CHECKING:
-    from typing import Any, Dict
+    from typing import Any, Dict, TextIO, Union
 
     from dsms.core.dsms import DSMS
 
@@ -21,17 +22,33 @@ class SparqlInterface:
     def __init__(self, dsms):
         """Initalize the Sparql interface"""
         self._dsms: "DSMS" = dsms
+        self._subgraph = Subgraph(dsms)
 
     def query(
         self, query: str, repository: str = "knowledge"
     ) -> "Dict[str, Any]":
         """Perform Sparql Query"""
         return _sparql_query(query, repository)
 
-    def update(self, filepath: str, repository: str = "knowledge") -> None:
+    def update(
+        self,
+        file_or_pathlike: "Union[str, TextIO]",
+        repository: str = "knowledge",
+    ) -> None:
         """Perform update query from local file"""
-        _sparql_update(filepath, self._dsms.config.encoding, repository)
-
-    def add_rdf(self, filepath: str, repository: str = "knowledge") -> None:
+        _sparql_update(
+            file_or_pathlike, self._dsms.config.encoding, repository
+        )
+
+    def insert(
+        self,
+        file_or_pathlike: "Union[str, TextIO]",
+        repository: str = "knowledge",
+    ) -> None:
         """Upload RDF to triplestore from local file"""
-        _add_rdf(filepath, self._dsms.config.encoding, repository)
+        _add_rdf(file_or_pathlike, self._dsms.config.encoding, repository)
+
+    @property
+    def subgraph(cls) -> Subgraph:
+        """Subgraph interface for DSMS"""
+        return cls._subgraph

dsms/knowledge/sparql_interface/subgraph.py

@@ -0,0 +1,44 @@
+"""DSMS Subgraph interface"""
+
+from typing import TYPE_CHECKING
+
+from dsms.knowledge.sparql_interface.utils import (
+    _create_subgraph,
+    _delete_subgraph,
+    _get_subgraph,
+    _update_subgraph,
+)
+
+if TYPE_CHECKING:
+    from rdflib import Graph
+
+    from dsms import DSMS
+
+
+class Subgraph:
+    """Subgraph interface for DSMS"""
+
+    def __init__(self, dsms):
+        """Initalize the Sparql interface"""
+        self._dsms: "DSMS" = dsms
+
+    def update(self, graph: "Graph", repository: str = "knowledge") -> None:
+        """Update a subgraph in the DSMS"""
+        _update_subgraph(graph, self._dsms.config.encoding, repository)
+
+    def create(self, graph: "Graph", repository: str = "knowledge") -> None:
+        """Create a subgraph in the DSMS"""
+        _create_subgraph(graph, self._dsms.config.encoding, repository)
+
+    def delete(self, identifier: str, repository: str = "knowledge") -> None:
+        """Delete a subgraph in the DSMS"""
+        _delete_subgraph(identifier, repository)
+
+    def get(
+        self,
+        identifier: str,
+        repository: str = "knowledge",
+        is_kitem_id: bool = False,
+    ) -> "Graph":
+        """Get a subgraph from the DSMS"""
+        return _get_subgraph(identifier, repository, is_kitem_id)

dsms/knowledge/sparql_interface/utils.py

@@ -2,12 +2,14 @@
 import io
 from typing import TYPE_CHECKING
 
-from rdflib import Graph
+from rdflib.plugins.sparql.results.jsonresults import JSONResult
 
 from dsms.core.utils import _kitem_id2uri, _perform_request
 
 if TYPE_CHECKING:
-    from typing import Any, Dict
+    from typing import Any, Dict, Optional, TextIO, Union
+
+    from rdflib import Graph
 
 
 def _sparql_query(query: str, repository: str) -> "Dict[str, Any]":
@@ -28,44 +30,64 @@ def _sparql_query(query: str, repository: str) -> "Dict[str, Any]":
             \n
             `{query}`"""
         ) from excep
-    return response["results"]["bindings"]
+    return response
 
 
 def _sparql_update(
-    filepath: str,
+    file_or_pathlike: "Union[str, TextIO]",
     encoding: str,
     repository: str,
 ) -> None:
     """Submit plain SPARQL-query to the DSMS instance."""
-
-    with open(filepath, mode="r+", encoding=encoding) as file:
-        response = _perform_request(
-            "api/knowledge/update-query",
-            "post",
-            files={"file": file},
-            params={"repository": repository},
-        )
+    response = _perform_request(
+        "api/knowledge/update-query",
+        "post",
+        files=_get_file_or_pathlike(file_or_pathlike, encoding),
+        params={"repository": repository},
+    )
     if not response.ok:
         raise RuntimeError(f"Sparql was not successful: {response.text}")
 
 
-def _add_rdf(filepath: str, encoding: str, repository: str) -> None:
-    """Create the subgraph in the remote backend"""
+def _get_file_or_pathlike(
+    file_or_pathlike: "Union[str, TextIO]", encoding: str
+) -> "TextIO":
+    if isinstance(file_or_pathlike, str):
+        with open(file_or_pathlike, mode="r+", encoding=encoding) as file:
+            files = {"file", file}
+    else:
+        if "read" not in dir(file_or_pathlike):
+            raise TypeError(
+                f"{file_or_pathlike} is neither a path"
+                f"or a file-like object."
+            )
+        files = {"file": file_or_pathlike}
+    return files
 
-    with open(filepath, mode="r+", encoding=encoding) as file:
-        response = _perform_request(
-            "api/knowledge/add-rdf",
-            "post",
-            files={"file": file},
-            params={"repository": repository},
-        )
+
+def _add_rdf(
+    file_or_pathlike: "Union[str, TextIO]",
+    encoding: str,
+    repository: str,
+    context: "Optional[str]" = None,
+) -> None:
+    """Create the subgraph in the remote backend"""
+    params = {"repository": repository}
+    if context:
+        params["context"] = context
+    response = _perform_request(
+        "api/knowledge/add-rdf",
+        "post",
+        files=_get_file_or_pathlike(file_or_pathlike, encoding),
+        params=params,
+    )
     if not response.ok:
         raise RuntimeError(
             f"Not able to create subgraph in backend: {response.text}"
         )
 
 
-def _delete_subgraph(identifier: str, encoding: str, repository: str) -> None:
+def _delete_subgraph(identifier: str, repository: str) -> None:
     """Get subgraph related to a certain dataset id."""
     query = f"""
     DELETE {{
@@ -79,42 +101,49 @@ def _delete_subgraph(identifier: str, encoding: str, repository: str) -> None:
             GRAPH ?g {{ ?s ?p ?o . }}
         }}
     }}"""
-    _sparql_update(query, encoding, repository)
+    response = _sparql_query(query, repository)
+    if not response.get("boolean"):
+        raise RuntimeError(
+            f"Deleteing subgraph was not successful: {response}"
+        )
+
 
+def _create_subgraph(graph: "Graph", encoding: str, respository: str) -> None:
+    """Create the subgraph in the remote backend"""
+    upload_file = io.BytesIO(graph.serialize(encoding=encoding))
+    _add_rdf(
+        upload_file, encoding, respository, context=f"<{graph.identifier}>"
+    )
 
-def _update_subgraph(graph: Graph, encoding: str, repository: str) -> None:
+
+def _update_subgraph(graph: "Graph", encoding: str, repository: str) -> None:
     """Update the subgraph in the remote backend"""
-    _delete_subgraph(graph.identifier, encoding, repository)
-    _add_rdf(graph, encoding, repository)
+    _delete_subgraph(graph.identifier, repository)
+    _create_subgraph(graph, encoding, repository)
 
 
-def _get_subgraph(kitem_id: str, repository: str) -> Graph:
+def _get_subgraph(
+    identifier: str, repository: str, is_kitem_id: bool = False
+) -> "Graph":
     """Get subgraph related to a certain dataset id."""
-    uri = _kitem_id2uri(kitem_id)
+    if is_kitem_id:
+        identifier = _kitem_id2uri(identifier)
     query = f"""
     SELECT DISTINCT
         ?s ?p ?o
     WHERE {{
         BIND(
-            <{uri}> as ?g
+            <{identifier}> as ?g
             )
         {{
             GRAPH ?g {{ ?s ?p ?o . }}
         }}
     }}"""
     data = _sparql_query(query, repository)
-
-    buffer = io.StringIO()
-    buffer.writelines(
-        f"<{row['s']['value']}> <{row['p']['value']}> <{row['o']['value']}> ."
-        for row in data
-    )
-    buffer.seek(0)
-
-    graph = Graph(identifier=uri)
-    graph.parse(buffer, format="n3")
+    graph = JSONResult(data)
+    graph.identifier = identifier
 
     if len(graph) == 0:
-        raise ValueError(f"Subgraph for id `{kitem_id}` does not exist.")
+        raise ValueError(f"Subgraph for id `{identifier}` does not exist.")
 
     return graph