ontology service

app/src/pages/workspaces_page/components/WorkspaceCardItem/styles.scss

@@ -1,7 +1,6 @@
 .workspace-card {
-  flex: 1;
+  width: calc(25% - 10px);
   max-height: fit-content;
-  min-width: 100%;
 }
 
 h5 {
@@ -14,10 +13,13 @@ p {
   overflow: hidden;
 }
 
-@media screen and (min-width: 768px) {
-  .workspace-card {
-    min-width: calc(768px / 3 - 20px);
-    max-width: calc(768px / 3 - 20px);
+@media (max-width: 768px) {
+  .workspace-card.bp5-card.bp5-elevation-2 {
+    width: calc(100% - 10px);
+  }
+  .workspaces-list {
+    flex-wrap: wrap;
+    justify-content: space-between;
   }
 }
 
@@ -28,5 +30,4 @@ p {
   & > *:not(:first-child) {
     margin-left: 10px;
   }
-  margin-top: 10px;
 }

app/src/pages/workspaces_page/styles.scss

@@ -17,15 +17,14 @@
 .workspaces-list {
   display: flex;
   gap: 10px;
+  padding: 10px;
+
   flex-wrap: wrap;
-  align-items: flex-start;
   align-content: flex-start;
-  flex-direction: column;
   width: 100%;
-  padding: 10px;
 }
 
-@media only screen and (min-width: 768px) {
+@media (max-width: 768px) {
   .workspaces-list {
     flex-direction: row;
   }

server/const/err_enums.py

@@ -2,6 +2,9 @@
 
 
 class ErrCodes(Enum):
+    # General
+    UNKNOWN_ERROR = -1
+    NOT_IMPLEMENTED = -2
     # FS Service
     FILE_NOT_FOUND = 0
     FILE_CORRUPTED = 1
@@ -10,3 +13,6 @@ class ErrCodes(Enum):
     WORKSPACE_METADATA_NOT_FOUND = 20
     WORKSPACE_METADATA_EXISTS = 21
     WORKSPACE_METADATA_ILLEGAL_UPDATE_OPERATION = 22
+
+    # Ontology Service
+    ONTOLOGY_NOT_FOUND = 40

server/models/ontology.py

@@ -275,7 +275,6 @@ class Ontology:
         classes (list[Class]): The classes in the ontology
         individuals (list[Individual]): The individuals in the ontology
         properties (list[Property]): The properties in the ontology
-        all_named_nodes (list[NamedNode]): All named nodes in the ontology
 
     """
 
@@ -285,7 +284,6 @@ class Ontology:
     classes: list[Class]
     individuals: list[Individual]
     properties: list[Property]
-    all_named_nodes: list[NamedNode]
 
     def to_dict(self):
         return {
@@ -301,10 +299,6 @@ def to_dict(self):
             "properties": [
                 prop.to_dict() for prop in self.properties
             ],
-            "all_named_nodes": [
-                node.to_dict()
-                for node in self.all_named_nodes
-            ],
         }
 
     @classmethod
@@ -325,8 +319,4 @@ def from_dict(cls, data):
                 Property.from_dict(prop)
                 for prop in data["properties"]
             ],
-            all_named_nodes=[
-                NamedNode.from_dict(node)
-                for node in data["all_named_nodes"]
-            ],
         )

server/service_protocols/ontology_service_protocol/__init__.py

@@ -34,7 +34,7 @@ def get_ontologies(
         ...
 
     def create_ontology(
-        self, name: str, content: bytes
+        self, name: str, base_uri: str, content: bytes
     ) -> Ontology:
         """
         Create an ontology

server/services/core/sqlite_db_service/tables/ontology.py

@@ -14,3 +14,4 @@ class OntologyTable(Base):
     )
     name: Mapped[str] = mapped_column(String)
     json_file_uuid: Mapped[str] = mapped_column(String)
+    ontology_file_uuid: Mapped[str] = mapped_column(String)

server/services/local/local_ontology_service.py

@@ -1,9 +1,12 @@
 import json
 import logging
+from uuid import uuid4
 
 from kink import inject
+from pkg_resources import FileMetadata
 from sqlalchemy import select
 
+from server.exceptions import ErrCodes, ServerException
 from server.models.ontology import Ontology
 from server.service_protocols.fs_service_protocol import (
     FSServiceProtocol,
@@ -15,19 +18,41 @@
 from server.services.local.local_fs_service import (
     LocalFSService,
 )
+from server.utils.ontology_indexer import OntologyIndexer
+from server.utils.rdf_loader import RDFLoader
 
 
 @inject
 class LocalOntologyService:
     def __init__(
         self,
         fs_service: LocalFSService,
+        ontology_indexer: OntologyIndexer,
         db_service: DBService,
     ):
         self.logger = logging.getLogger(__name__)
+        self.ontology_indexer: OntologyIndexer = (
+            ontology_indexer
+        )
         self.fs_service: FSServiceProtocol = fs_service
         self.db_service: DBService = db_service
 
+    def _get_from_ontology_table(
+        self, ontology_id: str
+    ) -> OntologyTable | None:
+        query = (
+            select(OntologyTable)
+            .where(OntologyTable.uuid == ontology_id)
+            .limit(1)
+        )
+
+        with self.db_service.get_session() as session:
+            result = session.execute(query).first()
+            if not result:
+                return None
+
+            return result[0]
+
     def get_ontology(self, ontology_id: str) -> Ontology:
         """
         Get ontology by id
@@ -42,26 +67,14 @@ def get_ontology(self, ontology_id: str) -> Ontology:
         self.logger.info(
             f"Getting ontology with id: {ontology_id}"
         )
-        query = (
-            select(OntologyTable)
-            .where(OntologyTable.uuid == ontology_id)
-            .limit(1)
+        ontology_table = self._get_from_ontology_table(
+            ontology_id
         )
 
-        ontology_table: OntologyTable | None = None
-
-        with self.db_service.get_session() as session:
-            result = session.execute(query).first()
-            if not result:
-                raise ValueError(
-                    f"Ontology with id {ontology_id} not found"
-                )
-
-            ontology_table = result[0]
-
         if not ontology_table:
-            raise ValueError(
-                f"Ontology with id {ontology_id} not found"
+            raise ServerException(
+                "Ontology not found",
+                ErrCodes.ONTOLOGY_NOT_FOUND,
             )
 
         file_bytes = (
@@ -114,5 +127,106 @@ def get_ontologies(
         return ontologies
 
     def create_ontology(
-        self, name: str, content: bytes
-    ) -> Ontology: ...
+        self, name: str, base_uri: str, content: bytes
+    ) -> Ontology:
+        self.logger.info(f"Creating ontology: {name}")
+        self.logger.info("Parsing ontology content")
+        g = RDFLoader.load_rdf_bytes(content)
+        self.logger.info(f"Indexing ontology: {name}")
+
+        all_classes = self.ontology_indexer.get_classes(
+            base_uri, g
+        )
+
+        all_properties = (
+            self.ontology_indexer.get_properties(
+                base_uri, g
+            )
+        )
+
+        all_individuals = (
+            self.ontology_indexer.get_individuals(
+                base_uri, g
+            )
+        )
+
+        self.logger.info("Indexing complete")
+        self.logger.info("Uploading ontology file")
+        file_metadata = self.fs_service.upload_file(
+            name, content
+        )
+        self.logger.info("File uploaded")
+
+        ontology = Ontology(
+            uuid=uuid4().hex,
+            file_uuid=file_metadata.uuid,
+            name=name,
+            classes=all_classes,
+            individuals=all_individuals,
+            properties=all_properties,
+        )
+
+        self.logger.info("Saving ontology to filesystem")
+
+        json_data = ontology.to_dict()
+
+        ontology_json_file = self.fs_service.upload_file(
+            f"{name}.json",
+            json.dumps(json_data).encode("utf-8"),
+        )
+        self.logger.info("Ontology saved to filesystem")
+
+        with self.db_service.get_session() as session:
+            session.add(
+                OntologyTable(
+                    uuid=ontology.uuid,
+                    name=ontology.name,
+                    json_file_uuid=ontology_json_file.uuid,
+                    ontology_file_uuid=file_metadata.uuid,
+                )
+            )
+            session.commit()
+
+        return ontology
+
+    def update_ontology(
+        self,
+        ontology_id: str,
+        name: str,
+        file_metadata: FileMetadata,
+    ) -> Ontology:
+        raise ServerException(
+            "Not implemented", ErrCodes.NOT_IMPLEMENTED
+        )
+
+    def delete_ontology(self, ontology_id: str):
+        self.logger.info(
+            f"Deleting ontology with id: {ontology_id}"
+        )
+
+        ontology_table = self._get_from_ontology_table(
+            ontology_id
+        )
+
+        if not ontology_table:
+            raise ServerException(
+                "Ontology not found",
+                ErrCodes.ONTOLOGY_NOT_FOUND,
+            )
+
+        self.fs_service.delete_file_with_uuid(
+            ontology_table.json_file_uuid
+        )
+        self.fs_service.delete_file_with_uuid(
+            ontology_table.ontology_file_uuid
+        )
+
+        with self.db_service.get_session() as session:
+            session.delete(ontology_table)
+            session.commit()
+
+        self.logger.info(
+            f"Ontology with id: {ontology_id} deleted"
+        )
+
+        return None