Rdf output adapter

.github/actions/setup/action.yaml

@@ -1,18 +1,18 @@
-name: 'Setup'
-description: 'Setup Python and Poetry'
+name: "Setup"
+description: "Setup Python and Poetry"
 inputs:
   PYTHON_VERSION:
-    description: 'Python version'
+    description: "Python version"
     default: 3.9
   POETRY_VERSION:
-    description: 'Poetry version'
+    description: "Poetry version"
     default: 1.5.1
 
 runs:
   using: "composite"
   steps:
     - name: Set up Python ${{inputs.PYTHON_VERSION}}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{inputs.PYTHON_VERSION}}
     - name: Load cached Poetry installation

.github/workflows/pr.yaml

@@ -7,8 +7,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        os: ["ubuntu-latest", "macos-13", "windows-latest"]
+        python-version: ["3.10", "3.11", "3.12"]
         neo4j-version: ["4.4-enterprise", "5.17.0-enterprise"]
         exclude:
           # Windows tests don't use the PostgreSQL/Neo4j Docker containers

biocypher/_config/biocypher_config.yaml

@@ -113,6 +113,10 @@ postgresql:
   # import_call_bin_prefix: '' # path to "psql"
   # import_call_file_prefix: '/path/to/files'
 
+rdf:
+  ### RDF configuration ###
+  rdf_format: turtle
+
 sqlite:
   ### SQLite configuration ###
 

biocypher/write/_batch_writer.py

@@ -6,6 +6,7 @@
 import re
 import glob
 
+from rdflib import Graph
 from more_itertools import peekable
 
 from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
@@ -117,6 +118,8 @@ def __init__(
         db_password: str = None,
         db_host: str = None,
         db_port: str = None,
+        rdf_format: str = None,
+        rdf_namespaces: dict = {},
     ):
         """
 
@@ -196,12 +199,20 @@ class contains all methods expected by a bach writer instance, some of
 
             db_port:
                 The database port.
+
+            rdf_format:
+                The format of RDF.
+
+            rdf_namespaces:
+                The namespaces for RDF.
         """
         self.db_name = db_name
         self.db_user = db_user
         self.db_password = db_password
         self.db_host = db_host or "localhost"
         self.db_port = db_port
+        self.rdf_format = rdf_format
+        self.rdf_namespaces = rdf_namespaces
 
         self.delim, self.escaped_delim = self._process_delimiter(delimiter)
         self.adelim, self.escaped_adelim = self._process_delimiter(

biocypher/write/_write.py

@@ -14,6 +14,7 @@
 """
 
 from biocypher._logger import logger
+from biocypher.write.graph._rdf import _RDFWriter
 from biocypher.write.graph._neo4j import _Neo4jBatchWriter
 from biocypher.write.graph._arangodb import _ArangoDBBatchWriter
 from biocypher.write.relational._sqlite import _SQLiteBatchWriter
@@ -43,6 +44,8 @@
     "ArangoDB": _ArangoDBBatchWriter,
     "sqlite": _SQLiteBatchWriter,
     "sqlite3": _SQLiteBatchWriter,
+    "rdf": _RDFWriter,
+    "RDF": _RDFWriter,
 }
 
 
@@ -102,4 +105,6 @@ def get_writer(
             db_user=dbms_config.get("user"),  # psql
             db_password=dbms_config.get("password"),  # psql
             db_port=dbms_config.get("port"),  # psql
+            rdf_format=dbms_config.get("rdf_format"),  # rdf
+            rdf_namespaces=dbms_config.get("rdf_namespaces"),  # rdf
         )