biocypher 0.5.39__tar.gz → 0.5.41__tar.gz

{biocypher-0.5.39 → biocypher-0.5.41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.5.39
+Version: 0.5.41
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT

{biocypher-0.5.39 → biocypher-0.5.41}/biocypher/_config/biocypher_config.yaml

@@ -3,7 +3,6 @@ Title: BioCypher python module configuration file
 ## Some options are not used by default. Uncomment them to use them.
 
 biocypher:
-
   ### Required parameters ###
   ## DBMS type
 
@@ -51,18 +50,17 @@ biocypher:
 
   # tail_ontologies:
   #   so:
-  #     url: test/so.owl
+  #     url: test/ontologies/so.owl
   #     head_join_node: sequence variant
   #     tail_join_node: sequence_variant
   #   mondo:
-  #     url: test/mondo.owl
+  #     url: test/ontologies/mondo.owl
   #     head_join_node: disease
   #     tail_join_node: disease
 
 ### DBMS configuration ###
 
 neo4j:
-
   ### Neo4j configuration ###
   ## Database name
 
@@ -80,8 +78,8 @@ neo4j:
 
   ## Neo4j admin import batch writer settings
 
-  delimiter: ';'
-  array_delimiter: '|'
+  delimiter: ";"
+  array_delimiter: "|"
   quote_character: "'"
 
   ## MultiDB functionality
@@ -104,8 +102,8 @@ postgresql:
 
   # PostgreSQL connection credentials
   database_name: postgres # DB name
-  user: postgres  # user name
-  password: postgres  # password
+  user: postgres # user name
+  password: postgres # password
   host: localhost # host
   port: 5432 # port
 
@@ -114,3 +112,15 @@ postgresql:
   delimiter: '\t'
   # import_call_bin_prefix: '' # path to "psql"
   # import_call_file_prefix: '/path/to/files'
+
+sqlite:
+  ### SQLite configuration ###
+
+  # SQLite connection credentials
+  database_name: sqlite.db # DB name
+
+  # SQLite import batch writer settings
+  quote_character: '"'
+  delimiter: '\t'
+  # import_call_bin_prefix: '' # path to "sqlite3"
+  # import_call_file_prefix: '/path/to/files'

{biocypher-0.5.39 → biocypher-0.5.41}/biocypher/_connect.py

@@ -11,11 +11,12 @@
 """
 BioCypher 'online' mode. Handles connection and manipulation of a running DBMS.
 """
+import subprocess
+
 from ._logger import logger
 
 logger.debug(f"Loading module {__name__}.")
 
-from typing import Optional
 from collections.abc import Iterable
 import itertools
 
@@ -24,7 +25,6 @@ import neo4j_utils
 from . import _misc
 from ._config import config as _config
 from ._create import BioCypherEdge, BioCypherNode
-from ._ontology import Ontology
 from ._translate import Translator
 
 __all__ = ["_Neo4jDriver"]
@@ -137,16 +137,43 @@ class _Neo4jDriver:
 
         logger.info("Creating constraints for node types in config.")
 
+        major_neo4j_version = int(self._get_neo4j_version().split(".")[0])
         # get structure
         for leaf in self.translator.ontology.mapping.extended_schema.items():
-            label = _misc.sentencecase_to_pascalcase(leaf[0])
+            label = _misc.sentencecase_to_pascalcase(leaf[0], sep=r"\s\.")
             if leaf[1]["represented_as"] == "node":
-                s = (
-                    f"CREATE CONSTRAINT `{label}_id` "
-                    f"IF NOT EXISTS ON (n:`{label}`) "
-                    "ASSERT n.id IS UNIQUE"
-                )
-                self._driver.query(s)
+                if major_neo4j_version >= 5:
+                    s = (
+                        f"CREATE CONSTRAINT `{label}_id` "
+                        f"IF NOT EXISTS FOR (n:`{label}`) "
+                        "REQUIRE n.id IS UNIQUE"
+                    )
+                    self._driver.query(s)
+                else:
+                    s = (
+                        f"CREATE CONSTRAINT `{label}_id` "
+                        f"IF NOT EXISTS ON (n:`{label}`) "
+                        "ASSERT n.id IS UNIQUE"
+                    )
+                    self._driver.query(s)
+
+    def _get_neo4j_version(self):
+        """Get neo4j version."""
+        try:
+            neo4j_version = self._driver.query(
+                """
+                    CALL dbms.components()
+                    YIELD name, versions, edition
+                    UNWIND versions AS version
+                    RETURN version AS version
+                """,
+            )[0][0]["version"]
+            return neo4j_version
+        except Exception as e:
+            logger.warning(
+                f"Error detecting Neo4j version: {e} use default version 4.0.0."
+            )
+            return "4.0.0"
 
     def add_nodes(self, id_type_tuples: Iterable[tuple]) -> tuple:
         """

{biocypher-0.5.39 → biocypher-0.5.41}/biocypher/_core.py

@@ -26,8 +26,8 @@ from ._logger import logger
 
 logger.debug(f"Loading module {__name__}.")
 
+from biocypher.write._write import DBMS_TO_CLASS, get_writer
 from ._get import Downloader
-from ._write import get_writer
 from ._config import config as _config
 from ._config import update_from_file as _file_update
 from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
@@ -40,7 +40,7 @@ from ._deduplicate import Deduplicator
 
 __all__ = ["BioCypher"]
 
-SUPPORTED_DBMS = ["neo4j", "postgresql"]
+SUPPORTED_DBMS = DBMS_TO_CLASS.keys()
 
 REQUIRED_CONFIG = [
     "dbms",
@@ -136,6 +136,10 @@ class BioCypher:
 
         if not self._schema_config_path:
             logger.warning("Running BioCypher without schema configuration.")
+        else:
+            logger.info(
+                f"Running BioCypher with schema configuration from {self._schema_config_path}."
+            )
 
         self._head_ontology = head_ontology or self.base_config["head_ontology"]
 
@@ -476,7 +480,7 @@ class BioCypher:
         if mt:
             msg = (
                 "Input entities not accounted for due to them not being "
-                "present in the `schema_config.yaml` configuration file "
+                f"present in the schema configuration file {self._schema_config_path} "
                 "(this is not necessarily a problem, if you did not intend "
                 "to include them in the database; see the log for details): \n"
             )

{biocypher-0.5.39 → biocypher-0.5.41}/biocypher/_metadata.py

@@ -19,7 +19,7 @@ import importlib.metadata
 
 import toml
 
-_VERSION = "0.5.39"
+_VERSION = "0.5.41"
 
 
 def get_metadata():

{biocypher-0.5.39 → biocypher-0.5.41}/biocypher/_misc.py

@@ -205,7 +205,7 @@ def sentencecase_to_snakecase(s: str) -> str:
     return stringcase.snakecase(s).lower()
 
 
-def sentencecase_to_pascalcase(s: str) -> str:
+def sentencecase_to_pascalcase(s: str, sep: str = r"\s") -> str:
     """
     Convert sentence case to PascalCase.
 
@@ -215,7 +215,11 @@ def sentencecase_to_pascalcase(s: str) -> str:
     Returns:
         string in PascalCase form
     """
-    return re.sub(r"(?:^| )([a-zA-Z])", lambda match: match.group(1).upper(), s)
+    return re.sub(
+        r"(?:^|[" + sep + "])([a-zA-Z])",
+        lambda match: match.group(1).upper(),
+        s,
+    )
 
 
 def to_lower_sentence_case(s: str) -> str: