Merge pull request #111 from monarch-initiative/pydantic-v2

Update to Pydantic v2

.github/workflows/test.yaml

@@ -46,4 +46,4 @@ jobs:
       #              run pytest
       #----------------------------------------------
       - name: Run tests
-        run: poetry run pytest tests
+        run: poetry run pytest tests

.gitignore

@@ -1,7 +1,7 @@
 # Default output / Generated / Unpacked data files
 output/
 tests/resources/source-files/string.tsv*
-
+.ruff_cache
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

examples/string-declarative/declarative-protein-links-detailed.py

@@ -1,7 +1,8 @@
 import re
 import uuid
 
-from biolink.pydanticmodel import PairwiseGeneToGeneInteraction, Protein
+# from biolink.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, Protein
+from koza.model.biolink.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, Protein
 
 from koza.cli_runner import get_koza_app
 

examples/string-w-custom-map/custom-map-protein-links-detailed.py

@@ -1,6 +1,7 @@
 import uuid
 
-from biolink.pydanticmodel import Gene, PairwiseGeneToGeneInteraction
+# from biolink.pydanticmodel_v2 import Gene, PairwiseGeneToGeneInteraction
+from koza.model.biolink.pydanticmodel_v2 import Gene, PairwiseGeneToGeneInteraction
 
 from koza.cli_runner import get_koza_app
 

examples/string-w-map/map-protein-links-detailed.py

@@ -1,6 +1,7 @@
 import uuid
 
-from biolink.pydanticmodel import Gene, PairwiseGeneToGeneInteraction
+# from biolink.pydanticmodel_v2 import Gene, PairwiseGeneToGeneInteraction
+from koza.model.biolink.pydanticmodel_v2 import Gene, PairwiseGeneToGeneInteraction
 
 from koza.cli_runner import get_koza_app
 

examples/string/protein-links-detailed.py

@@ -1,7 +1,8 @@
 import re
 import uuid
 
-from biolink.pydanticmodel import PairwiseGeneToGeneInteraction, Protein
+# from biolink.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, Protein
+from koza.model.biolink.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, Protein
 
 from koza.cli_runner import get_koza_app
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "koza"
-version = "0.4.0"
+version = "0.5.0"
 description = "Data transformation framework for LinkML data models"
 authors = [
     "The Monarch Initiative <[email protected]>",
@@ -16,8 +16,8 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.8"
-linkml-validator = ">=0.4.4"
-pydantic = "^1.10"
+linkml = ">=1.6.2"
+pydantic = "^2.4"
 pyyaml = ">=5.0.0"
 requests = "^2.24.0"
 ordered-set = ">=4.1.0"
@@ -30,7 +30,7 @@ sssom = "^0.3.41"
 black = "^23.10.0"
 ruff = "*"
 pytest = ">=6.0.0"
-biolink-model = ">=3.0.1"
+biolink-model = ">=3.0.1" # ">=3.5.5"
 dask = ">=2022.5.2"
 mkdocs = ">=1.4.2"
 mkdocs-material = ">=9.1.16"

src/koza/app.py

@@ -4,7 +4,7 @@
 from typing import Dict, Union
 import yaml
 
-from linkml_validator.validator import Validator
+# from linkml_validator.validator import Validator
 from pydantic.error_wrappers import ValidationError
 
 from koza.converter.kgx_converter import KGXConverter
@@ -43,7 +43,7 @@ def __init__(
         self.logger = logger
 
         if schema:
-            self.validator = Validator(schema=schema)
+            # self.validator = Validator(schema=schema)
             self.converter = KGXConverter()
 
         if source.config.depends_on is not None:
@@ -84,7 +84,8 @@ def process_sources(self):
         is_first = True
         transform_module = None
 
-        self.logger.info(f"Transforming source: {self.source.config.name}")
+        if self.logger:
+            self.logger.info(f"Transforming source: {self.source.config.name}")
         if self.source.config.transform_mode == 'flat':
             while True:
                 try:
@@ -94,11 +95,13 @@ def process_sources(self):
                     else:
                         importlib.reload(transform_module)
                 except MapItemException as mie:
-                    self.logger.debug(f"{str(mie)} not found in map")
+                    if self.logger:
+                        self.logger.debug(f"{str(mie)} not found in map")
                 except NextRowException:
                     continue
                 except ValidationError as ve:
-                    self.logger.error(f"Validation error while processing: {self.source.last_row}")
+                    if self.logger:
+                        self.logger.error(f"Validation error while processing: {self.source.last_row}")
                     raise ve
                 except StopIteration:
                     break