Releases pydantic pin, upgrades to pydantic v2 Refs #54

Author: sjoerdk

dicomtrolley/core.py

@@ -13,8 +13,7 @@
     TypeVar,
 )
 
-from pydantic import Field, ValidationError
-from pydantic.class_validators import validator
+from pydantic import Field, ValidationError, field_validator
 from pydantic.main import BaseModel
 from pydicom.datadict import tag_for_keyword
 from pydicom.dataset import Dataset
@@ -608,8 +607,8 @@ class Query(BaseModel):
     query_level: QueryLevels = (
         QueryLevels.STUDY
     )  # to which depth to return results
-    max_study_date: Optional[datetime]
-    min_study_date: Optional[datetime]
+    max_study_date: Optional[datetime] = None
+    min_study_date: Optional[datetime] = None
     include_fields: List[str] = Field([])  #
 
     class Config:
@@ -657,7 +656,8 @@ def validate_keyword(keyword):
         if not tag_for_keyword(keyword):
             raise ValueError(f"{keyword} is not a valid DICOM keyword")
 
-    @validator("include_fields")
+    @field_validator("include_fields")
+    @classmethod
     def include_fields_check(cls, include_fields, values):  # noqa: B902, N805
         """Include fields should be valid dicom tag names"""
         for field in include_fields:
@@ -684,7 +684,7 @@ class ExtendedQuery(Query):
     StudyDescription: str = ""
     SeriesDescription: str = ""
     InstitutionalDepartmentName: str = ""
-    PatientBirthDate: Optional[date]
+    PatientBirthDate: Optional[date] = None
 
 
 class Searcher:

dicomtrolley/mint.py

@@ -6,7 +6,7 @@
 from xml.etree import ElementTree
 from xml.etree.ElementTree import ParseError
 
-from pydantic.class_validators import root_validator
+from pydantic import model_validator
 from pydicom.dataelem import DataElement
 from pydicom.dataset import Dataset
 
@@ -159,11 +159,11 @@ class MintQuery(ExtendedQuery):
 
     limit: int = 0  # how many results to return. 0 = all
 
-    @root_validator()
+    @model_validator(mode="after")
     def min_max_study_date_xor(cls, values):  # noqa: B902, N805
         """Min and max should both be given or both be empty"""
-        min_date = values.get("min_study_date")
-        max_date = values.get("max_study_date")
+        min_date = values.min_study_date
+        max_date = values.max_study_date
         if min_date and not max_date:
             raise ValueError(
                 f"min_study_date parameter was passed"
@@ -177,14 +177,18 @@ def min_max_study_date_xor(cls, values):  # noqa: B902, N805
             )
         return values
 
-    @root_validator()
-    def include_fields_check(cls, values):  # noqa: B902, N805
+    @model_validator(mode="after")
+    def include_fields_check(self):
         """Include fields should match query level"""
-        include_fields = values.get("include_fields")
+        if isinstance(self, list):
+            # Interplay with base Query field_validator for include fields
+            return self  # don't check
+        else:
+            include_fields = self.include_fields
         if not include_fields:
-            return values  # May not exist if include_fields is invalid type
+            return self  # May not exist if include_fields is invalid type
 
-        query_level = values.get("query_level")
+        query_level = self.query_level
         if query_level:  # May be None for child classes
             valid_fields = get_valid_fields(query_level=query_level)
             for field in include_fields:
@@ -193,7 +197,7 @@ def include_fields_check(cls, values):  # noqa: B902, N805
                         f'"{field}" is not a valid include field for query '
                         f"level {query_level}. Valid fields: {valid_fields}"
                     )
-        return values
+        return self
 
     def __str__(self):
         return str(self.as_parameters())

dicomtrolley/qido_rs.py

@@ -11,7 +11,7 @@
 from datetime import datetime
 from typing import Dict, List, Optional, Sequence, Union
 
-from pydantic import root_validator
+from pydantic import model_validator
 from pydicom import Dataset
 from requests import Response
 
@@ -39,11 +39,11 @@ class QidoRSQueryBase(Query):
     limit: int = 0  # How many results to return. 0 = all
     offset: int = 0  # Number of skipped results
 
-    @root_validator()  # type: ignore
-    def min_max_study_date_xor(cls, values):  # noqa: B902, N805
+    @model_validator(mode="after")
+    def min_max_study_date_xor(self):  # noqa: B902, N805
         """Min and max should both be given or both be empty"""
-        min_date = values.get("min_study_date")
-        max_date = values.get("max_study_date")
+        min_date = self.min_study_date
+        max_date = self.max_study_date
         if min_date and not max_date:
             raise ValueError(
                 f"min_study_date parameter was passed"
@@ -55,7 +55,7 @@ def min_max_study_date_xor(cls, values):  # noqa: B902, N805
                 f"max_study_date parameter was passed ({max_date}), "
                 f"but min_study_date was not. Both need to be given"
             )
-        return values
+        return self
 
     @staticmethod
     def date_to_str(date_in: Optional[datetime]) -> str:
@@ -158,8 +158,8 @@ class HierarchicalQuery(QidoRSQueryBase):
     Faster than relationalQuery, but requires more information
     """
 
-    @root_validator()  # type: ignore
-    def uids_should_be_hierarchical(cls, values):  # noqa: B902, N805
+    @model_validator(mode="after")
+    def uids_should_be_hierarchical(self):
         """Any object uids passed should conform to study->series->instance"""
         order = ["StudyInstanceUID", "SeriesInstanceUID", "SOPInstanceUID"]
 
@@ -182,14 +182,13 @@ def assert_parents_filled(a_hierarchy, value_dict):
             else:
                 return assert_parents_filled(a_hierarchy, value_dict)
 
-        assert_parents_filled(order, values)
+        assert_parents_filled(order, self.dict())
+        return self
 
-        return values
-
-    @root_validator()  # type: ignore
-    def uids_should_match_query_level(cls, values):  # noqa: B902, N805
+    @model_validator(mode="after")
+    def uids_should_match_query_level(self):
         """If a query is for instance level, there should be study and series UIDs"""
-        query_level = values["query_level"]
+        query_level = self.query_level
 
         def assert_key_exists(values_in, query_level_in, missing_key_in):
             if not values_in.get(missing_key_in):
@@ -199,6 +198,7 @@ def assert_key_exists(values_in, query_level_in, missing_key_in):
                     f"a QIDO-RS relational query"
                 )
 
+        values = self.dict()
         if query_level == QueryLevels.STUDY:
             pass  # Fine. you can always look for some studies
         elif query_level == QueryLevels.SERIES:
@@ -207,7 +207,7 @@ def assert_key_exists(values_in, query_level_in, missing_key_in):
             assert_key_exists(values, query_level, "SeriesInstanceUID")
             assert_key_exists(values, query_level, "StudyInstanceUID")
 
-        return values
+        return self
 
     def uri_base(self) -> str:
         """WADO-RS url to call when performing this query. Full URI also needs
@@ -294,17 +294,15 @@ class RelationalQuery(QidoRSQueryBase):
     Allows broader searches than HierarchicalQuery, but can be slower
     """
 
-    @root_validator()  # type: ignore
-    def query_level_should_be_series_or_instance(
-        cls, values  # noqa: B902, N805
-    ):
+    @model_validator(mode="after")
+    def query_level_should_be_series_or_instance(self):
         """A relational query only makes sense for the instance and series levels.
         If you want to look for studies, us a hierarchical query
         """
-        if values.get("query_level") == QueryLevels.STUDY:
+        if self.query_level == QueryLevels.STUDY:
             raise ValueError(STUDY_VALUE_ERROR_TEXT)
 
-        return values
+        return self
 
     def uri_base(self) -> str:
         """WADO-RS url to call when performing this query. Full URI also needs

pyproject.toml

@@ -19,7 +19,7 @@ requests-futures = "^1.0.0"
 pynetdicom = "^1.5.6"
 Jinja2 = "^3.0.3"
 requests-toolbelt = "^1.0.0"
-pydantic = "1.8.2"
+pydantic = "^2.9.1"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.4.0"

tests/test_integration.py

@@ -39,7 +39,7 @@ def test_dicom_query_mint_cast(requests_mock, a_mint):
     set_mock_response(requests_mock, MINT_SEARCH_INSTANCE_LEVEL_ANY)
     with pytest.raises(DICOMTrolleyError):
         # should fail, casting to mint would lose unsupported StudyID parameter
-        a_mint.find_studies(DICOMQuery(StudyID=123))
+        a_mint.find_studies(DICOMQuery(StudyID="123"))
 
 
 def test_from_query():

tests/test_rad69.py

@@ -85,9 +85,9 @@ def test_rad69_error_from_server(
     with pytest.raises(DICOMTrolleyError) as e:
         a_rad69.get_dataset(
             InstanceReference(
-                study_uid=1,
-                series_uid=2,
-                instance_uid=3,
+                study_uid="1",
+                series_uid="2",
+                instance_uid="3",
             )
         )
     assert re.match(error_contains, str(e))
@@ -244,8 +244,8 @@ def test_wado_datasets_async(a_rad69, requests_mock):
     )
 
     instances = [
-        InstanceReference(study_uid=1, series_uid=2, instance_uid=3),
-        InstanceReference(study_uid=4, series_uid=5, instance_uid=6),
+        InstanceReference(study_uid="1", series_uid="2", instance_uid="3"),
+        InstanceReference(study_uid="4", series_uid="5", instance_uid="6"),
     ]
     a_rad69.use_async = True
     datasets = [x for x in a_rad69.datasets(instances)]