nci-cidc-api-modules 1.2.38__py3-none-any.whl → 1.2.40__py3-none-any.whl

cidc_api/models/pydantic/stage2/contact.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Contact(Base):

cidc_api/models/pydantic/stage2/demographic.py

@@ -2,7 +2,7 @@ from typing import Self, Annotated, List
 
 from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, model_validator, field_validator, BeforeValidator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     Sex,
     Race,

cidc_api/models/pydantic/stage2/disease.py

@@ -1,7 +1,7 @@
 from pydantic import NonPositiveInt, model_validator, BeforeValidator
 from typing import List, Self, Annotated, get_args
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     TumorGrade,
     CancerStageSystem,

cidc_api/models/pydantic/stage2/exposure.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, ExposureType
 
 

cidc_api/models/pydantic/stage2/file.py

@@ -1,5 +1,5 @@
 from datetime import datetime
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import ChecksumType, FileFormat
 
 
@@ -8,7 +8,7 @@ class File(Base):
     file_id: int | None = None
 
     # The unique identifier for the associated trial
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/gvhd_diagnosis_acute.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDDiagnosisAcuteAssessmentSystem,
     GVHDDiagnosisAcuteAssessmentSystemVersion,

cidc_api/models/pydantic/stage2/gvhd_diagnosis_chronic.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDDiagnosisChronicAssessmentSystem,
     GVHDDiagnosisChronicAssessmentSystemVersion,

cidc_api/models/pydantic/stage2/gvhd_organ_acute.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDOrgan,
     GVHDOrganAcuteStage,

cidc_api/models/pydantic/stage2/gvhd_organ_chronic.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDOrgan,
     GVHDOrganChronicScore,

cidc_api/models/pydantic/stage2/institution.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Institution(Base):

cidc_api/models/pydantic/stage2/medical_history.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, PositiveFloat, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import TobaccoSmokingStatus
 
 

cidc_api/models/pydantic/stage2/other_clinical_endpoint.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
 
 

cidc_api/models/pydantic/stage2/other_malignancy.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonPositiveInt, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 

cidc_api/models/pydantic/stage2/participant.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU
 from cidc_api.models.types import OffStudyReason
 
@@ -16,13 +16,16 @@ class Participant(Base):
     participant_id: str | None = None
 
     # The participant identifier assigned by the clinical trial team overseeing the study
-    native_participant_id: str | None = None
+    native_participant_id: str
 
     # The globally unique participant identifier assigned by the CIMAC network. e.g. C8P29A7
     cimac_participant_id: str | None = None
 
     # The unique identifier for the associated trial that the participant is participating in
-    trial_id: int | None = None
+    trial_id: str | None = None
+
+    # The version number of the trial dataset. e.g. "1.0"
+    version: str | None = None
 
     # Indicates if the individual is no longer actively participating in the clinical trial.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14834973%20and%20ver_nr=1

cidc_api/models/pydantic/stage2/prior_treatment.py

@@ -2,7 +2,7 @@ from typing import Self, Annotated, List
 
 from pydantic import NonPositiveInt, NegativeInt, model_validator, BeforeValidator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
 
 
@@ -41,9 +41,9 @@ class PriorTreatment(Base):
     # If prior treatment is "Stem cell transplant", indicates what stem cell donor type used.
     prior_treatment_stem_cell_donor_type: StemCellDonorType | None = None
 
-    # If prior treatment is "Stem cell transplant", indicates the number of days from the transplant
-    # date to the start of the current treatment.
-    prior_treatment_days_to_prior_transplant: NegativeInt | None = None
+    # If prior treatment is "Stem cell transplant", indicates the number of days from enrollment
+    # to the prior transplant. This must be a negative number.
+    prior_treatment_days_from_transplant_to_treatment_initiation: NegativeInt | None = None
 
     @model_validator(mode="after")
     def validate_description_cr(self) -> Self:

cidc_api/models/pydantic/stage2/publication.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Publication(Base):
@@ -6,7 +6,7 @@ class Publication(Base):
     publication_id: int | None = None
 
     # The unique internal identifier for the associated Trial record
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/radiotherapy_dose.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     YNU,
     RadiotherapyProcedure,

cidc_api/models/pydantic/stage2/response.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 
 
@@ -44,7 +44,7 @@ class Response(Base):
     evaluable_for_efficacy: bool
 
     # Days from enrollment date to the last time the patient's vital status was verified.
-    days_to_last_vital_status: NonNegativeInt | None = None
+    days_to_last_vital_status: NonNegativeInt | None = None  # TODO: Needs CR check
 
     @model_validator(mode="after")
     def validate_cause_of_death_cr(self) -> Self:

cidc_api/models/pydantic/stage2/response_by_system.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import PositiveInt, model_validator, NonNegativeInt
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
 
 

cidc_api/models/pydantic/stage2/shipment.py

@@ -1,6 +1,6 @@
 from datetime import datetime
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import AssayPriority, AssayType, Courier, ShipmentCondition, ShipmentQuality
 
 
@@ -12,7 +12,7 @@ class Shipment(Base):
     institution_id: int | None = None
 
     # The unique internal identifier for the associated trial.
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/shipment_specimen.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class ShipmentSpecimen(Base):

cidc_api/models/pydantic/stage2/specimen.py

@@ -1,6 +1,6 @@
 from datetime import datetime
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     UberonAnatomicalTerm,
     ICDO3MorphologicalCode,
@@ -66,7 +66,7 @@ class Specimen(Base):
     # Categorical description of timepoint at which the sample was taken.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5899851%20and%20ver_nr=1
     # Note: CIDC doesn't conform to this CDE's PVs
-    collection_event_name: str | None = None
+    collection_event_name: str
 
     # The type of the specimen
     specimen_type: SpecimenType | None = None
@@ -208,4 +208,7 @@ class Specimen(Base):
     date_ingested: datetime | None = None
 
     # Days from enrollment date to date specimen was collected.
-    days_to_specimen_collection: int | None = None
+    days_to_specimen_collection: int
+
+    # The location within the body from which a specimen was originally obtained as captured in the Uberon anatomical term.
+    organ_site_of_collection: UberonAnatomicalTerm

cidc_api/models/pydantic/stage2/stem_cell_transplant.py

@@ -1,5 +1,5 @@
 from pydantic import NonNegativeInt
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     StemCellDonorType,
     AllogeneicDonorType,
@@ -26,7 +26,7 @@ class StemCellTransplant(Base):
     allogeneic_donor_type: AllogeneicDonorType | None = None
 
     # Source of the stem cells used for transplant.
-    stem_cells_source: StemCellSource
+    stem_cell_source: StemCellSource
 
     # Days from the enrollment date to the date of the stem cell transplant.
     days_to_transplant: NonNegativeInt

cidc_api/models/pydantic/stage2/surgery.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
 
 

cidc_api/models/pydantic/stage2/therapy_agent_dose.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, TherapyAgentDoseUnits
 
 

cidc_api/models/pydantic/stage2/treatment.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, OffTreatmentReason
 
 

cidc_api/models/pydantic/stage2/trial.py

@@ -2,8 +2,8 @@ from datetime import datetime
 from pydantic import BeforeValidator
 from typing import List, Annotated
 
-from .base import Base
-from cidc_api.models.types import TrialOrganization, TrialFundingAgency, AssayType, AgeGroup
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import TrialOrganization, TrialFundingAgency, AssayType, AgeGroup, PrimaryPurposeType
 
 
 class Trial(Base):
@@ -12,7 +12,7 @@ class Trial(Base):
 
     # The unique identifier for the clinical trial. e.g. "GU16-287","BACCI"
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5054234%20and%20ver_nr=1
-    trial_id: str | None = None  # TODO: Fix stage2 trial_id to not be nullable, once stage 1 models are complete
+    trial_id: str | None = None
 
     # The version number of the trial dataset. e.g. "1.0"
     version: str | None = None
@@ -69,6 +69,10 @@ class Trial(Base):
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16333703%20and%20ver_nr=1
     dates_of_conduct_end: datetime | None = None
 
+    # A classification of the study based upon the primary intent of the study's activities.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=11160683%20and%20ver_nr=1
+    primary_purpose_type: PrimaryPurposeType
+
     # The image of the trial data schema
     schema_file_id: int | None = None
 
@@ -81,11 +85,5 @@ class Trial(Base):
     # The list of assays that CIDC expects to receive for this trial.
     expected_assays: List[AssayType] = []
 
-    # Is the cancer studying a liquid tumor type?
-    is_liquid_tumor_trial: bool = False
-
     # The dbgap study accession number associated with the trial.
-    dbgap_study_accession: str | None = None
-
-    # The internal version identifier for this specific trial dataset.
-    version: str
+    dbgap_study_accession: str

cidc_api/models/types.py

@@ -26,6 +26,7 @@ AgeGroup = Literal[
     "Pediatric",
 ]
 
+
 TrialOrganization = Literal[
     "ECOG-ACRIN",
     "SWOG",
@@ -59,6 +60,34 @@ TrialFundingAgency = Literal[
 ]
 
 
+PrimaryPurposeType = Literal[
+    "Adverse Effect Mitigation Study",
+    "Ancillary Study",
+    "Basic Science  Research ",
+    "Correlative Study",
+    "Cure Study",
+    "Device Feasibility Study",
+    "Diagnosis Study",
+    "Disease Modifying Treatment Study",
+    "Early Detection Study",
+    "Education Training Clinical Study",
+    "Epidemiology  Research ",
+    "Genomics Research",
+    "Health Services Research",
+    "Imaging Research",
+    "Interventional Study",
+    "Observational Study",
+    "Outcomes Research",
+    "Prevention Study",
+    "Proteomic Research",
+    "Rehabilitation Clinical Study ",
+    "Screening Study",
+    "Supportive Care Study",
+    "Transcriptomics Research",
+    "Treatment Study",
+]
+
+
 AssayType = Literal[
     "Olink",
     "WES",
@@ -285,7 +314,6 @@ CancerStageAJCC = Literal[
 
 
 CancerStageFIGO = Literal[
-    "value",
     "Stage I",
     "Stage IA",
     "Stage IA1",

cidc_api/shared/gcloud_client.py

@@ -449,9 +449,9 @@ def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str):
 
     # TODO: specify sheet in xlsx file and/or accept tsv and xls files
     if blob_name[-3:] == "csv":
-        return strip_whitespaces(pd.read_csv(temp_file))
+        return strip_whitespaces(pd.read_csv(temp_file, dtype=str, keep_default_na=False))
     elif blob_name[-4:] == "xlsx":
-        return strip_whitespaces(pd.read_excel(temp_file))
+        return strip_whitespaces(pd.read_excel(temp_file, dtype=str, keep_default_na=False))
     else:
         raise Exception("Can only read csv or xlsx files")
 

cidc_api/shared/utils.py

@@ -15,5 +15,6 @@ def strip_whitespaces(df, sheet=None):
 
     df.rename(columns=_stripper, inplace=True)
     df = df.map(_stripper)
+    df.replace("", None, inplace=True)
 
     return df

{nci_cidc_api_modules-1.2.38.dist-info → nci_cidc_api_modules-1.2.40.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.38
+Version: 1.2.40
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -8,34 +8,34 @@ Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: certifi>=2025.11.12
-Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.5
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.19.0
 Requires-Dist: flask>=3.1.2
 Requires-Dist: flask-migrate>=4.1.0
 Requires-Dist: flask-sqlalchemy>=3.1.1
 Requires-Dist: flask-talisman>=0.7.0
-Requires-Dist: google-auth==2.43.0
+Requires-Dist: google-auth==2.45.0
 Requires-Dist: google-api-python-client>=2.187.0
-Requires-Dist: google-cloud-bigquery>=3.38.0
-Requires-Dist: google-cloud-pubsub>=2.33.0
-Requires-Dist: google-cloud-secret-manager>=2.25.0
-Requires-Dist: google-cloud-storage>=3.6.0
+Requires-Dist: google-cloud-bigquery>=3.39.0
+Requires-Dist: google-cloud-pubsub>=2.34.0
+Requires-Dist: google-cloud-secret-manager>=2.26.0
+Requires-Dist: google-cloud-storage>=3.7.0
 Requires-Dist: jinja2>=3.1.6
-Requires-Dist: joserfc>=1.5.0
-Requires-Dist: marshmallow>=4.1.0
+Requires-Dist: joserfc>=1.6.0
+Requires-Dist: marshmallow>=4.1.2
 Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.3.5
+Requires-Dist: numpy>=2.4.0
 Requires-Dist: packaging>=25.0
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: pyarrow>=22.0.0
 Requires-Dist: pydantic~=2.12.5
 Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
-Requires-Dist: sqlalchemy>=2.0.44
+Requires-Dist: sqlalchemy>=2.0.45
 Requires-Dist: sqlalchemy-mixins~=2.0.5
 Requires-Dist: werkzeug>=3.1.4
-Requires-Dist: opentelemetry-api>=1.38.0
-Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.38.0
-Requires-Dist: opentelemetry-sdk>=1.38.0
+Requires-Dist: opentelemetry-api>=1.39.1
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.39.1
+Requires-Dist: opentelemetry-sdk>=1.39.1
 Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0