nci-cidc-api-modules 1.2.45__py3-none-any.whl → 1.2.53__py3-none-any.whl

cidc_api/models/pydantic/stage1/treatment.py

@@ -1,11 +1,11 @@
-from typing import Self
-
-from pydantic import model_validator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, OffTreatmentReason
 
 
+@forced_validators
 class Treatment(Base):
     __data_category__ = "treatment"
     __cardinality__ = "many"
@@ -37,14 +37,28 @@ class Treatment(Base):
     # If "Other" is selected for "off_treatment_reason", provide a description of the reason.
     off_treatment_reason_other: str | None = None
 
-    @model_validator(mode="after")
-    def validate_off_treatment_reason_cr(self) -> Self:
-        if self.off_treatment == "Yes" and not self.off_treatment_reason:
-            raise ValueError('If off_treatment is "Yes", please provide off_treatment_reason.')
-        return self
-
-    @model_validator(mode="after")
-    def validate_off_treatment_reason_other_cr(self) -> Self:
-        if self.off_treatment_reason == "Other" and not self.off_treatment_reason_other:
-            raise ValueError('If off_treatment_reason is "Other", please provide off_treatment_reason_other.')
-        return self
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_cr(cls, data, info) -> None:
+        off_treatment = data.get("off_treatment", None)
+        off_treatment_reason = data.get("off_treatment_reason", None)
+
+        if off_treatment == "Yes" and not off_treatment_reason:
+            raise ValueLocError(
+                'If off_treatment is "Yes", please provide off_treatment_reason.',
+                loc="off_treatment_reason",
+            )
+        return off_treatment_reason
+
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_other_cr(cls, data, info) -> None:
+        off_treatment_reason = data.get("off_treatment_reason", None)
+        off_treatment_reason_other = data.get("off_treatment_reason_other", None)
+
+        if off_treatment_reason == "Other" and not off_treatment_reason_other:
+            raise ValueLocError(
+                'If off_treatment_reason is "Other", please provide off_treatment_reason_other.',
+                loc="off_treatment_reason_other",
+            )
+        return off_treatment_reason_other

cidc_api/shared/file_handling.py

@@ -14,6 +14,8 @@ from ..telemetry import trace_
 
 logger = get_logger(__name__)
 
+MASTER_APPENDIX_A_VERSION_PREFIX = "Master Appendix A Version:"
+
 
 @trace_()
 def set_current_file(

cidc_api/shared/gcloud_client.py

@@ -61,6 +61,7 @@ from ..config.settings import (
     GOOGLE_HL_CLINICAL_VALIDATION_TOPIC,
     GOOGLE_DL_CLINICAL_VALIDATION_TOPIC,
     GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC,
+    GOOGLE_CLINICAL_DATA_INGESTION_PROCESSING_TOPIC,
     TESTING,
     ENV,
     IS_EMAIL_ON,
@@ -479,13 +480,24 @@ async def async_gcs_files_to_pandas_dataframes(bucket_name: str, blob_names: Lis
 
     for blob_name, contents in zip(blob_names, all_contents):
         extension = blob_name.split(".")[-1]
-        dataframes.append(prepare_dataframe(extension, contents))
+        try:
+            dataframes.append(prepare_dataframe(extension, contents))
+        except pd.errors.EmptyDataError:
+            logger.warning(f"The dataframe retrieved from {blob_name} was empty!")
     return dataframes
 
 
+async def async_gcs_files_to_bytes(bucket_name: str, blob_names: List[str]) -> List[DataFrame]:
+    """Async reads a XLSX or CSV files from Google Cloud Storage into a list of raw bytes"""
+
+    all_contents = await asyncio.gather(
+        *[async_get_file_bytes_from_gcs(bucket_name, blob_name) for blob_name in blob_names]
+    )
+    return all_contents
+
+
 async def async_get_file_bytes_from_gcs(bucket_name: str, blob_name: str) -> io.BytesIO:
     """Async reads a file from Google Cloud Storage and returns it as BytesIO."""
-
     async with Storage() as client:
         sheet_data = await client.download(bucket_name, blob_name)
     return io.BytesIO(sheet_data)
@@ -1056,6 +1068,12 @@ def publish_assay_metadata_validation(job_id: int) -> None:
     _report = _encode_and_publish(str(job_id), GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC)
 
 
+def publish_clinical_data_ingestion(job_id: int) -> None:
+    """Start ingestion of clinical data job"""
+    # Start asynchronously
+    _report = _encode_and_publish(str(job_id), GOOGLE_CLINICAL_DATA_INGESTION_PROCESSING_TOPIC)
+
+
 def send_email(to_emails: List[str], subject: str, html_content: str, **kw) -> None:
     """
     Publish an email-to-send to the emails topic.

{nci_cidc_api_modules-1.2.45.dist-info → nci_cidc_api_modules-1.2.53.dist-info}/METADATA

@@ -1,30 +1,31 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.45
+Version: 1.2.53
 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
 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]>=1.19.0
+Requires-Dist: cachetools>=6.2.4
+Requires-Dist: certifi>=2026.1.4
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.20.0
 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: gcloud-aio-storage~=9.6.1
-Requires-Dist: google-auth==2.45.0
-Requires-Dist: google-api-python-client>=2.187.0
-Requires-Dist: google-cloud-bigquery>=3.39.0
+Requires-Dist: google-api-python-client>=2.188.0
+Requires-Dist: google-auth==2.47.0
+Requires-Dist: google-cloud-bigquery>=3.40.0
 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: google-cloud-storage>=3.8.0
 Requires-Dist: jinja2>=3.1.6
-Requires-Dist: joserfc>=1.6.0
-Requires-Dist: marshmallow>=4.1.2
+Requires-Dist: joserfc>=1.6.1
+Requires-Dist: marshmallow>=4.2.0
 Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.4.0
+Requires-Dist: numpy>=2.4.1
 Requires-Dist: packaging>=25.0
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: pyarrow>=22.0.0
@@ -33,7 +34,7 @@ Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
 Requires-Dist: sqlalchemy>=2.0.45
 Requires-Dist: sqlalchemy-mixins~=2.0.5
-Requires-Dist: werkzeug>=3.1.4
+Requires-Dist: werkzeug>=3.1.5
 Requires-Dist: opentelemetry-api>=1.39.1
 Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.39.1
 Requires-Dist: opentelemetry-sdk>=1.39.1
@@ -42,7 +43,7 @@ Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
 Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
 Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
-Requires-Dist: nci-cidc-schemas==0.28.11
+Requires-Dist: nci-cidc-schemas==0.28.12
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.45.dist-info → nci_cidc_api_modules-1.2.53.dist-info}/RECORD

@@ -1,14 +1,16 @@
-cidc_api/__init__.py,sha256=TdZZy40X_55kxtHKjwbGqPrDr5qQe_uUz_Fvup_EuNI,23
+boot.py,sha256=oS_16OgU34iDxyFNpJl5rb5KbfbsCXroUCNLwVPxPNg,416
+cidc_api/__init__.py,sha256=X7WSWc7i6nvghhrqNxUUTAI8_CLJ7jRVdust93y4RdY,23
 cidc_api/telemetry.py,sha256=LuZWkG8CKCn23O41RTNxEOQwMmfpp-fQ6zSInZhVJg8,3333
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
 cidc_api/config/db.py,sha256=mEz8ugjvRNGylCqDYHaaMqaZfDh7sbd76BowmfBvq5c,2428
 cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
 cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
-cidc_api/config/settings.py,sha256=Zql6Gxb5MNBW-rxcDNIPUqPiYHnD9nxd2-ievHaEYcI,4744
+cidc_api/config/settings.py,sha256=IlOSJhSyYYK4XQQ4uBdD58kXO-a2AHPWTSN1AT95b9Y,4545
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/data.py,sha256=TyVXk5jJO1NN05CLqejLf5BPp6yLSNNxPmFOgXUnA1M,1313
+cidc_api/models/errors.py,sha256=UncRrh-4v0CR5mpLO0erWD1y9ctus3Nk6XOSvrTjfco,338
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
-cidc_api/models/models.py,sha256=DTt0eFkFVVxVn23Aqr6TA8CQ7qb2hdqQ0xVJ3RakBBw,153684
+cidc_api/models/models.py,sha256=RycbGNQHIud9mqCyIH_yrnN7PVSFwbUCjP6pe6sX5VA,154106
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/types.py,sha256=WVOTEH61FH5aGVwRbEcfNOce8NLjiEnl1ixtPWav2OA,30058
 cidc_api/models/db/stage1/__init__.py,sha256=zsxOSoogzL_xZ8B5OwcwLXvAmm6g2GYx1Zf6LLw8dq8,1917
@@ -79,32 +81,32 @@ cidc_api/models/db/stage2/trial_orm.py,sha256=7_5kA1Yv80GFQykK8AIlFC0vtrsb2H8xLs
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
 cidc_api/models/files/facets.py,sha256=vieZ3z_tYB29NqtvNzvKqajVwxM5ZLLZKeyQTq5lheU,33776
-cidc_api/models/pydantic/base.py,sha256=6Lsf4fekIS1E-DwZmgCXlfm3Qq9_23dA_v3iz1w2JoA,1427
+cidc_api/models/pydantic/base.py,sha256=sL_0PwEH2vS8BMT_w-zL7CPeaU-R7ih5afRigX6k2DM,4069
 cidc_api/models/pydantic/stage1/__init__.py,sha256=H-NDjCd8isHTgZ7sqz-MIbzC-PpW1kEtR-x-Dyc8r6Q,1667
 cidc_api/models/pydantic/stage1/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
-cidc_api/models/pydantic/stage1/adverse_event.py,sha256=zPy02xoRQeyaXBSmqDdQt4BaRTD6OHBjycVHVtBaAow,3880
+cidc_api/models/pydantic/stage1/adverse_event.py,sha256=ZW5iVnMmX7NtZcsgDAjzPorWPZDSJSmTXGK1EsU9AaQ,5167
 cidc_api/models/pydantic/stage1/baseline_clinical_assessment.py,sha256=5FYvtOVf_nIK1h3xTs3vQgJe2ivQSVHt_wfrTSDgVxU,1119
-cidc_api/models/pydantic/stage1/comorbidity.py,sha256=dk4SJnkaaju-boexf2SW_rNNGXl-Os2LR5lnIxCb-dA,1413
+cidc_api/models/pydantic/stage1/comorbidity.py,sha256=IfxFb0dZAdCY--Ze5kiZ3CrzVKJtuknpcpvrQ3ki-gI,1769
 cidc_api/models/pydantic/stage1/consent_group.py,sha256=aP_nd0GKK6K7VH-6IZRSDDX2RxFM_j9B36FIRGwysOU,1216
-cidc_api/models/pydantic/stage1/demographic.py,sha256=X0YoFdK7S8JQ9p_Jm3l-R5HgEl9sZnZVFXrECA2i_zw,6007
-cidc_api/models/pydantic/stage1/disease.py,sha256=fwK1FSxTm33BzViGTNsb6AahoDc2BTTXMitCGY3KyDk,7650
-cidc_api/models/pydantic/stage1/exposure.py,sha256=ERoVQLuNWynw2zugh5bVdUT0NzNbJ6fIUmKhPSCQfqk,1306
+cidc_api/models/pydantic/stage1/demographic.py,sha256=9r3AFlymwFLwbV0YCHQt1tqTc1g2ywT3zCD66StkYHA,6872
+cidc_api/models/pydantic/stage1/disease.py,sha256=G8d2iqsMhmDA3uxjOitxzmlFKIRxyUMp-o-H7eUfZFg,9250
+cidc_api/models/pydantic/stage1/exposure.py,sha256=bd9gUmOQ7ge-xvoxD17pX95MKxfHKD2xNaFEJAMAkn4,1571
 cidc_api/models/pydantic/stage1/gvhd_diagnosis_acute.py,sha256=jVMoWuLfspOZtOpC7rg1EzdvEAg8qEabcTaS6RRobZ8,1395
 cidc_api/models/pydantic/stage1/gvhd_diagnosis_chronic.py,sha256=SRwkAL07YyIZM4bYCqm01aKqSvj3yRmpsqFKxAZEZoM,1382
 cidc_api/models/pydantic/stage1/gvhd_organ_acute.py,sha256=VxlNGRJYjm9tW2lyLll8pD0t9JZs18gicnH-Ci_nR2I,771
 cidc_api/models/pydantic/stage1/gvhd_organ_chronic.py,sha256=Fnp1Qm-ZDDtDLrgOAnEOUnQVNWI9WrTSomiFPStGmjc,810
-cidc_api/models/pydantic/stage1/medical_history.py,sha256=IXtEvXrrLhTt6JEsj2MpDiZtLAkmrrsUS4aoe7sxans,1697
-cidc_api/models/pydantic/stage1/other_malignancy.py,sha256=V-Jru6uukipocKs7lDbmkGyJsHBxlM3A3NJoTShjJ9I,2188
-cidc_api/models/pydantic/stage1/participant.py,sha256=iDQrwYYtJY_XrkdbhsRNZuL44ighvW8JHCGxH-qo8jk,2199
+cidc_api/models/pydantic/stage1/medical_history.py,sha256=z-cE_ChyWUKTvWjVhKMUAYvap9YfpZn6Z2BiHhBXx6g,2000
+cidc_api/models/pydantic/stage1/other_malignancy.py,sha256=VIzhbkauaDfZdPxhTYpqNtwYBxE_4osE9wyZ67LQJx4,2622
+cidc_api/models/pydantic/stage1/participant.py,sha256=QfRkK2okY7nM84y9QMK12kZLURBGk-HNWWHL4pQZjec,2655
 cidc_api/models/pydantic/stage1/prior_treatment.py,sha256=axhyPHwYCoIvcIonjyPJ95HUyaAXqIuOd6hhoDM3LJU,2101
-cidc_api/models/pydantic/stage1/radiotherapy_dose.py,sha256=c5q0TxPOrYHX9KTd9he5B01zirKgcCxMnvW_7adzCrI,3327
-cidc_api/models/pydantic/stage1/response.py,sha256=rPqfYZhaZRcA1E7dkGOaHe9f2_YIcIg9-KtIPSTh1s8,2886
-cidc_api/models/pydantic/stage1/response_by_system.py,sha256=f8ZnLfNXGJLCfFL1X2jxlSUJPGvJKnOCf6PYbJVMXW8,4909
+cidc_api/models/pydantic/stage1/radiotherapy_dose.py,sha256=gDaL1OQuSuTauml6HafBiVvBn8gcynS3G1fa9KNhEPA,3833
+cidc_api/models/pydantic/stage1/response.py,sha256=TJlKmUz9SypbbDnv6iSmLb4KPEuFUPe9Q8iNSGsLbfI,3491
+cidc_api/models/pydantic/stage1/response_by_system.py,sha256=gjyo_jDyc2xHNNrUwoFqH3Fz51v2eSr3JRHkH0xwVqI,9851
 cidc_api/models/pydantic/stage1/specimen.py,sha256=scDekZ-RtXOQTTLburhqT3RF4KM34iY9NAV1wYi_HSg,1281
 cidc_api/models/pydantic/stage1/stem_cell_transplant.py,sha256=XsDVUksqbIprPxHwLlwHGyji4jsIFNMcIk-S0H4rDnQ,1228
-cidc_api/models/pydantic/stage1/surgery.py,sha256=53NrET_kNOlXXPP-mH5ecIPrNqDpDQt5s9WfsjPDM-s,2149
-cidc_api/models/pydantic/stage1/therapy_agent_dose.py,sha256=Y2L0vAqkfA5eI2qg7iQrqzCORwbkjyVEsthc6f5HKas,3021
-cidc_api/models/pydantic/stage1/treatment.py,sha256=1TeBaDJ352IfB10AtJH2iREdex3SZgDRXNUkhT0FZMo,2033
+cidc_api/models/pydantic/stage1/surgery.py,sha256=sHPzYMNusYIQrC6gjWopwxo0j9BNOq_Tcl6HKAMvuAQ,2421
+cidc_api/models/pydantic/stage1/therapy_agent_dose.py,sha256=XX7JM4CdvTuAsbI5rI4wYDcbevP46BetTk_z7N_EL-M,3527
+cidc_api/models/pydantic/stage1/treatment.py,sha256=eEjCcmkLdPmS2kg9dtUm3pt9apo1sRypBbte_xUVAYU,2607
 cidc_api/models/pydantic/stage1/trial.py,sha256=EFsMVMxxHbPeaBb6JG9JpX1qjtoho2t-GZnaI0gsYrY,1859
 cidc_api/models/pydantic/stage2/__init__.py,sha256=OQRG5wFkNsyAU_0KI1W5PDn8pBDe1EJDcgKZ19shh_g,2331
 cidc_api/models/pydantic/stage2/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
@@ -153,13 +155,13 @@ cidc_api/shared/assay_handling.py,sha256=zzWSqQ-ddLVzX5IuHvsaSib2H1lnjXpo9Lbxaoq
 cidc_api/shared/auth.py,sha256=EIP9AKokLNrI79Fkpv3P7WdzaddJIsuGGICc1W494X0,9110
 cidc_api/shared/email_layout.html,sha256=pBoTNw3ACHH-ncZFaNvcy5bXMqPwizR78usb0uCYtIc,7670
 cidc_api/shared/emails.py,sha256=8kNFEaSnKpY-GX_iE59QUhSp3c4_uzy3SpHYt2QjuqI,6121
-cidc_api/shared/file_handling.py,sha256=ObsLvBrkwHo6Nv48GvFXDKElNNl4inGpxv--001H_xc,5843
-cidc_api/shared/gcloud_client.py,sha256=0B13MRF_CUMbzaKtKVDd9fxErNdNGBpxfkknQ5deu7w,39972
+cidc_api/shared/file_handling.py,sha256=9MZXx5RfXO3A_pXf8Ulb7DQEuyp9j12eO9ad-PcTBXo,5908
+cidc_api/shared/gcloud_client.py,sha256=EJ2ZzZ0gwDOZx18PEzXil4F-jpruacShkVIoecw8qzY,40751
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
 cidc_api/shared/utils.py,sha256=-gLnzxCR9E6h0plt2xrNisUG5_Y6GhhVwz3DgDIzpvs,367
-nci_cidc_api_modules-1.2.45.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.45.dist-info/METADATA,sha256=ierSCHEAC0omx7bg4gjb-XPMPRTK_Qs6VMJXdW65C6A,40270
-nci_cidc_api_modules-1.2.45.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.45.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.45.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.53.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.53.dist-info/METADATA,sha256=JWWYI8eyF0_QbM-bqoNO5N_jsnoocDjNiwKR1Ba4x9Y,40301
+nci_cidc_api_modules-1.2.53.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+nci_cidc_api_modules-1.2.53.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
+nci_cidc_api_modules-1.2.53.dist-info/RECORD,,

{nci_cidc_api_modules-1.2.45.dist-info → nci_cidc_api_modules-1.2.53.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{nci_cidc_api_modules-1.2.45.dist-info → nci_cidc_api_modules-1.2.53.dist-info}/top_level.txt

@@ -1 +1,2 @@
+boot
 cidc_api