nci-cidc-api-modules 1.2.55__py3-none-any.whl → 1.2.56__py3-none-any.whl

cidc_api/__init__.py

@@ -1 +1 @@
-__version__ = "1.2.55"
+__version__ = "1.2.56"

cidc_api/config/db.py

@@ -35,6 +35,8 @@ def init_db(app: Flask):
     """Connect `app` to the database and run migrations"""
     db.init_app(app)
     Migrate(app, db, app.config["MIGRATIONS_PATH"])
+    with app.app_context():
+        upgrade(app.config["MIGRATIONS_PATH"])
 
 
 def get_sqlalchemy_database_uri(testing: bool = False) -> str:

cidc_api/models/pydantic/stage1/response_by_system.py

@@ -176,6 +176,19 @@ class ResponseBySystem(Base):
                     loc="days_to_best_response",
                 )
 
+    @forced_validator
+    @classmethod
+    def validate_progression_free_survival_disease_progression_chronology(cls, data, info) -> None:
+        progression = data.get("progression", None)
+        days_to_disease_progression = data.get("days_to_disease_progression", None)
+        progression_free_survival = data.get("progression_free_survival", None)
+
+        if progression == "Yes" and progression_free_survival != days_to_disease_progression:
+            raise ValueLocError(
+                'Violate "progression_free_survival" = "days_to_disease_progression" when progression is PFS event',
+                loc="progression_free_survival",
+            )
+
     @model_validator(mode="after")
     def validate_days_to_last_vital_status_chronology(self) -> Self:
         if not self.response:
@@ -218,3 +231,52 @@ class ResponseBySystem(Base):
                 loc="days_to_death,days_to_first_response,days_to_best_response,days_to_disease_progression",
             )
         return self
+
+    @model_validator(mode="after")
+    def validate_progression_free_survival_death_chronology(self) -> Self:
+        if not self.response:
+            return self
+
+        if (
+            self.progression_free_survival_event == "Yes"
+            and self.progression == "No"
+            and self.progression_free_survival != self.response.days_to_death
+        ):
+            raise ValueLocError(
+                'Violate "progression_free_survival" = "days_to_death" when death is PFS event',
+                loc="progression_free_survival",
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_progression_free_survival_event_no_or_unknown(self) -> Self:
+        if not self.response:
+            return self
+
+        pfs_event = self.progression_free_survival_event
+        if pfs_event in ["No", "Unknown"] and (self.days_to_disease_progression or self.response.days_to_death):
+            raise ValueLocError(
+                'Violate "days_to_death" and "days_to_disease_progression" should be blank when PFS event is "No" or "Unknown"',
+                loc="progression_free_survival_event",
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_progression_free_survival_event_consistent(self) -> Self:
+        if not self.response:
+            return self
+
+        progressed_or_dead = self.progression == "Yes" or self.response.survival_status == "Dead"
+        no_progression_and_alive = self.progression == "No" and self.response.survival_status == "Alive"
+        pfs_event = self.progression_free_survival_event
+        if (
+            (pfs_event == "Yes" and not progressed_or_dead)
+            or (progressed_or_dead and pfs_event != "Yes")
+            or (pfs_event == "No" and not no_progression_and_alive)
+            or (no_progression_and_alive and pfs_event != "No")
+        ):
+            raise ValueLocError(
+                'Inconsistent flags for "progression_free_survival_event","progression" and "survival_status"',
+                loc="progression_free_survival_event",
+            )
+        return self

{nci_cidc_api_modules-1.2.55.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.55
+Version: 1.2.56
 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

{nci_cidc_api_modules-1.2.55.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/RECORD

@@ -1,8 +1,8 @@
 boot.py,sha256=a5zD_ORheoOy3CuEIwjM9jcR4_Phngz6nc-E6RYIEj8,585
-cidc_api/__init__.py,sha256=w_Cy0hYe3h0VvVjywA1usJthx3ML2-hIuBZUa0GHWxg,23
+cidc_api/__init__.py,sha256=vHvjSAme38UPREXXcNqyijbgVzmFAnAOgLeqHeHpZAM,23
 cidc_api/telemetry.py,sha256=SRPXhN1O4P2jYaRN_K4hAhFURygrzzRrkQsGZmghUUQ,3355
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
-cidc_api/config/db.py,sha256=MHBQH2Ccf2J5cDpMwHJ704_ovl6i38DSF4Mktdfbr0g,2353
+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=IlOSJhSyYYK4XQQ4uBdD58kXO-a2AHPWTSN1AT95b9Y,4545
@@ -102,7 +102,7 @@ cidc_api/models/pydantic/stage1/participant.py,sha256=QfRkK2okY7nM84y9QMK12kZLUR
 cidc_api/models/pydantic/stage1/prior_treatment.py,sha256=axhyPHwYCoIvcIonjyPJ95HUyaAXqIuOd6hhoDM3LJU,2101
 cidc_api/models/pydantic/stage1/radiotherapy_dose.py,sha256=8TbBqx_BYzwygQE-LxlSEK2ntIAFlTpAq_GS479TabI,3839
 cidc_api/models/pydantic/stage1/response.py,sha256=hq5_eJ2BEaVH8pdU444p3AKHuZMdLsoDZcMA3XQa8Rw,3491
-cidc_api/models/pydantic/stage1/response_by_system.py,sha256=vW0Xj_hYRa3W-JbqJgvty559_B9x5UIySaAOhIDVMOs,9853
+cidc_api/models/pydantic/stage1/response_by_system.py,sha256=0QbGX-ZTiAbLTXtcu8irukC4E72rS1ARrCCnTyboTno,12622
 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=sHPzYMNusYIQrC6gjWopwxo0j9BNOq_Tcl6HKAMvuAQ,2421
@@ -156,8 +156,8 @@ cidc_api/shared/gcloud_client.py,sha256=EJ2ZzZ0gwDOZx18PEzXil4F-jpruacShkVIoecw8
 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-1.2.55.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.55.dist-info/METADATA,sha256=YILYITn86Z9qxxYBWpgS7WujFQ1fbIiQ4VrOUoevit0,40301
-nci_cidc_api_modules-1.2.55.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-nci_cidc_api_modules-1.2.55.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
-nci_cidc_api_modules-1.2.55.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.56.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.56.dist-info/METADATA,sha256=NS_GSV4rLWWKJ7vN5bxj3fISWowaOS8feJS-SHaXci4,40301
+nci_cidc_api_modules-1.2.56.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+nci_cidc_api_modules-1.2.56.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
+nci_cidc_api_modules-1.2.56.dist-info/RECORD,,