nci-cidc-api-modules 1.2.55__tar.gz → 1.2.56__tar.gz

{nci_cidc_api_modules-1.2.55/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.56}/PKG-INFO

@@ -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-1.2.56/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.56"

{nci_cidc_api_modules-1.2.55 → nci_cidc_api_modules-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:

{nci_cidc_api_modules-1.2.55/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.56/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 → nci_cidc_api_modules-1.2.56/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -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/cidc_api/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.55"