nci-cidc-api-modules 1.2.56__py3-none-any.whl → 1.2.57__py3-none-any.whl

cidc_api/__init__.py

@@ -1 +1 @@
-__version__ = "1.2.56"
+__version__ = "1.2.57"

cidc_api/code_systems/app.py

@@ -0,0 +1,126 @@
+from pathlib import Path
+from typing import Iterable
+from time import perf_counter
+
+from textual import on
+from textual.app import App, ComposeResult
+from textual.containers import Container
+from textual.widgets import Button, DirectoryTree, Footer, Header, Log, Select
+
+from cidc_api.code_systems.importer import delete_data, import_data, load_app
+
+
+class FilteredDirectoryTree(DirectoryTree):
+    def filter_paths(self, paths: Iterable[Path]) -> Iterable[Path]:
+        return [path for path in paths if path.name.endswith(".csv")]
+
+    def on_directory_tree_file_selected(self, event: DirectoryTree.FileSelected) -> None:
+        """Called when a file is selected in the directory tree."""
+        # log = self.app.query_one(Log)
+        # log.write_line(f"Selected file: {event.path.parent.name}/{event.path.name}")
+
+
+class CodeSystems(App):
+    """A Textual app to manage code systems."""
+
+    CSS = """
+    Select { width: 40%; margin: 1;}
+    FilteredDirectoryTree { margin-left: 2; }
+    Button, Log { margin: 1 2; }
+    Container { height: 10; }
+    #results { margin: 1; text-style: bold; }
+    """
+
+    BINDINGS = [("d", "toggle_dark", "Toggle dark mode"), ("q", "quit", "Quit the app")]
+    SELECT_OPTIONS = [(code, code) for code in ["Ctcae60", "Icdo3"]]
+
+    def compose(self) -> ComposeResult:
+        """Create child widgets for the app."""
+        yield Header()
+        yield Select(self.SELECT_OPTIONS, prompt="Select code system")
+        with Container(id="tree-container"):
+            yield FilteredDirectoryTree(Path(__file__).resolve().parent / "data")
+        yield Button("Import data", variant="primary", disabled=True)
+        yield Log()
+        yield Footer()
+
+    @on(Select.Changed)
+    async def check_select(self, event: Select.Changed):
+
+        old_tree = self.query_one(FilteredDirectoryTree)
+        await old_tree.remove()
+
+        folder_name = event.value
+        new_path = Path(__file__).resolve().parent / "data" / folder_name
+        new_tree = FilteredDirectoryTree(str(new_path))
+        await self.query_one("#tree-container").mount(new_tree)
+        new_tree.focus()  # optional: set focus to the new tree
+
+        self.maybe_enable_button()
+
+    @on(DirectoryTree.FileSelected)
+    def check_tree(self, _event: DirectoryTree.FileSelected):
+        self.maybe_enable_button()
+
+    def maybe_enable_button(self):
+        button_widget = self.query_one(Button)
+        code_system_widget = self.query_one(Select)
+        file_path_widget = self.query_one(FilteredDirectoryTree)
+        button_widget.disabled = not (
+            code_system_widget.value != Select.BLANK and file_path_widget.cursor_node.data.path.is_file()
+        )
+
+    # def on_ready(self) -> None:
+    #     log = self.query_one(Log)
+    #     log.write_line("Hello!")
+
+    def action_toggle_dark(self) -> None:
+        """An action to toggle dark mode."""
+        self.theme = "textual-dark" if self.theme == "textual-light" else "textual-light"
+
+    async def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Event handler called when the button is pressed."""
+        code_system_widget = self.query_one(Select)
+        file_path_widget = self.query_one(FilteredDirectoryTree)
+        log_widget = self.query_one(Log)
+
+        log_widget.clear()
+        code_system = code_system_widget.value
+        file_path = file_path_widget.cursor_node.data.path
+
+        button = event.button
+        button.disabled = True
+        old_label = button.label
+        button.label = "Running task, please wait..."
+        await self.run_task(log_widget, code_system, file_path)
+        button.disabled = False
+        button.label = old_label
+
+    async def run_task(self, log_widget: Log, code_system: str, file_path: Path) -> None:
+        log_widget.write_line("Loading app ...")
+        start = perf_counter()
+
+        flask_app, db, model = await load_app(code_system)
+        table_name = model.__tablename__
+        schema = model.__table__.schema
+        log_widget.write_line(f"{perf_counter() - start:.3f} seconds to load app.\n\n")
+
+        with flask_app.app_context():
+            engine = db.engine
+
+            log_widget.write_line("Deleting data ...")
+            start = perf_counter()
+            msg = await delete_data(engine, f"{schema}.{table_name}")
+            log_widget.write_line(msg)
+            log_widget.write_line(f"{perf_counter() - start:.3f} seconds to delete data.\n\n")
+
+            log_widget.write_line("Importing data ...")
+            start = perf_counter()
+            msg = await import_data(engine, file_path, f"{schema}.{table_name}")
+            log_widget.write_line(msg)
+            log_widget.write_line(f"{perf_counter() - start:.3f} seconds to import data.")
+
+
+if __name__ == "__main__":
+    app = CodeSystems()
+    app.run()

cidc_api/code_systems/ctcae.py

@@ -0,0 +1,34 @@
+# Stubbed to accept any string
+def is_ctcae_event_term(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Stubbed to accept any string
+def is_ctcae_event_code(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Stubbed to accept any string
+def is_ctcae_severity_grade(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Stubbed to accept any string
+def is_ctcae_system_organ_class(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Determines if the CTCAE term is one of the "Other, specify" types of terms for which we include
+# additional data about the AE.
+def is_ctcae_other_term(v):
+    if isinstance(v, str):
+        return "Other, specify" in v
+    return False

cidc_api/code_systems/gvhd.py

@@ -0,0 +1,6 @@
+# Stubbed to accept any string
+# Should support MAGIC and Modified Glucksberg
+def is_gvhd_organ(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v

cidc_api/code_systems/icd10cm.py

@@ -0,0 +1,12 @@
+# Stubbed to accept any string
+def is_ICD10CM_code(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Stubbed to accept any string
+def is_ICD10CM_term(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v

cidc_api/code_systems/icdo3.py

@@ -0,0 +1,12 @@
+# Stubbed to accept any string
+def is_ICDO3_code(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v
+
+
+# Stubbed to accept any string
+def is_ICDO3_term(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v

cidc_api/code_systems/importer.py

@@ -0,0 +1,108 @@
+# pylint: disable=import-outside-toplevel,broad-except,invalid-name,redefined-outer-name
+
+from os import environ
+from pathlib import Path
+import asyncio
+import importlib
+
+
+async def load_app(model):
+    print("Loading app ...")
+
+    # async load to allow reporting progress in UI
+    flask_app_mod = await asyncio.to_thread(importlib.import_module, "cidc_api.app")
+    db_mod = await asyncio.to_thread(importlib.import_module, "cidc_api.config.db")
+    code_systems = await asyncio.to_thread(importlib.import_module, "cidc_api.models.code_systems")
+
+    return flask_app_mod.app, db_mod.db, getattr(code_systems, model)
+
+
+async def import_data(engine, file_path, table_name):
+    print("Importing data ...")
+
+    conn = engine.raw_connection()
+    cursor = conn.cursor()
+
+    try:
+        with open(file_path, "r", encoding="utf-8") as file:
+            # define the COPY command, specifying STDIN for the file-like object
+            sql = f"COPY {table_name} FROM STDIN WITH CSV HEADER"
+
+            # execute the copy operation
+            cursor.copy_expert(sql, file)
+
+        msg = f"Number of rows copied: {cursor.rowcount}"
+        conn.commit()
+
+    except Exception as exc:
+        conn.rollback()
+        msg = f"Error during COPY command: {exc}"
+
+    finally:
+        cursor.close()
+        conn.close()
+
+    return msg
+
+
+async def delete_data(engine, table_name):
+    print("Deleting data ...")
+
+    conn = engine.raw_connection()
+    cursor = conn.cursor()
+
+    try:
+        cursor.execute(f"TRUNCATE TABLE {table_name} RESTART IDENTITY")
+        msg = "Table truncated successfully."
+        conn.commit()
+
+    except Exception as exc:
+        conn.rollback()
+        msg = f"Error during TRUNCATE command: {exc}"
+
+    finally:
+        cursor.close()
+        conn.close()
+
+    return msg
+
+
+async def call_local(table_name, file_path):
+    from dotenv import load_dotenv
+    from sqlalchemy import create_engine
+
+    load_dotenv()
+
+    engine = create_engine(environ.get("POSTGRES_URI"))
+    msg = await import_data(engine, file_path, table_name)
+
+    return msg
+
+
+if __name__ == "__main__":
+    model = "Ctcae60"
+    file_path = Path(__file__).resolve().parent / "data/ctcae_6.0.csv"
+
+    # model = "Icdo3"
+    # file_path = Path(__file__).resolve().parent / "data/icdo3.csv"
+
+    # direct connection with conn string from env
+    # from dotenv import load_dotenv
+    # from sqlalchemy import create_engine
+    # load_dotenv()
+    # engine = create_engine(environ.get("POSTGRES_URI"))
+    # msg = asyncio.run(import_data(engine, file_path, table_name))
+
+    app, db, model = asyncio.run(load_app(model))
+    table_name = model.__tablename__
+    schema = model.__table__.schema
+    table_name = f"{schema}.{table_name}"
+
+    with app.app_context():
+        engine = db.engine
+
+        msg = asyncio.run(delete_data(engine, table_name))
+        print(msg)
+
+        msg = asyncio.run(import_data(engine, file_path, table_name))
+        print(msg)

cidc_api/code_systems/uberon.py

@@ -0,0 +1,5 @@
+# Stubbed to accept any string
+def is_uberon_term(v):
+    if not isinstance(v, str):
+        raise TypeError("Value must be a string")
+    return v

cidc_api/models/dataset.py

@@ -11,7 +11,6 @@ from cidc_api.models.db.stage2 import all_models as stage2_all_db_models
 from cidc_api.models.db.stage1 import TrialORM as s1TrialORM
 from cidc_api.models.db.stage2 import TrialORM as s2TrialORM
 
-
 standard_data_categories = [
     model.__data_category__ for model in stage1_all_models if hasattr(model, "__data_category__")
 ]

cidc_api/models/db/stage1/__init__.py

@@ -24,7 +24,6 @@ from .therapy_agent_dose_orm import TherapyAgentDoseORM
 from .treatment_orm import TreatmentORM
 from .trial_orm import TrialORM
 
-
 __all__ = [
     "AdditionalTreatmentORM",
     "AdverseEventORM",

cidc_api/models/db/stage2/__init__.py

@@ -35,7 +35,6 @@ from .therapy_agent_dose_orm import TherapyAgentDoseORM
 from .treatment_orm import TreatmentORM
 from .trial_orm import TrialORM
 
-
 __all__ = [
     "AdditionalTreatmentORM",
     "AdministrativePersonORM",

cidc_api/models/files/details.py

@@ -1,7 +1,6 @@
 from typing import NamedTuple
 from typing_extensions import Literal
 
-
 FilePurpose = Literal["source", "analysis", "clinical", "miscellaneous"]
 
 

cidc_api/models/pydantic/stage1/__init__.py

@@ -24,7 +24,6 @@ from .therapy_agent_dose import TherapyAgentDose
 from .treatment import Treatment
 from .trial import Trial
 
-
 __all__ = [
     "AdditionalTreatment",
     "AdverseEvent",

cidc_api/models/pydantic/stage1/response_by_system.py

@@ -8,7 +8,6 @@ from cidc_api.models.pydantic.base import Base
 from cidc_api.models.pydantic.stage1.response import Response
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
-
 negative_response_values = [
     "Progressive Disease",
     "Stable Disease",

cidc_api/models/pydantic/stage2/__init__.py

@@ -35,7 +35,6 @@ from .therapy_agent_dose import TherapyAgentDose
 from .treatment import Treatment
 from .trial import Trial
 
-
 __all__ = [
     "AdditionalTreatment",
     "AdministrativePerson",

cidc_api/models/pydantic/stage2/response_by_system.py

@@ -8,7 +8,6 @@ from cidc_api.models.pydantic.base import Base
 from cidc_api.models.pydantic.stage1.response import Response
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
-
 negative_response_values = [
     "Progressive Disease",
     "Stable Disease",

cidc_api/shared/gcloud_client.py

@@ -70,7 +70,6 @@ from ..config.settings import (
 )
 from ..shared.utils import strip_whitespaces
 
-
 os.environ["TZ"] = "UTC"
 logger = get_logger(__name__)
 

cidc_api/shared/jose.py

@@ -8,7 +8,6 @@ from cachetools import cached, TTLCache
 # loacal modules
 from ..config.settings import AUTH0_DOMAIN, AUTH0_CLIENT_ID
 
-
 ALGORITHMS = ["RS256"]
 TIMEOUT_IN_SECONDS = 20
 PUBLIC_KEYS_CACHE = TTLCache(maxsize=3600, ttl=1024)  # 1 hour, 1 MB

{nci_cidc_api_modules-1.2.56.dist-info → nci_cidc_api_modules-1.2.57.dist-info}/METADATA

@@ -1,49 +1,48 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.56
+Version: 1.2.57
 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: 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: cachetools~=7.0.0
+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-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>=3.8.0
-Requires-Dist: jinja2>=3.1.6
-Requires-Dist: joserfc>=1.6.1
-Requires-Dist: marshmallow>=4.2.0
-Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.4.1
-Requires-Dist: packaging>=25.0
-Requires-Dist: pandas>=2.3.3
-Requires-Dist: pyarrow>=22.0.0
+Requires-Dist: google-api-python-client~=2.188.0
+Requires-Dist: google-auth==2.48.0
+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~=3.9.0
+Requires-Dist: jinja2~=3.1.6
+Requires-Dist: joserfc~=1.6.1
+Requires-Dist: marshmallow~=4.2.1
+Requires-Dist: marshmallow-sqlalchemy~=1.4.2
+Requires-Dist: numpy~=2.4.2
+Requires-Dist: pandas~=3.0.0
+Requires-Dist: pyarrow~=23.0.0
 Requires-Dist: pydantic~=2.12.5
-Requires-Dist: python-dotenv>=1.2.1
-Requires-Dist: requests>=2.32.5
-Requires-Dist: sqlalchemy>=2.0.45
+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>=3.1.5
-Requires-Dist: opentelemetry-api>=1.39.1
-Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.39.1
-Requires-Dist: opentelemetry-sdk>=1.39.1
-Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
-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==0.28.12
+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
+Requires-Dist: opentelemetry-instrumentation-flask~=0.59b0
+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==0.28.13
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.56.dist-info → nci_cidc_api_modules-1.2.57.dist-info}/RECORD

@@ -1,6 +1,14 @@
 boot.py,sha256=a5zD_ORheoOy3CuEIwjM9jcR4_Phngz6nc-E6RYIEj8,585
-cidc_api/__init__.py,sha256=vHvjSAme38UPREXXcNqyijbgVzmFAnAOgLeqHeHpZAM,23
+cidc_api/__init__.py,sha256=4bvatwbfE15IIgVfHJZH8d-WXGATbSGcT6GSdTUc1l0,23
 cidc_api/telemetry.py,sha256=SRPXhN1O4P2jYaRN_K4hAhFURygrzzRrkQsGZmghUUQ,3355
+cidc_api/code_systems/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cidc_api/code_systems/app.py,sha256=nyv7MBkOaZlB8trRCerWlOPOU9Hy-qCu71t8aLX1iQY,4804
+cidc_api/code_systems/ctcae.py,sha256=H5JvDQ5R5kYbK37UxjhmXMnKD3d40HmG0DONxfhNxnE,871
+cidc_api/code_systems/gvhd.py,sha256=r5jbHEa5yos0tmghjiruAeXI-r-4lU81JKCUpMHtO14,194
+cidc_api/code_systems/icd10cm.py,sha256=K1vbTQB75uAQeKgj0U9izhtMKVb2vqp69_hyx3z_jro,300
+cidc_api/code_systems/icdo3.py,sha256=A19yNX5-9Gs3X83kXcTlGgsXDTTJ9yR2dxEIoBVmpmU,296
+cidc_api/code_systems/importer.py,sha256=61lu0FF0r_2Q6UX_UWMO_qP9J56Xphj4RVX5EdYb8Vw,2959
+cidc_api/code_systems/uberon.py,sha256=BO2mYNDvPzZyLdhL_ZjCyEgHSLHuVifnTJvfktUfVWA,148
 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
@@ -8,13 +16,13 @@ cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,14
 cidc_api/config/settings.py,sha256=IlOSJhSyYYK4XQQ4uBdD58kXO-a2AHPWTSN1AT95b9Y,4545
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/code_systems.py,sha256=YR-SGg1UnCElHjibUauAFAs9ENLd7tT28V3sc-NQ4xk,918
-cidc_api/models/dataset.py,sha256=pz5CAzKioKCuArcXqD5MaLm-MnSRlr4I2VgNapGGjPA,3021
+cidc_api/models/dataset.py,sha256=1rz2Gww5wsqWqXOOZ7hWY0lL2H3lA5YZ1k7u5zc5el8,3020
 cidc_api/models/errors.py,sha256=UncRrh-4v0CR5mpLO0erWD1y9ctus3Nk6XOSvrTjfco,338
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
 cidc_api/models/models.py,sha256=RycbGNQHIud9mqCyIH_yrnN7PVSFwbUCjP6pe6sX5VA,154106
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/types.py,sha256=V0N3RrrnP5bgj44bv3Aet1Mw424KgkcAOfv3QJRyRQI,30112
-cidc_api/models/db/stage1/__init__.py,sha256=zsxOSoogzL_xZ8B5OwcwLXvAmm6g2GYx1Zf6LLw8dq8,1917
+cidc_api/models/db/stage1/__init__.py,sha256=4RIPYj7FZfFIk7N15mUPfuB_2DOQX_NmJSxvKASFUFA,1916
 cidc_api/models/db/stage1/additional_treatment_orm.py,sha256=Oe1wfYEOlMKAvNrOTCCnyXeEqAZtHSLk6d4ChIL2J58,1200
 cidc_api/models/db/stage1/adverse_event_orm.py,sha256=vhDDVMaksvXflH8unJJDlHL_8_SCFqWy0GWwxKSpge8,2194
 cidc_api/models/db/stage1/base_orm.py,sha256=izKizTf2W1fCK2CRUeyuErJbOaxNp6d299n4gqKWHDQ,246
@@ -41,7 +49,7 @@ cidc_api/models/db/stage1/surgery_orm.py,sha256=LaodgOnH4BJwt0Svvd37Q2RmdxNqa1sp
 cidc_api/models/db/stage1/therapy_agent_dose_orm.py,sha256=lwL1asNtJ70JRLTm5SXH7S8DZiQ0-oHGmc1sA5MbXR8,1580
 cidc_api/models/db/stage1/treatment_orm.py,sha256=qEuGOJATfOBJyKVmBaDEg0nRK2j65_HlmOoelkAvzec,1899
 cidc_api/models/db/stage1/trial_orm.py,sha256=orXC7srYEU_CY9m9VNE_1-iYP559Oqe6g8-NqdHXbto,1282
-cidc_api/models/db/stage2/__init__.py,sha256=R33BM1VDKJya5uuyYnPoGFVfhSViclIOklSoHH-EtBQ,2691
+cidc_api/models/db/stage2/__init__.py,sha256=9KE50cL-l6T1GY4Hm4MRLPzoZQ-V_2syOIX0LEMISLc,2690
 cidc_api/models/db/stage2/additional_treatment_orm.py,sha256=bq_E9h-AeYjhaYHaKUHmQ1k_OSP1OtNeu6bupA-ZKP4,1198
 cidc_api/models/db/stage2/administrative_person_orm.py,sha256=49Mon6yLXjTRM-pypTL2R0qlIT1eJRqSaMGKNubjVak,1290
 cidc_api/models/db/stage2/administrative_role_assignment_orm.py,sha256=vi8Xwe3Xz7QlRSTO4zVSd-42YMAfBnY3RNWFrh90f-Y,1292
@@ -80,10 +88,10 @@ cidc_api/models/db/stage2/therapy_agent_dose_orm.py,sha256=obAA7uvTWvSc_1E80_9cP
 cidc_api/models/db/stage2/treatment_orm.py,sha256=WGLvAVR1SlGpT-j11eAtq2waNHhCN-ywE43mDZWdK_Y,2193
 cidc_api/models/db/stage2/trial_orm.py,sha256=ijQLs1JjalXcS-s0HDv2_O2HoPL7Xvv_9AXtGeFc6BU,2821
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
-cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
+cidc_api/models/files/details.py,sha256=EIk5yaUHtATOumxiHSZs2UtBWrAQRqIdZZn6d4oVuRQ,65152
 cidc_api/models/files/facets.py,sha256=vieZ3z_tYB29NqtvNzvKqajVwxM5ZLLZKeyQTq5lheU,33776
 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/__init__.py,sha256=4H1YlqHFbcaX62sA3NkHg025eSXtFxEwj1UPWhyXfHw,1666
 cidc_api/models/pydantic/stage1/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
 cidc_api/models/pydantic/stage1/adverse_event.py,sha256=PanE03MgP70M_i3glCeBCtScuG4zIpyKiJZfeNAOOBc,5176
 cidc_api/models/pydantic/stage1/baseline_clinical_assessment.py,sha256=5FYvtOVf_nIK1h3xTs3vQgJe2ivQSVHt_wfrTSDgVxU,1119
@@ -102,14 +110,14 @@ 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=0QbGX-ZTiAbLTXtcu8irukC4E72rS1ARrCCnTyboTno,12622
+cidc_api/models/pydantic/stage1/response_by_system.py,sha256=JcsKCWTHaxubbaUTOpFs2U6EDjOTuqYog-GZXXAoBMg,12621
 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
 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=EfY7HZEn7HT_N5-g4hkYtAM5BQ3yiMRCtj4rm12UQ7U,1909
-cidc_api/models/pydantic/stage2/__init__.py,sha256=OQRG5wFkNsyAU_0KI1W5PDn8pBDe1EJDcgKZ19shh_g,2331
+cidc_api/models/pydantic/stage2/__init__.py,sha256=jBLPaYfgZWqBL6fohtyKQxsjRbl0N4dtfnNdyEYLc1Y,2330
 cidc_api/models/pydantic/stage2/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
 cidc_api/models/pydantic/stage2/administrative_person.py,sha256=3UYRgGLP7RukwZYTvQEnviDxBvWXj1uqditsoLJOw0s,1552
 cidc_api/models/pydantic/stage2/administrative_role_assignment.py,sha256=kWUciVSnczjejdBSlynsVxSQ4dytDdgw9OxSvgzParg,536
@@ -137,7 +145,7 @@ cidc_api/models/pydantic/stage2/prior_treatment.py,sha256=axhyPHwYCoIvcIonjyPJ95
 cidc_api/models/pydantic/stage2/publication.py,sha256=GBuvqBf0lyOoopN1S-3qX310xFxhixk7oDJLuGzLuiw,1817
 cidc_api/models/pydantic/stage2/radiotherapy_dose.py,sha256=8TbBqx_BYzwygQE-LxlSEK2ntIAFlTpAq_GS479TabI,3839
 cidc_api/models/pydantic/stage2/response.py,sha256=hq5_eJ2BEaVH8pdU444p3AKHuZMdLsoDZcMA3XQa8Rw,3491
-cidc_api/models/pydantic/stage2/response_by_system.py,sha256=vW0Xj_hYRa3W-JbqJgvty559_B9x5UIySaAOhIDVMOs,9853
+cidc_api/models/pydantic/stage2/response_by_system.py,sha256=G5fZltd1szrtz0eyQ5IIbOwQUTMEqPy-f3JKe8OucZM,9852
 cidc_api/models/pydantic/stage2/shipment.py,sha256=dsZcDPikCRS3cjr58EGHHJ2gjir78J4cdHh_1SwFyrQ,1595
 cidc_api/models/pydantic/stage2/shipment_specimen.py,sha256=exR7joXsH3Xd-o5vJV_Z-az33Edr8BBm5LCDv01iMI4,488
 cidc_api/models/pydantic/stage2/specimen.py,sha256=scDekZ-RtXOQTTLburhqT3RF4KM34iY9NAV1wYi_HSg,1281
@@ -152,12 +160,12 @@ 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=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/gcloud_client.py,sha256=nhyU11hZ049bez3-QaPC-Y3NZ-1t7o9XwT_QkE9ds6k,40750
+cidc_api/shared/jose.py,sha256=gNXVjZMHMPRfG6hoTeDxRi4HjbIo_JTBnZ6C9LaHh1I,1829
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
 cidc_api/shared/utils.py,sha256=-gLnzxCR9E6h0plt2xrNisUG5_Y6GhhVwz3DgDIzpvs,367
-nci_cidc_api_modules-1.2.56.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,,
+nci_cidc_api_modules-1.2.57.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.57.dist-info/METADATA,sha256=dJEJsXit5jKfR1MP7cwOpF1F4s4lP2Mg_W_Q-z1L51w,40270
+nci_cidc_api_modules-1.2.57.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+nci_cidc_api_modules-1.2.57.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
+nci_cidc_api_modules-1.2.57.dist-info/RECORD,,