nci-cidc-api-modules 1.0.1__tar.gz → 1.0.4__tar.gz

{nci_cidc_api_modules-1.0.1/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.0.4}/PKG-INFO

@@ -1,29 +1,31 @@
 Metadata-Version: 2.1
 Name: nci_cidc_api_modules
-Version: 1.0.1
+Version: 1.0.4
 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: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug==2.0.3
-Requires-Dist: flask~=2.0.3
+Requires-Dist: werkzeug==2.3.8
+Requires-Dist: flask==2.2.5
 Requires-Dist: flask-migrate==2.5.2
-Requires-Dist: flask-sqlalchemy~=2.4.0
+Requires-Dist: flask-sqlalchemy==2.5.1
 Requires-Dist: sqlalchemy~=1.3.0
 Requires-Dist: marshmallow==3.19.0
 Requires-Dist: marshmallow-sqlalchemy==0.22.3
-Requires-Dist: google-cloud-storage~=1.35.0
+Requires-Dist: google-cloud-storage==1.35.1
 Requires-Dist: google-cloud-secret-manager==2.16.2
 Requires-Dist: google-cloud-pubsub==0.43.0
-Requires-Dist: google-cloud-bigquery==3.3.5
+Requires-Dist: google-cloud-bigquery==3.18.0
 Requires-Dist: google-api-python-client==2.64.0
+Requires-Dist: packaging>=20.0.0
+Requires-Dist: pyarrow==14.0.1
 Requires-Dist: pandas<2,>=1
 Requires-Dist: python-dotenv==0.10.3
-Requires-Dist: requests==2.22.0
-Requires-Dist: jinja2~=3.0.3
-Requires-Dist: nci-cidc-schemas~=0.26.28
+Requires-Dist: requests==2.31.0
+Requires-Dist: jinja2==3.1.3
+Requires-Dist: nci-cidc-schemas==0.26.29
 
 # NCI CIDC API <!-- omit in TOC -->
 

{nci_cidc_api_modules-1.0.1 → nci_cidc_api_modules-1.0.4/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,29 +1,31 @@
 Metadata-Version: 2.1
 Name: nci_cidc_api_modules
-Version: 1.0.1
+Version: 1.0.4
 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: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug==2.0.3
-Requires-Dist: flask~=2.0.3
+Requires-Dist: werkzeug==2.3.8
+Requires-Dist: flask==2.2.5
 Requires-Dist: flask-migrate==2.5.2
-Requires-Dist: flask-sqlalchemy~=2.4.0
+Requires-Dist: flask-sqlalchemy==2.5.1
 Requires-Dist: sqlalchemy~=1.3.0
 Requires-Dist: marshmallow==3.19.0
 Requires-Dist: marshmallow-sqlalchemy==0.22.3
-Requires-Dist: google-cloud-storage~=1.35.0
+Requires-Dist: google-cloud-storage==1.35.1
 Requires-Dist: google-cloud-secret-manager==2.16.2
 Requires-Dist: google-cloud-pubsub==0.43.0
-Requires-Dist: google-cloud-bigquery==3.3.5
+Requires-Dist: google-cloud-bigquery==3.18.0
 Requires-Dist: google-api-python-client==2.64.0
+Requires-Dist: packaging>=20.0.0
+Requires-Dist: pyarrow==14.0.1
 Requires-Dist: pandas<2,>=1
 Requires-Dist: python-dotenv==0.10.3
-Requires-Dist: requests==2.22.0
-Requires-Dist: jinja2~=3.0.3
-Requires-Dist: nci-cidc-schemas~=0.26.28
+Requires-Dist: requests==2.31.0
+Requires-Dist: jinja2==3.1.3
+Requires-Dist: nci-cidc-schemas==0.26.29
 
 # NCI CIDC API <!-- omit in TOC -->
 

{nci_cidc_api_modules-1.0.1 → nci_cidc_api_modules-1.0.4}/nci_cidc_api_modules.egg-info/requires.txt

@@ -1,17 +1,19 @@
-werkzeug==2.0.3
-flask~=2.0.3
+werkzeug==2.3.8
+flask==2.2.5
 flask-migrate==2.5.2
-flask-sqlalchemy~=2.4.0
+flask-sqlalchemy==2.5.1
 sqlalchemy~=1.3.0
 marshmallow==3.19.0
 marshmallow-sqlalchemy==0.22.3
-google-cloud-storage~=1.35.0
+google-cloud-storage==1.35.1
 google-cloud-secret-manager==2.16.2
 google-cloud-pubsub==0.43.0
-google-cloud-bigquery==3.3.5
+google-cloud-bigquery==3.18.0
 google-api-python-client==2.64.0
+packaging>=20.0.0
+pyarrow==14.0.1
 pandas<2,>=1
 python-dotenv==0.10.3
-requests==2.22.0
-jinja2~=3.0.3
-nci-cidc-schemas~=0.26.28
+requests==2.31.0
+jinja2==3.1.3
+nci-cidc-schemas==0.26.29

nci_cidc_api_modules-1.0.4/pyproject.toml

@@ -0,0 +1,67 @@
+[tool.black]
+exclude = "migrations"
+target-version = ["py36"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+# configure a webdriver for testing Dash dashboards
+# addopts = "--webdriver Chrome --headless"
+
+[tool.poetry]
+name = "cidc-api-gae"
+version = "1.0.2"
+description = ""
+authors = []
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.10"
+flask-cors = "3.0.9"
+flask-cachecontrol = "0.3.0"
+six = "1.13.0"
+python-jose = "3.0.1"
+psycopg2-binary = ">=2,<3"
+packaging = "19.2"
+protobuf = "3.20.3"
+gunicorn = "^21.2.0"
+gevent = "23.9.1"
+psycogreen = "1.0.2"
+webargs = "6.0.0"
+dash = "2.15.0"
+markupsafe = "2.1.5"
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=8.0.1,<8.1.0"
+black = "22.3.0"
+pre-commit = "2.9.2"
+ipython = "8.13.0"
+flask-shell-ipython = "0.5.1"
+webdriver-manager = "^4.0.1"
+percy = "2.0.2"
+selenium = "3.141.0"
+bs4 = "0.0.1"
+
+
+[tool.poetry.group.modules.dependencies]
+werkzeug = "2.3.8"
+flask = "2.2.5"
+flask-migrate = "2.5.2"
+flask-sqlalchemy = "2.5.1"
+sqlalchemy = ">=1.3.0,<1.4.0"
+marshmallow = "3.19.0"
+marshmallow-sqlalchemy = "0.22.3"
+google-cloud-storage = ">=1.35.0,<1.36.0"
+google-cloud-secret-manager = "2.16.2"
+google-cloud-pubsub = "0.43.0"
+google-cloud-bigquery = "3.3.5"
+google-api-python-client = "2.64.0"
+pandas = ">=1,<2"
+python-dotenv = "0.10.3"
+requests = "2.31.0"
+jinja2 = "3.1.3"
+nci-cidc-schemas = "0.26.29"
+
+# keep the existing build step
+# [build-system]
+# requires = ["poetry-core"]
+# build-backend = "poetry.core.masonry.api"

nci_cidc_api_modules-1.0.4/requirements.modules.txt

@@ -0,0 +1,19 @@
+werkzeug==2.3.8
+flask==2.2.5
+flask-migrate==2.5.2
+flask-sqlalchemy==2.5.1
+sqlalchemy~=1.3.0
+marshmallow==3.19.0
+marshmallow-sqlalchemy==0.22.3
+google-cloud-storage==1.35.1
+google-cloud-secret-manager==2.16.2
+google-cloud-pubsub==0.43.0
+google-cloud-bigquery==3.18.0
+google-api-python-client==2.64.0
+packaging>=20.0.0
+pyarrow==14.0.1
+pandas>=1,<2
+python-dotenv==0.10.3
+requests==2.31.0
+jinja2==3.1.3
+nci-cidc-schemas==0.26.29

{nci_cidc_api_modules-1.0.1 → nci_cidc_api_modules-1.0.4}/setup.py

@@ -1,4 +1,4 @@
-"""Package up cidc_api/models.py for use in other services."""
+"""Bundle up packages from cidc_api for use in other services."""
 
 from setuptools import setup
 

{nci_cidc_api_modules-1.0.1 → nci_cidc_api_modules-1.0.4}/tests/test_api.py

@@ -3,6 +3,7 @@
 This file doesn't contain tests for methods that don't directly correspond
 to data resources, like endpoints that handle upload-related functionality.
 """
+
 import os
 
 os.environ["TZ"] = "UTC"
@@ -246,7 +247,7 @@ def test_resource_post(resource, config, cidc_api, clean_db, monkeypatch):
             item = config["model"].find_by_id(response.json["id"]).__dict__
             assert_dict_contains(item, config["json"])
     else:
-        assert response.status_code == 405
+        assert response.status_code == 404
 
 
 @pytest.mark.parametrize("resource, config", resource_requests.items())
@@ -454,6 +455,10 @@ def test_endpoint_urls(cidc_api):
         "/users/data_access_report",
     }
 
+    # TODO: remove extra_endpoints_for_tests
+    extra_endpoints_for_tests = {"/bad_request", "/key_error"}
+    expected_endpoints = expected_endpoints | extra_endpoints_for_tests
+
     # Check that every endpoint included in the API is expected.
     endpoints = set(
         [
@@ -465,25 +470,17 @@ def test_endpoint_urls(cidc_api):
     assert endpoints == expected_endpoints
 
 
+# TODO: these tests should be triggered from regular routes
 def test_exception_handler(clean_cidc_api):
     """
     Ensure that the API handles HTTPExceptions in its routes as expected.
     """
-    message = "uh oh!"
-
-    @clean_cidc_api.route("/bad_request")
-    def raise_bad_request():
-        raise BadRequest(message)
-
-    @clean_cidc_api.route("/key_error")
-    def raise_key_error():
-        raise KeyError(message)
 
     client = clean_cidc_api.test_client()
 
     res = client.get("/bad_request")
     assert res.status_code == 400
-    assert res.json == {"_status": "ERR", "_error": {"message": message}}
+    assert res.json == {"_status": "ERR", "_error": {"message": "bad_request"}}
 
     res = client.get("/key_error")
     assert res.status_code == 500

nci_cidc_api_modules-1.0.1/pyproject.toml

@@ -1,8 +0,0 @@
-[tool.black]
-exclude = "migrations"
-target-version = ["py36"]
-
-[tool.pytest.ini_options]
-minversion = "6.0"
-# configure a webdriver for testing Dash dashboards
-addopts = "--webdriver Chrome --headless"

nci_cidc_api_modules-1.0.1/requirements.modules.txt

@@ -1,18 +0,0 @@
-werkzeug==2.0.3
-flask~=2.0.3
-flask-migrate==2.5.2
-flask-sqlalchemy~=2.4.0
-sqlalchemy~=1.3.0
-marshmallow==3.19.0
-marshmallow-sqlalchemy==0.22.3
-google-cloud-storage~=1.35.0
-google-cloud-secret-manager==2.16.2
-google-cloud-pubsub==0.43.0
-google-cloud-bigquery==3.3.5
-google-api-python-client==2.64.0
-pandas>=1,<2
-python-dotenv==0.10.3
-requests==2.22.0
-# pin jinja version to resolve cidc-schemas dependency issue
-jinja2~=3.0.3
-nci-cidc-schemas~=0.26.28