diff --git a/convertPheno_server/makefile b/convertPheno_server/makefile index 194b0f09..c18ede04 100644 --- a/convertPheno_server/makefile +++ b/convertPheno_server/makefile @@ -112,3 +112,7 @@ sonar: github-codespaces-curltest: curl https://${GITHUB_CODESPACES_ID}-5001.app.github.dev/api/curltest -H "X-Github-Token: ${GITHUB_TOKEN}" + +upgrade_deps: + # poetry self add poetry-plugin-up + poetry up diff --git a/convertPheno_server/poetry.lock b/convertPheno_server/poetry.lock index 4f569f63..c13691f4 100644 --- a/convertPheno_server/poetry.lock +++ b/convertPheno_server/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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and platform_system == "Windows" +cryptography==41.0.7 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +deprecated==1.2.14 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +docker==6.1.3 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +flask-cors==4.0.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +flask-limiter==3.5.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +flask-restx==1.2.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +flask-sqlalchemy==3.1.1 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +flask==2.2.5 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +genson==1.2.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +greenlet==3.0.1 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") +idna==3.6 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +importlib-resources==6.1.1 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +itsdangerous==2.1.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +jinja2==3.1.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +jsonschema==4.17.3 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +limits==3.7.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +markdown-it-py==3.0.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +markupsafe==2.1.3 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +mdurl==0.1.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +ordered-set==4.1.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +packaging==23.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +psycopg2-binary==2.9.9 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pycparser==2.21 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pygments==2.17.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pyjwt==2.8.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pyrsistent==0.20.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pytz==2023.3.post1 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +pywin32==306 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" and sys_platform == "win32" +requests==2.31.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +rich==13.7.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +six==1.16.0 ; python_full_version >= "3.10.6" and python_version < "4" +sqlalchemy==2.0.23 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +typing-extensions==4.8.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +urllib3==2.1.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +websocket-client==1.7.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +werkzeug==2.3.8 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" +wrapt==1.16.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" diff --git a/convertPheno_server/server/app.py b/convertPheno_server/server/app.py index c28b84e9..c8b4eedd 100644 --- a/convertPheno_server/server/app.py +++ b/convertPheno_server/server/app.py @@ -59,6 +59,8 @@ def on_json_loading_failed(self, e): db = SQLAlchemy(app) +# TODO app.before_first_request +# is deprecated from flask 2.3.0 onwards @app.before_first_request def create_tables(): """Create all sql tables""" diff --git a/convertPheno_server/tests/reports/coverage/coverage.xml b/convertPheno_server/tests/reports/coverage/coverage.xml index c49cd71f..c4d27961 100644 --- a/convertPheno_server/tests/reports/coverage/coverage.xml +++ b/convertPheno_server/tests/reports/coverage/coverage.xml @@ -1,6 +1,6 @@ - - + + server @@ -32,27 +32,27 @@ - - + - - - - - - - - - - + + + + + + + + + - - + + + + @@ -1040,9 +1040,9 @@ - + - + @@ -1086,19 +1086,19 @@ - - - - - - - - + + + + + + + + - + @@ -1139,12 +1139,12 @@ - - - - - - + + + + + +