managed to upgrade some python libraries

CNAG-Biomedical-Informatics · Dec 8, 2023 · d6f6955 · d6f6955
1 parent 38e4eb1
commit d6f6955
Show file tree

Hide file tree

Showing 6 changed files with 769 additions and 981 deletions.
diff --git 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
diff --git a/convertPheno_server/pyproject.toml b/convertPheno_server/pyproject.toml
@@ -9,35 +9,35 @@ packages = []
 
 [tool.poetry.dependencies]
 python = "^3.10.6"
-anytree = "^2.8.0"
-cryptography = "^41.0.3"
-flask-restx = "^1.1.0"
+anytree = "^2.12.1"
+cryptography = "^41.0.7"
+docker = "^6.1.3"
+flask-restx = "^1.2.0"
 flask = "2.2.5"
-flask-cors = "^3.0.10"
-flask-sqlalchemy = "^3.0.3"
+flask-cors = "^4.0.0"
+flask-sqlalchemy = "^3.1.1"
 Flask-Limiter = "^3.5.0"
 genson = "^1.2.2"
 jsonschema = "^4.17.3"
-psycopg2-binary = "^2.9.6"
-pyjwt = "^2.6.0"
-docker = "^6.1.3"
+psycopg2-binary = "^2.9.9"
+pyjwt = "^2.8.0"
+requests = "^2.31.0"
 
 [tool.poetry.group.test.dependencies]
-pytest = "^7.3.1"
-pytest-cov = "^4.0.0"
-pytest-mock = "^3.10.0"
+pytest = "^7.4.2"
+pytest-cov = "^4.1.0"
 python-dotenv = "^1.0.0"
+pytest-mock = "^3.12.0"
 
 [tool.poetry.group.dev.dependencies]
-flake8 = "^6.0.0"
+black = "^23.11.0"
+flake8 = "^6.1.0"
 flake8-html = "^0.4.3"
-requests = "^2.30.0"
-black = "^23.3.0"
-ruff = "^0.0.265"
-pylint = "^2.17.4"
+pylint = "^3.0.2"
+ruff = "^0.1.7"
 
 [tool.poetry.group.prod.dependencies]
-gunicorn = "^20.1.0"
+gunicorn = "^21.2.0"
 
 [build-system]
 requires = ["poetry-core"]

diff --git a/convertPheno_server/requirements.txt b/convertPheno_server/requirements.txt
@@ -1,47 +1,45 @@
-aniso8601==9.0.1 ; python_full_version == "3.10.6"
-anytree==2.9.0 ; python_full_version == "3.10.6"
-attrs==23.1.0 ; python_full_version == "3.10.6"
-certifi==2023.7.22 ; python_full_version == "3.10.6"
-cffi==1.15.1 ; python_full_version == "3.10.6"
-charset-normalizer==3.2.0 ; python_full_version == "3.10.6"
-click==8.1.7 ; python_full_version == "3.10.6"
-colorama==0.4.6 ; python_full_version == "3.10.6" and platform_system == "Windows"
-cryptography==41.0.3 ; python_full_version == "3.10.6"
-deprecated==1.2.14 ; python_full_version == "3.10.6"
-docker==6.1.3 ; python_full_version == "3.10.6"
-flask-cors==3.0.10 ; python_full_version == "3.10.6"
-flask-limiter==3.5.0 ; python_full_version == "3.10.6"
-flask-restx==1.1.0 ; python_full_version == "3.10.6"
-flask-sqlalchemy==3.0.5 ; python_full_version == "3.10.6"
-flask==2.2.5 ; python_full_version == "3.10.6"
-genson==1.2.2 ; python_full_version == "3.10.6"
-greenlet==2.0.2 ; python_full_version == "3.10.6" and platform_machine == "aarch64" or python_full_version == "3.10.6" and platform_machine == "ppc64le" or python_full_version == "3.10.6" and platform_machine == "x86_64" or python_full_version == "3.10.6" and platform_machine == "amd64" or python_full_version == "3.10.6" and platform_machine == "AMD64" or python_full_version == "3.10.6" and platform_machine == "win32" or python_full_version == "3.10.6" and platform_machine == "WIN32"
-idna==3.4 ; python_full_version == "3.10.6"
-importlib-resources==6.0.1 ; python_full_version == "3.10.6"
-itsdangerous==2.1.2 ; python_full_version == "3.10.6"
-jinja2==3.1.2 ; python_full_version == "3.10.6"
-jsonschema-specifications==2023.7.1 ; python_full_version == "3.10.6"
-jsonschema==4.19.0 ; python_full_version == "3.10.6"
-limits==3.6.0 ; python_full_version == "3.10.6"
-markdown-it-py==3.0.0 ; python_full_version == "3.10.6"
-markupsafe==2.1.3 ; python_full_version == "3.10.6"
-mdurl==0.1.2 ; python_full_version == "3.10.6"
-ordered-set==4.1.0 ; python_full_version == "3.10.6"
-packaging==23.1 ; python_full_version == "3.10.6"
-psycopg2-binary==2.9.7 ; python_full_version == "3.10.6"
-pycparser==2.21 ; python_full_version == "3.10.6"
-pygments==2.16.1 ; python_full_version == "3.10.6"
-pyjwt==2.8.0 ; python_full_version == "3.10.6"
-pytz==2023.3.post1 ; python_full_version == "3.10.6"
-pywin32==306 ; sys_platform == "win32" and python_full_version == "3.10.6"
-referencing==0.30.2 ; python_full_version == "3.10.6"
-requests==2.31.0 ; python_full_version == "3.10.6"
-rich==13.5.2 ; python_full_version == "3.10.6"
-rpds-py==0.10.2 ; python_full_version == "3.10.6"
-six==1.16.0 ; python_full_version == "3.10.6"
-sqlalchemy==2.0.20 ; python_full_version == "3.10.6"
-typing-extensions==4.7.1 ; python_full_version == "3.10.6"
-urllib3==2.0.4 ; python_full_version == "3.10.6"
-websocket-client==1.6.2 ; python_full_version == "3.10.6"
-werkzeug==2.3.7 ; python_full_version == "3.10.6"
-wrapt==1.15.0 ; python_full_version == "3.10.6"
+aniso8601==9.0.1 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+anytree==2.12.1 ; python_full_version >= "3.10.6" and python_version < "4"
+attrs==23.1.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+certifi==2023.11.17 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+cffi==1.16.0 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+charset-normalizer==3.3.2 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+click==8.1.7 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0"
+colorama==0.4.6 ; python_full_version >= "3.10.6" and python_full_version < "4.0.0" 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
@@ -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
@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
-<coverage version="7.3.1" timestamp="1702037998737" lines-valid="1274" lines-covered="948" line-rate="0.7441" branches-valid="439" branches-covered="296" branch-rate="0.6743" complexity="0">
-	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.3.1 -->
+<coverage version="7.3.2" timestamp="1702064855918" lines-valid="1274" lines-covered="960" line-rate="0.7535" branches-valid="439" branches-covered="301" branch-rate="0.6856" complexity="0">
+	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.3.2 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
 		<source>server</source>
@@ -32,27 +32,27 @@
 						<line number="57" hits="1"/>
 						<line number="58" hits="1"/>
 						<line number="59" hits="1"/>
-						<line number="62" hits="1"/>
-						<line number="63" hits="1"/>
+						<line number="64" hits="1"/>
 						<line number="65" hits="1"/>
-						<line number="80" hits="1"/>
-						<line number="81" hits="1"/>
-						<line number="85" hits="0"/>
-						<line number="86" hits="0"/>
-						<line number="89" hits="0"/>
-						<line number="92" hits="1"/>
-						<line number="93" hits="1"/>
-						<line number="97" hits="0"/>
-						<line number="117" hits="1"/>
-						<line number="118" hits="1"/>
+						<line number="67" hits="1"/>
+						<line number="82" hits="1"/>
+						<line number="83" hits="1"/>
+						<line number="87" hits="0"/>
+						<line number="88" hits="0"/>
+						<line number="91" hits="0"/>
+						<line number="94" hits="1"/>
+						<line number="95" hits="1"/>
+						<line number="99" hits="0"/>
 						<line number="119" hits="1"/>
 						<line number="120" hits="1"/>
 						<line number="121" hits="1"/>
-						<line number="124" hits="1"/>
-						<line number="125" hits="1"/>
+						<line number="122" hits="1"/>
+						<line number="123" hits="1"/>
 						<line number="126" hits="1"/>
 						<line number="127" hits="1"/>
 						<line number="128" hits="1"/>
+						<line number="129" hits="1"/>
+						<line number="130" hits="1"/>
 					</lines>
 				</class>
 				<class name="model.py" filename="model.py" complexity="0" line-rate="1" branch-rate="1">
@@ -1040,9 +1040,9 @@
 				</class>
 			</classes>
 		</package>
-		<package name="utils" line-rate="0.5733" branch-rate="0.6207" complexity="0">
+		<package name="utils" line-rate="0.6124" branch-rate="0.7069" complexity="0">
 			<classes>
-				<class name="convert_pheno.py" filename="utils/convert_pheno.py" complexity="0" line-rate="0.8039" branch-rate="0.4">
+				<class name="convert_pheno.py" filename="utils/convert_pheno.py" complexity="0" line-rate="0.9412" branch-rate="0.7">
 					<methods/>
 					<lines>
 						<line number="12" hits="1"/>
@@ -1086,19 +1086,19 @@
 						<line number="105" hits="1"/>
 						<line number="106" hits="1"/>
 						<line number="108" hits="1"/>
-						<line number="110" hits="1" branch="true" condition-coverage="50% (1/2)" missing-branches="111"/>
-						<line number="111" hits="0"/>
-						<line number="113" hits="0" branch="true" condition-coverage="0% (0/2)" missing-branches="114,117"/>
-						<line number="114" hits="0"/>
-						<line number="115" hits="0"/>
-						<line number="117" hits="0" branch="true" condition-coverage="0% (0/2)" missing-branches="118,121"/>
-						<line number="118" hits="0"/>
-						<line number="119" hits="0"/>
+						<line number="110" hits="1" branch="true" condition-coverage="100% (2/2)"/>
+						<line number="111" hits="1"/>
+						<line number="113" hits="1" branch="true" condition-coverage="50% (1/2)" missing-branches="117"/>
+						<line number="114" hits="1"/>
+						<line number="115" hits="1"/>
+						<line number="117" hits="1" branch="true" condition-coverage="50% (1/2)" missing-branches="121"/>
+						<line number="118" hits="1"/>
+						<line number="119" hits="1"/>
 						<line number="121" hits="1"/>
 						<line number="124" hits="1"/>
 					</lines>
 				</class>
-				<class name="db_helpers.py" filename="utils/db_helpers.py" complexity="0" line-rate="0.7755" branch-rate="0.6875">
+				<class name="db_helpers.py" filename="utils/db_helpers.py" complexity="0" line-rate="0.8776" branch-rate="0.8125">
 					<methods/>
 					<lines>
 						<line number="12" hits="1"/>
@@ -1139,12 +1139,12 @@
 						<line number="74" hits="1" branch="true" condition-coverage="100% (2/2)"/>
 						<line number="75" hits="1"/>
 						<line number="76" hits="1"/>
-						<line number="78" hits="1" branch="true" condition-coverage="50% (1/2)" missing-branches="79"/>
-						<line number="79" hits="0"/>
-						<line number="80" hits="0"/>
-						<line number="81" hits="0" branch="true" condition-coverage="0% (0/2)" missing-branches="82,84"/>
-						<line number="82" hits="0"/>
-						<line number="84" hits="0"/>
+						<line number="78" hits="1" branch="true" condition-coverage="100% (2/2)"/>
+						<line number="79" hits="1"/>
+						<line number="80" hits="1"/>
+						<line number="81" hits="1" branch="true" condition-coverage="50% (1/2)" missing-branches="84"/>
+						<line number="82" hits="1"/>
+						<line number="84" hits="1"/>
 						<line number="86" hits="1"/>
 						<line number="89" hits="1"/>
 						<line number="96" hits="1"/>