diff --git a/applications/accounts-api/Dockerfile b/applications/accounts-api/Dockerfile index 0d8f6e645..c3f9ea104 100644 --- a/applications/accounts-api/Dockerfile +++ b/applications/accounts-api/Dockerfile @@ -13,5 +13,3 @@ RUN pip3 install --no-cache-dir -r requirements.txt COPY backend /usr/src/app RUN pip3 install -e . - -ENTRYPOINT gunicorn --workers=$WORKERS --bind=0.0.0.0:$PORT $MODULE_NAME.__main__:app diff --git a/applications/accounts-api/backend/requirements.txt b/applications/accounts-api/backend/requirements.txt index f9289e172..68760177c 100644 --- a/applications/accounts-api/backend/requirements.txt +++ b/applications/accounts-api/backend/requirements.txt @@ -1,11 +1,9 @@ -connexion[swagger-ui] >= 2.6.0; python_version>="3.6" -# 2.3 is the last version that supports python 3.4-3.5 -connexion[swagger-ui] <= 2.3.0; python_version=="3.5" or python_version=="3.4" -# connexion requires werkzeug but connexion < 2.4.0 does not install werkzeug -# we must peg werkzeug versions below to fix connexion -# https://github.com/zalando/connexion/pull/1044 -werkzeug == 2.2.3; python_version=="3.5" or python_version=="3.4" -swagger-ui-bundle >= 0.0.2 -python_dateutil >= 2.6.0 -setuptools >= 21.0.0 -cloudharness +connexion[swagger-ui,flask,uvicorn]>=3.0.0,<4.0.0 +swagger-ui-bundle>=1.1.0 +python_dateutil>=2.9.0 +setuptools>=21.0.0 +uvicorn +# Following some unnecessary requirements to make sure they can be installed +psycopg2-binary +sqlalchemy<2.0.0 +scipy \ No newline at end of file diff --git a/applications/accounts-api/backend/setup.py b/applications/accounts-api/backend/setup.py index e16a0a2e5..705dcf730 100644 --- a/applications/accounts-api/backend/setup.py +++ b/applications/accounts-api/backend/setup.py @@ -14,10 +14,10 @@ # http://pypi.python.org/pypi/setuptools REQUIRES = [ - "connexion>=2.0.2", - "swagger-ui-bundle>=0.0.2", - "python_dateutil>=2.6.0", - "cloudharness" + "connexion[swagger-ui,flask,uvicorn]>=3.0.0,<4.0.0", + "Flask", + "swagger-ui-bundle", + "cloudharness", ] setup( diff --git a/applications/accounts/deploy/resources/realm.json b/applications/accounts/deploy/resources/realm.json index 80888301c..c9d38951e 100644 --- a/applications/accounts/deploy/resources/realm.json +++ b/applications/accounts/deploy/resources/realm.json @@ -322,6 +322,34 @@ "offline_access", "microprofile-jwt" ] + }, + { + "clientId": "idp-arc", + "name": "idp-arc", + "enabled": true, + "publicClient": true, + "standardFlowEnabled": true, + "implicitFlowEnabled": false, + "directAccessGrantsEnabled": false, + "serviceAccountsEnabled": false, + "protocol": "openid-connect", + "rootUrl": "{{ .Values.idpArc.rootUrl }}", + "redirectUris": [ + "{{ .Values.idpArc.rootUrl }}/*" + ], + "webOrigins": [ + "{{ .Values.idpArc.rootUrl }}" + ], + "attributes": { + "pkce.code.challenge.method": "S256" + }, + "fullScopeAllowed": true, + "defaultClientScopes": [ + "web-origins", "profile", "roles", "email" + ], + "optionalClientScopes": [ + "offline_access", "{{ .Values.apps.accounts.admin.role }}-scope" + ] } ], "clientScopes": [ diff --git a/applications/jupyterlab/Dockerfile b/applications/jupyterlab/Dockerfile index 9799c8b93..3b142019c 100644 --- a/applications/jupyterlab/Dockerfile +++ b/applications/jupyterlab/Dockerfile @@ -77,15 +77,15 @@ USER root RUN conda install conda-forge::nest-simulator ENV NEST_HOME=/opt/conda -USER jovyan - -#### Install Python packages +#### Install Python packages (as root to avoid permission issues with conda-managed packages) RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip && \ pip install backports.tarfile>=1.2 # temp fix for error: ImportError: cannot import name 'tarfile' from 'backports' RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ pip install -r requirements.txt --upgrade --no-cache-dir +USER jovyan + # Compile NEURON mod files for PyNN RUN cd /opt/conda/lib/python3.12/site-packages/pyNN/neuron/nmodl && nrnivmodl diff --git a/applications/jupyterlab/requirements.txt b/applications/jupyterlab/requirements.txt index cce0760db..cd64d940d 100644 --- a/applications/jupyterlab/requirements.txt +++ b/applications/jupyterlab/requirements.txt @@ -3,7 +3,7 @@ pyelectro neurotune #### NEURON & NetPyNE -neuron +neuron<9 # Install specific version of NetPyNE git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne diff --git a/applications/netpyne/Dockerfile b/applications/netpyne/Dockerfile index eca06eea7..f5788e99a 100644 --- a/applications/netpyne/Dockerfile +++ b/applications/netpyne/Dockerfile @@ -1,6 +1,6 @@ -FROM node:18 AS jsbuild +FROM node:16-bullseye AS jsbuild ARG APP_DIR=dependencies/NetPyNE-UI ENV FOLDER=netpyne diff --git a/deployment-configuration/values-template-dev.yaml b/deployment-configuration/values-template-dev.yaml index 6b178e827..2a11a72d1 100644 --- a/deployment-configuration/values-template-dev.yaml +++ b/deployment-configuration/values-template-dev.yaml @@ -1,2 +1,12 @@ backup: - active: false \ No newline at end of file + active: false + +idpArc: + rootUrl: "https://idp-arc.idp-arc.dev.metacell.us" + +ingress: + annotations: + nginx.ingress.kubernetes.io/enable-cors: "true" + nginx.ingress.kubernetes.io/cors-allow-origin: "https://idp-arc.idp-arc.dev.metacell.us" + nginx.ingress.kubernetes.io/cors-allow-credentials: "true" + nginx.ingress.kubernetes.io/cors-allow-headers: "Authorization, Content-Type" diff --git a/deployment/codefresh-dev.yaml b/deployment/codefresh-dev.yaml index 0c3bd2ece..6f2f4e58f 100644 --- a/deployment/codefresh-dev.yaml +++ b/deployment/codefresh-dev.yaml @@ -31,7 +31,7 @@ steps: title: Cloning NetPyNE-UI.git repository... type: git-clone repo: https://github.com/MetaCell/NetPyNE-UI.git - revision: 1.1.0 + revision: osb2-dev working_directory: applications/netpyne/dependencies/ git: github clone_nwb-explorer_git_development_nwb-explorer: