MetaCell
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@@ -11,3 +11,7 @@ skaffold.yaml
 applications/workspaces/backend/static
 .overrides
 **/*.sqlite3
+
+applications/portal/frontend/src/assets/atlas/salk_cord_10um/*
+applications/portal/backend/persistent/*
+applications/portal/backend/data/*
@@ -7,23 +7,51 @@ The SALK Mouse Cord Atlas
 ### Prerequisites
 
 The SALK deployment is built on top of [CloudHarness](https://github.com/MetaCell/cloud-harness).
-The deployment process is based on Python 3.7+ scripts. It is recommended to setup a virtual 
-environment first.
+CloudHarness is a base infrastructure and common utilities for microservice applications deployed on Kubernetes.
+
+CloudHarness and SALK use Python 3.9, it is recommended to setup a virtual environment first.
 
 With conda: 
 ```bash
-conda create --name salk python=3.7
+conda create --name salk python=3.9
 conda activate salk
 ```
 
 To install CloudHarness:
 
 ```
-git clone --branch release/1.0.0 https://github.com/MetaCell/cloud-harness.git
+git clone --branch release/2.1.0 https://github.com/MetaCell/cloud-harness.git
 cd cloud-harness
 pip install -r requirements.txt
 ```
 
+
+
+## Deploy to a K8s cluster
+
+Make sure that you are using the correct K8s context (check `kubectl config get-contexts`)
+Or set your context using `kubectl config set-context`
+
+Requirements:
+* helm installed (https://helm.sh/docs/intro/install/)
+* kubectl installed (https://kubernetes.io/docs/tasks/tools/)
+* skaffold installed (https://skaffold.dev/docs/install/)
+
+
+```bash
+conda activate salk
+
+# prepare the Helm chart
+harness-deployment cloud-harness . -t <docker tag> -d <the.domain.com> -r <docker registry> -rs <docker registry secret> -n <namespace> -e prod -i portal
+
+# build the images
+skaffold build
+
+# install the application
+helm upgrade salk ./deployment/helm --install --reset-values --version 0.0.1 --namespace <namespace> --values ./deployment/helm/values.yaml --timeout 600s
+```
+
+
 ## Development setup
 
 Minikube is recommended to setup locally. The procedure is different depending on where Minikube is installed.
@@ -33,7 +61,7 @@ Run the `setup.sh` script to setup your minikube cluster.
 The script will also build all Docker images and installs the deployment using `skaffold`
 
 Requirements:
-* minikube installed
-* kubectl installed
-* skaffold installed
-* helm installed
+* helm installed (https://helm.sh/docs/intro/install/)
+* kubectl installed (https://kubernetes.io/docs/tasks/tools/)
+* minikube installed (https://minikube.sigs.k8s.io/docs/start/)
+* skaffold installed (https://skaffold.dev/docs/install/)
@@ -2,4 +2,5 @@ public
 dist
 node_modules
 .vscode
-
+backend/static/*
+frontend/src/assets/atlas/*
@@ -18,6 +18,7 @@ RUN python3 -m pip install -r requirements.txt --no-cache-dir --upgrade
 
 COPY backend/requirements.txt backend/setup.py .
 RUN python3 -m pip install -e .
+RUN apt-get update && apt-get install poppler-utils -y
 
 COPY backend ${APP_DIR}
 RUN python3 manage.py collectstatic --noinput
@@ -28,16 +29,18 @@ RUN mkdir -p ${APP_DIR}/static/www
 RUN python3 manage.py generate_canal_images salk_cord_10um
 RUN python3 manage.py generate_grid_images salk_cord_10um
 RUN python3 manage.py generate_lamina_images salk_cord_10um
-RUN python3 manage.py generate_annotation_images salk_cord_10um
+RUN python3 manage.py generate_grey_and_white_matter_images salk_cord_10um
+RUN python3 manage.py split_meshes salk_cord_10um
 
 # compile frontend
-FROM node:16-alpine as frontend
+FROM node:18-alpine as frontend
 
 ENV BUILDDIR=/builddir
 ENV APP_DIR=/usr/src/app
 
 COPY --from=backend ${APP_DIR}/persistent/ ${BUILDDIR}/src/assets/atlas/salk_cord_10um/
-RUN rm -rf ${BUILDDIR}/src/assets/atlas/salk_cord_10um/*.sqlite3
+RUN rm -rf ${BUILDDIR}/src/assets/atlas/salk_cord_10um/populations/*
+RUN rm -rf ${BUILDDIR}/src/assets/atlas/salk_cord_10um/*.json && rm -rf ${BUILDDIR}/src/assets/atlas/salk_cord_10um/*.sqlite3
 COPY frontend/package.json ${BUILDDIR}/package.json
 COPY frontend/yarn.lock ${BUILDDIR}/yarn.lock
 WORKDIR ${BUILDDIR}
 
@@ -35,6 +35,15 @@ sudo ln -s "$NVM_DIR/versions/node/$(nvm version)/bin/npm" "/usr/local/bin/npm"
 The local webpack dev server uses [keycloak_dev.json](src/assets/keycloak_dev.json) for connecting to the keycloak accounts system.
 Please check this file and change the domain according to your setup.
 
+
+### Generate SALK Cord images
+
+To generate SALK Cord images, once all the requirements for backend is installed, activate the virtual environment. And run the following command to generate the Salk Cord images .
+```
+./generate_images.sh
+```
+
+
 ### Self Signed Certificates
 
 When running on a local minikube please make sure you import the generated cacert certificates. The certificate file is most likely to be found here ./deployment/helm/resources/certs/cacert.crt