diff --git a/.github/workflows/kubernetes-charts-build.yaml b/.github/workflows/kubernetes-charts-build.yaml index aee72a1..2c22ccf 100644 --- a/.github/workflows/kubernetes-charts-build.yaml +++ b/.github/workflows/kubernetes-charts-build.yaml @@ -20,7 +20,7 @@ defaults: jobs: helm-lint-test: runs-on: ubuntu-latest - if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform-toolkit' + if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform' steps: - name: Checkout uses: actions/checkout@v5.0.0 @@ -130,7 +130,7 @@ jobs: run: | helm package ./medcat-service-helm --version ${{ steps.version.outputs.chart_version }} helm package ./medcat-trainer-helm --version ${{ steps.version.outputs.chart_version }} --dependency-update - helm package ./cogstack-helm-ce --version ${{ steps.version.outputs.chart_version }} --dependency-update + helm package ./cogstack-ce-helm --version ${{ steps.version.outputs.chart_version }} --dependency-update - name: Helm OCI login to Docker Hub run: helm registry login registry-1.docker.io -u ${{ secrets.DOCKERHUB_USERNAME }} -p ${{ secrets.DOCKERHUB_TOKEN }} @@ -139,7 +139,7 @@ jobs: run: | helm push ./medcat-service-helm-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems helm push ./medcat-trainer-helm-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems - helm push ./cogstack-helm-ce-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems + helm push ./cogstack-ce-helm-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems - name: Release uses: softprops/action-gh-release@v2 diff --git a/.github/workflows/observability-docker.yml b/.github/workflows/observability-docker.yml index d6aa6a1..e505cda 100644 --- a/.github/workflows/observability-docker.yml +++ b/.github/workflows/observability-docker.yml @@ -16,7 +16,7 @@ on: jobs: docker: runs-on: ubuntu-latest - if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform-toolkit' + if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform' strategy: matrix: # This should be replaced with Docker Bake instead include: diff --git a/docs/docs/cogstack-ce/tutorial/quickstart-installation.md b/docs/docs/cogstack-ce/tutorial/quickstart-installation.md index 2ebf8de..95cc1b3 100644 --- a/docs/docs/cogstack-ce/tutorial/quickstart-installation.md +++ b/docs/docs/cogstack-ce/tutorial/quickstart-installation.md @@ -14,7 +14,7 @@ The install should take around 15 minutes, and by the end of this tutorial you w Run: ```sh -helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce --timeout 15m +helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-ce-helm --timeout 15m ``` This command will install Cogstack community edition with all the default values. @@ -55,8 +55,7 @@ If you use a custom namespace or Helm release name, add the namespace or replace 2. Open JupyterHub by opening http://127.0.0.1:8000 in a web browser -Jupyter should start up, and present a login screen. - +Jupyter should start up, and present a login screen. ## Next step: run the bundled notebook diff --git a/docs/docs/index.md b/docs/docs/index.md index 4be37ac..73b6d9c 100644 --- a/docs/docs/index.md +++ b/docs/docs/index.md @@ -21,10 +21,10 @@ Deploy the CogStack Community Edition on an existing Kubernetes cluster using he ```sh $ helm install \ - cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce \ + cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-ce-helm \ --timeout=15m0s ---> 100% -Pulled: registry-1.docker.io/cogstacksystems/cogstack-helm-ce:0.0.1 +Pulled: registry-1.docker.io/cogstacksystems/cogstack-ce-helm:0.0.1 Digest: sha256:02e8ad3df7173270f7fdeb3e1ed5133427cec06ffc15b4ce763fa9bb062c8df1 NAME: cogstack @@ -66,7 +66,7 @@ The AI and Data Engineering layer comprises of: - MLOps tooling for model training and validation !!! tip - Many of these apps and tools are open source and available on GitHub (subject to the licensing in each project), in the [CogStack GitHub](https://github.com/CogStack). +Many of these apps and tools are open source and available on GitHub (subject to the licensing in each project), in the [CogStack GitHub](https://github.com/CogStack). The public documentation on this page covers these open source community offerings. diff --git a/docs/docs/platform/deployment/helm/charts/_index.md b/docs/docs/platform/deployment/helm/charts/_index.md index 161525c..5137aac 100644 --- a/docs/docs/platform/deployment/helm/charts/_index.md +++ b/docs/docs/platform/deployment/helm/charts/_index.md @@ -11,12 +11,11 @@ The Helm charts for CogStack are published to Docker Hub, which is an OCI-compli https://hub.docker.com/r/cogstacksystems/medcat-trainer-helm - **CogStack CE (Community Edition, umbrella chart):** - https://hub.docker.com/r/cogstacksystems/cogstack-helm-ce + https://hub.docker.com/r/cogstacksystems/cogstack-ce-helm - [MedCAT Service Helm](medcat-service-helm.md) - [MedCAT Trainer Helm](medcat-trainer-helm.md) - -- [CogStack CE Helm](cogstack-ce-helm.md) +- [CogStack Community Edition Helm](cogstack-ce-helm.md) ## Chart Publishing diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index dfbdbfd..be76973 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -47,7 +47,7 @@ nav: - MedCAT: https://docs.cogstack.org/projects/nlp - MedCAT Trainer: https://docs.cogstack.org/projects/medcat-trainer/ - Tutorials: - - Medcat Service Tutorial: platform/cogstack-ai/medcat-service-tutorial.ipynb + - Medcat Service Tutorial: platform/cogstack-ai/medcat-service-tutorial.ipynb - Data Engineering: - Data Engineering: data-engineering/index.md - Data pipelines: overview/Data pipelines.md @@ -69,7 +69,7 @@ nav: - Charts Overview: platform/deployment/helm/charts/_index.md - MedCAT Service Helm: platform/deployment/helm/charts/medcat-service-helm.md - MedCAT Trainer Helm: platform/deployment/helm/charts/medcat-trainer-helm.md - - Cogstack CE Helm: platform/deployment/helm/charts/cogstack-helm-ce.md + - Cogstack CE Helm: platform/deployment/helm/charts/cogstack-ce-helm.md - Examples: - Examples: platform/deployment/examples/_index.md - AWS Kubernetes EKS: platform/deployment/examples/aws-kubernetes-eks.md diff --git a/docs/scripts/copy_files_from_repo.py b/docs/scripts/copy_files_from_repo.py index 2a36454..c6b4d04 100644 --- a/docs/scripts/copy_files_from_repo.py +++ b/docs/scripts/copy_files_from_repo.py @@ -22,11 +22,11 @@ # Add more entries here to copy additional static files into documentation. COPY_SPECS = [ { - "sourceFilePath": "helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-service-tutorial.ipynb", + "sourceFilePath": "helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-service-tutorial.ipynb", "outputFilePath": "platform/cogstack-ai/medcat-service-tutorial.ipynb", }, { - "sourceFilePath": "helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb", + "sourceFilePath": "helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb", "outputFilePath": "cogstack-ce/tutorial/medcat-opensearch-e2e.ipynb", }, ] diff --git a/helm-charts/cogstack-helm-ce/.helmignore b/helm-charts/cogstack-ce-helm/.helmignore similarity index 100% rename from helm-charts/cogstack-helm-ce/.helmignore rename to helm-charts/cogstack-ce-helm/.helmignore diff --git a/helm-charts/cogstack-helm-ce/Chart.lock b/helm-charts/cogstack-ce-helm/Chart.lock similarity index 100% rename from helm-charts/cogstack-helm-ce/Chart.lock rename to helm-charts/cogstack-ce-helm/Chart.lock diff --git a/helm-charts/cogstack-helm-ce/Chart.yaml b/helm-charts/cogstack-ce-helm/Chart.yaml similarity index 98% rename from helm-charts/cogstack-helm-ce/Chart.yaml rename to helm-charts/cogstack-ce-helm/Chart.yaml index 0f67497..3af6f32 100644 --- a/helm-charts/cogstack-helm-ce/Chart.yaml +++ b/helm-charts/cogstack-ce-helm/Chart.yaml @@ -1,5 +1,5 @@ apiVersion: v2 -name: cogstack-helm-ce +name: cogstack-ce-helm description: CogStack Community Edition Helm Chart # A chart can be either an 'application' or a 'library' chart. diff --git a/helm-charts/cogstack-helm-ce/README.md b/helm-charts/cogstack-ce-helm/README.md similarity index 94% rename from helm-charts/cogstack-helm-ce/README.md rename to helm-charts/cogstack-ce-helm/README.md index 7a8de49..31199e9 100644 --- a/helm-charts/cogstack-helm-ce/README.md +++ b/helm-charts/cogstack-ce-helm/README.md @@ -1,4 +1,4 @@ -# CogStack Helm Community Edition +# CogStack Community Edition Helm Chart This is a all in one helm chart that runs CogStack on Kubernetes @@ -11,6 +11,9 @@ This chart is an umbrella chart that deploys: | **MedCAT** | Medical Concept Annotation Tool — NER and linking for clinical text. | | **AnonCAT** | De-identification service (MedCAT in DEID mode) for anonymising text. | | **MedCAT Trainer** | Training and model management for MedCAT, with Solr and PostgreSQL. | +| **OpenSearch** | Search and analytics engine powering logs and document indexing for CogStack. | +| **OpenSearch Dashboards** | Visualization and analytics UI for OpenSearch data. | +| **JupyterHub** | Multi-user notebook server for interactive data science workflows. | ## Prerequisites @@ -20,7 +23,7 @@ This chart is an umbrella chart that deploys: ## Installation ```sh -helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce +helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-ce-helm ``` ## Configuration @@ -115,7 +118,7 @@ kubectl delete namespace cogstack | medcat-trainer.env.CSRF_TRUSTED_ORIGINS | string | `"http://localhost:8080"` | CSRF trusted origins for the MedCAT Trainer frontend (set for your deployment/port-forward). | | medcat-trainer.image.tag | string | `"latest@sha256:103215a7540ad614c32866f4cb00ddd91e7aff37cea9abc25dc226c577f9506d"` | MedCAT Trainer image tag (can be a digest-pinned tag). | | medcat-trainer.provisioning.enabled | bool | `true` | Enable provisioning of projects and models on startup. | -| medcat-trainer.provisioning.existingConfigMap.name | string | `"cogstack-helm-ce-example-trainer-provisioining"` | Existing ConfigMap name containing the provisioning configuration. | +| medcat-trainer.provisioning.existingConfigMap.name | string | `"cogstack-ce-helm-example-trainer-provisioining"` | Existing ConfigMap name containing the provisioning configuration. | | nameOverride | string | `""` | This is to override the chart name. | | opensearch-dashboards.enabled | bool | `true` | Deploy an opensearch-dashboards instance | | opensearch.enabled | bool | `true` | Deploy an opensearch cluster | diff --git a/helm-charts/cogstack-helm-ce/README.md.gotmpl b/helm-charts/cogstack-ce-helm/README.md.gotmpl similarity index 87% rename from helm-charts/cogstack-helm-ce/README.md.gotmpl rename to helm-charts/cogstack-ce-helm/README.md.gotmpl index ba10b0d..317866b 100644 --- a/helm-charts/cogstack-helm-ce/README.md.gotmpl +++ b/helm-charts/cogstack-ce-helm/README.md.gotmpl @@ -1,4 +1,4 @@ -# CogStack Helm Community Edition +# CogStack Community Edition Helm Chart This is a all in one helm chart that runs CogStack on Kubernetes @@ -11,6 +11,10 @@ This chart is an umbrella chart that deploys: | **MedCAT** | Medical Concept Annotation Tool — NER and linking for clinical text. | | **AnonCAT** | De-identification service (MedCAT in DEID mode) for anonymising text. | | **MedCAT Trainer** | Training and model management for MedCAT, with Solr and PostgreSQL. | +| **OpenSearch** | Search and analytics engine powering logs and document indexing for CogStack. | +| **OpenSearch Dashboards** | Visualization and analytics UI for OpenSearch data. | +| **JupyterHub** | Multi-user notebook server for interactive data science workflows. | + ## Prerequisites @@ -20,7 +24,7 @@ This chart is an umbrella chart that deploys: ## Installation ```sh -helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce +helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-ce-helm ``` ## Configuration diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/Chart.lock b/helm-charts/cogstack-ce-helm/charts/jupyterhub/Chart.lock similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/Chart.lock rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/Chart.lock diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/Chart.yaml b/helm-charts/cogstack-ce-helm/charts/jupyterhub/Chart.yaml similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/Chart.yaml rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/Chart.yaml diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md b/helm-charts/cogstack-ce-helm/charts/jupyterhub/README.md similarity index 99% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/README.md index 1c4f551..4fd3cc8 100644 --- a/helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md +++ b/helm-charts/cogstack-ce-helm/charts/jupyterhub/README.md @@ -14,7 +14,7 @@ A Helm chart for CogStack Jupyter Hub using official JupyterHub chart | Key | Type | Default | Description | |-----|------|---------|-------------| -| jupyterhub.cull.enabled | bool | false, so pods stay running indefinitely d | Enable culling of user pods | +| jupyterhub.cull.enabled | bool | false, so pods stay running indefinitely | Enable culling of user pods | | jupyterhub.hub.config.Authenticator.admin_users[0] | string | `"admin"` | | | jupyterhub.hub.config.DummyAuthenticator.password | string | `"SuperSecret"` | | | jupyterhub.hub.config.JupyterHub.authenticator_class | string | `"dummy"` | | diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md.gotmpl b/helm-charts/cogstack-ce-helm/charts/jupyterhub/README.md.gotmpl similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md.gotmpl rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/README.md.gotmpl diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb b/helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-opensearch-e2e.ipynb diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-service-tutorial.ipynb b/helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-service-tutorial.ipynb similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/examples/medcat-service-tutorial.ipynb rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/examples/medcat-service-tutorial.ipynb diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/templates/examples-configmap.yaml b/helm-charts/cogstack-ce-helm/charts/jupyterhub/templates/examples-configmap.yaml similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/templates/examples-configmap.yaml rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/templates/examples-configmap.yaml diff --git a/helm-charts/cogstack-helm-ce/charts/jupyterhub/values.yaml b/helm-charts/cogstack-ce-helm/charts/jupyterhub/values.yaml similarity index 100% rename from helm-charts/cogstack-helm-ce/charts/jupyterhub/values.yaml rename to helm-charts/cogstack-ce-helm/charts/jupyterhub/values.yaml diff --git a/helm-charts/cogstack-helm-ce/ci/ci-values.yaml b/helm-charts/cogstack-ce-helm/ci/ci-values.yaml similarity index 100% rename from helm-charts/cogstack-helm-ce/ci/ci-values.yaml rename to helm-charts/cogstack-ce-helm/ci/ci-values.yaml diff --git a/helm-charts/cogstack-helm-ce/provisioning/base_index_settings.json b/helm-charts/cogstack-ce-helm/provisioning/base_index_settings.json similarity index 100% rename from helm-charts/cogstack-helm-ce/provisioning/base_index_settings.json rename to helm-charts/cogstack-ce-helm/provisioning/base_index_settings.json diff --git a/helm-charts/cogstack-helm-ce/provisioning/dashboards.ndjson b/helm-charts/cogstack-ce-helm/provisioning/dashboards.ndjson similarity index 100% rename from helm-charts/cogstack-helm-ce/provisioning/dashboards.ndjson rename to helm-charts/cogstack-ce-helm/provisioning/dashboards.ndjson diff --git a/helm-charts/cogstack-helm-ce/provisioning/generate_synthetic_bulk_ndjson.py b/helm-charts/cogstack-ce-helm/provisioning/generate_synthetic_bulk_ndjson.py similarity index 100% rename from helm-charts/cogstack-helm-ce/provisioning/generate_synthetic_bulk_ndjson.py rename to helm-charts/cogstack-ce-helm/provisioning/generate_synthetic_bulk_ndjson.py diff --git a/helm-charts/cogstack-helm-ce/provisioning/opensearch-provisioning.sh b/helm-charts/cogstack-ce-helm/provisioning/opensearch-provisioning.sh similarity index 100% rename from helm-charts/cogstack-helm-ce/provisioning/opensearch-provisioning.sh rename to helm-charts/cogstack-ce-helm/provisioning/opensearch-provisioning.sh diff --git a/helm-charts/cogstack-helm-ce/templates/NOTES.txt b/helm-charts/cogstack-ce-helm/templates/NOTES.txt similarity index 100% rename from helm-charts/cogstack-helm-ce/templates/NOTES.txt rename to helm-charts/cogstack-ce-helm/templates/NOTES.txt diff --git a/helm-charts/cogstack-helm-ce/templates/_helpers.tpl b/helm-charts/cogstack-ce-helm/templates/_helpers.tpl similarity index 82% rename from helm-charts/cogstack-helm-ce/templates/_helpers.tpl rename to helm-charts/cogstack-ce-helm/templates/_helpers.tpl index ad7acb9..1987250 100644 --- a/helm-charts/cogstack-helm-ce/templates/_helpers.tpl +++ b/helm-charts/cogstack-ce-helm/templates/_helpers.tpl @@ -1,7 +1,7 @@ {{/* Expand the name of the chart. */}} -{{- define "cogstack-helm-ce.name" -}} +{{- define "cogstack-ce-helm.name" -}} {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }} {{- end }} @@ -10,7 +10,7 @@ Create a default fully qualified app name. We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec). If release name contains chart name it will be used as a full name. */}} -{{- define "cogstack-helm-ce.fullname" -}} +{{- define "cogstack-ce-helm.fullname" -}} {{- if .Values.fullnameOverride }} {{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }} {{- else }} @@ -26,16 +26,16 @@ If release name contains chart name it will be used as a full name. {{/* Create chart name and version as used by the chart label. */}} -{{- define "cogstack-helm-ce.chart" -}} +{{- define "cogstack-ce-helm.chart" -}} {{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }} {{- end }} {{/* Common labels */}} -{{- define "cogstack-helm-ce.labels" -}} -helm.sh/chart: {{ include "cogstack-helm-ce.chart" . }} -{{ include "cogstack-helm-ce.selectorLabels" . }} +{{- define "cogstack-ce-helm.labels" -}} +helm.sh/chart: {{ include "cogstack-ce-helm.chart" . }} +{{ include "cogstack-ce-helm.selectorLabels" . }} {{- if .Chart.AppVersion }} app.kubernetes.io/version: {{ .Chart.AppVersion | quote }} {{- end }} @@ -45,17 +45,17 @@ app.kubernetes.io/managed-by: {{ .Release.Service }} {{/* Selector labels */}} -{{- define "cogstack-helm-ce.selectorLabels" -}} -app.kubernetes.io/name: {{ include "cogstack-helm-ce.name" . }} +{{- define "cogstack-ce-helm.selectorLabels" -}} +app.kubernetes.io/name: {{ include "cogstack-ce-helm.name" . }} app.kubernetes.io/instance: {{ .Release.Name }} {{- end }} {{/* Create the name of the service account to use */}} -{{- define "cogstack-helm-ce.serviceAccountName" -}} +{{- define "cogstack-ce-helm.serviceAccountName" -}} {{- if .Values.serviceAccount.create }} -{{- default (include "cogstack-helm-ce.fullname" .) .Values.serviceAccount.name }} +{{- default (include "cogstack-ce-helm.fullname" .) .Values.serviceAccount.name }} {{- else }} {{- default "default" .Values.serviceAccount.name }} {{- end }} diff --git a/helm-charts/cogstack-helm-ce/templates/medcat-trainer-provisioining.yaml b/helm-charts/cogstack-ce-helm/templates/medcat-trainer-provisioining.yaml similarity index 90% rename from helm-charts/cogstack-helm-ce/templates/medcat-trainer-provisioining.yaml rename to helm-charts/cogstack-ce-helm/templates/medcat-trainer-provisioining.yaml index b0a50c4..a94dccc 100644 --- a/helm-charts/cogstack-helm-ce/templates/medcat-trainer-provisioining.yaml +++ b/helm-charts/cogstack-ce-helm/templates/medcat-trainer-provisioining.yaml @@ -1,4 +1,4 @@ -{{- if and (index .Values "medcat-trainer" "provisioning" "enabled") (eq (index .Values "medcat-trainer" "provisioning" "existingConfigMap" "name") "cogstack-helm-ce-example-trainer-provisioining") }} +{{- if and (index .Values "medcat-trainer" "provisioning" "enabled") (eq (index .Values "medcat-trainer" "provisioning" "existingConfigMap" "name") "cogstack-ce-helm-example-trainer-provisioining") }} apiVersion: v1 kind: ConfigMap metadata: @@ -15,7 +15,7 @@ data: description: "Example project for medcat trainer using MedCAT Service" annotationGuidelineLink: "https://docs.google.com/document/d/1xxelBOYbyVzJ7vLlztP2q1Kw9F5Vr1pRwblgrXPS7QM/edit?usp=sharing" useModelService: true - modelServiceUrl: "http://{{ include "cogstack-helm-ce.fullname" . }}-medcat-service:5000" + modelServiceUrl: "http://{{ include "cogstack-ce-helm.fullname" . }}-medcat-service:5000" - dataset: name: "Example Dataset - psych.csv - deid" url: "https://raw.githubusercontent.com/CogStack/cogstack-nlp/be9825f151da2d3b6faac80d49e5be91a1629c68/medcat-trainer/notebook_docs/example_data/psych.csv" @@ -25,5 +25,5 @@ data: description: "Example project for medcat trainer using AnonCAT Service" annotationGuidelineLink: "https://docs.google.com/document/d/1xxelBOYbyVzJ7vLlztP2q1Kw9F5Vr1pRwblgrXPS7QM/edit?usp=sharing" useModelService: true - modelServiceUrl: "http://{{ include "cogstack-helm-ce.fullname" . }}-anoncat-service:5000" + modelServiceUrl: "http://{{ include "cogstack-ce-helm.fullname" . }}-anoncat-service:5000" {{- end }} \ No newline at end of file diff --git a/helm-charts/cogstack-helm-ce/templates/opensearch-provisioning-config-map.yaml b/helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-config-map.yaml similarity index 100% rename from helm-charts/cogstack-helm-ce/templates/opensearch-provisioning-config-map.yaml rename to helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-config-map.yaml diff --git a/helm-charts/cogstack-helm-ce/templates/opensearch-provisioning-post-install.yaml b/helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-post-install.yaml similarity index 93% rename from helm-charts/cogstack-helm-ce/templates/opensearch-provisioning-post-install.yaml rename to helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-post-install.yaml index 39317e7..f46a81b 100644 --- a/helm-charts/cogstack-helm-ce/templates/opensearch-provisioning-post-install.yaml +++ b/helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-post-install.yaml @@ -3,13 +3,13 @@ apiVersion: v1 kind: Pod metadata: labels: - {{- include "cogstack-helm-ce.labels" . | nindent 4 }} + {{- include "cogstack-ce-helm.labels" . | nindent 4 }} annotations: "helm.sh/hook": post-install,post-upgrade "helm.sh/hook-weight": "1" "helm.sh/hook-delete-policy": hook-succeeded,before-hook-creation #"helm.sh/hook-delete-policy": before-hook-creation - name: {{ include "cogstack-helm-ce.fullname" . }}-opensearch-provisioning + name: {{ include "cogstack-ce-helm.fullname" . }}-opensearch-provisioning spec: restartPolicy: OnFailure containers: diff --git a/helm-charts/cogstack-helm-ce/values.yaml b/helm-charts/cogstack-ce-helm/values.yaml similarity index 97% rename from helm-charts/cogstack-helm-ce/values.yaml rename to helm-charts/cogstack-ce-helm/values.yaml index ce48bf1..76ac6e6 100644 --- a/helm-charts/cogstack-helm-ce/values.yaml +++ b/helm-charts/cogstack-ce-helm/values.yaml @@ -1,4 +1,4 @@ -# Default values for cogstack-helm-ce. +# Default values for cogstack-ce-helm. # This is a YAML-formatted file. # Declare variables to be passed into your templates. @@ -49,7 +49,7 @@ medcat-trainer: enabled: true existingConfigMap: # -- Existing ConfigMap name containing the provisioning configuration. - name: "cogstack-helm-ce-example-trainer-provisioining" + name: "cogstack-ce-helm-example-trainer-provisioining" env: # -- CSRF trusted origins for the MedCAT Trainer frontend (set for your deployment/port-forward). CSRF_TRUSTED_ORIGINS: "http://localhost:8080" diff --git a/helm-charts/local_dev_startup.sh b/helm-charts/local_dev_startup.sh index f94906d..a641a2a 100644 --- a/helm-charts/local_dev_startup.sh +++ b/helm-charts/local_dev_startup.sh @@ -25,9 +25,9 @@ helm test medcat-service --logs ## helm install trainer-registry oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm --wait --timeout 5m0s -helm upgrade cogstack-helm-ce ./cogstack-helm-ce --install +helm upgrade cogstack-ce-helm ./cogstack-ce-helm --install # Stop any running port forwards # ps -ef | grep '[p]ort-forward' | awk '{print $2}' | xargs -r kill -# Port forward all services in cogstack-helm-ce -# helm get notes cogstack-helm-ce | bash \ No newline at end of file +# Port forward all services in cogstack-ce-helm +# helm get notes cogstack-ce-helm | bash \ No newline at end of file