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alhendricksonalhendrickson
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build(helm): Fix helm chart testing. Fix lint issues. Bump trainer version (#43)
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Lines changed: 51 additions & 44 deletions

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‎.github/workflows/kubernetes-charts-build.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -20,42 +20,45 @@ jobs:
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if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform-toolkit'
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v5.0.0
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with:
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fetch-depth: 0
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- name: Set up Helm
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uses: azure/setup-helm@v4.3.0
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with:
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version: v3.18.3
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uses: azure/setup-helm@v4.3.1
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- uses: actions/setup-python@v5.3.0
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- uses: actions/setup-python@v6.0.0
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with:
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python-version: '3.x'
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check-latest: true
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- name: Set up chart-testing
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uses: helm/chart-testing-action@v2.7.0
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uses: helm/chart-testing-action@v2.8.0
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- name: Run chart-testing (list-changed)
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id: list-changed
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working-directory: .
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run: |
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changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch}})
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changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts)
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if [[ -n "$changed" ]]; then
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echo "changed=true" >> "$GITHUB_UTPUT"
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echo "changed=true" >> "$GITHUB_OUTPUT"
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fi
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- name: Run chart-testing (lint)
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if: steps.list-changed.outputs.changed == 'true'
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run: ct lint --target-branch ${{ github.event.repository.default_branch }}
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working-directory: .
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env:
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CT_CHECK_VERSION_INCREMENT: "false"
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run: ct lint --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts
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- name: Create kind cluster
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if: steps.list-changed.outputs.changed == 'true'
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uses: helm/kind-action@v1.12.0
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- name: Run chart-testing (install)
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if: steps.list-changed.outputs.changed == 'true'
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run: ct install --target-branch ${{ github.event.repository.default_branch }}
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working-directory: .
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run: ct install --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts
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helm-publish:
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runs-on: ubuntu-latest

‎deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -21,14 +21,18 @@ version: 0.0.1
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# incremented each time you make changes to the application. Versions are not expected to
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# follow Semantic Versioning. They should reflect the version the application is using.
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# It is recommended to use it with quotes.
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appVersion: "latest"
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appVersion: "3.5.1"
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maintainers:
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- name: alhendrickson
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email: alistair@cogstack.org
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# Chart.yaml
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dependencies:
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- name: solr
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version: "9.6.10"
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repository: "oci://registry-1.docker.io/bitnamicharts"
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- name: postgresql
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version: 16.7.27
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repository: "oci://registry-1.docker.io/bitnamicharts"
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condition: postgresql.enabled
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- name: solr
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version: "9.6.10"
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repository: "oci://registry-1.docker.io/bitnamicharts"
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- name: postgresql
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version: 16.7.27
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repository: "oci://registry-1.docker.io/bitnamicharts"
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condition: postgresql.enabled

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -11,5 +11,5 @@ spec:
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- name: wget
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image: busybox
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command: ['wget']
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args: ['{{ include "medcat-trainer-helm.fullname" . }}-nginx:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
14+
args: ['{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
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restartPolicy: Never

‎deployment/kubernetes/charts/medcat-trainer-helm/values.yaml‎

Lines changed: 25 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ image:
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# This sets the pull policy for images.
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pullPolicy: Always
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# Overrides the image tag whose default is the chart appVersion.
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tag: "latest"
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# tag: "latest"
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nginxImage:
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repository: nginx
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pullPolicy: IfNotPresent
@@ -26,7 +26,7 @@ env:
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EMAIL_PORT: "465"
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EMAIL_USER: "example@cogstack.org"
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ENV: "non-prod"
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LOAD_EXAMPLES: "1"
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LOAD_EXAMPLES: "0"
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LOAD_NUM_DOC_PAGES: "10"
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MAX_DATASET_SIZE: "10000"
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MAX_MEDCAT_MODELS: "2"
@@ -55,7 +55,7 @@ postgresql:
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repository: bitnamilegacy/postgresql
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# Pin legacy version of postgresql following bitnami change to remove free images. Match prefect version
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tag: 17.6.0-debian-12-r4
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persistence:
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media:
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# Size of PVC for files like model packs and other media downloaded by medcat trainer
@@ -64,28 +64,28 @@ persistence:
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# Size of the PVC for the static HTML site
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size: 100Mi
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sqlite:
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# Size of the PVC for the Sqlite database
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# Size of the PVC for the Sqlite database
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size: 100Mi
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# Size of the PVC for the Sqlite backups
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backupDbSize: 300Mi
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storageClassName: ""
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# MedCAT config as described here: https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py
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medcatConfig: |
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cat.linking.optim = {'type': 'standard', 'lr': 0.1}
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cat.linking.filter_before_disamb = True
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# 20 - INFO; 10 - DEBUG
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cat.general.log_level = 20
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# Recommended is to have this one negative
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cat.linking.similarity_threshold = -5
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# And this one to be used as the real th
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cat.linking.similarity_threshold_trainer = -5
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# Used for limiting the number of occ of a concept in a project
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cat.general.cui_count_limit = 100000000
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# Is unlink full
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cat.general.full_unlink = False
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# use this spacy model
88-
cat.general.spacy_model = 'en_core_web_md'
75+
cat.linking.optim = {'type': 'standard', 'lr': 0.1}
76+
cat.linking.filter_before_disamb = True
77+
# 20 - INFO; 10 - DEBUG
78+
cat.general.log_level = 20
79+
# Recommended is to have this one negative
80+
cat.linking.similarity_threshold = -5
81+
# And this one to be used as the real th
82+
cat.linking.similarity_threshold_trainer = -5
83+
# Used for limiting the number of occ of a concept in a project
84+
cat.general.cui_count_limit = 100000000
85+
# Is unlink full
86+
cat.general.full_unlink = False
87+
# use this spacy model
88+
cat.general.spacy_model = 'en_core_web_md'
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solr:
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replicaCount: 1
@@ -109,10 +109,10 @@ solr:
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image:
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repository: bitnamilegacy/zookeeper
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tag: 3.9.3-debian-12-r22
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replicaCount: 1 #
112+
replicaCount: 1
113113
persistence:
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size: 1Gi # Default is 8Gi
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114+
# Set size of the PVC for zookeper. Default is 8Gi
115+
size: 1Gi
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117117
# This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
118118
imagePullSecrets: []
@@ -164,9 +164,10 @@ service:
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type: ClusterIP
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# This sets the ports more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#field-spec-ports
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port: 8001
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apiPort: 8000 # Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
167+
# Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
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apiPort: 8000
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# nodePort: 30001
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# This block is for setting up the ingress for more information can be found here: https://kubernetes.io/docs/concepts/services-networking/ingress/
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ingress:
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enabled: false
@@ -224,7 +225,6 @@ nginx:
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path: /nginx/health/live
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port: http
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# This section is for setting up autoscaling more information can be found here: https://kubernetes.io/docs/concepts/workloads/autoscaling/
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autoscaling:
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enabled: false
@@ -253,4 +253,4 @@ tolerations: []
253253
affinity: {}
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# Runtime class name for the pod (e.g., "nvidia" for GPU workloads)
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runtimeClassName: ""
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runtimeClassName: ""

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