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chore: deployment startup ordering (#108)
1. xtramcp backend needs to be started and ready before paperdebugger backend attempts connection. Currently, this is manually ensured. We can enforce an ordering with a startup gate by including in the `initContainer` of paperdebugger. 2. Add healthcheck node to check for xtramcp start-up before starting PD pod. Additional: - Propose to remove defaults for some secrets and allow backend processing logic to handle instead. Future: re-try logic for for more robust handling of connection re-try. This will also facilitate re-establishing connection during pod failures.
1 parent 594373f commit de12255

5 files changed

Lines changed: 42 additions & 30 deletions

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‎hack/dev.sh‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -6,20 +6,21 @@ ROOT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." &>/dev/null && pwd)
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cd $ROOT_DIR
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OPENAI_BASE_URL=${OPENAI_BASE_URL:-https://api.openai.com/v1}
9-
OPENAI_API_KEY=${OPENAI_API_KEY:-sk-dummy-OPENAI_API_KEY}
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OPENAI_API_KEY=${OPENAI_API_KEY:-}
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INFERENCE_BASE_URL=${INFERENCE_BASE_URL:-https://inference.paperdebugger.workers.dev}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-sk-dummy-OPEN-ROUTER}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-}
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MCP_BASIC_KEY=${MCP_BASIC_KEY:-sk-dummy-MCP_BASIC_KEY}
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MCP_PAPERSCORE_KEY=${MCP_PAPERSCORE_KEY:-sk-dummy-MCP_PAPERSCORE_KEY}
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XTRAMCP_OPENAI_BASE_URL=${XTRAMCP_OPENAI_BASE_URL:-https://api.openai.com/v1}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-sk-dummy-XTRAMCP_OPENAI_API_KEY}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-}
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XTRAMCP_OPENREVIEW_BASE_URL=${XTRAMCP_OPENREVIEW_BASE_URL:-https://api2.openreview.net}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-dummy-XTRAMCP_OPENREVIEW_USERNAME}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-dummy-XTRAMCP_OPENREVIEW_PASSWORD}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-dummy-crossref-email-address}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-dummy-doi-email-address}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-postgresql://dummy-arxiv-metadata-db-url}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-mongodb://dummy-mongo-uri}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-}
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XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-}
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PAPERDEBUGGER_IMAGE=${PAPERDEBUGGER_IMAGE:-ghcr.io/paperdebugger/sharelatex-paperdebugger:latest}
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MONGO_URI=${MONGO_URI:-}
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GHCR_DOCKER_CONFIG=${GHCR_DOCKER_CONFIG:-dummy-ghcr-docker-config}
@@ -42,6 +43,7 @@ helm template $ROOT_DIR/helm-chart \
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--set-string xtramcp_openreview_password=$XTRAMCP_OPENREVIEW_PASSWORD \
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--set-string xtramcp_crossref_email_address=$XTRAMCP_CROSSREF_EMAIL_ADDRESS \
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--set-string xtramcp_doi_email_address=$XTRAMCP_DOI_EMAIL_ADDRESS \
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--set-string xtramcp_acl_metadata_db_url=$XTRAMCP_ACL_METADATA_DB_URL \
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--set-string xtramcp_arxiv_metadata_db_url=$XTRAMCP_ARXIV_METADATA_DB_URL \
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--set-string xtramcp_mongo_uri=$XTRAMCP_MONGO_URI \
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--set-string paperdebugger.image=$PAPERDEBUGGER_IMAGE \

‎hack/prd.sh‎

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Original file line numberDiff line numberDiff line change
@@ -8,19 +8,19 @@ cd $ROOT_DIR
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OPENAI_BASE_URL=${OPENAI_BASE_URL:-https://api.openai.com/v1}
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OPENAI_API_KEY=${OPENAI_API_KEY:-}
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INFERENCE_BASE_URL=${INFERENCE_BASE_URL:-https://inference.paperdebugger.workers.dev}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-sk-dummy-OPEN-ROUTER}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-}
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MCP_BASIC_KEY=${MCP_BASIC_KEY:-sk-dummy-MCP_BASIC_KEY}
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MCP_PAPERSCORE_KEY=${MCP_PAPERSCORE_KEY:-sk-dummy-MCP_PAPERSCORE_KEY}
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XTRAMCP_OPENAI_BASE_URL=${XTRAMCP_OPENAI_BASE_URL:-https://api.openai.com/v1}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-sk-dummy-XTRAMCP_OPENAI_API_KEY}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-}
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XTRAMCP_OPENREVIEW_BASE_URL=${XTRAMCP_OPENREVIEW_BASE_URL:-https://api2.openreview.net}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-dummy-XTRAMCP_OPENREVIEW_USERNAME}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-dummy-XTRAMCP_OPENREVIEW_PASSWORD}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-dummy-crossref-email-address}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-dummy-doi-email-address}
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XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-postgresql://dummy-acl-metadata-db-url}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-postgresql://dummy-arxiv-metadata-db-url}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-mongodb://dummy-mongo-uri}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-}
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XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-}
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PAPERDEBUGGER_IMAGE=${PAPERDEBUGGER_IMAGE:-ghcr.io/paperdebugger/sharelatex-paperdebugger:latest}
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MONGO_URI=${MONGO_URI:-}
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GHCR_DOCKER_CONFIG=${GHCR_DOCKER_CONFIG:-dummy-ghcr-docker-config}

‎hack/stg.sh‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -8,19 +8,19 @@ cd $ROOT_DIR
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OPENAI_BASE_URL=${OPENAI_BASE_URL:-https://api.openai.com/v1}
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OPENAI_API_KEY=${OPENAI_API_KEY:-}
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INFERENCE_BASE_URL=${INFERENCE_BASE_URL:-https://inference.paperdebugger.workers.dev}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-sk-dummy-OPEN-ROUTER}
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INFERENCE_API_KEY=${INFERENCE_API_KEY:-}
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MCP_BASIC_KEY=${MCP_BASIC_KEY:-sk-dummy-MCP_BASIC_KEY}
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MCP_PAPERSCORE_KEY=${MCP_PAPERSCORE_KEY:-sk-dummy-MCP_PAPERSCORE_KEY}
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XTRAMCP_OPENAI_BASE_URL=${XTRAMCP_OPENAI_BASE_URL:-https://api.openai.com/v1}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-sk-dummy-XTRAMCP_OPENAI_API_KEY}
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XTRAMCP_OPENAI_API_KEY=${XTRAMCP_OPENAI_API_KEY:-}
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XTRAMCP_OPENREVIEW_BASE_URL=${XTRAMCP_OPENREVIEW_BASE_URL:-https://api2.openreview.net}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-dummy-XTRAMCP_OPENREVIEW_USERNAME}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-dummy-XTRAMCP_OPENREVIEW_PASSWORD}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-dummy-crossref-email-address}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-dummy-doi-email-address}
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XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-postgresql://dummy-acl-metadata-db-url}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-postgresql://dummy-arxiv-metadata-db-url}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-mongodb://dummy-mongo-uri}
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XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-}
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XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-}
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XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-}
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XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-}
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XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-}
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XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-}
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XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-}
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PAPERDEBUGGER_IMAGE=${PAPERDEBUGGER_IMAGE:-ghcr.io/paperdebugger/sharelatex-paperdebugger:latest}
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MONGO_URI=${MONGO_URI:-}
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GHCR_DOCKER_CONFIG=${GHCR_DOCKER_CONFIG:-dummy-ghcr-docker-config}

‎helm-chart/templates/paperdebugger.yaml‎

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@@ -15,8 +15,8 @@ spec:
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spec:
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imagePullSecrets:
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- name: ghcr-secret
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{{ if .Values.mongo.in_cluster }}
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initContainers:
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{{- if .Values.mongo.in_cluster }}
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- name: init-mongodb
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image: mongo:latest
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command:
@@ -26,7 +26,17 @@ spec:
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"--eval",
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'db.isMaster().primary || rs.initiate({_id: "in-cluster", members: [{_id: 0, host: "mongo:27017"}]})',
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]
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{{ end }}
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{{- end }}
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- name: wait-for-xtramcp-port
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image: busybox:1.36
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command: ["sh", "-c"]
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args:
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- |
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echo "Waiting for xtramcp health endpoint..."
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until wget -q --spider http://paperdebugger-xtramcp-server:8080/health; do
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sleep 2
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done
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echo "xtramcp is healthy."
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containers:
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- name: paperdebugger
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image: {{ .Values.paperdebugger.image }}

‎helm-chart/values.yaml‎

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@@ -14,7 +14,7 @@ paperdebuggerMcpServer:
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image: ghcr.io/paperdebugger/paperdebugger-mcp-server:main-14409c5
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paperdebuggerXtraMcpServer:
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image: ghcr.io/paperdebugger/xtragpt-mcp-server:sha-3bfcca3
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image: ghcr.io/paperdebugger/xtragpt-mcp-server:sha-95f70ce
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mongo:
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in_cluster: true

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