search

A Helm chart for Helx Search components. This chart installs Dug, TranQL , Airflow and Redis.

Architecture of Search Chart

For full architeture overview please refer to our documentation here.

Note

When installing you might notice a warning from bitnami postgres chart about the use of unknown postgres docker image, that warning is safe to ignore.

Values

Dug API Server

Key	Type	Default	Description
api.certMountPath	string	"/usr/lib/ssl/certs/ca_elastic.crt"	Default location to elastic search tls certificate
api.deployment	object	{"apiPort":5551,"apiTimeout":10,"apiWorkers":8,"extraEnv":[],"imagePullSecrets":[],"logLevel":"INFO","resources":{"limits":{"cpu":2,"memory":"2Gi"},"requests":{"cpu":"500m","memory":"1Gi"}}}	Deployment pod Configuration
api.elasticScheme	string	"https"	Connection Scheme to elastic search
api.image	object	{"pullPolicy":"Always","repository":"containers.renci.org/helxplatform/dug","tag":""}	Container image
api.replicas	int	4	Number of relicas for Dug API server
api.service.annotations	object	{}	Search service annotation
api.service.apiPort	string	"5551"	API port on deployment
api.service.name	string	"search-api"	This should match release name in this example the helm release name was search
api.service.port	string	"5551"	Service port
api.service.type	string	"ClusterIP"	Service type

Koios Chat UI

Key	Type	Default	Description
chat	object	{"apiPort":8080,"config":{"api_url":null,"public_url":null},"enabled":false,"image":{"repository":"containers.renci.org/helxplatform/koios-ui","tag":"v0.0.1"},"replicas":1,"resources":{},"root_path":"/chat","service":{"type":"ClusterIP"}}	Configuration option for Dug chatbot UI
chat_2	object	{"apiPort":8080,"config":{"api_url":null,"public_url":null},"enabled":false,"image":{"repository":"containers.renci.org/helxplatform/koios-ui","tag":"v1.0.0"},"replicas":1,"resources":{},"root_path":"/chat-v2","service":{"type":"ClusterIP"}}	Configuration option for Dug chatbot UI

Application Config

Key	Type	Default	Description
config.annotation.annotator_type	string	"sapbert"	Annotator type to use , options are sapbert or monarch
config.annotation.monarch	object	{"url":"https://api.monarchinitiative.org/api/nlp/annotate/entities?min_length=4&longest_only=false&include_abbreviation=false&include_acronym=false&include_numbers=false&content="}	Monarch annotator config
config.annotation.normalizer_url	string	"https://nodenormalization-sri.renci.org/get_normalized_nodes?conflate=false&description=true&curie="	Node normalization url to use during annotation
config.annotation.sapbert	object	{"annotator_url":"https://sap-qdrant.apps.renci.org/annotate/","bagel":{"enabled":false,"llm_args":{"access_key":"","llm_model_name":"gpt-4o-2024-05-13","organization":""},"prompt":"bagel/ask_classes","url":"https://bagel.apps.renci.org/group_synonyms_openai"},"classification_url":"https://med-nemo.apps.renci.org/annotate/","score_threshold":0.8}	Sapbert annotator config
config.annotation.synonymizer_url	string	"https://name-resolution-sri.renci.org/reverse_lookup"	Name resolution url to use to find synonyms
config.element_mappings	string	""	colon seperated mappings list by comma, eg : dbgap:Non-HEAL Studies,bacpac:HEAL Research Programs, used to map parser outputs to other values.
config.input_sets	string	"bdc:v2.0,topmed:v2.0"	Input dataset to include during ingestion. These refer to repo names on lakefs. With version (branch) tags.
config.kgx_data_sets	string	"baseline-graph:v5.0,cde-graph:v5.0"	Knowledge graph input datasets to ingest for the dug Knowledge graph. These are lakefs repo names with version(branches) as tags.
config.lakefs.access_key	string	"accesskey"	Lakefs access key
config.lakefs.branch	string	"main"	Branch to write output files to.
config.lakefs.enabled	bool	true	Enables lakefs usage for input and output on data ingest.
config.lakefs.host	string	"https://lakefs.apps.renci.org"	Lakefs host address
config.lakefs.repo	string	"test-repo"	Lakefs repo to write outputs to
config.lakefs.secret_key	string	"secretkey"	Lakefs secret key
config.node_to_queries_enabled	string	"false"	Enables CDE extraction from Knowledge graph.

Elasticsearch

Key	Type	Default	Description
elasticsearch	object	{"clusterHealthCheckParams":"wait_for_status=green&timeout=1s","enabled":true,"esJavaOpts":"-Xmx6g -Xms6g -Dlog4j2.disable.jmx=true -Dlog4j2.formatMsgNoLookups=true","extraEnvs":[{"name":"ELASTIC_PASSWORD","valueFrom":{"secretKeyRef":{"key":"password","name":"search-elastic-secret"}}},{"name":"ELASTIC_USERNAME","valueFrom":{"secretKeyRef":{"key":"username","name":"search-elastic-secret"}}},{"name":"LOG4J_FORMAT_MSG_NO_LOOKUPS","value":"true"}],"imageTag":"8.19.6","maxUnavailable":0,"replicas":3,"resources":{"limits":{"cpu":1,"ephemeral-storage":"256Mi","memory":"8G"},"requests":{"cpu":1,"ephemeral-storage":"256Mi","memory":"8G"}},"secret":{"enabled":false},"sysctlInitContainer":{"enabled":false}}	Elastic search for more information checkout full elasticsearch chart options at https://github.com/elastic/helm-charts/tree/v8.5.1

Ingress

Key	Type	Default	Description
ingress	object	`{"annotations":{"nginx.ingress.kubernetes.io/cors-allow-headers":"Content-Type","nginx.ingress.kubernetes.io/cors-allow-methods":"POST, OPTIONS","nginx.ingress.kubernetes.io/cors-allow-origin":"*","nginx.ingress.kubernetes.io/enable-cors":"true"},"basicAuth":{"enabled":false,"password":"","username":""},"className":"","enabled":false,"hosts":[{"host":"chart-example.local"}],"labels":{},"pathType":"ImplementationSpecific","paths":[{"name":"ui","path":"/","port":80,"prepend":true},{"name":"tranql","path":"/tranql","port":8081,"prepend":true},{"name":"api-server","path":"/airflow","port":8080,"prepend":true}],"rewrite_paths":[{"name":"api","path":"/search-api(/	$)(.*)","port":5551,"prepend":true}],"tls":[]}`

Redis

Key	Type	Default	Description
redis	object	{"auth":{"existingSecret":"search-redis-secret","existingSecretPasswordKey":"password"},"clusterDomain":"cluster.local","commonConfiguration":"# Enable AOF https://redis.io/topics/persistence#append-only-file\nappendonly no\n# Disable RDB persistence, AOF persistence already enabled.\nsave 300 100000","enabled":true,"fullnameOverride":"","image":{"registry":"containers.renci.org","repository":"helxplatform/falkor","tag":"v4.14.4-alpine"},"master":{"command":"","extraFlags":["--loadmodule","/var/lib/falkordb/bin/falkordb.so","THREAD_COUNT","8","OMP_THREAD_COUNT","16"],"livenessProbe":{"enabled":false},"persistence":{"size":"50Gi"},"readinessProbe":{"enabled":true,"failureThreshold":1,"periodSeconds":1},"resources":{"limits":{"cpu":2,"memory":"45Gi"},"requests":{"cpu":1,"memory":"45Gi"}}},"replica":{"autoscaling":{"enabled":false,"maxReplicas":1,"minReplicas":1,"targetCPU":100},"extraFlags":["--loadmodule","/FalkorDB/bin/src/falkordb.so","THREAD_COUNT","8","OMP_THREAD_COUNT","16"],"livenessProbe":{"enabled":false},"persistence":{"size":"50G"},"readinessProbe":{"enabled":true,"failureThreshold":1,"periodSeconds":1,"successThreshold":5},"replicaCount":0,"resources":{"limits":{"cpu":2,"memory":"45Gi"},"requests":{"cpu":1,"memory":"45Gi"}}},"serviceAccount":{"create":false},"usePassword":true}	Redis (Redis Graph) for more information checkout full redis chart options at https://github.com/bitnami/charts/tree/redis/18.1.1/bitnami/redis

Elastic / Redis secrets

Key	Type	Default	Description
secrets	object	{"elastic":{"name":"search-elastic-secret","passwordKey":"password","user":"elastic","userKey":"username"},"redis":{"name":"search-redis-secret","passwordKey":"password"}}	Secrets for passwords

Tranql

Key	Type	Default	Description
tranql	object	{"enabled":true,"existingRedis":{"host":"","port":6379,"secret":"search-redis-secret","secretPasswordKey":"password"},"extraEnv":[{"name":"WEB_PATH_PREFIX","value":"/tranql"}],"gunicorn":{"workerCount":1,"workerTimeout":1600},"redis":{"enabled":false},"resources":{"limits":{"cpu":2,"memory":"2G"},"requests":{"cpu":"500m","memory":"2G"}},"webPrefix":"/tranql"}	Tranql API configuration. Please refer to https://github.com/helxplatform/tranql-chart/tree/main for more details.

Dug (Helx) UI

Key	Type	Default	Description
ui	object	{"config":{"analytics":{"enabled":false},"brand_description":{"html":"<html></html>"},"brand_name":"","hidden_result_tabs":"cdes","meta":{"description":"Dug semantic search","title":"Dug semantic search"},"search":{"enabled":"true","url":""},"support":{"faqs_url":"","help_portal_url":"","user_guide_url":""},"tranql_enabled":"true","tranql_url":"","workspaces":{"enabled":"false"}},"enabled":false}	Dug search UI configuration please refer to https://github.com/helxplatform/ui-chart/tree/master for more options

Other Values

Key	Type	Default	Description
airflow.airflowVersion	string	"3.1.1"
airflow.apiServer.resources.limits.cpu	int	1
airflow.apiServer.resources.limits.memory	string	"2Gi"
airflow.config.api.auth_backends	string	"airflow.api.auth.backend.basic_auth"
airflow.config.core.internal_api_secret_key	string	"{{ .Values.webserverSecretKey }}"
airflow.dagProcessor.enabled	bool	true
airflow.dagProcessor.logGroomerSidecar.enabled	bool	false
airflow.dagProcessor.resources.limits.cpu	int	2
airflow.dagProcessor.resources.limits.memory	string	"2Gi"
airflow.dags.gitSync.branch	string	"main"
airflow.dags.gitSync.enabled	bool	true
airflow.dags.gitSync.repo	string	"https://github.com/helxplatform/roger.git"
airflow.dags.gitSync.subPath	string	"dags"
airflow.dags.persistence.enabled	bool	false
airflow.data.metadataConnection.pass	string	"postgres"
airflow.defaultAirflowRepository	string	"airflow"
airflow.executor	string	"KubernetesExecutor"
airflow.extraEnv	string	"- name: ROGER_LAKEFS__CONFIG_ENABLED\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_enabled\n- name: ROGER_LAKEFS__CONFIG_HOST\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_host\n- name: ROGER_LAKEFS__CONFIG_ACCESS__KEY__ID\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_access_key_id\n- name: ROGER_LAKEFS__CONFIG_SECRET__ACCESS__KEY\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_secret_access_key\n- name: ROGER_LAKEFS__CONFIG_BRANCH\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_branch\n- name: ROGER_LAKEFS__CONFIG_REPO\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: lakefs_repo\n- name: ROGER_ANNOTATION_NORMALIZER\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: normalizer_url\n- name: ROGER_ANNOTATION_ANNOTATOR__TYPE\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_type\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_MONARCH_URL\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_monarch_url\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_CLASSIFICATION__URL\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_classification_url\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_ANNOTATOR__URL\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_annotator_url\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_ENABLED\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_enabled\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_URL\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_url\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_PROMPT\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_prompt\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_LLM__ARGS_LLM__MODEL__NAME\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_llm_model_name\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_LLM__ARGS_ORGANIZATION\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_llm_organization\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_BAGEL_LLM__ARGS_ACCESS__KEY\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_bagel_llm_access_key\n- name: ROGER_ANNOTATION_ANNOTATOR__ARGS_SAPBERT_SCORE__THRESHOLD\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: annotator_sapbert_score_threshold\n- name: ROGER_ANNOTATION_SYNONYM__SERVICE\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: synonymizer_url\n- name: ROGER_DATA_DIR\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: data_directory\n- name: ROGER_DUG__INPUTS_DATA__SETS\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: input_sets\n- name: ROGER_ELASTICSEARCH_HOST\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-elastic-config\"\n key: host\n- name: ROGER_ELASTICSEARCH_PASSWORD\n valueFrom:\n secretKeyRef:\n name: \"{{ .Release.Name }}-elastic-secret\"\n key: password\n- name: ROGER_ELASTICSEARCH_USERNAME\n valueFrom:\n secretKeyRef:\n name: \"{{ .Release.Name }}-elastic-secret\"\n key: username\n- name: ROGER_REDISGRAPH_HOST\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-redis-config\"\n key: host\n- name: ROGER_REDISGRAPH_GRAPH\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-redis-config\"\n key: graph\n- name: ROGER_REDISGRAPH_PASSWORD\n valueFrom:\n secretKeyRef:\n name: \"{{ .Release.Name }}-redis-secret\"\n key: password\n- name: ROGER_REDISGRAPH_PORT\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-redis-config\"\n key: port\n- name: ROGER_S3_ACCESS__KEY\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: s3_access_key\n- name: ROGER_S3_BUCKET\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: s3_bucket\n- name: ROGER_S3_HOST\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: s3_host\n- name: ROGER_S3_SECRET__KEY\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: s3_secret_key\n- name: ROGER_KGX_DATA__SETS\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: kgx_data_sets\n- name: ROGER_INDEXING_NODE__TO__ELEMENT__QUERIES_ENABLED\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: node_to_queries_enabled\n- name: ROGER_INDEXING_ELEMENT__MAPPING\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: element_mappings\n- name: ROGER_ELASTICSEARCH_NBOOST__HOST\n value: nboost $ TODO compute this\n- name: ROGER_INDEXING_TRANQL__ENDPOINT\n valueFrom:\n configMapKeyRef:\n name: \"{{ .Release.Name }}-data-config\"\n key: tranql_endpoint\n- name: AIRFLOW__KUBERNETES_EXECUTOR__DELETE_WORKER_PODS\n value: \"FALSE\"\n- name: \"AIRFLOW__LOGGING__LOGGING_LEVEL\"\n value: \"DEBUG\"\n- name: \"AIRFLOW__LOGGING__BASE_LOG_FOLDER\"\n value: \"/opt/airflow/share/logs\"\n- name: \"AIRFLOW__WEBSERVER__APPLICATION_ROOT\"\n value: \"/airflow\"\n- name: ROGER_ELASTICSEARCH_SCHEME\n value: \"https\"\n- name: ROGER_ELASTICSEARCH_CA__PATH\n value: \"/opt/certs/es.crt\"\n"
airflow.images.airflow.repository	string	"containers.renci.org/helxplatform/airflow"
airflow.images.airflow.tag	string	"3.1.1"
airflow.postgresql.auth.password	string	"postgres"
airflow.postgresql.auth.postgresPassword	string	"postgres"
airflow.postgresql.image.registry	string	"containers.renci.org"
airflow.postgresql.image.repository	string	"vgl/postgres-alpine"
airflow.postgresql.image.tag	string	"18.0.1"
airflow.redis.enabled	bool	false
airflow.redis.serviceAccount.create	bool	false
airflow.scheduler.env[0].name	string	"AIRFLOW__CORE__EXECUTOR"
airflow.scheduler.env[0].value	string	"KubernetesExecutor"
airflow.scheduler.livenessProbe.command[0]	string	"bash"
airflow.scheduler.livenessProbe.command[1]	string	"-c"
airflow.scheduler.livenessProbe.command[2]	string	"airflow jobs check --job-type SchedulerJob --hostname \"$(hostname)\"\n"
airflow.scheduler.logGroomerSidecar.enabled	bool	false
airflow.scheduler.resources.limits.cpu	int	1
airflow.scheduler.resources.limits.memory	string	"2Gi"
airflow.scheduler.startupProbe.command[0]	string	"bash"
airflow.scheduler.startupProbe.command[1]	string	"-c"
airflow.scheduler.startupProbe.command[2]	string	"airflow jobs check --job-type SchedulerJob --hostname \"$(hostname)\"\n"
airflow.statsd.enabled	bool	false
airflow.triggerer.enabled	bool	false
airflow.volumeMounts[0].mountPath	string	"/opt/airflow/share/data"
airflow.volumeMounts[0].name	string	"airflow-data"
airflow.volumeMounts[1].mountPath	string	"/opt/airflow/share/logs"
airflow.volumeMounts[1].name	string	"airflow-logs"
airflow.volumeMounts[2].mountPath	string	"/opt/certs/es.crt"
airflow.volumeMounts[2].name	string	"es-cert"
airflow.volumeMounts[2].subPath	string	"ca.crt"
airflow.volumes[0].name	string	"airflow-data"
airflow.volumes[0].persistentVolumeClaim.claimName	string	"search-data"
airflow.volumes[1].name	string	"es-cert"
airflow.volumes[1].secret.defaultMode	int	511
airflow.volumes[1].secret.secretName	string	"elasticsearch-master-certs"
airflow.volumes[2].name	string	"airflow-logs"
airflow.volumes[2].persistentVolumeClaim.claimName	string	"search-airflow-logs"
airflow.webServer.defaultUser.email	string	"admin@example.com"
airflow.webServer.defaultUser.enabled	bool	true
airflow.webServer.defaultUser.firstName	string	"admin"
airflow.webServer.defaultUser.lastName	string	"user"
airflow.webServer.defaultUser.password	string	"admin"
airflow.webServer.defaultUser.role	string	"Admin"
airflow.webServer.defaultUser.username	string	"admin"
airflow.webserverSecretKey	string	"your-secret-key-here"
airflow.workers.logGroomerSidecar.enabled	bool	false
airflow.workers.replicas	int	0
fullnameOverride	string	""
nameOverride	string	""