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11.0 11.0 5.0 1.27 MB

A collection of Helm charts

Home Page: https://chgl.github.io/charts

License: MIT License

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chart helm helm-charts kubernetes

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charts's Issues

Parsing error in ohdsi - postgresql chart

Hi @chgl ,
I tried to pull the latest chart and deploy. I get this error message:
Error: parse error at (ohdsi/charts/postgresql/charts/common/templates/_secrets.tpl:84): function "lookup" not defined

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Awaiting Schedule

These updates are awaiting their schedule. Click on a checkbox to get an update now.

chore(deps): update all non-major dependencies (actions/upload-artifact, common, docker.io/bitnami/postgresql, github/codeql-action, minio, postgresql, sigstore/cosign-installer)

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

chore(deps): update mcr.microsoft.com/mssql/server:2022-latest docker digest to c1aa8af

Detected dependencies

github-actions

.github/workflows/check-links.yaml

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

actions/cache v4.0.2@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9

lycheeverse/lychee-action v1.10.0@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621

micalevisk/last-issue-action v2.3.0@0d40124cc99ac8601c2516007f0c98ef3d27537b

peter-evans/create-issue-from-file v5.0.0@24452a72d85239eacf1468b0f1982a9f3fec4c94

ubuntu 22.04

.github/workflows/ci.yaml

step-security/harden-runner v2.9.1@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

actions/cache v4.0.2@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9

step-security/harden-runner v2.9.1@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

helm/chart-testing-action v2.6.1@e6669bcd63d7cb57cb4380c33043eebe5d111992

helm/kind-action v1.10.0@0025e74a8c7512023d06dc019c617aa3cf561fde

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

EndBug/add-and-commit v9.1.4@a94899bca583c204427a224a7af87c02f9b325d5

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

ubuntu 22.04

ubuntu 22.04

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

ubuntu 22.04

.github/workflows/mega-linter.yml

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

oxsecurity/megalinter v7.13.0@bacb5f8674e3730b904ca4d20c8bd477bc51b1a7

actions/upload-artifact v4.3.5@89ef406dd8d7e03cfd12d9e0a4a378f454709029

ubuntu 22.04

.github/workflows/release.yaml

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

helm/chart-releaser-action v1.6.0@a917fd15b20e8b64b94d9158ad54cd6345335584

sigstore/cosign-installer v3.5.0@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

ubuntu 22.04

.github/workflows/scorecards.yaml

actions/checkout v4.1.7@692973e3d937129bcbf40652eb9f2f61becf3332

ossf/scorecard-action v2.4.0@62b2cac7ed8198b15735ed49ab1e5cf35480ba46

actions/upload-artifact v4.3.5@89ef406dd8d7e03cfd12d9e0a4a378f454709029

github/codeql-action v3.25.15@afb54ba388a7dca6ecae48f608c4ff05ff4cc77a

helm-values

charts/fhir-server-exporter/values.yaml

ghcr.io/chgl/fhir-server-exporter v2.3.7@sha256:3a368d8e8ca496b3a5347c4a52e789806252c232efd38746a55fbc2780756ed7

docker.io/curlimages/curl 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4

charts/fhir-server/values.yaml

mcr.microsoft.com/healthcareapis/r4-fhir-server 4.0.218@sha256:d3f817db5215bd99df6e0285c1e7d295391622f0b0a4aa5723a2733c23cd6ab0

mcr.microsoft.com/mssql/server 2022-latest@sha256:c4369c38385eba011c10906dc8892425831275bb035d5ce69656da8e29de50d8

docker.io/curlimages/curl 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4

charts/magnifhir/values.yaml

ghcr.io/chgl/magnifhir v1.5.2@sha256:13f121613edd4e52051e864892fa532714c9ab935688c00fb9b772f502c413e9

docker.io/curlimages/curl 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4

charts/ohdsi/values.yaml

docker.io/ohdsi/webapi 2.14.0@sha256:582b59b186fde5936081c1df6e41cba53e45e112d5b4875ddfda1e4dee4b2981

docker.io/bitnami/postgresql 16.3.0-debian-12-r23@sha256:865e341baf49006e32b3e72254a15a81c939178cb9c48fcd9faf1c0ac4b49664

docker.io/ohdsi/atlas 2.14.1@sha256:bd095ed794a6619f877d72c13ecfc22c8bb8a863937392857866e4bd6015157f

docker.io/docker/whalesay latest@sha256:178598e51a26abbc958b8a2e48825c90bc22e641de3d31e18aaf55f3258ba93b

docker.io/ohdsi/broadsea-achilles sha-bccd396@sha256:a881063aff6200d0d368ec30eb633381465fb8aa15e7d7138b7d48b6256a6feb

docker.io/curlimages/curl 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4

charts/pathling-server/values.yaml

docker.io/aehrc/pathling 7.0.1@sha256:70177a4eb7a20a5edba7a4957ac6cd245c29e3c306e98c5de59fe2974c1f71b8

docker.io/curlimages/curl 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4

helmv3

charts/fhir-server-exporter/Chart.yaml

common 2.21.0

charts/fhir-server/Chart.yaml

common 2.21.0

charts/magnifhir/Chart.yaml

common 2.21.0

charts/ohdsi/Chart.yaml

postgresql 15.5.20

common 2.21.0

charts/pathling-server/Chart.yaml

minio 14.6.32

common 2.21.0

regex

.github/workflows/ci.yaml

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

.github/workflows/release.yaml

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

README.md

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

ghcr.io/chgl/kube-powertools v2.3.16@sha256:b6a3c4e90c464625993680560780f2888f6df75b6564066cc51aea7a67c67074

Check this box to trigger a request for Renovate to run again on this repository

[ohdsi] Note memory recommendations for webapi in values.yaml

2+ GB per OHDSI/WebAPI#1811 (comment)

Atlas error: Unable to connect to an instance of the WebAPI

[ohdsi] annotate the CDM init job to run as a post-install helm hook

The CDM init job should be annotated and run as a post-install helm hook: https://helm.sh/docs/topics/charts_hooks/#the-available-hooks

Error while creating cohort

I get following error while creating a cohort. Any suggestion on where the issue might be?

2021-10-29 22:21:24.229 ERROR http-nio-8080-exec-4 org.ohdsi.webapi.util.GenericExceptionMapper -  - java.lang.NoClassDefFoundError: org/graalvm/polyglot/PolyglotException
	at org.ohdsi.analysis.versioning.CdmVersionUtils.determineCdmCompatibility(CdmVersionUtils.java:27)
	at org.ohdsi.analysis.versioning.VersionedSerializer.serialize(VersionedSerializer.java:21)
	at org.ohdsi.analysis.versioning.VersionedSerializer.serialize(VersionedSerializer.java:9)
	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:292)
	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3697)
	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:3073)
	at org.ohdsi.analysis.Utils.serialize(Utils.java:172)
	at org.ohdsi.analysis.Utils.serialize(Utils.java:165)
	at org.ohdsi.webapi.service.CohortDefinitionService.createCohortDefinition(CohortDefinitionService.java:406)
	at org.ohdsi.webapi.service.CohortDefinitionService$$FastClassBySpringCGLIB$$3ea7ee83.invoke(<generated>)

Issue with Launching WebAPI using Helm Charts

Expected behavior:
Trying to launch the ohdsi-Webapi on a minikube cluster and following the steps that are outlined here:
https://github.com/chgl/charts/tree/master/charts/ohdsi

The installation and update were successful but neither the atlas or webapi endpoint are working. Opening the minikube dashboard and going to the pods shows that all 3 pods (ohdsi-atlas, ohdsi-postgresql, and ohdsi-webapi) have errored with the falling error message:

"Failed to pull image "busybox:1.32": rpc error: code = Unknown desc = Error response from daemon: Get https://registry-1.docker.io/v2/: dial tcp: lookup registry-1.docker.io on 192.168.64.1:53: read udp 192.168.64.2:44156->192.168.64.1:53: i/o timeout"

Have tried deleting and reinstalling using Helm along with reinstalling Docker but neither has made any change.

Actual behavior
Once helm install is run and the endpoints are given, the WebAPI and Atlas should be running

Steps to reproduce behavior
https://github.com/chgl/charts/tree/master/charts/ohdsi
Follow the steps outlined here

[fhir-server-exporter] Container fails to start in current chart version 1.0.7

Hi,

Just to note, with current chart version 1.0.7 the container crashes with

Failed to create CoreCLR, HRESULT: 0x80070008

We don't have this behavior in 1.0.6 and earlier. I suspect a bug in the .NET base image, maybe this is a temporary one.

Cheers!

webapi is not responding on startup

webapi and atlas pods are running but only atlas responds while webapi doesn't work (doing curl from a pod other than atlas and webapi). When I look at the logs in webapi it seems service has started (logs added later in the issue). How long does it take for webapi to start reponding (I have waited few minutes). Are there any suggestions on how to fix a non-responding webapi pod. Is this behavior expected behavior on startup?

WebAPI's tail logs

2021-06-21 15:32:19.128 INFO main org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainer -  - Tomcat started on port(s): 8080 (http)
2021-06-21 15:32:19.136 INFO main org.ohdsi.webapi.WebApi -  - Started WebApi in 22.833 seconds (JVM running for 23.702)
2021-06-21 15:42:19.147 INFO taskScheduler-2 org.ohdsi.webapi.executionengine.service.ScriptExecutionServiceImpl -  - Invalidating execution engine based analyses
2021-06-21 15:52:19.171 INFO taskScheduler-10 org.ohdsi.webapi.executionengine.service.ScriptExecutionServiceImpl -  - Invalidating execution engine based analyses
Jun 21, 2021 3:52:44 PM org.glassfish.jersey.server.ApplicationHandler bindProvidersAndResources
WARNING: Component of class interface org.ohdsi.webapi.service.IRAnalysisResource cannot be instantiated and will be ignored.
Jun 21, 2021 3:52:44 PM org.glassfish.jersey.internal.Errors logErrors
WARNING: The following warnings have been detected: WARNING: The (sub)resource method createAnalysis in org.ohdsi.webapi.service.IRAnalysisResource contains empty path annotation.
WARNING: The (sub)resource method getIRAnalysisList in org.ohdsi.webapi.service.IRAnalysisResource contains empty path annotation.
WARNING: The (sub)resource method list in org.ohdsi.webapi.feanalysis.FeAnalysisController contains empty path annotation.
WARNING: The (sub)resource method createAnalysis in org.ohdsi.webapi.feanalysis.FeAnalysisController contains empty path annotation.
WARNING: The (sub)resource method createConceptSet in org.ohdsi.webapi.service.ConceptSetService contains empty path annotation.
WARNING: The (sub)resource method getConceptSets in org.ohdsi.webapi.service.ConceptSetService contains empty path annotation.
WARNING: The (sub)resource method list in org.ohdsi.webapi.pathway.PathwayController contains empty path annotation.
WARNING: The (sub)resource method create in org.ohdsi.webapi.pathway.PathwayController contains empty path annotation.
WARNING: A HTTP GET method, public org.ohdsi.webapi.job.JobExecutionResource org.ohdsi.webapi.service.CDMResultsService.warmCache(java.lang.String,org.ohdsi.webapi.service.CDMResultsService), should not consume any entity.
WARNING: The (sub)resource method list in org.ohdsi.webapi.job.NotificationController contains empty path annotation.
WARNING: The (sub)resource method getInfo in org.ohdsi.webapi.info.InfoService contains empty path annotation.
WARNING: The (sub)resource method list in org.ohdsi.webapi.cohortcharacterization.CcController contains empty path annotation.
WARNING: The (sub)resource method create in org.ohdsi.webapi.cohortcharacterization.CcController contains empty path annotation.
WARNING: The (sub)resource method getCohortDefinitionList in org.ohdsi.webapi.service.CohortDefinitionService contains empty path annotation.
WARNING: The (sub)resource method createCohortDefinition in org.ohdsi.webapi.service.CohortDefinitionService contains empty path annotation.
WARNING: The (sub)resource method getPermissions in org.ohdsi.webapi.security.PermissionController contains empty path annotation.
WARNING: The (sub)resource method createJob in org.ohdsi.webapi.user.importer.UserImportJobController contains empty path annotation.
WARNING: The (sub)resource method listJobs in org.ohdsi.webapi.user.importer.UserImportJobController contains empty path annotation.
WARNING: The (sub)resource method getAnalysisList in org.ohdsi.webapi.estimation.EstimationController contains empty path annotation.
WARNING: The (sub)resource method createEstimation in org.ohdsi.webapi.estimation.EstimationController contains empty path annotation.
WARNING: The (sub)resource method getFeasibilityStudyList in org.ohdsi.webapi.service.FeasibilityService contains empty path annotation.
WARNING: The (sub)resource method createStudy in org.ohdsi.webapi.service.FeasibilityService contains empty path annotation.
WARNING: The (sub)resource method createSource in org.ohdsi.webapi.source.SourceController contains empty path annotation.
WARNING: The (sub)resource method createAnalysis in org.ohdsi.webapi.prediction.PredictionController contains empty path annotation.
WARNING: The (sub)resource method getAnalysisList in org.ohdsi.webapi.prediction.PredictionController contains empty path annotation.

[ohdsi] add out-of-the-box support for solr

https://github.com/bitnami/charts/tree/master/bitnami/solr

OHDSI/WebAPI#1091 (comment)

[ohdsi] make achilles cronjob history limit configurable

https://kubernetes.io/docs/reference/kubernetes-api/workload-resources/cron-job-v1/

successfulJobsHistoryLimit
failedJobsHistoryLimit

Action Required: Fix Renovate Configuration

There is an error with this repository's Renovate configuration that needs to be fixed. As a precaution, Renovate will stop PRs until it is resolved.

Location: .renovaterc.json
Error type: The renovate configuration file contains some invalid settings
Message: Invalid configuration option: packageRules[2].matchDepNames , packageRules[2]: Each packageRule must contain at least one match* or exclude* selector. Rule: {"matchDepNames ":["postgresql","docker.io/bitnami/postgresql","minio"],"extends":["schedule:monthly"]}

ohdsi - Postgresql - Issues deploying to K8s

Hi @chgl ,
As you mentioned, I am moving this topic from OHDSI/Broadsea#23

Two main issues that I saw in the Postgresql deployment:

No cpu limit specified in the values: and hence I got this message:
create Pod ohdsi-postgresql-0 in StatefulSet ohdsi-postgresql failed error: Pod "ohdsi-postgresql-0" is invalid: spec.containers[0].resources.requests: Invalid value: "250m": must be less than or equal to cpu limit

So I am trying to update the values to include this.

mkdir: cannot create directory ‘/bitnami/postgresql/data’: Permission denied
I am looking into this issue. Maybe I should create a PVC first and use that in the values.

I will update once I do these.

Thanks,

[fhir-server-exporter] interpret fhir server url and name as a template

allows setting values such as "{{ .Release.Name }}" to simplify configuration.

hard coded schema name when WebAPI comes up

Hi @chgl ,
I was working on the CDM init container and noticed one issue.

I am using the schema name webapi for storing all the webapi database objects and I am using cdm for storing the CDM data.

I have used the above two schema names in my values.yaml and also the webapi.db.schema is set to webapi.

However, I still see the webapi container crashing with the following error. It looks like it is looking at a schema named OHDSI by default.

I have these for the extraEnv in webapi:

  - name: "datasource.cdm.schema"
      value: "cdm"
    - name: "datasource.ohdsi.schema"
      value: "webapi"
    - name: "spring.jpa.properties.hibernate.default_schema"
      value: "webapi"
    - name: "spring.batch.repository.tableprefix"
      value: "webapi.BATCH_"
    - name: "flyway_schemas"
      value: "webapi"
    - name: "flyway.placeholders.ohdsiSchema"
      value: "webapi"

	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.base/java.lang.reflect.Method.invoke(Unknown Source)
	at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
	at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
	at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
	at org.springframework.boot.loader.WarLauncher.main(WarLauncher.java:59)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'flyway' defined in class path resource [org/ohdsi/webapi/FlywayConfig.class]: Invocation of init method failed; nested exception is org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateSqlException: 
Migration V1.0.0.1__schema-create_spring_batch.sql failed
---------------------------------------------------------
SQL State  : 3F000
Error Code : 0
Message    : ERROR: schema "ohdsi" does not exist
  Position: 14
Location   : db/migration/postgresql/V1.0.0.1__schema-create_spring_batch.sql (/var/lib/ohdsi/webapi/WEB-INF/classes/db/migration/postgresql/V1.0.0.1__schema-create_spring_batch.sql)
Line       : 1
Statement  : CREATE TABLE ohdsi.BATCH_JOB_INSTANCE  (
	JOB_INSTANCE_ID BIGINT  NOT NULL PRIMARY KEY ,
	VERSION BIGINT ,
	JOB_NAME VARCHAR(100) NOT NULL,
	JOB_KEY VARCHAR(32) NOT NULL,
	constraint JOB_INST_UN unique (JOB_NAME, JOB_KEY)
) 
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1630)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:297)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
	at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1139)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1067)
	at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
	at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
	... 26 more
Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateSqlException: 
Migration V1.0.0.1__schema-create_spring_batch.sql failed
---------------------------------------------------------
SQL State  : 3F000
Error Code : 0
Message    : ERROR: schema "ohdsi" does not exist
  Position: 14
Location   : db/migration/postgresql/V1.0.0.1__schema-create_spring_batch.sql (/var/lib/ohdsi/webapi/WEB-INF/classes/db/migration/postgresql/V1.0.0.1__schema-create_spring_batch.sql)

posgtgres user password for ohdsi chart

Hi @chgl ,
I was able to install both Atlas and WebAPI using a Postgres DB that I had provisioned outside of the chart.

Now, I am back to trying it via the chart.

I see that the postgesql pod and service are getting created. I am trying to to go into the pod and see the tables that have been created. I tried to do psql -U postgres

None of the passwords listed in the auto created secret(ohdsi-postgresql ) works
(postgresql-password: xxx==
postgresql-postgres-password: yyy==)

WebAPI is also not able to authenticate with the password defined in the secret.

Any idea what is missing ?
Thanks again for your tips and help.