From: Oliver H. <o....@dk...> - 2023-08-25 11:47:02
|
Hi Petri, I followed the update instruction, chipster seems to run, but two questions remain: 1) I added > image: > tag: v4.7.2 to ~/values.yaml Should this be removed after successful update again? Or should it stay there? 2) There seem to be 3 remnants from the old version (top 3 of below list): > Every 2.0s: kubectl get pod > > NAME READY STATUS > RESTARTS AGE > type-service-7ff4944dd6-zzdrl 0/1 ContainerStatusUnknown 7 > (33m ago) 21d > toolbox-86f7994cf9-wl6lc 0/1 Error 12 > (33m ago) 129d > backup-77c55fc4df-7ccl4 0/1 Error > 11 129d > chipster-session-db-postgresql-0 1/1 Running > 0 27m > chipster-job-history-postgresql-0 1/1 Running > 0 27m > chipster-auth-postgresql-0 1/1 Running > 0 26m > auth-9d654f456-9h9x8 1/1 Running 3 > (22m ago) 26m > service-locator-57c4fd5486-5gptt 1/1 Running 4 > (21m ago) 26m > session-db-66996d7bf9-64l7m 1/1 Running 4 > (21m ago) 26m > toolbox-c88ccc85d-fr6wx 1/1 Running 4 > (21m ago) 26m > backup-dc7fdc458-v2vxh 1/1 Running 4 > (21m ago) 26m > file-storage-0 1/1 Running 4 > (21m ago) 22m > type-service-6c6db85655-bb69q 1/1 Running 4 > (21m ago) 26m > scheduler-66fb56bcd6-xkpm4 1/1 Running 5 > (21m ago) 26m > session-worker-6f49c987b6-5z6hp 1/1 Running 5 > (20m ago) 26m > job-history-689477cc4c-5tqmp 1/1 Running 5 > (21m ago) 26m > web-server-84f8784bc9-ksjjx 1/1 Running 5 > (20m ago) 26m > file-broker-7679bf556b-vp2vb 1/1 Running 5 > (20m ago) 26m Is there something left to do with them? Some further suggestions: 1) You linked to the #updates tag in the k3s/README.md document. For the new images one needs to jump ahead/up in the same document following the link in "If there is a newer Chipster container image version available", which is somehow confusing. My suggestion is: there should be a single "UPDATE" document which can be followed from top to down. The only jumps in there should be when skipping something not necessary and the jump should never be ahead/up but always downwards. 2) It isn't clear in which folder the update procedure has to be started. Where should I be, when I do the first step "git pull" ? Actually it is "~/git/chipster-openshift/k3s", I always have to explore it again, because last time I had to is months ago. 3) Add something about updating the Ubuntu system to the Update-Document. Currently we run Ubuntu 20.04.6 LTS on the chipster server. A 'do-release-upgrade' is shown at login, of course I hesitate to do this. Some information would be nice, if chipster is still considerung Ubuntu 20.04 as best operating system or if it is already safe to upgrade to a newer version. 4) Can I see any version information in the chipster webgui? Like, if a user wants to see the current version(s) of the system? I did a brief search for it and didn't found anything. It isn't that much important but somehow some kind of software standard, to expose version information to the user. I think there are several versions (chipster, chipster-tools,...) to be shown somewhere. Best regards, Oli Am 24.08.2023 um 10:35 schrieb Chipster: > Hi, > > Chipster v4.7.2 has been released. This version includes a small, but incompatible change in the Chipster Rest API, so this requires you to update the backend services and the web app at the same time. > > We have started to add version tags to our container images to avoid inadvertant changes in your Chipster. Please follow the update instructions inhttps://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates to start using these new tagged images in your installation. The instructions now also ask you to pull all images at once, which additionally makes sure that your installation won't depend on our image registry anymore after the installation. > > The container image repository has changed, but the update instructions will take care of this for you. The old Helm templates used the latest images in a image repository docker-registry.rahti.csc.fi/chipster-images/ . We didn't want to push the new images in the same repository, because it could have broken the current installations. From now own the images are released in a new repository docker-registry.rahti.csc.fi/chipster-images-release/ . We'll try to keep the old repository available until end of year 2023. Let us know if you have problems in the update procedure so that we can try to sort them out before this. > > When testing the update procedure, my ingress refused any new connections until Ubuntu was rebooted. I don't know why this happened because we didn't change the K3s version or ingress configuration. Just don't be alarmed if this happens until you have rebooted Ubuntu. > > Technical details about the API change: > > Chipster has a few API endpoints, where the UserID is sent in the URL. For example the web app used to make a request to get the details of the User object from a URL /auth/users/jaas%2F<username> . Unfortunately the UserID (jaas%2F<username>) contains a forward slash character "/", which is also a separator in the URL path. Until now we tried to URL encode the slash to "%2F". This worked fine in the Kubernetes Ingress Controller Traefik, used in K3s. However, this prevented Chipster deployments in other Kubernetes releases, where NGINX Ingress Controller is used, because the NGINX (understandably) decoded the URL path already before the Chipster endpoint. We have now changed these API endpoints to pass the UserID in the query parameter instead: /auth/users?userId=jaas%2F<username> . Albeit breaking Rest API conventions, be hope this change makes Chipster easier to deploy in different environments. > > Best regards, > Petri / Chipster team > > _______________________________________________ > Chipster-tech mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-tech -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |