From 24781c9f429c8b8317368f6e79c5e6bfb7cb661a Mon Sep 17 00:00:00 2001 From: Github aggregate action Date: Mon, 19 Aug 2024 07:13:28 +0000 Subject: [PATCH] Update from neicnordic/sensitive-data-archive at 07:13 on 2024-08-19 --- docs/dictionary/wordlist.txt | 64 ++++++++++++++++++---------------- docs/guides/charts-overview.md | 15 +++++--- 2 files changed, 44 insertions(+), 35 deletions(-) diff --git a/docs/dictionary/wordlist.txt b/docs/dictionary/wordlist.txt index 7f15f23..2a874ae 100644 --- a/docs/dictionary/wordlist.txt +++ b/docs/dictionary/wordlist.txt @@ -1,10 +1,33 @@ +ACCESSIONROUTING +BIGINT +Bigpicture +CENTERPREFIX +DNS +FK +FS +HOSTKEY +INGESTROUTING +JWTPUBKEYURL +MAPPINGROUTING +Mina's +NSS +NetworkPolicy +PEMKEYPASS +PEMKEYPATH +PGDATA +PREFETCHCOUNT +RegisterFile +SPRINGFRAMEWORK +SYNCPUBKEYPATH +SetAccessionID +TCP +UDP aaf aai aaiconnectprofile abug accessionid accessionids -ACCESSIONROUTING accesskey ack'ed acked @@ -15,8 +38,8 @@ aissue aj amqp amqps -apis apiVersion +apis assignees assigneesreencrypts atitle @@ -25,13 +48,12 @@ automagically autonumber backend backupArchive -backuppubkey backupRoutingKey +backuppubkey bbug +bfac bigint -BIGINT bigpicture -Bigpicture blockquote bmi bugfix @@ -40,7 +62,6 @@ cacert ccacd cega cegamq -CENTERPREFIX centralega centralega's cgktxeg @@ -73,8 +94,8 @@ datasetid datasetids datasets dbPassword -dbschema dbUser +dbschema ddfqevq decrypt decryptable @@ -85,15 +106,15 @@ decryptor dev discoverable dns -DNS doi dsn ebi ecc +ef ega +ega's egac egaf -ega's egas endcoordinate env @@ -106,9 +127,7 @@ fileid filepath filesystem fjddcmrvlawqmvrbly -FK formsubmission -FS funders getarchived getheader @@ -122,7 +141,6 @@ golangci gopath gradle helpdesk -HOSTKEY hostname howto href @@ -131,7 +149,6 @@ https ietf img incrementing -INGESTROUTING init initd initdb @@ -147,12 +164,11 @@ jwk jwt jwtKey jwtPub +jwtSecret jwtpubeyurl jwtpubkeypath jwtpubkeyurl -JWTPUBKEYURL jwts -jwtSecret jwttoken keyfile keypair @@ -168,7 +184,6 @@ localmq logstash makefile mapfilestodataset -MAPPINGROUTING markcompleted markready matchLabels @@ -176,7 +191,6 @@ microservice microservices migratedb mina -Mina's minio miniostorage misspelled words: @@ -195,12 +209,10 @@ namespaceSelector nbis neic neicnordic -NetworkPolicy nginx nodeport notls nss -NSS oidc ol oldpath @@ -215,15 +227,12 @@ orgs ou pacx pem -PEMKEYPASS -PEMKEYPATH -PGDATA pgvolume phenome pkcs png -podman podSelector +podman policyTypes posix postgres @@ -231,7 +240,6 @@ postgresAdminPassword postgresql pre prefetchcount -PREFETCHCOUNT prepended programmatically publickey @@ -249,7 +257,6 @@ reencrypted reencrypting reencrypts registerfile -RegisterFile repo reqs requesters @@ -261,11 +268,10 @@ samtools schemas sda sda's -secretkey secretName +secretkey sequenceDiagram setaccessionid -SetAccessionID setarchived sftp sftpinbox @@ -273,7 +279,6 @@ sha smth somedir speciffic -SPRINGFRAMEWORK src sshd ssl @@ -286,10 +291,8 @@ submitters svc svg syncapi -SYNCPUBKEYPATH sysdevs tada -TCP testsuite thumbsup tls @@ -298,7 +301,6 @@ tryggve tsd ttl tz -UDP ui uio unencrypted diff --git a/docs/guides/charts-overview.md b/docs/guides/charts-overview.md index 057224f..2fd2b50 100644 --- a/docs/guides/charts-overview.md +++ b/docs/guides/charts-overview.md @@ -1,24 +1,27 @@ # Sensitive Data Archive Helm Charts + + ## Charts overview The `neicnordic` Helm repository contains the following charts (for configuration details click on the links below): - [sda-svc - SDA services](https://github.com/neicnordic/sensitive-data-archive/blob/main/charts/sda-svc/README.md) - This chart deploys the service components needed to operate the Sensitive Data Archive solution. The charts may include additional service components that might be beneficial for administrative operations or extending the Sensitive Data Archive solutions to facilitate different use cases. + This chart deploys the service components needed to operate the Sensitive Data Archive (SDA) solution. It may include additional service components that might be beneficial for administrative operations or extending the SDA solution to facilitate different use cases. - [sda-db - SDA database](https://github.com/neicnordic/sensitive-data-archive/blob/main/charts/sda-db/README.md) This chart deploys a pre-configured database ([PostgreSQL](https://www.postgresql.org/)) instance for Sensitive Data Archive, the database schemas are designed to adhere to [European Genome-Phenome Archive](https://ega-archive.org/) federated archiving model. -- [sda-mq - SDA Message broker](https://github.com/neicnordic/sensitive-data-archive/blob/main/charts/sda-mq/README.md) +- [sda-mq - SDA message broker](https://github.com/neicnordic/sensitive-data-archive/blob/main/charts/sda-mq/README.md) This chart deploys a pre-configured message broker ([RabbitMQ](https://www.rabbitmq.com/)) designed for [European Genome-Phenome Archive](https://ega-archive.org/) federated messaging between `CentralEGA` and Local/Federated EGAs but also configurable to support Standalone SDA deployments. - [sda-orch - SDA orchestrate service](https://github.com/neicnordic/sensitive-data-archive/blob/main/charts/sda-orch/README.md) This chart deploys an orchestration service for the Sensitive Data Archive solution. This is a helper service designed to curate the ingestion flow in an automated manner when the SDA solution is deployed and configured as standalone (non-federated). + **Note:** The `sda-orch` chart may be out of date and is thus not guaranteed to be functional. ## Usage @@ -54,6 +57,8 @@ To configure a Helm chart with your own values, you can copy the default `values helm show values neicnordic/ > .yaml ``` +**Note** that Kubernetes resources, such as secrets, may be required for a chart to function properly. All necessary resources should be created in the Kubernetes cluster before installing the chart. + Then, you can install the chart with the following command: ```sh @@ -62,9 +67,11 @@ helm install my-release -f .yaml neicnordic/ Example: +First create the secret containing the crypt4gh keypair and passphrase before the chart is deployed (see e.g. [here](https://github.com/neicnordic/sensitive-data-archive/blob/cc66756318bfac5fd92ef22f9763e69b42ed5c3c/.github/integration/scripts/charts/dependencies.sh#L17)). Then edit the `values.yaml` to your liking and install the chart: + ```sh helm show values neicnordic/sda-svc > my-values.yaml -vi my-values.yaml +vi my-values.yaml # modify with your own settings helm install my-release neicnordic/sda-svc -f my-values.yaml ``` @@ -72,7 +79,7 @@ For quick reference to Helm's chart management capabilities see [here](https://h ## Uninstalling the Chart -To uninstall/delete the `my-release` deployment: +To uninstall the `my-release` deployment: ```sh helm delete my-release