Update from neicnordic/sensitive-data-archive at 07:13 on 2024-08-19

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
@@ -168,15 +184,13 @@ localmq
 logstash
 makefile
 mapfilestodataset
-MAPPINGROUTING
 markcompleted
 markready
 matchLabels
 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
@@ -215,23 +227,19 @@ orgs
 ou
 pacx
 pem
-PEMKEYPASS
-PEMKEYPATH
-PGDATA
 pgvolume
 phenome
 pkcs
 png
-podman
 podSelector
+podman
 policyTypes
 posix
 postgres
 postgresAdminPassword
 postgresql
 pre
 prefetchcount
-PREFETCHCOUNT
 prepended
 programmatically
 publickey
@@ -249,7 +257,6 @@ reencrypted
 reencrypting
 reencrypts
 registerfile
-RegisterFile
 repo
 reqs
 requesters
@@ -261,19 +268,17 @@ samtools
 schemas
 sda
 sda's
-secretkey
 secretName
+secretkey
 sequenceDiagram
 setaccessionid
-SetAccessionID
 setarchived
 sftp
 sftpinbox
 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

docs/guides/charts-overview.md

@@ -1,24 +1,27 @@
 # Sensitive Data Archive Helm Charts
 
+<!-- Developer Comment: please keep in mind that contents below will appear as inline markdown sections in the NeIC SDA Handbook guide [Deploying on Kubernetes](https://neic-sda.readthedocs.io/en/latest/guides/deploy-k8s/) page. -->
+
 ## 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/<chart-name> > <values-filename>.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
@@ -62,17 +67,19 @@ helm install my-release -f <values-filename>.yaml neicnordic/<chart-name>
 
 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
 ```
 
 For quick reference to Helm's chart management capabilities see [here](https://helm.sh/docs/intro/cheatsheet/#chart-management).
 
 ## Uninstalling the Chart
 
-To uninstall/delete the `my-release` deployment:
+To uninstall the `my-release` deployment:
 
 ```sh
 helm delete my-release