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Docs/add helm chart install instructions (#127)
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aaperis authored Aug 14, 2024
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3 changes: 2 additions & 1 deletion aggregate-mappings.json
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Expand Up @@ -10,6 +10,7 @@
"sda/cmd/sync/sync.md": "docs/services/sync.md",
"sda-sftp-inbox/README.md": "docs/services/sftpinbox.md",
"./GETTINGSTARTED.md": "docs/guides/sda-dev-test-doc.md",
"sda/sda.md": "docs/services/sda.md"
"sda/sda.md": "docs/services/sda.md",
"charts/README.md": "docs/guides/charts-overview.md"
}
}
68 changes: 35 additions & 33 deletions docs/dictionary/wordlist.txt
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@@ -1,33 +1,10 @@
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
Expand All @@ -38,21 +15,23 @@ aissue
aj
amqp
amqps
apiVersion
apis
assigneesreencrypts
apiVersion
assignees
assigneesreencrypts
atitle
auth
automagically
autonumber
backend
backupArchive
backupRoutingKey
backuppubkey
backupRoutingKey
bbug
bigint
BIGINT
bigpicture
Bigpicture
blockquote
bmi
bugfix
Expand All @@ -61,10 +40,12 @@ cacert
ccacd
cega
cegamq
CENTERPREFIX
centralega
centralega's
cgktxeg
chacha
cheatsheet
checksumed
checksums
chunksize
Expand Down Expand Up @@ -92,8 +73,8 @@ datasetid
datasetids
datasets
dbPassword
dbUser
dbschema
dbUser
ddfqevq
decrypt
decryptable
Expand All @@ -104,14 +85,15 @@ decryptor
dev
discoverable
dns
DNS
doi
dsn
ebi
ecc
ega
ega's
egac
egaf
ega's
egas
endcoordinate
env
Expand All @@ -124,7 +106,9 @@ fileid
filepath
filesystem
fjddcmrvlawqmvrbly
FK
formsubmission
FS
funders
getarchived
getheader
Expand All @@ -138,6 +122,7 @@ golangci
gopath
gradle
helpdesk
HOSTKEY
hostname
howto
href
Expand All @@ -146,6 +131,7 @@ https
ietf
img
incrementing
INGESTROUTING
init
initd
initdb
Expand All @@ -161,11 +147,12 @@ jwk
jwt
jwtKey
jwtPub
jwtSecret
jwtpubeyurl
jwtpubkeypath
jwtpubkeyurl
JWTPUBKEYURL
jwts
jwtSecret
jwttoken
keyfile
keypair
Expand All @@ -181,13 +168,15 @@ localmq
logstash
makefile
mapfilestodataset
MAPPINGROUTING
markcompleted
markready
matchLabels
microservice
microservices
migratedb
mina
Mina's
minio
miniostorage
misspelled words:
Expand All @@ -206,10 +195,12 @@ namespaceSelector
nbis
neic
neicnordic
NetworkPolicy
nginx
nodeport
notls
nss
NSS
oidc
ol
oldpath
Expand All @@ -218,24 +209,29 @@ openid
openjdk
openshift
openssl
orch
orchestrator
orgs
ou
pacx
pem
PEMKEYPASS
PEMKEYPATH
PGDATA
pgvolume
phenome
pkcs
png
podSelector
podman
podSelector
policyTypes
posix
postgres
postgresAdminPassword
postgresql
pre
prefetchcount
PREFETCHCOUNT
prepended
programmatically
publickey
Expand All @@ -249,10 +245,11 @@ receival
recive
recommned
reencrypt
reencrypts
reencrypted
reencrypting
reencrypts
registerfile
RegisterFile
repo
reqs
requesters
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schemas
sda
sda's
secretName
secretkey
secretName
sequenceDiagram
setaccessionid
SetAccessionID
setarchived
sftp
sftpinbox
sha
smth
somedir
speciffic
SPRINGFRAMEWORK
src
sshd
ssl
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svc
svg
syncapi
SYNCPUBKEYPATH
sysdevs
tada
TCP
testsuite
thumbsup
tls
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tsd
ttl
tz
UDP
ui
uio
unencrypted
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86 changes: 86 additions & 0 deletions docs/guides/charts-overview.md
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# 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.

- [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)

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).

## Usage

[Helm](https://helm.sh) must be installed to use the charts.
Please refer to Helm's [documentation](https://helm.sh/docs/) to get started.

With Helm properly installed, add the `neicnordic` Helm repository as follows:

```sh
helm repo add neicnordic https://neicnordic.github.io/sensitive-data-archive
helm repo update
```

You can then run

```sh
helm search repo neicnordic
```

to see the available charts.

## Installing the Charts

To install a chart with the release name `my-release`:

```sh
helm install my-release neicnordic/<chart-name>
```

To configure a Helm chart with your own values, you can copy the default `values.yaml` file from the chart to your local directory and modify it as needed, or using helm:

```sh
helm show values neicnordic/<chart-name> > <values-filename>.yaml
```

Then, you can install the chart with the following command:

```sh
helm install my-release -f <values-filename>.yaml neicnordic/<chart-name>
```

Example:

```sh
helm show values neicnordic/sda-svc > my-values.yaml
vi my-values.yaml
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:

```sh
helm delete my-release
```

The command removes all the Kubernetes components associated with the chart and deletes the release.

## System requirements

- kubernetes minimal version required for running the helm charts is `>= 1.25`
- helm minimal version required for running the charts is `>=3.5`
29 changes: 8 additions & 21 deletions docs/guides/deploy-k8s.md
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Expand Up @@ -23,25 +23,10 @@ The services could be divided into two trust boundaries

The innermost trust zone contains the database and the archive, which be can accessed only from internal cluster.

## Charts overview

### sda-db - Database component for Sensitive Data Archive (SDA) installation

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 - RabbitMQ component for Sensitive Data Archive (SDA) installation

This chart deploys a pre-configured message broker ([RabbitMQ](https://www.rabbitmq.com/)) designed to work [European Genome-Phenome Archive](https://ega-archive.org/) federated messaging interface between `CentralEGA` and Local/Federated EGAs.

### sda-svc - Components for Sensitive Data Archive (SDA) installation

This chart deploys the service components needed to operate the Sensitive Data Archive solution for running a Federated EGA node.
The charts may include additional service components that might be beneficial for administrative operations or extending the Sensitive Data Archive solutions to facilitate other use cases.

## System requirements

- kubernetes minimal version required for running the helm charts is `>= 1.25`
- helm minimal version required for running the charts is `>=3.5`
{%
include-markdown "./charts-overview.md"
start="# Sensitive Data Archive Helm Charts"
%}

### Resource estimation

Expand All @@ -66,13 +51,15 @@ The table below reflects the minimum required resources to run the services in t
| sftpinbox | 100m | 128Mi | - |
| doa | 100m | 128Mi | - |

Here, minimal lists of variables requiring configuration, in addition to the defaults, are provided in the respective `values.yml` file for each of the Helm charts.
## Chart configuration

Here we provide minimal lists of variables that require configuration in addition to the defaults, so as to achieve a working deployment of the `sensitive data archive`. These variables can be set in the respective `values.yml` file for each of the Helm charts:

- [SDA services](#sda-services-chart)
- [RabbitMQ](#rabbitmq-chart)
- [SDA Database](#database-chart)

in order to achieve a working deployment of the `sensitive data archive`. In the following it is assumed that a *federated* setup is being deployed.
In what follows it is assumed that a [*federated*](/docs/structure.md#federated-vs-stand-alone) setup is being deployed.

### SDA services chart

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