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docs/deployment-docker-compose.md
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## TL;DR ## TL;DR
If you have [:simple-docker: Docker](https://docs.docker.com/engine/install/) already installed on your system, you can If you have [Docker](https://docs.docker.com/engine/install/) already installed on your system, you can install DBRepo with:
install DBRepo with:
```shell ```shell
curl -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/install.sh | sudo bash curl -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/install.sh | bash
``` ```
## Architecture ## Architecture
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docs/deployment-helm.md
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To install DBRepo in your existing cluster, download the sample [`values.yaml`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-deployment/-/raw/master/charts/dbrepo-core/values.yaml?inline=false) To install DBRepo in your existing cluster, download the sample [`values.yaml`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-deployment/-/raw/master/charts/dbrepo-core/values.yaml?inline=false)
for your deployment and update the variables `hostname` and `authAdminApiUrl` to your domain. for your deployment and update the variables `hostname` and `authAdminApiUrl` to your domain.
If you have [:simple-helm: Helm](https://helm.sh/docs/intro/install/) already installed on your system, you can If you have [Helm](https://helm.sh/docs/intro/install/) already installed on your system, you can
install DBRepo with: install DBRepo with:
```shell ```shell
...@@ -26,59 +26,3 @@ helm upgrade --install dbrepo \ ...@@ -26,59 +26,3 @@ helm upgrade --install dbrepo \
![Architecture Kubernetes Azure](images/architecture-core.svg) ![Architecture Kubernetes Azure](images/architecture-core.svg)
<figcaption>Architecture of the services on Kubernetes</figcaption> <figcaption>Architecture of the services on Kubernetes</figcaption>
</figure> </figure>
## Chart values
| Key | Type | Default | Description |
|---------------------------------|--------|------------------------------------|------------------------------------------------------------------------------------------------------------|
| `replicaCount` | int | `1` | Number of replicas (pods) to launch. |
| `nameOverride` | string | `""` | A name in place of the chart name for `app:` labels. |
| `fullnameOverride` | string | `""` | A name to substitute for the full names of resources. |
| `imagePullPolicy` | string | `Always` | Override for the image pull policy, e.g. `IfNotPresent` |
| `adminEmail` | string | `noreply@example.com` | E-mail address for OAI-PMH metadata. |
| `repositoryName` | string | `Database Repository` | Repository name for OAI-PMH metadata. |
| `hostname` | string | `example.com` | Domain name for the deployment, should not contain `https://` or any path. |
| `uiLogo` | string | `/logo.png` | Path to the logo, you can mount the file via a configmap or volume. |
| `uiIcon` | string | `/favicon.ico` | Path to the favicon, you can mount the file via a configmap or volume. |
| `uiVersion` | string | `latest` | Subtitle of the repository displayed in the UI. |
| `uiTitle` | string | `Database Repository` | Title of the repository displayed in the UI. |
| `uiKeycloakLoginUrl` | string | `/api/auth/` | Link to the authentication service login page. |
| `uiBrokerLoginUrl` | string | `/broker/` | Link to the broker service login page. |
| `uiForceSsl` | bool | `true` | Force SSL in the frontend on all resources and links. Disable this for insecure file uploads. |
| `uiUploadPath` | string | `/tmp/` | Path to upload files into the shared volume. |
| `authClientId` | string | `dbrepo-client` | Id of the client within keycloak that the backend services should use for communication with keycloak. |
| `authClientSecret` | string | `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG` | Secret of this client. This should be changed. |
| `authUsername` | string | `fda` | Authentication service admin username that the backend services should use. |
| `authPassword` | string | `fda` | Authentication service admin password that the backend services should use. |
| `authAdminApiUrl` | string | `https://example.com/api/auth` | Backend authentication URL that points to the keycloak instance. |
| `brokerUsername` | string | `broker` | Broker service admin username that the backend services should use. |
| `brokerPassword` | string | `broker` | Broker service admin password that the backend services should use. |
| `brokerEndpoint` | string | `http://broker-service` | Endpoint URL of the broker service. |
| `datacitePassword` | string | `""` | Password of a DataCite Fabrica user to mint DOIs (optional). |
| `datacitePrefix` | string | `""` | DOI prefix (optional). |
| `dataciteUrl` | string | `https://api.datacite.org` | DataCite Fabrica API endpoint URL (optional). |
| `dataciteUsername` | string | `""` | Username of a DataCite Fabrica user to mint DOIs (optional). |
| `metadataDbDatabase` | string | `fda` | Database name of the metadata database. |
| `metadataDbHost` | string | `metadata-db` | Hostname of the metadata database, this can be a domain name for e.g. managed database deployments. |
| `metadataDbJdbcExtraArgs` | string | `""` | Additional arguments for the JDBC protocol to e.g. enforce SSL with `?useSSL=true` |
| `metadataDbPassword` | string | `dbrepo` | Password of the root user that can access the metadata database. |
| `metadataDbUsername` | string | `root` | Username of the root user that can access the metadata database. |
| `metadataDbReplicationUsername` | string | `replicator` | Replication username. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `metadataDbReplicationPassword` | string | `replicator` | Replication password. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `authDb` | string | `keycloak` | Database name of the authentication service database. |
| `authDbHost` | string | `auth-db` | Hostname of the metadata database, this can be a domain name for e.g. managed database deployments. |
| `authDbType` | string | `mariadb` | JDBC database type for the authentication service (keycloak). |
| `authDbPassword` | string | `dbrepo` | Password of the root user that can access the authentication database. |
| `authDbUsername` | string | `root` | Username of the root user that can access the authentication database. |
| `authDbReplicationUsername` | string | `replicator` | Replication username. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `authDbReplicationPassword` | string | `replicator` | Replication password. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `dataDbPassword` | string | `dbrepo` | Password of the root user that can access the data database. |
| `dataDbUsername` | string | `root` | Username of the root user that can access the data database. |
| `dataDbReplicationUsername` | string | `replicator` | Replication username. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `dataDbReplicationPassword` | string | `replicator` | Replication password. Set to `""` if no replication pod should be started (e.g. in a managed environment). |
| `searchPassword` | string | `admin` | Password of the user that can read and write into the search database. |
| `searchUsername` | string | `admin` | Username of the user that can read and write into the search database. |
| `additionalConfigMaps` | string | `[]` | Array of additional config maps. Set to e.g. `[ name: my-config, data: [ key: value ] ]`. |
| `additionalSecrets` | string | `[]` | Array of additional secrets. Set to e.g. `[ name: my-secret, data: [ key: b64_enc_value ] ]`. |
| `premiumStorageClassName` | string | `""` | StorageClass name for the shared volume. Must have `ReadWriteMany` capabilities. |
docs/deployment-kubernetes-azure.md
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### Hardware ### Hardware
For this small cloud, test deployment any public cloud provider would suffice, we recommend a For this small cloud, test deployment any public cloud provider would suffice, we recommend a
small [:simple-microsoftazure: Kubernetes Service](https://azure.microsoft.com/en-us/products/kubernetes-service) small [Kubernetes Service](https://azure.microsoft.com/en-us/products/kubernetes-service)
with Kubernetes version *1.24.10* and node sizes *Standard_B4ms* with Kubernetes version *1.24.10* and node sizes *Standard_B4ms*
- 4 vCPU cores - 4 vCPU cores
...@@ -44,7 +44,7 @@ supports: ...@@ -44,7 +44,7 @@ supports:
2. Hardlinks (TUSd creates lockfiles during upload) 2. Hardlinks (TUSd creates lockfiles during upload)
You will need to use a *StorageClass* of either `managed-*` or `azureblob-*` (after enabling the You will need to use a *StorageClass* of either `managed-*` or `azureblob-*` (after enabling the
proprietary [:simple-microsoftazure: CSI driver for BLOB storage](https://learn.microsoft.com/en-us/azure/aks/azure-blob-csi?tabs=NFS#azure-blob-storage-csi-driver-features) proprietary [CSI driver for BLOB storage](https://learn.microsoft.com/en-us/azure/aks/azure-blob-csi?tabs=NFS#azure-blob-storage-csi-driver-features)
in your Kubernetes Cluster). in your Kubernetes Cluster).
We recommend to create We recommend to create
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docs/stylesheets/extra.css
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--md-primary-fg-color--dark: #00537c /* darken 10% */; --md-primary-fg-color--dark: #00537c /* darken 10% */;
} }
figure img.img-border {
border: 1px solid #b3b3b3;
}
.md-main .md-content a:not(.action-button), .md-main .md-content a:not(.action-button),
.md-main .md-content a:not(.action-button) { .md-main .md-content a:not(.action-button) {
color: var(--md-typeset-color); color: var(--md-typeset-color);
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docs/system-databases-search.md
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## Security ## Security
(none) 1. Change the default credentials in the [Search Database Dashboard](../system-other-search-dashboard) with the default
credentials `admin:admin` and navigate to your username on the top right and click "Reset password".
<figure markdown>
![Data ingest](images/opensearch-dashboards-reset-pw.png){ .img-border }
<figcaption>Reset the admin password in Opensearch Dashboards</figcaption>
</figure>
docs/system-other-search-dashboard.md
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!!! debug "Debug Information" !!! debug "Debug Information"
* Ports: 5601/tcp * Ports: 5601/tcp
* UI: `http://:5601/` * UI: `http://:5601/admin/dashboard/`
## Overview ## Overview
It provides a *graphical user interface* (GUI) for an administrator to interact with It provides a *graphical user interface* (GUI) for an administrator to interact with
the [Search Database](../system-databases-search). the [Search Database](../system-databases-search).
<figure markdown>
![Data ingest](images/opensearch-dashboards.png){ .img-border }
<figcaption>Opensearch Dashboards on first start</figcaption>
</figure>
## Limitations ## Limitations
(none) (none)
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docs/system-other-ui.md
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## Overview ## Overview
It provides a *graphical user interface* (GUI) for a researcher to interact with the database repository's API. It provides a *user interface* (UI) for a researcher to interact with the database repository's API.
<figure markdown>
![Data ingest](images/ui.png){ .img-border }
<figcaption>User Interface</figcaption>
</figure>
<figure markdown> <figure markdown>
![UI microservice architecture detailed](images/architecture-ui.png) ![UI microservice architecture detailed](images/architecture-ui.png)
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