Document upload connector

.helmdocsignore

@@ -8,9 +8,6 @@ charts/radar-integration/
 charts/radar-jdbc-connector/
 charts/radar-output/
 charts/radar-s3-connector/
-charts/radar-upload-connect-backend/
-charts/radar-upload-connect-frontend/
-charts/radar-upload-source-connector/
 charts/s3-proxy/
 charts/smtp/
 charts/velero/

charts/management-portal/README.md

@@ -61,7 +61,7 @@ A Helm chart for RADAR-Base Management Portal
 | managementportal.common_privacy_policy_url | string | `"http://info.thehyve.nl/radar-cns-privacy-policy"` | Override with a publicly resolvable url of the privacy-policy url for your set-up. This can be overridden on a project basis as well. |
 | managementportal.oauth_checking_key_aliases_0 | string | `"radarbase-managementportal-ec"` | Keystore alias to sign JWT tokens from Management Portal |
 | managementportal.oauth_checking_key_aliases_1 | string | `"selfsigned"` | Keystore alias to sign JWT tokens from Management Portal |
-| managementportal.frontend_client_secret | string | `"xxx"` | OAuth Client secret of the Management Portal frontend application |
+| managementportal.frontend_client_secret | string | `"xxx"` | OAuth2 Client secret of the Management Portal frontend application |
 | managementportal.common_admin_password | string | `"xxx"` | Admin password of the default admin user created by the system |
 | smtp.enabled | bool | `false` | set to true, if SMTP server should be enabled. Required to be true for production setup |
 | smtp.host | string | `"smtp"` | Hostname of the SMTP server |
@@ -71,7 +71,7 @@ A Helm chart for RADAR-Base Management Portal
 | smtp.from | string | `"[email protected]"` | Email address which should be used to send activation emails |
 | smtp.starttls | bool | `false` | set to true,if ttls should be enabled |
 | smtp.auth | bool | `true` | set to true, if the account should be authenticated before sending emails |
-| oauth_clients | object | check values.yaml | Oauth Client configuration |
+| oauth_clients | object | check values.yaml | OAuth2 Client configuration |
 
 ## OAuth Client Configuration
 List of OAuth client configurations supported by RADAR-base. Each client should be enabled separately, if relevant and used in the installation.

charts/management-portal/values.yaml

@@ -113,7 +113,7 @@ managementportal:
   oauth_checking_key_aliases_0: radarbase-managementportal-ec
   # -- Keystore alias to sign JWT tokens from Management Portal
   oauth_checking_key_aliases_1: selfsigned
-  # -- OAuth Client secret of the Management Portal frontend application
+  # -- OAuth2 Client secret of the Management Portal frontend application
   frontend_client_secret: xxx
   # -- Admin password of the default admin user created by the system
   common_admin_password: xxx
@@ -137,7 +137,7 @@ smtp:
   # -- set to true, if the account should be authenticated before sending emails
   auth: true
 
-# -- Oauth Client configuration
+# -- OAuth2 Client configuration
 # @default -- check values.yaml
 oauth_clients:
   pRMT:

charts/radar-rest-sources-backend/README.md

@@ -55,7 +55,7 @@ A Helm chart for the backend application of RADAR-base Rest Sources Authorizer
 | postgres.ssl.enabled | bool | `false` | set to true of the connecting to postgres using SSL |
 | postgres.ssl.keystorepassword | string | `"keystorepassword"` |  |
 | managementportal_host | string | `"management-portal"` | hostname of the Management Portal |
-| client_secret | string | `"secret"` | OAuth client secret of the radar-rest-sources-backend client from Management Portal |
+| client_secret | string | `"secret"` | OAuth2 client secret of the radar-rest-sources-backend client from Management Portal |
 | restSourceClients.fitbit.enable | bool | `false` | set to true, if Fitbit client should be used |
 | restSourceClients.fitbit.sourceType | string | `"FitBit"` | Type of the data sources |
 | restSourceClients.fitbit.authorizationEndpoint | string | `"https://www.fitbit.com/oauth2/authorize"` | Authorization endpoint for Fitbit authentication and authorization |

charts/radar-rest-sources-backend/templates/configmap.yaml

@@ -20,9 +20,9 @@ data:
     auth:
       # Management Portal URL
       managementPortalUrl: http://{{ .Values.managementportal_host }}:8080/managementportal/
-      # OAuth2 Client id of more-promasys-sync application
+      # OAuth2 Client id of rest sources authorizer backend
       clientId: radar_rest_sources_auth_backend
-      # OAuth2 Client Secret of more_promasys_sync_client client
+      # OAuth2 Client Secret of rest sources authorizer backend client
       clientSecret: {{ .Values.client_secret }}
 
     database:

charts/radar-rest-sources-backend/values.yaml

@@ -93,7 +93,7 @@ postgres:
 # -- hostname of the Management Portal
 managementportal_host: management-portal
 
-# -- OAuth client secret of the radar-rest-sources-backend client from Management Portal
+# -- OAuth2 client secret of the radar-rest-sources-backend client from Management Portal
 client_secret: secret
 
 restSourceClients:

charts/radar-upload-connect-backend/Chart.yaml

@@ -1,10 +1,16 @@
 apiVersion: v1
 appVersion: "0.5.9"
-description: A Helm chart for Kubernetes
+description: A Helm chart for RADAR-base upload connector backend application.
 name: radar-upload-connect-backend
 version: 0.1.1
+sources: ["https://github.com/RADAR-base/radar-upload-source-connector"]
+deprecated: false
+type: application
+home: "https://radar-base.org"
 maintainers:
   - email: [email protected]
     name: Keyvan Hedayati
   - email: [email protected]
     name: Joris Borgdorff
+  - email: [email protected]
+    name: Nivethika Mahasivam

charts/radar-upload-connect-backend/README.md

@@ -0,0 +1,55 @@
+
+
+# radar-upload-connect-backend
+
+![Version: 0.1.1](https://img.shields.io/badge/Version-0.1.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 0.5.9](https://img.shields.io/badge/AppVersion-0.5.9-informational?style=flat-square)
+
+A Helm chart for RADAR-base upload connector backend application.
+
+**Homepage:** <https://radar-base.org>
+
+## Maintainers
+
+| Name | Email | Url |
+| ---- | ------ | --- |
+| Keyvan Hedayati | [email protected] |  |
+| Joris Borgdorff | [email protected] |  |
+| Nivethika Mahasivam | [email protected] |  |
+
+## Source Code
+
+* <https://github.com/RADAR-base/radar-upload-source-connector>
+
+## Prerequisites
+* Kubernetes 1.17+
+* Kubectl 1.17+
+* Helm 3.1.0+
+
+## Values
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| replicaCount | int | `2` | Number of radar-upload-connect-backend replicas to deploy |
+| image.repository | string | `"radarbase/radar-upload-connect-backend"` | radar-upload-connect-backend image repository |
+| image.tag | string | `"0.5.9"` | radar-upload-connect-backend image tag (immutable tags are recommended) Overrides the image tag whose default is the chart appVersion. |
+| image.pullPolicy | string | `"IfNotPresent"` | radar-upload-connect-backend image pull policy |
+| nameOverride | string | `""` | String to partially override radar-upload-connect-backend.fullname template with a string (will prepend the release name) |
+| fullnameOverride | string | `""` | String to fully override radar-upload-connect-backend.fullname template with a string |
+| service.type | string | `"ClusterIP"` | Kubernetes Service type |
+| service.port | int | `8085` | radar-upload-connect-backend port |
+| ingress.enabled | bool | `true` | Enable ingress controller resource |
+| ingress.annotations | object | check values.yaml | Annotations that define default ingress class, certificate issuer and proxy settings |
+| ingress.path | string | `"/upload/api/?(.*)"` | Path within the url structure |
+| ingress.hosts | list | `["localhost"]` | Host to listen to requests to |
+| ingress.tls.secretName | string | `"radar-base-tls"` | Name of the secret containing TLS certificates |
+| resources.requests | object | `{"cpu":"100m","memory":"2Gi"}` | CPU/Memory resource requests |
+| nodeSelector | object | `{}` | Node labels for pod assignment |
+| tolerations | list | `[]` | Toleration labels for pod assignment |
+| affinity | object | `{}` | Affinity labels for pod assignment |
+| client_id | string | `"radar_upload_backend"` | OAuth2 client id of the upload connect backend application |
+| client_secret | string | `"secret"` | OAuth2 client secret of the upload connect backend |
+| postgres.host | string | `"radar-upload-postgresql-postgresql"` | Host name of the database to store uploaded data and metadata |
+| postgres.user | string | `"postgres"` | Database username |
+| postgres.password | string | `"password"` | Database password |
+| managementportal_host | string | `"management-portal"` | Host name of the management portal application |
+| serverName | string | `"localhost"` | Server name or domain name |

charts/radar-upload-connect-backend/README.md.gotmpl

@@ -0,0 +1,16 @@
+{{ template "chart.header" . }}
+{{ template "chart.deprecationWarning" . }}
+
+{{ template "chart.badgesSection" . }}
+
+{{ template "chart.description" . }}
+
+{{ template "chart.homepageLine" . }}
+
+{{ template "chart.maintainersSection" . }}
+
+{{ template "chart.sourcesSection" . }}
+
+{{ template "common.prerequisites" . }}
+
+{{ template "chart.valuesSection" . }}

charts/radar-upload-connect-backend/values.yaml

@@ -2,32 +2,47 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
+# -- Number of radar-upload-connect-backend replicas to deploy
 replicaCount: 2
 
 image:
+  # -- radar-upload-connect-backend image repository
   repository: radarbase/radar-upload-connect-backend
+  # -- radar-upload-connect-backend image tag (immutable tags are recommended)
+  # Overrides the image tag whose default is the chart appVersion.
   tag: 0.5.9
+  # -- radar-upload-connect-backend image pull policy
   pullPolicy: IfNotPresent
 
+# -- String to partially override radar-upload-connect-backend.fullname template with a string (will prepend the release name)
 nameOverride: ""
+# -- String to fully override radar-upload-connect-backend.fullname template with a string
 fullnameOverride: ""
 
 service:
+  # -- Kubernetes Service type
   type: ClusterIP
+  # -- radar-upload-connect-backend port
   port: 8085
 
 ingress:
+  # -- Enable ingress controller resource
   enabled: true
+  # -- Annotations that define default ingress class, certificate issuer and proxy settings
+  # @default -- check values.yaml
   annotations:
     kubernetes.io/ingress.class: nginx
     cert-manager.io/cluster-issuer: letsencrypt-prod
     nginx.ingress.kubernetes.io/rewrite-target: /$1
     nginx.ingress.kubernetes.io/proxy-body-size: 200m
     nginx.ingress.kubernetes.io/proxy-request-buffering: "off"
+  # -- Path within the url structure
   path: "/upload/api/?(.*)"
+  # -- Host to listen to requests to
   hosts:
     - localhost
   tls:
+    # -- Name of the secret containing TLS certificates
     secretName: radar-base-tls
 
 resources:
@@ -38,35 +53,33 @@ resources:
   # limits:
   #   cpu: 100m
   #   memory: 128Mi
+
+  # -- CPU/Memory resource requests
   requests:
     cpu: 100m
     memory: 2Gi
 
-persistence:
-  enabled: true
-  ## If defined, storageClassName: <storageClass>
-  ## If set to "-", storageClassName: "", which disables dynamic provisioning
-  ## If undefined (the default) or set to null, no storageClassName spec is
-  ##   set, choosing the default provisioner.  (gp2 on AWS, standard on
-  ##   GKE, AWS & OpenStack)
-  ##
-  # storageClass: "-"
-  ##
-  ## If you want to reuse an existing claim, you can pass the name of the PVC using
-  ## the existingClaim variable
-  existingClaim: radar-output
-
+# -- Node labels for pod assignment
 nodeSelector: {}
 
+# -- Toleration labels for pod assignment
 tolerations: []
 
+# -- Affinity labels for pod assignment
 affinity: {}
 
+# -- OAuth2 client id of the upload connect backend application
 client_id: radar_upload_backend
+# -- OAuth2 client secret of the upload connect backend
 client_secret: secret
 postgres:
+  # -- Host name of the database to store uploaded data and metadata
   host: radar-upload-postgresql-postgresql
+  # -- Database username
   user: postgres
+  # -- Database password
   password: password
+# -- Host name of the management portal application
 managementportal_host: management-portal
+# -- Server name or domain name
 serverName: localhost

charts/radar-upload-connect-frontend/Chart.yaml

@@ -1,10 +1,16 @@
 apiVersion: v1
 appVersion: "0.5.9"
-description: A Helm chart for Kubernetes
+description: A Helm chart for RADAR-base upload connector frontend application
 name: radar-upload-connect-frontend
 version: 0.1.1
+sources: ["https://github.com/RADAR-base/radar-upload-source-connector"]
+deprecated: false
+type: application
+home: "https://radar-base.org"
 maintainers:
   - email: [email protected]
     name: Keyvan Hedayati
   - email: [email protected]
     name: Joris Borgdorff
+  - email: [email protected]
+    name: Nivethika Mahasivam

charts/radar-upload-connect-frontend/README.md

@@ -0,0 +1,50 @@
+
+
+# radar-upload-connect-frontend
+
+![Version: 0.1.1](https://img.shields.io/badge/Version-0.1.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 0.5.9](https://img.shields.io/badge/AppVersion-0.5.9-informational?style=flat-square)
+
+A Helm chart for RADAR-base upload connector frontend application
+
+**Homepage:** <https://radar-base.org>
+
+## Maintainers
+
+| Name | Email | Url |
+| ---- | ------ | --- |
+| Keyvan Hedayati | [email protected] |  |
+| Joris Borgdorff | [email protected] |  |
+| Nivethika Mahasivam | [email protected] |  |
+
+## Source Code
+
+* <https://github.com/RADAR-base/radar-upload-source-connector>
+
+## Prerequisites
+* Kubernetes 1.17+
+* Kubectl 1.17+
+* Helm 3.1.0+
+
+## Values
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| replicaCount | int | `2` | Number of radar-upload-connect-frontend replicas to deploy |
+| image.repository | string | `"radarbase/radar-upload-connect-frontend"` | radar-upload-connect-frontend image repository |
+| image.tag | string | `"0.5.9"` | radar-upload-connect-frontend image tag (immutable tags are recommended) Overrides the image tag whose default is the chart appVersion. |
+| image.pullPolicy | string | `"IfNotPresent"` | radar-upload-connect-frontend image pull policy |
+| nameOverride | string | `""` | String to partially override radar-upload-connect-frontend.fullname template with a string (will prepend the release name) |
+| fullnameOverride | string | `""` | String to fully override radar-upload-connect-frontend.fullname template with a string |
+| service.type | string | `"ClusterIP"` | Kubernetes Service type |
+| service.port | int | `80` | radar-upload-connect-frontend port |
+| ingress.enabled | bool | `true` | Enable ingress controller resource |
+| ingress.annotations | object | check values.yaml | Annotations that define default ingress class, certificate issuer |
+| ingress.path | string | `"/upload/?(.*)"` | Path within the url structure |
+| ingress.hosts | list | `["localhost"]` | Host to listen to requests to |
+| ingress.tls.secretName | string | `"radar-base-tls"` | Name of the secret containing TLS certificates |
+| resources.requests | object | `{"cpu":"100m","memory":"128Mi"}` | CPU/Memory resource requests |
+| nodeSelector | object | `{}` | Node labels for pod assignment |
+| tolerations | list | `[]` | Toleration labels for pod assignment |
+| affinity | object | `{}` | Affinity labels for pod assignment |
+| server_name | string | `"localhost"` | Server name or domain name |
+| vue_app_client_id | string | `"radar_upload_frontend"` | OAuth2 client id of the upload connect frontend application |

charts/radar-upload-connect-frontend/README.md.gotmpl

@@ -0,0 +1,16 @@
+{{ template "chart.header" . }}
+{{ template "chart.deprecationWarning" . }}
+
+{{ template "chart.badgesSection" . }}
+
+{{ template "chart.description" . }}
+
+{{ template "chart.homepageLine" . }}
+
+{{ template "chart.maintainersSection" . }}
+
+{{ template "chart.sourcesSection" . }}
+
+{{ template "common.prerequisites" . }}
+
+{{ template "chart.valuesSection" . }}