Merge pull request #10 from nfdi4health/feat/dataverse6-1

feat(k8s.dataverse): Upgrade to dataverse 6.1

k8s/dataverse/Chart.yaml

@@ -15,10 +15,10 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.3.4
+version: 0.3.6
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "5.13.0"
+appVersion: "6.1.0"

k8s/dataverse/README.md

@@ -1,25 +1,6 @@
 # Install dataverse
 `helm install my-dataverse ./dataverse`
 
-# Access dataverse via localhost port forwarding
-`export DATAVERSE_POD="my-dataverse-dataverse-0"`
-
-`kubectl port-forward pods/${DATAVERSE_POD} 8080:8080`
-# Configure custom schema
-## Update SOLR fields with custom metadata info
-The charts persona contains a valid solr schema which is used by default. 
-If you alter a MDS block you manually need to refresh the solr core.
-### Login into the solr helper container and execute the update 
-`export SOLR_POD="my-dataverse-dataverse-solr-0"`
-
-`kubectl exec -i -t $SOLR_POD --container dataverse-solr-config  -- /bin/sh`
-
-`curl "http://${DATAVERSE_HOSTNAME}:8080/api/admin/index/solr/schema" | /scripts/update-fields.sh /template/conf/schema.xml`
-
-`cp /template/conf/schema.xml /var/solr/data/collection1/schema.xml `
-
-`curl "http://localhost:8983/solr/admin/cores?action=RELOAD&core=collection1"`
-
 # Backup & Restore
 ## Restore database backup
 
@@ -74,8 +55,8 @@ Postgres is configured to automatically create and store a logical backup in S3.
 
 7. Configure and sync postgres secrets with k8s.
 
-   The default postgres deployment creates at least three k8s secrets. Since you just loaded a backup they are out of sync.
-   Either those secrets must be updated with the values of the backup or the  values within the db mut be updated.
+   The  postgres deployment creates at least three k8s secrets. Since you just loaded a backup they (k8s secret) are out of sync.
+   Either those k8s secrets must be updated with the values from the just loaded backup or the database must be adapted to the values of the k8s secrets
    We update the values within the db. First, we obtain list of accounts to update, then we obtain the passwords and update the db values.
 
    Get the list of accounts:

k8s/dataverse/persona/nfdi4health/init.sh

@@ -10,7 +10,7 @@ SELF_LOCATION=${BOOTSTRAP_DIR}/${PERSONA}/
 echo "SELF_LOCATION"
 echo $SELF_LOCATION
 
-echo "Running dev setup-all.sh (INSECURE MODE)"
+echo "Running base setup-all.sh (INSECURE MODE)"
 "${BOOTSTRAP_DIR}"/base/setup-all.sh --insecure -p=admin1 | tee /tmp/setup-all.sh.out
 API_TOKEN=$(grep apiToken "/tmp/setup-all.sh.out" | jq ".data.apiToken" | tr -d \")
 export API_TOKEN

k8s/dataverse/persona/nfdi4health/schema.xml

@@ -246,7 +246,7 @@
     <!-- SCHEMA-FIELDS::BEGIN -->
     <field name="accessToSources" type="text_en" multiValued="false" stored="true" indexed="true"/>
     <field name="actionsToMinimizeLoss" type="text_en" multiValued="false" stored="true" indexed="true"/>
-    <field name="alternativeTitle" type="text_en" multiValued="false" stored="true" indexed="true"/>
+    <field name="alternativeTitle" type="text_en" multiValued="true" stored="true" indexed="true"/>
     <field name="alternativeURL" type="text_en" multiValued="false" stored="true" indexed="true"/>
     <field name="astroFacility" type="text_en" multiValued="true" stored="true" indexed="true"/>
     <field name="astroInstrument" type="text_en" multiValued="true" stored="true" indexed="true"/>

k8s/dataverse/templates/NOTES.txt

@@ -2,21 +2,32 @@ Thank you for installing {{ .Chart.Name }}.
 
 Your release is named {{ .Release.Name }}.
 
-Here are some tasks to perform :)
+## Interact with the instance
 
-## Enable admin api via localhost port forwarding
-### Allow all API calls
 `kubectl port-forward pods/{{ .Release.Name }}-dataverse-0  8080:8080`
+Once the port forward is active you can interact with dataverse UI via http://localhost:8080 and via API.
+API request are treated by dataverse as they originate from localhost.
 
-`curl -X PUT -d allow http://localhost:8080/api/admin/settings/:BlockedApiPolicy`
 
 ## Update SOLR fields with custom metadata info
-Login into the solr helper container and execute the update
+The `schema.xml` file within the persona nfdi4health contains adaptions for the included custom metadata blocks.
+This means SOLR is configured for the personal out of the box! Once you alter a metadata blocks via the API,
+the change must be manually adapted to the solr configuration. The following snippet will walk you through the task:
+
+Connect to the solr helper container, and open a remote shell:
 `kubectl exec -i -t {{ .Release.Name }}-dataverse-solr-0 --container dataverse-solr-config  -- /bin/sh`
 
+In the shell you can invoke the following commands:
+
+Depending on your change it may be necessary to drop the complete index. You can use this call.
+`curl -X POST -H 'Content-Type: application/json' 'http://localhost:8983/solr/collection1/update?commit=true' -d '{ "delete": {"query":"*:*"} }'`
+
+Obtains the schema from dataverse and apply it to the default solr template
 `curl "http://${DATAVERSE_HOSTNAME}:8080/api/admin/index/solr/schema" | /scripts/update-fields.sh /template/conf/schema.xml`
 
+Copies the schema into the core
 `cp /template/conf/schema.xml /var/solr/data/collection1/schema.xml`
 
+Tell SOLR to reload the configuration.
 `curl "http://localhost:8983/solr/admin/cores?action=RELOAD&core=collection1"`
 

k8s/dataverse/templates/dataverse-baker.yaml

@@ -5,7 +5,7 @@ metadata:
   labels:
     app.kubernetes.io/name: dataverse
     app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-    app.kubernetes.io/version: "5.13"
+    app.kubernetes.io/version: {{ .Chart.AppVersion }}
     app.kubernetes.io/component: bootstrap
     app.kubernetes.io/part-of: dataverse
   annotations:
@@ -18,12 +18,12 @@ spec:
       labels:
         app.kubernetes.io/name: dataverse
         app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-        app.kubernetes.io/version: "5.13"
+        app.kubernetes.io/version: {{ .Chart.AppVersion }}
         app.kubernetes.io/component: bootstrap
         app.kubernetes.io/part-of: dataverse
     spec:
       containers:
-        - image:  gdcc/configbaker:alpha
+        - image: {{ .Values.images.configbaker}}
           name: dataverse-configbaker
           command: [ "bootstrap.sh", "-u", "http://{{ .Release.Name }}-dataverse-svc:8080","nfdi4health" ]
           env:

k8s/dataverse/templates/dataverse-pod.yaml

@@ -5,7 +5,7 @@ metadata:
   labels:
     app.kubernetes.io/name: dataverse
     app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-    app.kubernetes.io/version: "5.13"
+    app.kubernetes.io/version: {{ .Chart.AppVersion }}
     app.kubernetes.io/component: dataverse
     app.kubernetes.io/part-of: dataverse
 spec:
@@ -25,7 +25,7 @@ spec:
   selector:
     app.kubernetes.io/name: dataverse
     app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-    app.kubernetes.io/version: "5.13"
+    app.kubernetes.io/version: {{ .Chart.AppVersion }}
     app.kubernetes.io/component: dataverse
     app.kubernetes.io/part-of: dataverse
 ---
@@ -36,7 +36,7 @@ metadata:
   labels:
     app.kubernetes.io/name: dataverse
     app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-    app.kubernetes.io/version: "5.13"
+    app.kubernetes.io/version: {{ .Chart.AppVersion }}
     app.kubernetes.io/component: dataverse
     app.kubernetes.io/part-of: dataverse
 spec:
@@ -45,15 +45,15 @@ spec:
     matchLabels:
       app.kubernetes.io/name: dataverse
       app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-      app.kubernetes.io/version: "5.13"
+      app.kubernetes.io/version: {{ .Chart.AppVersion }}
       app.kubernetes.io/component: dataverse
       app.kubernetes.io/part-of: dataverse
   template:
     metadata:
       labels:
         app.kubernetes.io/name: dataverse
         app.kubernetes.io/instance: dataverse-{{ .Release.Name }}
-        app.kubernetes.io/version: "5.13"
+        app.kubernetes.io/version: {{ .Chart.AppVersion }}
         app.kubernetes.io/component: dataverse
         app.kubernetes.io/part-of: dataverse
     spec:

k8s/dataverse/templates/solr-config-map.yaml

@@ -5,7 +5,7 @@ metadata:
   labels:
     app.kubernetes.io/name: solr
     app.kubernetes.io/instance: solr-{{ .Release.Name }}
-    app.kubernetes.io/version: "8.11.2"
+    app.kubernetes.io/version: "9.5.0"
     app.kubernetes.io/component: solr
     app.kubernetes.io/part-of: dataverse
 data:

k8s/dataverse/templates/solr.yaml

@@ -10,7 +10,7 @@ spec:
   selector:
       app.kubernetes.io/name: solr
       app.kubernetes.io/instance: solr-{{ .Release.Name }}
-      app.kubernetes.io/version: "8.11.2"
+      app.kubernetes.io/version: "9.5.0"
       app.kubernetes.io/component: solr
       app.kubernetes.io/part-of: dataverse
 ---
@@ -21,7 +21,7 @@ metadata:
   labels:
     app.kubernetes.io/name: solr
     app.kubernetes.io/instance: solr-{{ .Release.Name }}
-    app.kubernetes.io/version: "8.11.2"
+    app.kubernetes.io/version: "9.5.0"
     app.kubernetes.io/component: solr
     app.kubernetes.io/part-of: dataverse
 spec:
@@ -38,7 +38,7 @@ metadata:
   labels:
     app.kubernetes.io/name: solr
     app.kubernetes.io/instance: solr-{{ .Release.Name }}
-    app.kubernetes.io/version: "8.11.2"
+    app.kubernetes.io/version: "9.5.0"
     app.kubernetes.io/component: solr
     app.kubernetes.io/part-of: dataverse
 spec:
@@ -55,7 +55,7 @@ metadata:
   labels:
     app.kubernetes.io/name: solr
     app.kubernetes.io/instance: solr-{{ .Release.Name }}
-    app.kubernetes.io/version: "8.11.2"
+    app.kubernetes.io/version: "9.5.0"
     app.kubernetes.io/component: solr
     app.kubernetes.io/part-of: dataverse
 spec:
@@ -64,22 +64,22 @@ spec:
     matchLabels:
       app.kubernetes.io/name: solr
       app.kubernetes.io/instance: solr-{{ .Release.Name }}
-      app.kubernetes.io/version: "8.11.2"
+      app.kubernetes.io/version: "9.5.0"
       app.kubernetes.io/component: solr
       app.kubernetes.io/part-of: dataverse
   template:
     metadata:
       labels:
         app.kubernetes.io/name: solr
         app.kubernetes.io/instance: solr-{{ .Release.Name }}
-        app.kubernetes.io/version: "8.11.2"
+        app.kubernetes.io/version: "9.5.0"
         app.kubernetes.io/component: solr
         app.kubernetes.io/part-of: dataverse
     spec:
       securityContext:
         fsGroup: 8983
       containers:
-      - image: gdcc/configbaker:unstable
+      - image: {{.Values.images.configbaker}}
         name: dataverse-solr-config
         env:
           - name: DATAVERSE_SOLR_HOST
@@ -97,7 +97,7 @@ spec:
           - mountPath: /schema/
             name: cfgmap
       - name: solr
-        image: solr:8.11.2
+        image: solr:9.5.0
         command: [ "/bin/bash", "-c" ]
         args: [ "sleep 30; precreate-core collection1 /solr-template; solr-foreground -Djetty.host=0.0.0.0" ]
         env:

k8s/dataverse/values.yaml

@@ -17,4 +17,5 @@ dataverse:
     requests:
       memory: "500Mi"
 images:
-  backend: gitlab.zbmed.de:5050/km/nfdi4health/registersearch/dataverse:a8a721be01ff4953061f1eb00337ef187bcf5c4f
+  backend: gdcc/dataverse:alpha
+  configbaker: gdcc/configbaker:alpha