Merge pull request #34 from nfdi4health/feat/dv-permalinks

feat(k8s.dataverse): update Dataverse configuration for Permalinks

k8s/dataverse/Chart.yaml

@@ -15,7 +15,7 @@ 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: 0.8.0
+version: 0.8.1
 
 # 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

k8s/dataverse/persona/nfdi4health/generate-permalink.sql

@@ -1,47 +1,33 @@
--- A script for creating, through a database stored procedure, sequential
--- 8 character identifiers from a base36 representation of current timestamp.
--- Adapted from: https://guides.dataverse.org/en/latest/_downloads/772201110a1c1b429e7c3336b6e9d36d/identifier_from_timestamp.sql
+-- Adapted from: https://github.com/IQSS/dataverse/blob/a36db2d7df0d9976c00179b82f11cfb338a6cfc8/doc/sphinx-guides/source/_static/util/createsequence.sql
 
-CREATE OR REPLACE FUNCTION base36_encode(
-  IN digits bigint, IN min_width int = 0)
-RETURNS varchar AS $$
+DO $$
 DECLARE
-chars char[];
-    ret varchar;
-    val bigint;
+last_val bigint;
 BEGIN
-    chars := ARRAY[
-      '0','1','2','3','4','5','6','7','8','9',
-      'A','B','C','D','E','F','G','H','I','J',
-      'K','L','M','N','O','P','Q','R','S','T',
-      'U','V','W','X','Y','Z'];
-    val := digits;
-    ret := '';
-    IF val < 0 THEN
-        val := val * -1;
-END IF;
-    WHILE val != 0 LOOP
-        ret := chars[(val % 36)+1] || ret;
-        val := val / 36;
-END LOOP;
+    -- Get the last value of the existing sequence
+    SELECT last_value INTO last_val FROM dvobject_id_seq;
 
-    IF min_width > 0 AND char_length(ret) < min_width THEN
-        ret := lpad(ret, min_width, '0');
-END IF;
+    -- Create the new sequence with the desired start and min values
+    EXECUTE format('
+            CREATE SEQUENCE datasetidentifier_seq
+            INCREMENT BY 1
+            MINVALUE %s
+            MAXVALUE 9223372036854775807
+            CACHE 1
+        ', last_val + 1);
+END $$;
 
-RETURN ret;
-END;
-$$ LANGUAGE plpgsql IMMUTABLE;
+ALTER TABLE datasetidentifier_seq OWNER TO "dataverse";
 
+-- And now create a PostgreSQL FUNCTION, for JPA to
+-- access as a NamedStoredProcedure:
 
 CREATE OR REPLACE FUNCTION generateIdentifierFromStoredProcedure()
 RETURNS varchar AS $$
 DECLARE
-curr_time_msec bigint;
-    identifier varchar;
+identifier varchar;
 BEGIN
-    curr_time_msec := extract(epoch from now())*1000;
-    identifier := base36_encode(curr_time_msec);
+    identifier := nextval('datasetidentifier_seq')::varchar;
 RETURN identifier;
 END;
 $$ LANGUAGE plpgsql IMMUTABLE;

k8s/dataverse/persona/nfdi4health/init.sh

@@ -22,10 +22,6 @@ echo "# hide progress meter
 # fail script on server error
 --fail-with-body" > ~/.curlrc
 
-echo "Configuring PID permalink generator function"
-PGPASSWORD=$DATAVERSE_DB_PASSWORD psql -h $DATAVERSE_DB_HOST -U $DATAVERSE_DB_USER < /scripts/bootstrap/nfdi4health/generate-permalink.sql
-echo
-
 echo "Setting superuser status"
 curl -X PUT "${DATAVERSE_URL}/api/admin/superuser/dataverseAdmin" -d true
 echo
@@ -141,6 +137,12 @@ while IFS= read -r DATAVERSE; do
   fi
 done <<< "${DATAVERSES}"
 
+# This should be done after creating dataverses if we want a chance of keeping the database IDs and Permalink IDs of our
+# datasets in sync
+echo "Configuring PID permalink generator function"
+PGPASSWORD=$DATAVERSE_DB_PASSWORD psql -h $DATAVERSE_DB_HOST -U $DATAVERSE_DB_USER < /scripts/bootstrap/nfdi4health/generate-permalink.sql
+echo
+
 # Last step as existence of one block is the indicator for a complete bootstrapped installation
 echo "Load custom metadata blocks"
 #curl -X POST -H "Content-type: text/tab-separated-values" $DATAVERSE_HOST/api/admin/datasetfield/load --upload-file customMDS.tsv

k8s/dataverse/templates/dataverse-pod.yaml

@@ -97,26 +97,18 @@ spec:
             - name: DATAVERSE_PID_PROVIDERS
               value: "fake,csh,ctgov,euctr,per,isrctn,ctri,jprn,actrn,drks"
             - name: DATAVERSE_PID_DEFAULT_PROVIDER
-              value: "fake"
-            - name: DATAVERSE_PID_FAKE_TYPE
-              value: "FAKE"
-            - name: DATAVERSE_PID_FAKE_LABEL
-              value: "Fake DOI Provider"
-            - name: DATAVERSE_PID_FAKE_SHOULDER
-              value: "FK2/"
-            - name: DATAVERSE_PID_FAKE_AUTHORITY
-              value: "10.5072"
+              value: "csh"
             - name: DATAVERSE_PID_CSH_TYPE
               value: "perma"
             - name: DATAVERSE_PID_CSH_LABEL
               value: "Permalink Provider"
             - name: DATAVERSE_PID_CSH_AUTHORITY
               value: {{.Values.dataverse.pid.permalink.authority}}
             - name: DATAVERSE_PID_CSH_SHOULDER
-              value: {{.Values.dataverse.pid.permalink.shoulder}}
-            - name: DATAVERSE_PID_CSH_BASE_URL
+              value: ""
+            - name: DATAVERSE_PID_CSH_PERMALINK_BASE_URL
               value: {{.Values.dataverse.pid.permalink.base_url}}
-            - name: DATAVERSE_PID_CSH_SEPARATOR
+            - name: DATAVERSE_PID_CSH_PERMALINK_SEPARATOR
               value: {{.Values.dataverse.pid.permalink.separator | quote}}
             - name: DATAVERSE_PID_CSH_IDENTIFIER_GENERATION_STYLE
               value: "storedProcGenerated"