Merge pull request #19 from nfdi4health/feat/dv-permalinks

feat: Permalinks in Dataverse

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

@@ -0,0 +1,47 @@
+-- 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
+
+CREATE OR REPLACE FUNCTION base36_encode(
+  IN digits bigint, IN min_width int = 0)
+RETURNS varchar AS $$
+DECLARE
+chars char[];
+    ret varchar;
+    val bigint;
+BEGIN
+    chars := ARRAY[
+      '0','1','2','3','4','5','6','7','8','9',
+      'A','B','C','D','E','F','G','H','I','J',
+      'K','L','M','N','O','P','Q','R','S','T',
+      'U','V','W','X','Y','Z'];
+    val := digits;
+    ret := '';
+    IF val < 0 THEN
+        val := val * -1;
+END IF;
+    WHILE val != 0 LOOP
+        ret := chars[(val % 36)+1] || ret;
+        val := val / 36;
+END LOOP;
+
+    IF min_width > 0 AND char_length(ret) < min_width THEN
+        ret := lpad(ret, min_width, '0');
+END IF;
+
+RETURN ret;
+END;
+$$ LANGUAGE plpgsql IMMUTABLE;
+
+
+CREATE OR REPLACE FUNCTION generateIdentifierFromStoredProcedure()
+RETURNS varchar AS $$
+DECLARE
+curr_time_msec bigint;
+    identifier varchar;
+BEGIN
+    curr_time_msec := extract(epoch from now())*1000;
+    identifier := base36_encode(curr_time_msec);
+RETURN identifier;
+END;
+$$ LANGUAGE plpgsql IMMUTABLE;

k8s/dataverse/persona/nfdi4health/init.sh

@@ -22,8 +22,8 @@ echo "# hide progress meter
 # fail script on server error
 --fail-with-body" > ~/.curlrc
 
-echo "Setting DOI provider to FAKE"
-curl -s -H "X-Dataverse-key:$API_TOKEN" -X PUT -d FAKE $DATAVERSE_URL/api/admin/settings/:DoiProvider
+echo "Configuring PID permalink generator function"
+PGPASSWORD=$DATAVERSE_DB_PASSWORD psql -h $DATAVERSE_DB_HOST -U $DATAVERSE_DB_USER < /scripts/bootstrap/nfdi4health/generate-permalink.sql
 echo
 
 echo "Setting superuser status"

k8s/dataverse/templates/dataverse-baker.yaml

@@ -37,6 +37,18 @@ spec:
               value: "/roles"
             - name: USERS_PATH
               value: "/users"
+            - name: DATAVERSE_DB_HOST
+              value: "{{ .Release.Name }}-dataverse-postgres-pooler"
+            - name: DATAVERSE_DB_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: dataverse.{{ .Release.Name }}-dataverse-postgres.credentials.postgresql.acid.zalan.do
+                  key: password
+            - name: DATAVERSE_DB_USER
+              valueFrom:
+                secretKeyRef:
+                  name: dataverse.{{ .Release.Name }}-dataverse-postgres.credentials.postgresql.acid.zalan.do
+                  key: username
           volumeMounts:
             - name: script
               mountPath: "/scripts/bootstrap/nfdi4health"

k8s/dataverse/templates/dataverse-pod.yaml

@@ -95,7 +95,7 @@ spec:
             - name: DATAVERSE_DB_VALIDATION_CLASSNAME
               value: "org.glassfish.api.jdbc.validation.PostgresConnectionValidation"
             - name: DATAVERSE_PID_PROVIDERS
-              value: "fake"
+              value: "fake,csh,ctgov,euctr,per,isrctn,ctri,jprn,actrn,drks"
             - name: DATAVERSE_PID_DEFAULT_PROVIDER
               value: "fake"
             - name: DATAVERSE_PID_FAKE_TYPE
@@ -106,6 +106,104 @@ spec:
               value: "FK2/"
             - name: DATAVERSE_PID_FAKE_AUTHORITY
               value: "10.5072"
+            - 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: {{.Values.dataverse.pid.permalink.base_url}}
+            - name: DATAVERSE_PID_CSH_SEPARATOR
+              value: {{.Values.dataverse.pid.permalink.separator}}
+            - name: DATAVERSE_PID_CSH_IDENTIFIER_GENERATION_STYLE
+              value: "storedProcGenerated"
+            - name: DATAVERSE_PID_CTGOV_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_CTGOV_LABEL
+              value: "CT.gov Permalink Provider"
+            - name: DATAVERSE_PID_CTGOV_AUTHORITY
+              value: "NCT"
+            - name: DATAVERSE_PID_CTGOV_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_CTGOV_PERMALINK_BASE_URL
+              value: "https://clinicaltrials.gov/study/"
+            - name: DATAVERSE_PID_EUCTR_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_EUCTR_LABEL
+              value: "ICTRP EUCTR Permalink Provider"
+            - name: DATAVERSE_PID_EUCTR_AUTHORITY
+              value: "EUCTR"
+            - name: DATAVERSE_PID_EUCTR_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_EUCTR_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_PER_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_PER_LABEL
+              value: "ICTRP PER Permalink Provider"
+            - name: DATAVERSE_PID_PER_AUTHORITY
+              value: "PER"
+            - name: DATAVERSE_PID_PER_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_PER_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_PER_PERMALINK_SEPARATOR
+              value: "-"
+            - name: DATAVERSE_PID_ISRCTN_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_ISRCTN_LABEL
+              value: "ICTRP ISRCTN Permalink Provider"
+            - name: DATAVERSE_PID_ISRCTN_AUTHORITY
+              value: "ISRCTN"
+            - name: DATAVERSE_PID_ISRCTN_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_ISRCTN_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_CTRI_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_CTRI_LABEL
+              value: "ICTRP CTRI Permalink Provider"
+            - name: DATAVERSE_PID_CTRI_AUTHORITY
+              value: "CTRI"
+            - name: DATAVERSE_PID_CTRI_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_CTRI_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_CTRI_PERMALINK_SEPARATOR
+              value: "/"
+            - name: DATAVERSE_PID_JPRN_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_JPRN_LABEL
+              value: "ICTRP JPRN Permalink Provider"
+            - name: DATAVERSE_PID_JPRN_AUTHORITY
+              value: "JPRN-jRCT"
+            - name: DATAVERSE_PID_JPRN_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_JPRN_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_ACTRN_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_ACTRN_LABEL
+              value: "ICTRP ACTRN Permalink Provider"
+            - name: DATAVERSE_PID_ACTRN_AUTHORITY
+              value: "ACTRN"
+            - name: DATAVERSE_PID_ACTRN_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_ACTRN_PERMALINK_BASE_URL
+              value: "https://trialsearch.who.int/Trial2.aspx?TrialID="
+            - name: DATAVERSE_PID_DRKS_TYPE
+              value: "perma"
+            - name: DATAVERSE_PID_DRKS_LABEL
+              value: "DRKS Permalink Provider"
+            - name: DATAVERSE_PID_DRKS_AUTHORITY
+              value: "DRKS"
+            - name: DATAVERSE_PID_DRKS_SHOULDER
+              value: ""
+            - name: DATAVERSE_PID_DRKS_PERMALINK_BASE_URL
+              value: "https://drks.de/search/de/trial/"
             - name: DATAVERSE_DB_CONNECTION_VALIDATION_METHOD
               value: "custom-validation"
             # hack for https://dataverse.zulipchat.com/#narrow/stream/375812-containers/topic/MPC.20profile.20problem

k8s/dataverse/values.yaml

@@ -16,6 +16,12 @@ dataverse:
       memory: "4Gi"
     requests:
       memory: "1Gi"
+  pid:
+    permalink:
+      authority:
+      shoulder:
+      base_url:
+      separator:
 images:
   backend: ghcr.io/nfdi4health/csh-ui/dataverse:6.2
   configbaker: ghcr.io/nfdi4health/csh-ui/dataverse-baker:6.2