Merge pull request #111 from DataONEorg/develop

3.0.1 release

README.md

@@ -1,5 +1,7 @@
 # DataONE Indexer
 
+Also see [RELEASE-NOTES.md](./RELEASE-NOTES.md)
+
 The DataONE Indexer is a system that processes index tasks created by other components. The DataONE
 Indexer comprises three main subsystems, each defined by its own helm subsystem chart:
 

RELEASE-NOTES.md

@@ -0,0 +1,19 @@
+# dataone-indexer Release Notes
+
+## dataone-indexer version 3.0.1 & helm chart version 1.0.1
+
+* Release date: 2024-07-08
+* helm chart version 1.0.1
+  * Change `.Values.idxworker.cn_url` to `.Values.global.d1ClientCnUrl`
+  * Get `fullname` from metacat chart or provide in values.yaml
+  * Add simple 'exec' liveness probe. Remove readiness probe
+* dataone-indexer version 3.0.1
+  * Bump rmq amqp client to 5.21.0
+  * Add healthcheck code
+  * Exit app if unrecoverable exception occurs when started from `main()` method
+
+## dataone-indexer version 3.0.0 & helm chart version 1.0.0
+
+* Release date: 2024-04-25
+* helm chart version 1.0.0 -- first release of helm chart
+* dataone-indexer version 3.0.0 -- first release of dataone-indexer

docker/Dockerfile

@@ -18,7 +18,8 @@ RUN apt update && apt -y install \
     nano
 
 #Add a user & group with id=1001 and name=d1indexer
-RUN groupadd -g 1000 d1indexer && useradd -u 1000 -g 1000 d1indexer
+RUN groupadd -g 1000 d1indexer && useradd -u 1000 -g 1000 d1indexer \
+    && touch ./livenessprobe
 
 # The most recently built jar file is copied from the maven build directory to this dir by maven, so that
 # it can be copied to the image.
@@ -28,6 +29,7 @@ COPY ./docker/entrypoint.sh .
 # Change the ownership of the jar and sh files
 RUN chown d1indexer dataone-index-worker-${TAG}-shaded.jar
 RUN chown d1indexer entrypoint.sh
+RUN chown d1indexer livenessprobe
 
 #Run Container as d1indexer
 USER 1000

helm/Chart.lock

@@ -6,4 +6,4 @@ dependencies:
   repository: https://charts.bitnami.com/bitnami
   version: 6.2.3
 digest: sha256:8a0c7f616956207f7a5161ec1f5f3b58c432b8c8051ad4ef927dacee81c52be9
-generated: "2022-10-26T16:58:14.484158-08:00"
+generated: "2024-05-27T16:09:36.080811-07:00"

helm/Chart.yaml

@@ -21,19 +21,19 @@ 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: 1.0.0
+version: 1.0.1
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "3.0.0"
+appVersion: "3.0.1"
 
 # Chart dependencies
 dependencies:
-  - name: rabbitmq      # rabbitmq version 3.10.5 is deployed by chart version 10.1.14
+  - name: rabbitmq
     repository: https://charts.bitnami.com/bitnami
-    version: 10.1.14
+    version: 10.1.14    # rabbitmq version 3.10.5 is deployed by chart version 10.1.14
     condition: rabbitmq.enabled, global.rabbitmq.enabled
   - name: solr
     repository: https://charts.bitnami.com/bitnami

helm/config/dataone-indexer.properties

@@ -29,7 +29,7 @@ index.thread.number={{ .Values.idxworker.pool_size }}
 
 dataone.indexing.performance.logging.enabled=false
 
-D1Client.CN_URL={{ .Values.idxworker.cn_url }}
+D1Client.CN_URL={{ .Values.global.d1ClientCnUrl }}
 
 index.resourcemap.namespace=http://www.w3.org/TR/rdf-syntax-grammar;
 {{- print "" }}http://www.openarchives.org/ore/terms

helm/templates/_helpers.tpl

@@ -61,6 +61,24 @@ Create the name of the service account to use
 {{- end }}
 {{- end }}
 
+{{/*
+Check to see if '.Values.global "dataone-indexer.enabled' is set to true in the top-level metacat
+chart. If so, we know we're running as a subchart, and can infer the 'metacat.fullname'.
+If we're not running as a sub-chart, then we need to read the user-provided value from
+.Values.idxworker.metacatK8sFullName
+*/}}
+{{- define "get.metacat.fullname" -}}
+{{- if (index .Values.global "dataone-indexer.enabled") }}
+{{- if contains "metacat" (lower .Release.Name) }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-metacat" .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- else }}
+{{- default "MISSING-idxworker.metacatK8sFullName-MISSING" .Values.idxworker.metacatK8sFullName }}
+{{- end }}
+{{- end }}
+
 {{/*
 set MN url
 If we're running as a subchart, can use direct access without needing to go through ingress/https;
@@ -71,20 +89,23 @@ If connecting to an instance outside the cluster, should use https;
 {{- define "idxworker.mn.url" -}}
 {{- $mn_url := .Values.idxworker.mn_url }}
 {{- if not $mn_url }}
-{{- $mn_url = printf "http://%s-hl:8080/%s/d1/mn" .Release.Name .Values.global.metacatAppContext }}
+{{- $fullname := (include "get.metacat.fullname" .) }}
+{{- $mn_url = printf "http://%s-hl:8080/%s/d1/mn" $fullname .Values.global.metacatAppContext }}
 {{- end }}
 {{- $mn_url }}
 {{- end }}
 
 {{/*
 set Claim Name of existing PVC to use (typically the volume that is shared with metacat)
 Either use the value set in .Values.persistence.claimName, or if blank, autopopulate with
-  {podname}-metacat-{releaseName}-0 (e.g. metacatbrooke-metacat-metacatbrooke-0)
+  {podname}-metacat-{fullName}-0 (e.g. metacatbrooke-metacat-metacatbrooke-metacat-0)
+  (see 'idxworker.fullname' for logic behind how a 'fullname' is defined)
 */}}
 {{- define "idxworker.shared.claimName" -}}
 {{- $claimName := .Values.persistence.claimName }}
 {{- if not $claimName }}
-{{- $claimName = printf "%s-metacat-%s-0" .Release.Name .Release.Name }}
+{{- $fullname := (include "get.metacat.fullname" .) }}
+{{- $claimName = printf "%s-metacat-%s-0" .Release.Name $fullname }}
 {{- end }}
 {{- $claimName }}
 {{- end }}

helm/templates/deployment.yaml

@@ -25,8 +25,7 @@ spec:
         {{- toYaml . | nindent 8 }}
       {{- end }}
       {{- if .Values.affinity }}
-      affinity: {{- include "idxhelpers.tplvalues.render" (dict "value" .Values.affinity "context"
-      $) | nindent 8 }}
+      affinity: {{- include "idxhelpers.tplvalues.render" (dict "value" .Values.affinity "context" $) | nindent 8 }}
       {{- end }}
       {{- if .Values.nodeSelector }}
       nodeSelector: {{- include "idxhelpers.tplvalues.render" (dict "value" .Values.nodeSelector "context" $) | nindent 8 }}
@@ -52,15 +51,14 @@ spec:
             {{- toYaml .Values.securityContext | nindent 12 }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
-          # livenessProbe:
-          #   httpGet:
-          #     path: /
-          #     port: http
-          # readinessProbe:
-          #   httpGet:
-          #     path: /
-          #     port: http
-          #     initialDelaySeconds:
+          livenessProbe:
+            exec:
+              command:
+                - /bin/sh
+                - -c
+                - test $(($(date +%s) - $(stat -c %Y /var/lib/dataone-indexer/livenessprobe))) -lt 20
+            initialDelaySeconds: 20
+            periodSeconds: 15
           resources:
             {{- toYaml .Values.resources | nindent 12 }}
           volumeMounts:
@@ -130,18 +128,6 @@ spec:
               | grep -c "<schema name=\"dataone") == 1 ]]; do
               echo waiting for Solr Schema to be accessible at http://{{ $solrHost }}:
               {{- $solrPort }}$URI; sleep 1; done;
-      {{- with .Values.nodeSelector }}
-      nodeSelector:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      {{- with .Values.affinity }}
-      affinity:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      {{- with .Values.tolerations }}
-      tolerations:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
       volumes:
         - name: {{ .Release.Name }}-config-volume
           configMap:

helm/values.yaml

@@ -4,6 +4,9 @@
 
 global:
   solrPort: &global-solr-port 8983
+
+  ## @param global.metacatAppContext The application context used by the metacat installation
+  ##
   metacatAppContext: metacat
 
   ## @param global.storageClass default name of the storageClass to use for PVs
@@ -21,6 +24,10 @@ global:
   ##
   ephemeralVolumeStorageClass: csi-cephfs-sc-ephemeral
 
+  ## @param global.d1ClientCnUrl URL of the CN
+  ##
+  d1ClientCnUrl: "https://cn.dataone.org/cn"
+
 
 ## @section Dataone-Indexer Application-Specific Properties
 
@@ -109,15 +116,20 @@ persistence:
 idxworker:
   debug: "FALSE"
 
+  ## @param idxworker.metacatK8sFullName ignored if deployed as subchart, else use metacat.fullname
+  ## If deployed as a subchart, metacatK8sFullName will be ignored, and metacat.fullname will be
+  ## retrieved automatically from the top-level metacat chart. If this not a subchart, set
+  ## metacatK8sFullName to reflect the k8s "fullname" of the metacat installation being indexed.
+  ## Note there is some tricky logic involved in deciding what the fullname should be - see
+  ## "idxworker.fullname" in templates/_helpers.tpl, as an example.
+  ##
+  metacatK8sFullName: ""
+
   ## @param idxworker.mn_url URL of the metacat instance that depends upon this indexer
   ## Leave this value unset (mn_url: "") to have it automatically populated
   ##
   mn_url: ""
 
-  ## @param idxworker.cn_url URL of the CN
-  ##
-  cn_url: "https://cn.dataone.org/cn"
-
   ## @param idxworker.solrHostname hostname of the solr service to use
   ## Leave unset (solrHostname: "") to automatically populate when using solr bitnami subchart
   ##

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.dataone</groupId>
     <artifactId>dataone-index-worker</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <packaging>jar</packaging>
     <name>dataone-index-worker</name>
     <url>http://maven.apache.org</url>
@@ -249,7 +249,7 @@
         <dependency>
             <groupId>com.rabbitmq</groupId>
             <artifactId>amqp-client</artifactId>
-            <version>5.14.2</version>
+            <version>5.21.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>

src/main/java/org/dataone/cn/indexer/IndexWorker.java

@@ -2,12 +2,18 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.attribute.FileTime;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
+import java.util.concurrent.ScheduledExecutorService;
 
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.xpath.XPathExpressionException;
@@ -93,21 +99,23 @@ public class IndexWorker {
     private String specifiedThreadNumberStr = null;
     private int specifiedThreadNumber = 0;
     private ExecutorService executor = null;
-
-
+
     /**
      * Commandline main for the IndexWorker to be started.
-     * @param args
-     * @throws TimeoutException 
-     * @throws IOException 
-     * @throws ServiceFailure 
+     * @param args (not used -- command line args)
      */
-    public static void main(String[] args) throws IOException, TimeoutException, ServiceFailure {
+    public static void main(String[] args) {
         logger.info("IndexWorker.main - Starting index worker...");
         String propertyFile = null;
         loadExternalPropertiesFile(propertyFile);
-        IndexWorker worker = new IndexWorker();
-        worker.start();
+        try {
+            IndexWorker worker = new IndexWorker();
+            worker.start();
+        } catch (Exception e) {
+            logger.fatal("IndexWorker.main() exiting due to fatal error: " + e.getMessage(), e);
+            System.exit(1);
+        }
+        startLivenessProbe();
     }
 
     /**
@@ -224,7 +232,7 @@ public IndexWorker(Boolean initialize) throws IOException, TimeoutException, Ser
             OntologyModelService.getInstance();
         }
     }
-    
+
     /**
      * Initialize the RabbitMQ service
      * @throws IOException 
@@ -357,7 +365,7 @@ public void run() {
          };
          boolean autoAck = false;
          rabbitMQchannel.basicConsume(INDEX_QUEUE_NAME, autoAck, consumer);
-         logger.info("IndexWorker.start - Calling basicConsume and waiting for the comming messages");
+         logger.info("IndexWorker.start - Calling basicConsume and waiting for the coming messages");
     }
 
     /**
@@ -474,6 +482,20 @@ private void indexOjbect(IndexQueueMessageParser parser, long deliveryTag, boole
     public void stop() throws IOException, TimeoutException {
         rabbitMQchannel.close();
         rabbitMQconnection.close();
-        logger.info("IndexWorker.stop - stop the index queue conection.");
+        logger.info("IndexWorker.stop - stop the index queue connection.");
+    }
+
+    private static void startLivenessProbe() {
+        ScheduledExecutorService scheduler = Executors.newScheduledThreadPool(1);
+        Path path = Paths.get("./livenessprobe");
+        Runnable task = () -> {
+            try {
+                Files.setLastModifiedTime(path, FileTime.fromMillis(System.currentTimeMillis()));
+            } catch (IOException e) {
+                logger.error("IndexWorker.startLivenessProbe - failed to update file: " + path, e);
+            }
+        };
+        scheduler.scheduleAtFixedRate(task, 0, 10, TimeUnit.SECONDS);
+        logger.info("IndexWorker.startLivenessProbe - livenessProbe started");
     }
 }