CARDS-2021: PREMs: Automatically delete submitted survey responses ol…

…der than one year

prems-resources/backend/pom.xml

@@ -66,5 +66,13 @@
       <artifactId>org.osgi.framework</artifactId>
       <version>1.9.0</version>
     </dependency>
+    <dependency>
+      <groupId>org.osgi</groupId>
+      <artifactId>org.osgi.service.component</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.osgi</groupId>
+      <artifactId>org.osgi.service.component.annotations</artifactId>
+    </dependency>
   </dependencies>
 </project>

prems-resources/backend/src/main/java/io/uhndata/cards/prems/patients/internal/SubmittedFormsCleanupScheduler.java

@@ -0,0 +1,93 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package io.uhndata.cards.prems.patients.internal;
+
+import org.apache.sling.api.resource.ResourceResolverFactory;
+import org.apache.sling.commons.scheduler.ScheduleOptions;
+import org.apache.sling.commons.scheduler.Scheduler;
+import org.osgi.service.component.ComponentContext;
+import org.osgi.service.component.annotations.Activate;
+import org.osgi.service.component.annotations.Component;
+import org.osgi.service.component.annotations.Reference;
+import org.osgi.service.metatype.annotations.AttributeDefinition;
+import org.osgi.service.metatype.annotations.Designate;
+import org.osgi.service.metatype.annotations.ObjectClassDefinition;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import io.uhndata.cards.resolverProvider.ThreadResourceResolverProvider;
+
+/**
+ * Automatically delete submitted survey responses older than max age.
+ *
+ * @version $Id$
+ * @since 0.9.6
+ */
+@Designate(ocd = SubmittedFormsCleanupScheduler.Config.class, factory = true)
+@Component(immediate = true)
+public class SubmittedFormsCleanupScheduler
+{
+    /** Default log. */
+    private static final Logger LOGGER = LoggerFactory.getLogger(SubmittedFormsCleanupScheduler.class);
+
+    private static final String SCHEDULER_JOB_NAME = "SubmittedFormsCleanup";
+
+    /** Provides access to resources. */
+    @Reference
+    private ResourceResolverFactory resolverFactory;
+
+    /** For sharing the resource resolver with other services. */
+    @Reference
+    private ThreadResourceResolverProvider rrp;
+
+    /** The scheduler for rescheduling jobs. */
+    @Reference
+    private Scheduler scheduler;
+
+    @ObjectClassDefinition(name = "Submitted survey responses cleanup",
+        description = "Automatically delete submitted survey responses older than one max age")
+    public static @interface Config
+    {
+        /** Default value of how long the submissions can be kept in the database in days. */
+        int MAX_AGE = 365;
+
+        @AttributeDefinition(
+            name = "Max age of submitted survey responses",
+            description = "Days of how long submissions can be kept in the database")
+        int maxAgeDays() default MAX_AGE;
+    }
+
+    @Activate
+    private void activate(final Config config, final ComponentContext componentContext)
+    {
+        try {
+            // Every night at midnight
+            final ScheduleOptions options = this.scheduler.EXPR("0 0 0 * * ? *");
+            options.name(SCHEDULER_JOB_NAME);
+            options.canRunConcurrently(false);
+
+            final Runnable cleanupJob = new SubmittedFormsCleanupTask(this.resolverFactory, this.rrp,
+                config.maxAgeDays());
+            this.scheduler.schedule(cleanupJob, options);
+        } catch (final Exception e) {
+            LOGGER.error("UnsubmittedFormsCleanup failed to schedule: {}", e.getMessage(), e);
+        }
+    }
+}

prems-resources/backend/src/main/java/io/uhndata/cards/prems/patients/internal/SubmittedFormsCleanupTask.java

@@ -0,0 +1,123 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package io.uhndata.cards.prems.patients.internal;
+
+import java.time.ZonedDateTime;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.jcr.query.Query;
+
+import org.apache.sling.api.resource.LoginException;
+import org.apache.sling.api.resource.PersistenceException;
+import org.apache.sling.api.resource.Resource;
+import org.apache.sling.api.resource.ResourceResolver;
+import org.apache.sling.api.resource.ResourceResolverFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import io.uhndata.cards.resolverProvider.ThreadResourceResolverProvider;
+
+/**
+ * Periodically delete submitted survey responses older than max age.
+ *
+ * @version $Id$
+ * @since 0.9.6
+ */
+public class SubmittedFormsCleanupTask implements Runnable
+{
+
+    /** Default log. */
+    private static final Logger LOGGER = LoggerFactory.getLogger(SubmittedFormsCleanupTask.class);
+
+    /** Provides access to resources. */
+    private final ResourceResolverFactory resolverFactory;
+
+    /** For sharing the resource resolver with other services. */
+    private final ThreadResourceResolverProvider rrp;
+
+    private final int maxAgeDays;
+
+    /**
+     * @param resolverFactory a valid ResourceResolverFactory providing access to resources
+     * @param patientAccessConfiguration details on patient authentication for token lifetime purposes
+     * @param maxAgeDays OSGi config defines days of how long submissions can be kept in the database
+     */
+    SubmittedFormsCleanupTask(final ResourceResolverFactory resolverFactory, final ThreadResourceResolverProvider rrp,
+        final int maxAgeDays)
+    {
+        this.resolverFactory = resolverFactory;
+        this.rrp = rrp;
+        this.maxAgeDays = maxAgeDays;
+    }
+
+    @Override
+    public void run()
+    {
+        boolean mustPopResolver = false;
+        try (ResourceResolver resolver = this.resolverFactory
+            .getServiceResourceResolver(Map.of(ResourceResolverFactory.SUBSERVICE, "VisitFormsPreparation"))) {
+            this.rrp.push(resolver);
+            mustPopResolver = true;
+            // Gather the needed UUIDs to place in the query
+            final String visitInformationQuestionnaire =
+                (String) resolver.getResource("/Questionnaires/Visit information").getValueMap().get("jcr:uuid");
+            final String submitted = (String) resolver
+                .getResource("/Questionnaires/Visit information/surveys_submitted").getValueMap().get("jcr:uuid");
+
+            // Query:
+            final Iterator<Resource> resources = resolver.findResources(String.format(
+                // select the data forms
+                "select distinct dataForm.*"
+                    + "  from [cards:Form] as dataForm"
+                    // belonging to a visit
+                    + "  inner join [cards:Form] as visitInformation on visitInformation.subject = dataForm.subject"
+                    + "    inner join [cards:Answer] as submitted on isdescendantnode(submitted, visitInformation)"
+                    + " where"
+                    // link to the correct Visit Information questionnaire
+                    + "  visitInformation.questionnaire = '%1$s'"
+                    // the data form was last modified by the patient before the allowed timeframe
+                    + "  and dataForm.[jcr:lastModified] < '%2$s'"
+                    // the visit is submitted
+                    + "  and submitted.question = '%3$s'"
+                    + "  and submitted.value = 1"
+                    // exclude the Visit Information form itself
+                    + "  and dataForm.questionnaire <> '%1$s'",
+                visitInformationQuestionnaire, ZonedDateTime.now().minusDays(this.maxAgeDays), submitted),
+                Query.JCR_SQL2);
+            resources.forEachRemaining(form -> {
+                try {
+                    resolver.delete(form);
+                } catch (final PersistenceException e) {
+                    LOGGER.warn("Failed to delete expired survey form {}: {}", form.getPath(), e.getMessage());
+                }
+            });
+            resolver.commit();
+        } catch (final LoginException e) {
+            LOGGER.warn("Invalid setup, service rights not set up for the expired survey forms cleanup task");
+        } catch (final PersistenceException e) {
+            LOGGER.warn("Failed to delete expired survey responses forms: {}", e.getMessage());
+        } finally {
+            if (mustPopResolver) {
+                this.rrp.pop();
+            }
+        }
+    }
+}