Add healthcheck to our backend image

.github/workflows/reviewdog.yml

@@ -11,6 +11,7 @@ jobs:
         uses: reviewdog/action-shellcheck@v1
         with:
           github_token: ${{ secrets.github_token }}
+          reporter: github-pr-review
   # Use yamllint to lint yaml files
   yamllint:
     name: check / yamllint

add_healthcheck_config_to_server_xml.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+"""Script to modify a Tomcat server.xml file using Docker and plain text processing.
+
+This script fetches the server.xml file from a Docker container, adds a new
+HealthCheckValve element to the last Host in the XML, and saves the modified
+file locally.
+
+Make sure you have Docker installed and the necessary permissions to run it.
+
+Usage:
+    1. Adjust CONTAINER_TOMCAT_CONFIG_PATH, LOCAL_TOMCAT_CONFIG_PATH, and
+       BACKEND_IMAGE_TAG as needed.
+    2. Run the script.
+
+"""
+
+import subprocess
+import sys
+import os
+
+CONTAINER_TOMCAT_CONFIG_PATH = '/usr/local/tomcat/conf'
+LOCAL_TOMCAT_CONFIG_PATH = 'config/tomcat'
+BACKEND_IMAGE_TAG = os.getenv('BACKEND_IMAGE_TAG', 'dspace/dspace:dspace-7_x')
+
+CONTAINER_SERVER_XML = CONTAINER_TOMCAT_CONFIG_PATH + '/server.xml'
+LOCAL_SERVER_XML = LOCAL_TOMCAT_CONFIG_PATH + '/server.xml'
+
+# Indicate that we are fetching the server.xml file
+print("Fetching the server.xml file from the Docker container...")
+
+docker_command = [
+    'docker',
+    'run',
+    '--rm',
+    BACKEND_IMAGE_TAG,
+    'cat',
+    CONTAINER_SERVER_XML,
+]
+
+# Run the Docker command to fetch the server.xml file
+with subprocess.Popen(docker_command, cwd=LOCAL_TOMCAT_CONFIG_PATH, stdout=subprocess.PIPE,
+                      stderr=subprocess.PIPE) as process:
+    output, error = process.communicate()
+    if process.returncode != 0:
+        print("Error fetching the server.xml file:")
+        print("stdout:", output.decode('utf-8'))
+        print("stderr:", error.decode('utf-8'))
+        sys.exit(1)
+
+    # Write the fetched content to the local server.xml file
+    with open(LOCAL_SERVER_XML, 'wb') as local_file:
+        local_file.write(output)
+
+# Indicate that we are processing the server.xml file
+print("Processing the server.xml file...")
+
+# Identify the line number where we want to insert the new HealthCheckValve
+INSERT_LINE_NUMBER = None
+with open(LOCAL_SERVER_XML, 'r', encoding='utf-8') as xml_file:
+    lines = xml_file.readlines()
+    for i, line in enumerate(reversed(lines)):
+        if '</Host>' in line:
+            INSERT_LINE_NUMBER = len(lines) - i
+            break
+
+# Insert the new HealthCheckValve into the identified line
+if INSERT_LINE_NUMBER is not None:
+    lines.insert(INSERT_LINE_NUMBER,
+    '    <Valve className="org.apache.catalina.valves.HealthCheckValve"/>\n')
+
+# Write the modified content back to the local server.xml file
+with open(LOCAL_SERVER_XML, 'w', encoding='utf-8') as xml_file:
+    xml_file.writelines(lines)
+
+# Indicate success
+print("Modification complete. The modified server.xml file is saved locally.")
+
+sys.exit(0)

config/dspace/from_container/access-conditions.xml

@@ -0,0 +1,108 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans
+           http://www.springframework.org/schema/beans/spring-beans-2.5.xsd">
+
+	<bean id="uploadConfigurationDefault" class="org.dspace.submit.model.UploadConfiguration">
+		<property name="name" value="upload"/>
+		<property name="metadata" value="bitstream-metadata" />
+        <property name="options">
+            <list>
+                <ref bean="openAccess"/>
+                <ref bean="lease"/>
+                <ref bean="embargoed" />
+                <ref bean="administrator"/>
+                <!-- <ref bean="networkAdministration"/> -->
+            </list>
+        </property>
+    </bean>
+
+    <bean id="openAccess" class="org.dspace.submit.model.AccessConditionOption">
+        <property name="groupName" value="Anonymous"/>
+        <property name="name" value="openaccess"/>
+        <property name="hasStartDate" value="false"/>
+        <property name="hasEndDate" value="false"/>
+    </bean>
+    <bean id="lease" class="org.dspace.submit.model.AccessConditionOption">
+        <property name="groupName" value="Anonymous"/>
+        <property name="name" value="lease"/>
+        <property name="hasStartDate" value="false"/>
+        <property name="hasEndDate" value="true"/>
+        <property name="endDateLimit" value="+6MONTHS"/>
+    </bean>
+    <bean id="embargoed" class="org.dspace.submit.model.AccessConditionOption">
+        <property name="groupName" value="Anonymous"/>
+        <property name="name" value="embargo"/>
+        <property name="hasStartDate" value="true"/>
+        <property name="startDateLimit" value="+36MONTHS"/>
+        <property name="hasEndDate" value="false"/>
+    </bean>
+    <bean id="administrator" class="org.dspace.submit.model.AccessConditionOption">
+        <property name="groupName" value="Administrator"/>
+        <property name="name" value="administrator"/>
+        <property name="hasStartDate" value="false"/>
+        <property name="hasEndDate" value="false"/>
+    </bean>
+<!--     <bean id="networkAdministration" class="org.dspace.submit.model.AccessConditionOption">
+    	<property name="groupName" value="INSTITUTIONAL_NETWORK"/>
+        <property name="name" value="networkAdministration"/>
+        <property name="hasStartDate" value="false"/>
+        <property name="hasEndDate" value="false"/>
+    </bean> -->
+
+    <bean id="uploadConfigurationService" class="org.dspace.submit.model.UploadConfigurationService">
+        <property name="map">
+            <map>
+                <entry key="upload" value-ref="uploadConfigurationDefault" />
+            </map>
+        </property>
+    </bean>
+
+    <bean id="accessConditionConfigurationService" class="org.dspace.submit.model.AccessConditionConfigurationService" />
+
+    <bean id="accessConditionConfigurationDefault" class="org.dspace.submit.model.AccessConditionConfiguration">
+        <!-- This name must match the id of the step as defined in the item-submission.xml -->
+        <property name="name" value="itemAccessConditions"></property>
+        <property name="canChangeDiscoverable" value="true"></property>
+        <property name="options">
+            <list>
+                <ref bean="openAccess"/>
+                <ref bean="lease"/>
+                <ref bean="embargoed" />
+                <ref bean="administrator"/>
+            </list>
+        </property>
+    </bean>
+
+    <bean id="defaultBulkAccessConditionConfiguration"
+          class="org.dspace.app.bulkaccesscontrol.model.BulkAccessConditionConfiguration">
+        <property name="name" value="default"/>
+        <property name="itemAccessConditionOptions">
+            <list>
+                <ref bean="openAccess"/>
+                <ref bean="administrator"/>
+                <ref bean="embargoed" />
+                <ref bean="lease"/>
+            </list>
+        </property>
+        <property name="bitstreamAccessConditionOptions">
+            <list>
+                <ref bean="openAccess"/>
+                <ref bean="administrator"/>
+                <ref bean="embargoed" />
+                <ref bean="lease"/>
+            </list>
+        </property>
+    </bean>
+
+    <bean id="bulkAccessConditionConfigurationService"
+          class="org.dspace.app.bulkaccesscontrol.service.BulkAccessConditionConfigurationService">
+        <property name="bulkAccessConditionConfigurations">
+            <list>
+                <ref bean="defaultBulkAccessConditionConfiguration"/>
+            </list>
+        </property>
+    </bean>
+
+</beans>

config/dspace/from_container/bibtex-integration.xml

@@ -0,0 +1,63 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xmlns:context="http://www.springframework.org/schema/context"
+       xmlns:util="http://www.springframework.org/schema/util"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans
+           http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+           http://www.springframework.org/schema/context
+           http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
+       default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
+
+    <context:annotation-config/>
+    <!-- allows us to use spring annotations in beans -->
+
+    <util:map id="bibtexMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
+              value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
+        <description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
+            only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
+            what metadatafield is generated.
+        </description>
+        <entry key-ref="dcType" value-ref="bibtexTypeContrib" />
+        <entry key-ref="dcTitle" value-ref="bibtexTitleContrib" />
+        <entry key-ref="dcAuthors" value-ref="bibtexAuthorsContrib" />
+        <entry key-ref="dcJournal" value-ref="bibtexJournalContrib" />
+		<entry key-ref="dcIssued" value-ref="bibtexIssuedContrib" />
+		<entry key-ref="dcJissn" value-ref="bibtexJissnContrib" />    
+    </util:map>
+
+    <bean id="bibtexJissnContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+        <property name="field" ref="dcJissn"/>
+        <property name="key" value="ISSN" />
+    </bean>
+
+    <bean id="bibtexIssuedContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+        <property name="field" ref="dcIssued"/>
+        <property name="key" value="year" />
+    </bean>
+
+    <bean id="bibtexJournalContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+        <property name="field" ref="dcJournal"/>
+        <property name="key" value="journal" />
+    </bean>
+
+    <bean id="bibtexAuthorsContrib" class="org.dspace.importer.external.metadatamapping.contributor.SplitMetadataContributor">
+        <constructor-arg name="innerContributor">
+            <bean class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+                <property name="field" ref="dcAuthors"/>
+                <property name="key" value="author" />
+            </bean>
+        </constructor-arg>
+        <constructor-arg name="regex" value="\sand\s"/>
+    </bean>
+
+    <bean id="bibtexTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+        <property name="field" ref="dcTitle"/>
+        <property name="key" value="title" />
+    </bean>
+
+    <bean id="bibtexTypeContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
+        <property name="field" ref="dcType"/>
+        <property name="key" value="type" />
+    </bean>
+
+</beans>

config/dspace/from_container/bitstore.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd" default-lazy-init="true">
+
+    <bean name="org.dspace.storage.bitstore.BitstreamStorageService" class="org.dspace.storage.bitstore.BitstreamStorageServiceImpl">
+        <property name="incoming" value="${assetstore.index.primary}"/>
+        <property name="stores">
+            <map>
+                <entry key="0" value-ref="localStore"/>
+                <entry key="1" value-ref="s3Store"/>
+            </map>
+        </property>
+    </bean>
+
+    <bean name="localStore" class="org.dspace.storage.bitstore.DSBitStoreService" scope="singleton">
+        <property name="baseDir" value="${assetstore.dir}"/>
+    </bean>
+
+    <bean name="s3Store" class="org.dspace.storage.bitstore.S3BitStoreService" scope="singleton" lazy-init="true">
+        <property name="enabled" value="${assetstore.s3.enabled}"/>
+        <!-- AWS Security credentials, with policies for specified bucket -->
+        <property name="awsAccessKey" value="${assetstore.s3.awsAccessKey}"/>
+        <property name="awsSecretKey" value="${assetstore.s3.awsSecretKey}"/>
+        <property name="useRelativePath" value="${assetstore.s3.useRelativePath}"/>
+
+        <!-- S3 bucket name to store assets in. example: longsight-dspace-auk -->
+        <property name="bucketName" value="${assetstore.s3.bucketName}"/>
+
+        <!-- AWS S3 Region to use: {us-east-1, us-west-1, eu-west-1, eu-central-1, ap-southeast-1, ... } -->
+        <!-- Optional, sdk default is us-east-1 -->
+        <property name="awsRegionName" value="${assetstore.s3.awsRegionName}"/>
+
+        <!-- Subfolder to organize assets within the bucket, in case this bucket is shared  -->
+        <!-- Optional, default is root level of bucket -->
+        <property name="subfolder" value="${assetstore.s3.subfolder}"/>
+    </bean>
+
+    <!-- <bean name="localStore2 ... -->
+    <!-- <bean name="s3Store2 ... -->
+</beans>

config/dspace/from_container/cache.xml

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xmlns:cache="http://www.springframework.org/schema/cache"
+       xmlns:p="http://www.springframework.org/schema/p"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans
+                           http://www.springframework.org/schema/beans/spring-beans.xsd
+                           http://www.springframework.org/schema/cache
+                           http://www.springframework.org/schema/cache/spring-cache.xsd">
+
+    <cache:annotation-driven />
+    <bean id="cacheManager" class="org.springframework.cache.jcache.JCacheCacheManager">
+        <property name="cacheManager">
+            <bean class="org.springframework.cache.jcache.JCacheManagerFactoryBean">
+               <property name="cacheManagerUri" value="file:${dspace.dir}/config/ehcache.xml"/>
+            </bean>
+        </property>
+    </bean>
+
+</beans>