7000 mpconfig for JVM settings

doc/sphinx-guides/source/admin/make-data-count.rst

@@ -146,7 +146,9 @@ Configuring Your Dataverse Installation for Make Data Count Citations
 
 Please note: as explained in the note above about limitations, this feature is not available to Dataverse installations that use Handles.
 
-To configure your Dataverse installation to pull citations from the test vs. production DataCite server see :ref:`doi.dataciterestapiurlstring` in the Installation Guide.
+To configure your Dataverse installation to pull citations from the test vs.
+production DataCite server see :ref:`dataverse.pid.datacite.rest-api-url` in
+the Installation Guide.
 
 Please note that in the curl example, Bash environment variables are used with the idea that you can set a few environment variables and copy and paste the examples as is. For example, "$DOI" could become "doi:10.5072/FK2/BL2IBM" by issuing the following export command from Bash:
 

doc/sphinx-guides/source/api/native-api.rst

@@ -485,6 +485,8 @@ You should expect an HTTP 200 ("OK") response and JSON indicating the database I
 
 .. note:: Only a Dataverse installation account with superuser permissions is allowed to include files when creating a dataset via this API. Adding files this way only adds their file metadata to the database, you will need to manually add the physical files to the file system.
 
+.. _api-import-dataset:
+
 Import a Dataset into a Dataverse Collection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -2932,7 +2934,7 @@ Each user can get a dump of their basic information in JSON format by passing in
 
     curl -H "X-Dataverse-key:$API_TOKEN" $SERVER_URL/api/users/:me    
 
-.. _pids-api:
+
 
 Managing Harvesting Server and Sets
 -----------------------------------
@@ -3043,6 +3045,10 @@ The fully expanded example above (without the environment variables) looks like
 
 Only users with superuser permissions may delete harvesting sets.
 
+
+
+.. _pids-api:
+
 PIDs
 ----
 

doc/sphinx-guides/source/developers/testing.rst

@@ -79,6 +79,17 @@ greatly extended parameterized testing. Some guidance how to write those:
 - https://blog.codefx.org/libraries/junit-5-parameterized-tests/
 - See also some examples in our codebase.
 
+JUnit 5 Test Helper Extensions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Our codebase provides little helpers to ease dealing with state during tests.
+Some tests might need to change something which should be restored after the test ran.
+
+For unit tests, the most interesting part is to set a JVM setting just for the current test.
+Please use ``@JvmSetting(key = JvmSettings.XXX, value = "")`` annotation on a test method or
+a test class to set and clear the property automatically.
+
+
 Observing Changes to Code Coverage
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

modules/dataverse-parent/pom.xml

@@ -164,7 +164,7 @@
 
         <!-- Testing dependencies -->
         <testcontainers.version>1.15.0</testcontainers.version>
-        <microbean-mpconfig.version>0.4.1</microbean-mpconfig.version>
+        <smallrye-mpconfig.version>2.10.1</smallrye-mpconfig.version>
 
         <junit.version>4.13.1</junit.version>
         <junit.jupiter.version>5.7.0</junit.jupiter.version>

pom.xml

@@ -601,9 +601,9 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.microbean</groupId>
-            <artifactId>microbean-microprofile-config</artifactId>
-            <version>${microbean-mpconfig.version}</version>
+            <groupId>io.smallrye.config</groupId>
+            <artifactId>smallrye-config</artifactId>
+            <version>${smallrye-mpconfig.version}</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
@@ -641,10 +641,17 @@
                     <include>**/*.xml</include>
                     <include>**/firstNames/*.*</include>
                     <include>**/*.xsl</include>
-                    <include>**/*.properties</include>
                     <include>**/services/*</include>
                 </includes>
             </resource>
+            <resource>
+                <directory>src/main/resources</directory>
+                <!-- Filter files matching here for Maven properties and replace -->
+                <filtering>true</filtering>
+                <includes>
+                    <include>**/*.properties</include>
+                </includes>
+            </resource>
         </resources>
         <plugins>
             <plugin>

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

@@ -23,6 +23,8 @@
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.TypedQuery;
+
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import org.apache.commons.text.StringEscapeUtils;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
@@ -53,7 +55,11 @@ public class DOIDataCiteRegisterService {
 
     private DataCiteRESTfullClient getClient() throws IOException {
         if (client == null) {
-            client = new DataCiteRESTfullClient(System.getProperty("doi.baseurlstring"), System.getProperty("doi.username"), System.getProperty("doi.password"));
+            client = new DataCiteRESTfullClient(
+                JvmSettings.DATACITE_MDS_API_URL.lookup(),
+                JvmSettings.DATACITE_USERNAME.lookup(),
+                JvmSettings.DATACITE_PASSWORD.lookup()
+            );
         }
         return client;
     }

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java

@@ -13,6 +13,7 @@
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
 
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import org.apache.commons.httpclient.HttpException;
 import org.apache.commons.httpclient.HttpStatus;
 
@@ -219,9 +220,9 @@ public void deleteIdentifier(DvObject dvObject) throws IOException, HttpExceptio
     private void deleteDraftIdentifier(DvObject dvObject) throws IOException {
 
     	//ToDo - incorporate into DataCiteRESTfulClient
-        String baseUrl = systemConfig.getDataCiteRestApiUrlString();
-        String username = System.getProperty("doi.username");
-        String password = System.getProperty("doi.password");
+        String baseUrl = JvmSettings.DATACITE_REST_API_URL.lookup();
+        String username = JvmSettings.DATACITE_USERNAME.lookup();
+        String password = JvmSettings.DATACITE_PASSWORD.lookup();
         GlobalId doi = dvObject.getGlobalId();
         /**
          * Deletes the DOI from DataCite if it can. Returns 204 if PID was deleted

src/main/java/edu/harvard/iq/dataverse/DOIEZIdServiceBean.java

@@ -1,5 +1,6 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.ucsb.nceas.ezid.EZIDException;
 import edu.ucsb.nceas.ezid.EZIDService;
 import edu.ucsb.nceas.ezid.EZIDServiceRequest;
@@ -26,10 +27,10 @@ public class DOIEZIdServiceBean extends AbstractGlobalIdServiceBean {
 
     public DOIEZIdServiceBean() {
         logger.log(Level.FINE,"Constructor");
-        baseURLString = System.getProperty("doi.baseurlstring");
+        baseURLString = JvmSettings.EZID_API_URL.lookup();
         ezidService = new EZIDService(baseURLString);
-        USERNAME = System.getProperty("doi.username");
-        PASSWORD = System.getProperty("doi.password");
+        USERNAME = JvmSettings.EZID_USERNAME.lookup();
+        PASSWORD = JvmSettings.EZID_PASSWORD.lookup();
         logger.log(Level.FINE, "Using baseURLString {0}", baseURLString);
         try {
             ezidService.login(USERNAME, PASSWORD);

src/main/java/edu/harvard/iq/dataverse/Dataset.java

@@ -33,6 +33,8 @@
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
+
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.StringUtil;
 
@@ -515,11 +517,8 @@ private Collection<String> getCategoryNames() {
     @Deprecated 
     public Path getFileSystemDirectory() {
         Path studyDir = null;
-
-        String filesRootDirectory = System.getProperty("dataverse.files.directory");
-        if (filesRootDirectory == null || filesRootDirectory.equals("")) {
-            filesRootDirectory = "/tmp/files";
-        }
+
+        String filesRootDirectory = JvmSettings.FILES_DIRECTORY.lookup();
 
         if (this.getAlternativePersistentIndentifiers() != null && !this.getAlternativePersistentIndentifiers().isEmpty()) {
             for (AlternativePersistentIdentifier api : this.getAlternativePersistentIndentifiers()) {

src/main/java/edu/harvard/iq/dataverse/HandlenetServiceBean.java

@@ -24,8 +24,6 @@
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -34,6 +32,7 @@
 import java.security.PrivateKey;
 
 /* Handlenet imports: */
+import edu.harvard.iq.dataverse.util.SystemConfig;
 import net.handle.hdllib.AbstractMessage;
 import net.handle.hdllib.AbstractResponse;
 import net.handle.hdllib.AdminRecord;
@@ -247,21 +246,7 @@ private String getRegistrationUrl(DvObject dvObject) {
     }
 
     public String getSiteUrl() {
-        logger.log(Level.FINE,"getSiteUrl");
-        String hostUrl = System.getProperty("dataverse.siteUrl");
-        if (hostUrl != null && !"".equals(hostUrl)) {
-            return hostUrl;
-        }
-        String hostName = System.getProperty("dataverse.fqdn");
-        if (hostName == null) {
-            try {
-                hostName = InetAddress.getLocalHost().getCanonicalHostName();
-            } catch (UnknownHostException e) {
-                return null;
-            }
-        }
-        hostUrl = "https://" + hostName;
-        return hostUrl;
+        return SystemConfig.getDataverseSiteUrlStatic();
     }
 
     private byte[] readKey(final String file) {

src/main/java/edu/harvard/iq/dataverse/api/Info.java

@@ -1,5 +1,6 @@
 package edu.harvard.iq.dataverse.api;
 
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import javax.ejb.EJB;
@@ -44,7 +45,7 @@ public Response getInfo() {
     @GET
     @Path("server")
     public Response getServer() {
-        return response( req -> ok(systemConfig.getDataverseServer()));
+        return response( req -> ok(JvmSettings.FQDN.lookup()));
     }
 
     @GET

src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java

@@ -6,6 +6,7 @@
 import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitationsServiceBean;
 import edu.harvard.iq.dataverse.makedatacount.DatasetMetrics;
 import edu.harvard.iq.dataverse.makedatacount.DatasetMetricsServiceBean;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 
 import java.io.FileReader;
@@ -141,7 +142,10 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws Mal
             // DataCite wants "doi=", not "doi:".
             String authorityPlusIdentifier = persistentId.replaceFirst("doi:", "");
             // Request max page size and then loop to handle multiple pages
-            URL url = new URL(systemConfig.getDataCiteRestApiUrlString() + "/events?doi=" + authorityPlusIdentifier + "&source=crossref&page[size]=1000");
+            URL url = new URL(JvmSettings.DATACITE_REST_API_URL.lookup() +
+                              "/events?doi=" +
+                              authorityPlusIdentifier +
+                              "&source=crossref&page[size]=1000");
             logger.fine("Retrieving Citations from " + url.toString());
             boolean nextPage = true;
             JsonArrayBuilder dataBuilder = Json.createArrayBuilder();

src/main/java/edu/harvard/iq/dataverse/api/Pids.java

@@ -5,6 +5,7 @@
 import edu.harvard.iq.dataverse.engine.command.impl.DeletePidCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.ReservePidCommand;
 import edu.harvard.iq.dataverse.pidproviders.PidUtil;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.util.Arrays;
 import javax.ejb.Stateless;
@@ -46,9 +47,13 @@ public Response getPid(@QueryParam("persistentId") String persistentId) {
         } catch (WrappedResponse ex) {
             return error(Response.Status.FORBIDDEN, BundleUtil.getStringFromBundle("api.errors.invalidApiToken"));
         }
-        String baseUrl = systemConfig.getDataCiteRestApiUrlString();
-        String username = System.getProperty("doi.username");
-        String password = System.getProperty("doi.password");
+
+        // FIXME: Even before changing to MPCONFIG retrieval, this was pinned to be DataCite specific!
+        //        Should this be extended to EZID and other PID systems like Handle?
+        String baseUrl = JvmSettings.DATACITE_REST_API_URL.lookup();
+        String username = JvmSettings.DATACITE_USERNAME.lookup();
+        String password = JvmSettings.DATACITE_PASSWORD.lookup();
+
         try {
             JsonObjectBuilder result = PidUtil.queryDoi(persistentId, baseUrl, username, password);
             return ok(result);

src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java

@@ -1,5 +1,6 @@
 package edu.harvard.iq.dataverse.api.datadeposit;
 
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import java.io.File;
 import java.util.Arrays;
@@ -86,37 +87,32 @@ public boolean storeAndCheckBinary() {
 
     @Override
     public String getTempDirectory() {
-        String tmpFileDir = System.getProperty(SystemConfig.FILES_DIRECTORY);
-        if (tmpFileDir != null) {
-            String swordDirString = tmpFileDir + File.separator + "sword";
-            File swordDirFile = new File(swordDirString);
-            /**
-             * @todo Do we really need this check? It seems like we do because
-             * if you create a dataset via the native API and then later try to
-             * upload a file via SWORD, the directory defined by
-             * dataverse.files.directory may not exist and we get errors deep in
-             * the SWORD library code. Could maybe use a try catch in the doPost
-             * method of our SWORDv2MediaResourceServlet.
-             */
-            if (swordDirFile.exists()) {
+        // will throw a runtime exception when not found
+        String tmpFileDir = JvmSettings.FILES_DIRECTORY.lookup();
+
+        String swordDirString = tmpFileDir + File.separator + "sword";
+        File swordDirFile = new File(swordDirString);
+        /**
+         * @todo Do we really need this check? It seems like we do because
+         * if you create a dataset via the native API and then later try to
+         * upload a file via SWORD, the directory defined by
+         * dataverse.files.directory may not exist and we get errors deep in
+         * the SWORD library code. Could maybe use a try catch in the doPost
+         * method of our SWORDv2MediaResourceServlet.
+         */
+        if (swordDirFile.exists()) {
+            return swordDirString;
+        } else {
+            boolean mkdirSuccess = swordDirFile.mkdirs();
+            if (mkdirSuccess) {
+                logger.info("Created directory " + swordDirString);
                 return swordDirString;
             } else {
-                boolean mkdirSuccess = swordDirFile.mkdirs();
-                if (mkdirSuccess) {
-                    logger.info("Created directory " + swordDirString);
-                    return swordDirString;
-                } else {
-                    String msgForSwordUsers = ("Could not determine or create SWORD temp directory. Check logs for details.");
-                    logger.severe(msgForSwordUsers + " Failed to create " + swordDirString);
-                    // sadly, must throw RunTimeException to communicate with SWORD user
-                    throw new RuntimeException(msgForSwordUsers);
-                }
+                String msgForSwordUsers = ("Could not determine or create SWORD temp directory. Check logs for details.");
+                logger.severe(msgForSwordUsers + " Failed to create " + swordDirString);
+                // sadly, must throw RunTimeException to communicate with SWORD user
+                throw new RuntimeException(msgForSwordUsers);
             }
-        } else {
-            String msgForSwordUsers = ("JVM option \"" + SystemConfig.FILES_DIRECTORY + "\" not defined. Check logs for details.");
-            logger.severe(msgForSwordUsers);
-            // sadly, must throw RunTimeException to communicate with SWORD user
-            throw new RuntimeException(msgForSwordUsers);
         }
     }
 

src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java

@@ -59,6 +59,7 @@
 
 import org.apache.commons.io.IOUtils;
 
+import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.sql.Timestamp;
@@ -79,7 +80,7 @@
 @Dependent
 public class FileRecordJobListener implements ItemReadListener, StepListener, JobListener {
 
-    public static final String SEP = System.getProperty("file.separator");
+    public static final String SEP = File.separator;
 
     private static final UserNotification.Type notifyType = UserNotification.Type.FILESYSTEMIMPORT;
 

src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java

@@ -54,7 +54,7 @@
 @Dependent
 public class FileRecordReader extends AbstractItemReader {
 
-    public static final String SEP = System.getProperty("file.separator");
+    public static final String SEP = File.separator;
 
     @Inject
     JobContext jobContext;

src/main/java/edu/harvard/iq/dataverse/batch/util/LoggingUtil.java

@@ -154,8 +154,8 @@ public static Logger getJobLogger(String jobId) {
 	    try {
 		    Logger jobLogger = Logger.getLogger("job-"+jobId);
 		    FileHandler fh;
-		    String logDir = System.getProperty("com.sun.aas.instanceRoot") + System.getProperty("file.separator") 
-			    + "logs" + System.getProperty("file.separator") + "batch-jobs" + System.getProperty("file.separator");
+		    String logDir = System.getProperty("com.sun.aas.instanceRoot") + File.separator
+			    + "logs" + File.separator + "batch-jobs" + File.separator;
 		    checkCreateLogDirectory( logDir );
 		    fh = new FileHandler(logDir + "job-" + jobId + ".log");
 		    logger.log(Level.INFO, "JOB LOG: " + logDir + "job-" + jobId + ".log");