Merge pull request #5012 from evolvedbinary/6.x.x/hotfix/expath-impor…

…t-xquery-transient

[6.x.x] Fix an issue with XQuery transient imports within EXPath Package

exist-core/src/main/java/org/exist/client/InteractiveClient.java

@@ -2190,7 +2190,7 @@ public boolean run(final String args[]) throws Exception {
                 configFile = Optional.ofNullable(ConfigurationHelper.lookup((String) CONF_XML.get("")));
             }
         }
-        configFile.ifPresent(value -> properties.setProperty(CONFIGURATION, value.toAbsolutePath().toString()));
+        configFile.ifPresent(value -> properties.setProperty(CONFIGURATION, value.toString()));
 
         properties.putAll(loadClientProperties());
 

exist-core/src/main/java/org/exist/repo/ExistRepository.java

@@ -23,12 +23,17 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.exist.dom.persistent.BinaryDocument;
+import org.exist.security.PermissionDeniedException;
+import org.exist.source.DBSource;
 import org.exist.storage.BrokerPool;
 import org.exist.storage.BrokerPoolService;
 import org.exist.storage.BrokerPoolServiceException;
+import org.exist.storage.DBBroker;
 import org.exist.storage.NativeBroker;
 import org.exist.util.Configuration;
 import org.exist.util.FileUtils;
+import org.exist.xmldb.XmldbURI;
 import org.exist.xquery.ErrorCodes;
 import org.exist.xquery.Expression;
 import org.exist.xquery.Module;
@@ -41,7 +46,9 @@
 import org.expath.pkg.repo.PackageException;
 import org.expath.pkg.repo.Repository;
 import org.expath.pkg.repo.URISpace;
+import org.w3c.dom.Document;
 
+import javax.annotation.Nullable;
 import javax.xml.transform.Source;
 import javax.xml.transform.stream.StreamSource;
 import java.io.IOException;
@@ -273,6 +280,38 @@ public Path resolveXQueryModule(final String namespace) throws XPathException {
         return null;
     }
 
+    /**
+     * Attempt to lookup an XQuery from the filesystem in the database.
+     *
+     * @param broker the database broker
+     * @param xqueryPath the path to the xquery within the EXPath filesystem repo.
+     *
+     * @return the database source for the xquery, or null.
+     */
+    public @Nullable org.exist.source.Source resolveStoredXQueryModuleFromDb(final DBBroker broker, final Path xqueryPath) throws PermissionDeniedException {
+        if (!xqueryPath.startsWith(expathDir)) {
+            return null;
+        }
+
+        final String relXQueryPath = expathDir.relativize(xqueryPath).toString();
+
+        // 1. attempt to locate it within a library
+        XmldbURI xqueryDbPath = XmldbURI.create("xmldb:exist:///db/system/repo/" + relXQueryPath);
+        @Nullable Document doc = broker.getXMLResource(xqueryDbPath);
+        if (doc != null && doc instanceof BinaryDocument) {
+            return new DBSource(broker, (BinaryDocument) doc, false);
+        }
+
+        // 2. attempt to locate it within an app
+        xqueryDbPath = XmldbURI.create("xmldb:exist:///db/apps/" + relXQueryPath);
+        doc = broker.getXMLResource(xqueryDbPath);
+        if (doc != null && doc instanceof BinaryDocument) {
+            return new DBSource(broker, (BinaryDocument) doc, false);
+        }
+
+        return null;
+    }
+
     public Source resolveXSLTModule(final String namespace) throws PackageException {
         for (final Packages pp : myParent.listPackages()) {
             final Package pkg = pp.latest();

exist-core/src/main/java/org/exist/util/Configuration.java

@@ -127,6 +127,8 @@ public Configuration(String configFilename, Optional<Path> existHomeDirname) thr
         InputStream is = null;
         try {
 
+            existHomeDirname = existHomeDirname.map(Path::normalize);
+
             if(configFilename == null) {
                 // Default file name
                 configFilename = DatabaseImpl.CONF_XML;
@@ -164,7 +166,6 @@ public Configuration(String configFilename, Optional<Path> existHomeDirname) thr
                     }
                 }
 
-
                 Path configFile = Paths.get(configFilename);
 
                 if(!configFile.isAbsolute() && existHome.isPresent()) {
@@ -863,15 +864,15 @@ private void configureBackend( final Optional<Path> dbHome, Element con ) throws
         final String dataFiles = getConfigAttributeValue( con, BrokerPool.DATA_DIR_ATTRIBUTE );
 
         if (dataFiles != null) {
-            final Path df = ConfigurationHelper.lookup( dataFiles, dbHome );
+            final Path df = ConfigurationHelper.lookup(dataFiles, dbHome);
             if (!Files.isReadable(df)) {
                 try {
                     Files.createDirectories(df);
                 } catch (final IOException ioe) {
-                    throw new DatabaseConfigurationException("cannot read data directory: " + df.toAbsolutePath().toString(), ioe);
+                    throw new DatabaseConfigurationException("cannot read data directory: " + df, ioe);
                 }
             }
-            config.put(BrokerPool.PROPERTY_DATA_DIR, df.toAbsolutePath());
+            config.put(BrokerPool.PROPERTY_DATA_DIR, df);
             LOG.debug(BrokerPool.PROPERTY_DATA_DIR + ": {}", config.get(BrokerPool.PROPERTY_DATA_DIR));
         }
 
@@ -1090,9 +1091,9 @@ private void configureRecovery( final Optional<Path> dbHome, Element recovery )
             final Path rf = ConfigurationHelper.lookup( option, dbHome );
 
             if(!Files.isReadable(rf)) {
-                throw new DatabaseConfigurationException( "cannot read data directory: " + rf.toAbsolutePath());
+                throw new DatabaseConfigurationException( "cannot read data directory: " + rf);
             }
-            setProperty(Journal.PROPERTY_RECOVERY_JOURNAL_DIR, rf.toAbsolutePath());
+            setProperty(Journal.PROPERTY_RECOVERY_JOURNAL_DIR, rf);
             LOG.debug(Journal.PROPERTY_RECOVERY_JOURNAL_DIR + ": {}", config.get(Journal.PROPERTY_RECOVERY_JOURNAL_DIR));
         }
 

exist-core/src/main/java/org/exist/util/ConfigurationHelper.java

@@ -109,7 +109,7 @@ public static Optional<Path> getExistHome(final String config) {
         final Path userHomeRelativeConfig = userHome.resolve(config);
         if (Files.isDirectory(userHome) && Files.isRegularFile(userHomeRelativeConfig)) {
             final Path existHome = userHomeRelativeConfig.getParent().normalize();
-            LOG.debug("Got eXist home: {} from system property 'user.home': {}", existHome.toAbsolutePath().toString(), userHome.toAbsolutePath().toString());
+            LOG.debug("Got eXist home: {} from system property 'user.home': {}", existHome.toAbsolutePath(), userHome.toAbsolutePath());
             return Optional.of(existHome);
         }
 
@@ -119,7 +119,7 @@ public static Optional<Path> getExistHome(final String config) {
         final Path userDirRelativeConfig = userDir.resolve(config);
         if (Files.isDirectory(userDir) && Files.isRegularFile(userDirRelativeConfig)) {
             final Path existHome = userDirRelativeConfig.getParent().normalize();
-            LOG.debug("Got eXist home: {} from system property 'user.dir': {}", existHome.toAbsolutePath().toString(), userDir.toAbsolutePath().toString());
+            LOG.debug("Got eXist home: {} from system property 'user.dir': {}", existHome.toAbsolutePath(), userDir.toAbsolutePath());
             return Optional.of(existHome);
         }
 
@@ -132,7 +132,7 @@ public static Optional<Path> getExistHome(final String config) {
                     existHome = Paths.get(new URI(configUrl.getPath())).getParent().getParent().normalize();
                     LOG.warn("{} file was found on the classpath, but inside a Jar file! Derived EXIST_HOME from Jar's parent folder: {}", config, existHome);
                 } else {
-                    existHome = Paths.get(configUrl.toURI()).getParent();
+                    existHome = Paths.get(configUrl.toURI()).getParent().normalize();
                     if (FileUtils.fileName(existHome).equals("etc")) {
                         existHome = existHome.getParent().normalize();
                     }
@@ -179,15 +179,14 @@ public static Path lookup(final String path) {
      * @return the file handle
      */
     public static Path lookup(final String path, final Optional<Path> parent) {
-        // resolvePath is used for things like ~user/folder
-        final Path p = decodeUserHome(path);
-        if (p.isAbsolute()) {
-            return p;
+        // attempt to first resolve the path that is used for things like ~user/folder
+        Path p = decodeUserHome(path);
+        if (!p.isAbsolute()) {
+            p = parent
+                    .orElse(getExistHome().orElse(Paths.get(System.getProperty("user.dir"))))
+                    .resolve(path);
         }
-
-        return parent
-                .orElse(getExistHome().orElse(Paths.get(System.getProperty("user.dir"))))
-                .resolve(path);
+        return p.normalize().toAbsolutePath();
     }
 
 

exist-core/src/main/java/org/exist/util/SingleInstanceConfiguration.java

@@ -66,7 +66,7 @@ public SingleInstanceConfiguration(String configFilename, Optional<Path> existHo
     public static Optional<Path> getPath() {
         if (!_configFile.isPresent()) {
             final Path f = ConfigurationHelper.lookup("conf.xml");
-            return Optional.of(f.toAbsolutePath());
+            return Optional.of(f);
         }
         return _configFile;
     }

exist-core/src/main/java/org/exist/xquery/XQueryContext.java

@@ -30,6 +30,7 @@
 import java.net.URISyntaxException;
 import java.nio.charset.Charset;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.concurrent.CopyOnWriteArrayList;
 import java.util.concurrent.atomic.AtomicReference;
@@ -588,9 +589,28 @@ public Optional<ExistRepository> getRepository() {
 
             // use the resolved file or return null
             if (resolved != null) {
-                // build a module object from the file
-                final Source src = new FileSource(resolved, false);
-                return compileOrBorrowModule(prefix, namespace, "", src);
+
+                String location = "";
+
+                try {
+
+                    // see if the src exists in the database and if so, use that instead
+                    Source src = repo.get().resolveStoredXQueryModuleFromDb(getBroker(), resolved);
+                    if (src != null) {
+                        // NOTE(AR) set the location of the module to import relative to this module's load path - so that transient imports of the imported module will resolve correctly!
+                        location = Paths.get(XmldbURI.create(moduleLoadPath).getCollectionPath()).relativize(Paths.get(((DBSource)src).getDocumentPath().getCollectionPath())).toString();
+                    } else {
+                        // else, fallback to the one from the filesystem
+                        src = new FileSource(resolved, false);
+                    }
+
+                    // build a module object from the source
+                    final ExternalModule module = compileOrBorrowModule(prefix, namespace, location, src);
+                    return module;
+
+                } catch (final PermissionDeniedException e) {
+                    throw new XPathException(e.getMessage(), e);
+                }
             }
         }
 

exist-parent/pom.xml

@@ -394,7 +394,7 @@
             <dependency>
                 <groupId>org.expath.packaging</groupId>
                 <artifactId>pkg-java</artifactId>
-                <version>2.0.0</version>
+                <version>2.0.1</version>
             </dependency>
 
             <dependency>