Update support for iRODS

irods/pom.xml

@@ -24,6 +24,11 @@
     <packaging>jar</packaging>
 
     <dependencies>
+        <dependency>
+            <groupId>org.irods</groupId>
+            <artifactId>irods4j</artifactId>
+            <version>0.5.0-java8</version>
+        </dependency>
         <dependency>
             <groupId>ch.cyberduck</groupId>
             <artifactId>core</artifactId>
@@ -37,27 +42,10 @@
             <version>${project.version}</version>
         </dependency>
         <dependency>
-            <groupId>ch.iterate.jargon</groupId>
-            <artifactId>jargon-core</artifactId>
-            <version>4.2.0.1</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.claymoresystems</groupId>
-                    <artifactId>puretls</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.globus.jglobus</groupId>
-                    <artifactId>cog-jglobus</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.perf4j</groupId>
-                    <artifactId>perf4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>log4j</groupId>
-                    <artifactId>log4j</artifactId>
-                </exclusion>
-            </exclusions>
+            <artifactId>testcontainers</artifactId>
+            <groupId>org.testcontainers</groupId>
+            <version>1.21.3</version>
+            <scope>test</scope>
         </dependency>
     </dependencies>
 

irods/src/main/java/ch/cyberduck/core/irods/IRODSAttributesFinderFeature.java

@@ -1,7 +1,7 @@
 package ch.cyberduck.core.irods;
 
 /*
- * Copyright (c) 2002-2016 iterate GmbH. All rights reserved.
+ * Copyright (c) 2002-2025 iterate GmbH. All rights reserved.
  * https://cyberduck.io/
  *
  * This program is free software; you can redistribute it and/or modify
@@ -15,23 +15,33 @@
  * GNU General Public License for more details.
  */
 
+import ch.cyberduck.core.DefaultIOExceptionMappingService;
 import ch.cyberduck.core.ListProgressListener;
 import ch.cyberduck.core.Path;
 import ch.cyberduck.core.PathAttributes;
 import ch.cyberduck.core.exception.BackgroundException;
 import ch.cyberduck.core.exception.NotfoundException;
 import ch.cyberduck.core.features.AttributesAdapter;
 import ch.cyberduck.core.features.AttributesFinder;
-import ch.cyberduck.core.io.Checksum;
 
-import org.apache.commons.codec.binary.Base64;
-import org.apache.commons.codec.binary.Hex;
-import org.irods.jargon.core.exception.JargonException;
-import org.irods.jargon.core.pub.IRODSFileSystemAO;
-import org.irods.jargon.core.pub.domain.ObjStat;
-import org.irods.jargon.core.pub.io.IRODSFile;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.irods.irods4j.high_level.catalog.IRODSQuery;
+import org.irods.irods4j.high_level.connection.IRODSConnection;
+import org.irods.irods4j.high_level.vfs.IRODSFilesystem;
+import org.irods.irods4j.high_level.vfs.LogicalPath;
+import org.irods.irods4j.high_level.vfs.ObjectStatus;
+import org.irods.irods4j.low_level.api.IRODSException;
 
-public class IRODSAttributesFinderFeature implements AttributesFinder, AttributesAdapter<ObjStat> {
+import java.io.IOException;
+import java.util.List;
+
+public class IRODSAttributesFinderFeature implements AttributesFinder, AttributesAdapter<List<String>> {
+
+    private static final Logger log = LogManager.getLogger(IRODSAttributesFinderFeature.class);
+
+    private static final String REPLICA_STATUS_GOOD = "1";
+    private static final String REPLICA_STATUS_STALE = "0";
 
     private final IRODSSession session;
 
@@ -42,28 +52,79 @@ public IRODSAttributesFinderFeature(final IRODSSession session) {
     @Override
     public PathAttributes find(final Path file, final ListProgressListener listener) throws BackgroundException {
         try {
-            final IRODSFileSystemAO fs = session.getClient();
-            final IRODSFile f = fs.getIRODSFileFactory().instanceIRODSFile(file.getAbsolute());
-            if(!f.exists()) {
-                throw new NotfoundException(file.getAbsolute());
+            log.debug("looking up path attributes.");
+
+            final String logicalPath = file.getAbsolute();
+            final IRODSConnection conn = session.getClient();
+
+            ObjectStatus status = IRODSFilesystem.status(conn.getRcComm(), logicalPath);
+
+            if(IRODSFilesystem.isDataObject(status)) {
+                log.debug("data object exists in iRODS. fetching data using GenQuery2.");
+                String query = String.format(
+                        "select DATA_CREATE_TIME, DATA_MODIFY_TIME, DATA_SIZE, DATA_CHECKSUM, DATA_REPL_STATUS where COLL_NAME = '%s' and DATA_NAME = '%s' order by DATA_REPL_STATUS desc, DATA_MODIFY_TIME desc",
+                        LogicalPath.parentPath(logicalPath),
+                        LogicalPath.objectName(logicalPath));
+                log.debug("query = [{}]", query);
+                List<List<String>> rows = IRODSQuery.executeGenQuery2(conn.getRcComm(), query);
+
+                PathAttributes attrs = new PathAttributes();
+
+                if(!rows.isEmpty()) {
+                    List<String> row = rows.get(0);
+                    if(REPLICA_STATUS_STALE.equals(row.get(4)) || REPLICA_STATUS_GOOD.equals(row.get(4))) {
+                        setAttributes(attrs, row);
+                    }
+                }
+
+                return attrs;
             }
-            final ObjStat stats = fs.getObjStat(f.getAbsolutePath());
-            return this.toAttributes(stats);
+
+            if(IRODSFilesystem.isCollection(status)) {
+                log.debug("collection exists in iRODS. fetching data using GenQuery2.");
+                String query = String.format("select COLL_CREATE_TIME, COLL_MODIFY_TIME where COLL_NAME = '%s'", logicalPath);
+                log.debug("query = [{}]", query);
+                List<List<String>> rows = IRODSQuery.executeGenQuery2(conn.getRcComm(), query);
+
+                PathAttributes attrs = new PathAttributes();
+
+                if(!rows.isEmpty()) {
+                    // Collections do not have the same properties as data objects
+                    // so fill in the gaps to satisfy requirements of setAttributes.
+                    List<String> row = rows.get(0);
+                    row.add("0"); // Data size
+                    row.add("");  // Checksum
+                    row.add("");  // Replica status
+                    setAttributes(attrs, row);
+                }
+
+                return attrs;
+            }
+
+            throw new NotfoundException(logicalPath);
         }
-        catch(JargonException e) {
+        catch(IRODSException e) {
             throw new IRODSExceptionMappingService().map("Failure to read attributes of {0}", e, file);
         }
+        catch(IOException e) {
+            throw new DefaultIOExceptionMappingService().map("Failure to read attributes of {0}", e, file);
+        }
     }
 
     @Override
-    public PathAttributes toAttributes(final ObjStat stats) {
-        final PathAttributes attributes = new PathAttributes();
-        attributes.setModificationDate(stats.getModifiedAt().getTime());
-        attributes.setCreationDate(stats.getCreatedAt().getTime());
-        attributes.setSize(stats.getObjSize());
-        attributes.setChecksum(Checksum.parse(Hex.encodeHexString(Base64.decodeBase64(stats.getChecksum()))));
-        attributes.setOwner(stats.getOwnerName());
-        attributes.setGroup(stats.getOwnerZone());
-        return attributes;
+    public PathAttributes toAttributes(final List<String> row) {
+        PathAttributes attrs = new PathAttributes();
+        setAttributes(attrs, row);
+        return attrs;
+    }
+
+    private static void setAttributes(final PathAttributes attrs, final List<String> row) {
+        log.debug("path attribute info: created at [{}], modified at [{}], data size = [{}], checksum = [{}]",
+                row.get(0), row.get(1), row.get(2), row.get(3));
+        attrs.setCreationDate(Long.parseLong(row.get(0)) * 1000); // seconds to ms
+        attrs.setModificationDate(Long.parseLong(row.get(1)) * 1000);
+        attrs.setSize(Long.parseLong(row.get(2)));
+        attrs.setChecksum(IRODSChecksumUtils.toChecksum(row.get(3)));
     }
+
 }

irods/src/main/java/ch/cyberduck/core/irods/IRODSChecksumUtils.java

@@ -0,0 +1,52 @@
+package ch.cyberduck.core.irods;
+
+/*
+ * Copyright (c) 2002-2025 iterate GmbH. All rights reserved.
+ * https://cyberduck.io/
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ */
+
+import ch.cyberduck.core.io.Checksum;
+
+import org.apache.commons.codec.binary.Base64;
+import org.apache.commons.codec.binary.Hex;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+public final class IRODSChecksumUtils {
+
+    private static final Logger log = LogManager.getLogger(IRODSChecksumUtils.class);
+
+    public static Checksum toChecksum(String irodsChecksum) {
+        if(StringUtils.isBlank(irodsChecksum)) {
+            return Checksum.NONE;
+        }
+
+        int colon = irodsChecksum.indexOf(':');
+        if(-1 == colon) {
+            log.debug("no hash algorithm prefix found in iRODS checksum. ignoring checksum.");
+            return Checksum.NONE;
+        }
+
+        if(colon + 1 >= irodsChecksum.length()) {
+            log.debug("iRODS checksum may be corrupted. ignoring checksum.");
+            return Checksum.NONE;
+        }
+
+        log.debug("checksum from iRODS server is [{}].", irodsChecksum);
+        String checksum = irodsChecksum.substring(colon + 1);
+        checksum = Hex.encodeHexString(Base64.decodeBase64(checksum));
+        log.debug("base64-decoded, hex-encoded checksum is [{}].", checksum);
+        return Checksum.parse(checksum);
+    }
+}