http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/pom.xml ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/pom.xml b/modules/data-manager/data-manager-core/pom.xml new file mode 100644 index 0000000..0dfa59a --- /dev/null +++ b/modules/data-manager/data-manager-core/pom.xml @@ -0,0 +1,95 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project xmlns="http://maven.apache.org/POM/4.0.0"; + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> + <parent> + <artifactId>data-manager</artifactId> + <groupId>org.apache.airavata</groupId> + <version>0.16-SNAPSHOT</version> + <relativePath>../pom.xml</relativePath> + </parent> + + <modelVersion>4.0.0</modelVersion> + <artifactId>data-manager-core</artifactId> + <packaging>jar</packaging> + <name>Airavata Data Manager Core</name> + <url>http://airavata.apache.org/</url> + + <dependencies> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-data-models</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-registry-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-registry-cpi</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-commons</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-server-configuration</artifactId> + <version>${project.version}</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>data-manager-cpi</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-registry-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-registry-cpi</artifactId> + <version>${project.version}</version> + </dependency> + + <dependency> + <groupId>org.jglobus</groupId> + <artifactId>gss</artifactId> + <version>${jglobus.version}</version> + </dependency> + <dependency> + <groupId>org.jglobus</groupId> + <artifactId>gridftp</artifactId> + <version>${jglobus.version}</version> + </dependency> + <dependency> + <groupId>org.jglobus</groupId> + <artifactId>myproxy</artifactId> + <version>2.1.0</version> + </dependency> + + <dependency> + <groupId>org.bouncycastle</groupId> + <artifactId>bcprov-jdk16</artifactId> + <version>1.44</version> + </dependency> + + + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-databind</artifactId> + <version>2.5.3</version> + </dependency> + <dependency> + <groupId>org.mongodb</groupId> + <artifactId>mongo-java-driver</artifactId> + <version>3.0.0</version> + </dependency> + </dependencies> +</project> \ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerFactory.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerFactory.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerFactory.java new file mode 100644 index 0000000..af908a3 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerFactory.java @@ -0,0 +1,34 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import org.apache.airavata.data.manager.cpi.DataManager; +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class FileManagerFactory { + private final static Logger logger = LoggerFactory.getLogger(FileManagerFactory.class); + + public static DataManager getFileManager() throws DataManagerException { + return new FileManagerImpl(); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerImpl.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerImpl.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerImpl.java new file mode 100644 index 0000000..2570fc5 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileManagerImpl.java @@ -0,0 +1,78 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import org.apache.airavata.data.manager.cpi.DataManager; +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.apache.airavata.data.manager.cpi.FileTransferService; +import org.apache.airavata.data.manager.cpi.ReplicaCatalogService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + + +public class FileManagerImpl implements DataManager { + private final static Logger logger = LoggerFactory.getLogger(FileManagerImpl.class); + + /** + * Return file transfer service instance + * + * @return + */ + @Override + public FileTransferService getFileTransferService() throws DataManagerException { + try{ + return new FileTransferServiceImpl(); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + + /** + * Return replica catalog service instance + * + * @return + */ + @Override + public ReplicaCatalogService getReplicaCatalogService() throws DataManagerException { + try{ + return new ReplicaCatalogServiceImpl(); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + + /** + * Return metadata catalog service + * + * @return + */ + @Override + public MetadataCatalogService getMetadataCatalogService() throws DataManagerException { + try{ + return new MetadataCatalogServiceImpl(); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileTransferServiceImpl.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileTransferServiceImpl.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileTransferServiceImpl.java new file mode 100644 index 0000000..a782ba7 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/FileTransferServiceImpl.java @@ -0,0 +1,484 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import com.fasterxml.jackson.core.JsonProcessingException; +import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential; +import org.apache.airavata.data.manager.core.db.dao.FileTransferRequestDao; +import org.apache.airavata.data.manager.core.remote.client.RemoteStorageClient; +import org.apache.airavata.data.manager.core.remote.client.http.HTTPStorageClient; +import org.apache.airavata.data.manager.core.remote.client.scp.SCPStorageClient; +import org.apache.airavata.data.manager.core.remote.client.sftp.SFTPStorageClient; +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.apache.airavata.data.manager.cpi.FileTransferService; +import org.apache.airavata.model.data.transfer.*; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileWriter; +import java.io.IOException; +import java.net.InetAddress; +import java.util.List; +import java.util.UUID; + +public class FileTransferServiceImpl implements FileTransferService { + + private final static Logger logger = LoggerFactory.getLogger(FileTransferServiceImpl.class); + + private FileTransferRequestDao fileTransferRequestDao; + + public FileTransferServiceImpl() throws IOException { + this.fileTransferRequestDao = new FileTransferRequestDao(); + } + + /** + * Method to upload the give bytes to the destination storage system + * + * @param gatewayId + * @param username + * @param fileData + * @param destHostName + * @param destLoginName + * @param destPort + * @param destProtocol + * @param destinationPath + * @param destHostCredToken + * @return + * @throws DataManagerException + */ + @Override + public String uploadFile(String gatewayId, String username, byte[] fileData, String destHostName, String destLoginName, int destPort, + StorageResourceProtocol destProtocol, + String destinationPath, String destHostCredToken) throws DataManagerException { + long transferTime = System.currentTimeMillis(); + if(destProtocol == StorageResourceProtocol.SCP || destProtocol == StorageResourceProtocol.SFTP) { + Object credential = getCredential(destHostCredToken); + SSHCredential sshCredential; + if (credential instanceof SSHCredential) { + sshCredential = (SSHCredential) credential; + File srcFile = null; + FileWriter fileWriter = null; + FileTransferRequestModel fileTransferRequestModel = null; + try { + String srcFilePath = System.getProperty("java.io.tmpdir")+File.separator+ UUID.randomUUID().toString(); + srcFile = new File(srcFilePath); + fileWriter = new FileWriter(srcFile); + fileWriter.write(new String(fileData)); + fileWriter.close(); + RemoteStorageClient remoteStorageClient; + if(destProtocol == StorageResourceProtocol.SCP) + remoteStorageClient = new SCPStorageClient(destHostName, destPort, destLoginName, + sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + else + remoteStorageClient = new SFTPStorageClient(destHostName, destPort, destLoginName, + sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + + fileTransferRequestModel = new FileTransferRequestModel(); + fileTransferRequestModel.setGatewayId(gatewayId); + fileTransferRequestModel.setUsername(username); + fileTransferRequestModel.setSrcHostname(InetAddress.getLocalHost().getHostName()); + fileTransferRequestModel.setSrcProtocol(StorageResourceProtocol.LOCAL); + fileTransferRequestModel.setDestHostname(destHostName); + fileTransferRequestModel.setDestLoginName(destLoginName); + fileTransferRequestModel.setDestPort(destPort); + fileTransferRequestModel.setDestProtocol(destProtocol); + fileTransferRequestModel.setDestFilePath(destinationPath); + fileTransferRequestModel.setDestHostCredToken(destHostCredToken); + fileTransferRequestModel.setFileTransferMode(FileTransferMode.SYNC); + remoteStorageClient.writeFile(srcFile, destinationPath); + transferTime = System.currentTimeMillis() - transferTime; + fileTransferRequestModel.setTransferTime(transferTime); + fileTransferRequestModel.setTransferStatus(FileTransferStatus.COMPLETED); + fileTransferRequestModel.setCreatedTime(System.currentTimeMillis()); + fileTransferRequestModel.setLastModifiedType(fileTransferRequestModel.getCreatedTime()); + fileTransferRequestModel.setFileSize(srcFile.length()); + String transferId = fileTransferRequestDao.createFileTransferRequest(fileTransferRequestModel); + return transferId; + } catch (Exception e) { + logger.error(e.getMessage(), e); + if(fileTransferRequestModel != null) { + fileTransferRequestModel.setTransferStatus(FileTransferStatus.FAILED); + try { + fileTransferRequestDao.createFileTransferRequest(fileTransferRequestModel); + } catch (JsonProcessingException e1) { + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + throw new DataManagerException(e.getMessage()); + } finally { + if(srcFile != null) + srcFile.delete(); + if(fileWriter != null) + try { + fileWriter.close(); + } catch (IOException e) { + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + } else { + throw new DataManagerException("Only SSHCredential type is supported"); + } + }else{ + throw new DataManagerException(destProtocol.toString() + " protocol is not supported for this method"); + } + } + + /** + * Transfer file between two storage resources synchronously. Returns the file transfer request id + * + * @param gatewayId + * @param username + * @param srcHostname + * @param srcLoginName + * @param srcPort + * @param srcProtocol + * @param srcPath + * @param srcHostCredToken + * @param destHostname + * @param destLoginName + * @param destPort + * @param destProtocol + * @param destinationPath + * @param destHostCredToken + * @return + * @throws DataManagerException + */ + @Override + public String transferFile(String gatewayId, String username, String srcHostname, String srcLoginName, int srcPort, StorageResourceProtocol srcProtocol, + String srcPath, String srcHostCredToken, String destHostname, String destLoginName, int destPort, + StorageResourceProtocol destProtocol, String destinationPath, String destHostCredToken) + throws DataManagerException { + long transferTime = System.currentTimeMillis(); + File srcFile = null; + FileTransferRequestModel fileTransferRequestModel = null; + try{ + fileTransferRequestModel = new FileTransferRequestModel(); + fileTransferRequestModel.setGatewayId(gatewayId); + fileTransferRequestModel.setUsername(username); + fileTransferRequestModel.setSrcHostname(srcHostname); + fileTransferRequestModel.setSrcPort(srcPort); + fileTransferRequestModel.setSrcLoginName(srcLoginName); + fileTransferRequestModel.setSrcFilePath(srcPath); + fileTransferRequestModel.setSrcProtocol(srcProtocol); + fileTransferRequestModel.setSrcHostCredToken(srcHostCredToken); + fileTransferRequestModel.setDestHostname(destHostname); + fileTransferRequestModel.setDestPort(destPort); + fileTransferRequestModel.setDestLoginName(destLoginName); + fileTransferRequestModel.setDestFilePath(destinationPath); + fileTransferRequestModel.setDestProtocol(destProtocol); + fileTransferRequestModel.setDestHostCredToken(destHostCredToken); + fileTransferRequestModel.setCreatedTime(System.currentTimeMillis()); + fileTransferRequestModel.setLastModifiedType(fileTransferRequestModel.getCreatedTime()); + fileTransferRequestModel.setFileTransferMode(FileTransferMode.SYNC); + + if(srcProtocol == StorageResourceProtocol.HTTP || srcProtocol == StorageResourceProtocol.HTTPS || + srcProtocol == StorageResourceProtocol.SCP || srcProtocol == StorageResourceProtocol.SFTP){ + RemoteStorageClient srcClient = null; + if(srcProtocol == StorageResourceProtocol.HTTP){ + srcClient = new HTTPStorageClient(HTTPStorageClient.Protocol.HTTP, srcHostname, srcPort); + }else if(srcProtocol == StorageResourceProtocol.HTTPS){ + srcClient = new HTTPStorageClient(HTTPStorageClient.Protocol.HTTPS, srcHostname, srcPort); + }else if(srcProtocol == StorageResourceProtocol.SCP){ + Object credential = getCredential(srcHostCredToken); + if(credential instanceof SSHCredential){ + SSHCredential sshCredential = (SSHCredential) credential; + srcClient = new SCPStorageClient(srcHostname, srcPort, srcLoginName, sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + }else{ + throw new DataManagerException("Only support SSHCredentials for SCP host"); + } + }else{ + Object credential = getCredential(srcHostCredToken); + if(credential instanceof SSHCredential){ + SSHCredential sshCredential = (SSHCredential) credential; + srcClient = new SFTPStorageClient(srcHostname, srcPort, srcLoginName, sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + }else{ + throw new DataManagerException("Only support SSHCredentials for SFTP host"); + } + } + fileTransferRequestModel.setTransferStatus(FileTransferStatus.RUNNING); + srcFile = srcClient.readFile(srcPath); + }else{ + throw new DataManagerException("Unsupported src protocol " + srcProtocol); + } + + if(destProtocol == StorageResourceProtocol.SCP || destProtocol == StorageResourceProtocol.SFTP){ + RemoteStorageClient destClient = null; + if(destProtocol == StorageResourceProtocol.SCP){ + Object credential = getCredential(srcHostCredToken); + if(credential instanceof SSHCredential){ + SSHCredential sshCredential = (SSHCredential) credential; + destClient = new SCPStorageClient(srcHostname, srcPort, srcLoginName, sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + }else{ + throw new DataManagerException("Only support SSHCredentials for SCP host"); + } + }else{ + Object credential = getCredential(srcHostCredToken); + if(credential instanceof SSHCredential){ + SSHCredential sshCredential = (SSHCredential) credential; + destClient = new SFTPStorageClient(srcHostname, srcPort, srcLoginName, sshCredential.getPrivateKey(), + sshCredential.getPublicKey(), sshCredential.getPassphrase().getBytes()); + }else{ + throw new DataManagerException("Only support SSHCredentials for SFTP host"); + } + } + destClient.writeFile(srcFile, destinationPath); + transferTime = System.currentTimeMillis() - transferTime; + fileTransferRequestModel.setTransferTime(transferTime); + fileTransferRequestModel.setFileSize(srcFile.length()); + fileTransferRequestModel.setTransferStatus(FileTransferStatus.COMPLETED); + String transferId = fileTransferRequestDao.createFileTransferRequest(fileTransferRequestModel); + return transferId; + }else{ + throw new DataManagerException("Unsupported src protocol " + srcProtocol); + } + }catch (Exception e){ + logger.error(e.getMessage(), e); + if(fileTransferRequestModel != null) { + fileTransferRequestModel.setTransferStatus(FileTransferStatus.FAILED); + try { + fileTransferRequestDao.createFileTransferRequest(fileTransferRequestModel); + } catch (JsonProcessingException ex) { + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + throw new DataManagerException(e); + }finally { + if(srcFile != null) + srcFile.delete(); + } + } + + /** + * Transfer file between two storage resources asynchronously. Returns the file transfer request id + * + * @param gatewayId + * @param username + * @param srcHostname + * @param srcLoginName + * @param srcPort + * @param srcProtocol + * @param srcPath + * @param srcHostCredToken + * @param destHostname + * @param destLoginName + * @param destPort + * @param destProtocol + * @param destinationPath + * @param destHostCredToken + * @param callbackEmails + * @return + * @throws DataManagerException + */ + @Override + public String transferFileAsync(String gatewayId, String username, String srcHostname, String srcLoginName, int srcPort, StorageResourceProtocol srcProtocol, + String srcPath, String srcHostCredToken, String destHostname, String destLoginName, + int destPort, StorageResourceProtocol destProtocol, String destinationPath, + String destHostCredToken, String[] callbackEmails) throws DataManagerException { + return null; + } + + /** + * Get a directory listing of the specified source directory + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param path + * @param hostCredential + * @return + * @throws DataManagerException + */ + @Override + public List<LSEntryModel> getDirectoryListing(String hostname, String loginName, int port, StorageResourceProtocol protocol, + String path, String hostCredential) throws DataManagerException { + return null; + } + + /** + * Move file from one place to another inside the same storage resource + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param sourcePath + * @param destinationPath + * @throws DataManagerException + */ + @Override + public void moveFile(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String sourcePath, String destinationPath) throws DataManagerException { + + } + + /** + * Rename a file + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param sourcePath + * @param newName + * @throws DataManagerException + */ + @Override + public void renameFile(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String sourcePath, String newName) throws DataManagerException { + + } + + /** + * Create new directory + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param dirPath + * @throws DataManagerException + */ + @Override + public void mkdir(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String dirPath) throws DataManagerException { + + } + + /** + * Delete File in storage resource + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param filePath + * @throws DataManagerException + */ + @Override + public void deleteFile(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String filePath) throws DataManagerException { + + } + + /** + * Check whether the specified file exists + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param filePath + * @return + * @throws DataManagerException + */ + @Override + public boolean isExists(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String filePath) throws DataManagerException { + return false; + } + + /** + * Check whether the path points to a directory + * + * @param hostname + * @param loginName + * @param port + * @param protocol + * @param hostCredential + * @param filePath + * @return + * @throws DataManagerException + */ + @Override + public boolean isDirectory(String hostname, String loginName, int port, StorageResourceProtocol protocol, String hostCredential, + String filePath) throws DataManagerException { + return false; + } + + /** + * Method to retrieve file transfer status giving transfer id + * + * @param transferId + * @return + * @throws DataManagerException + */ + @Override + public FileTransferRequestModel getFileTransferRequestStatus(String transferId) throws DataManagerException { + try{ + return fileTransferRequestDao.getFileTransferRequest(transferId); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + + //TODO API Call to Credential Store + private SSHCredential getCredential(String credentialStoreToken) throws DataManagerException { + try{ + SSHCredential sshCredential = new SSHCredential(); + File privateKey = new File("/Users/supun/.ssh/id_rsa"); + byte[] privateKeyBytes = IOUtils.toByteArray(new FileInputStream(privateKey)); + File publicKey = new File("/Users/supun/.ssh/id_rsa.pub"); + byte[] publicKeyBytes = IOUtils.toByteArray(new FileInputStream(publicKey)); + String passPhrase = "cecilia@1990"; + sshCredential.setPrivateKey(privateKeyBytes); + sshCredential.setPublicKey(publicKeyBytes); + sshCredential.setPassphrase(passPhrase); + return sshCredential; + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + public static void main(String[] args) throws IOException, DataManagerException { + FileTransferServiceImpl fileTransferService = new FileTransferServiceImpl(); + String sourceFile = "fsgsdgsdgsdgsdg"; + String transferId = fileTransferService.uploadFile("default", "supun", sourceFile.getBytes(), "gw75.iu.xsede.org", + "pga", 22, StorageResourceProtocol.SCP, "/var/www/portals/test.file", null); + FileTransferRequestModel fileTransferRequestModel = fileTransferService.fileTransferRequestDao.getFileTransferRequest(transferId); + System.out.println("file transfer id:" + fileTransferRequestModel.getTransferId()); + + transferId = fileTransferService.transferFile("default", "supun", "gw75.iu.xsede.org", "pga", 22, StorageResourceProtocol.SCP, + "/var/www/portals/test.file", null, "gw75.iu.xsede.org", "pga", 22, StorageResourceProtocol.SCP, + "/var/www/portals/test2.file", null); + fileTransferRequestModel = fileTransferService.fileTransferRequestDao.getFileTransferRequest(transferId); + System.out.println("file transfer id:" + fileTransferRequestModel.getTransferId()); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogService.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogService.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogService.java new file mode 100644 index 0000000..15172a3 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogService.java @@ -0,0 +1,76 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.apache.airavata.model.data.metadata.MetadataModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class MetadataCatalogService implements org.apache.airavata.data.manager.cpi.MetadataCatalogService { + private final static Logger logger = LoggerFactory.getLogger(MetadataCatalogService.class); + + /** + * Create new metadata model + * + * @param metadataModel + * @return + * @throws DataManagerException + */ + @Override + public String createMetadata(MetadataModel metadataModel) throws DataManagerException { + return null; + } + + /** + * Update existing metadata model + * + * @param metadataModel + * @throws DataManagerException + */ + @Override + public void updateMetadata(MetadataModel metadataModel) throws DataManagerException { + + } + + /** + * Delete existing metadata model + * + * @param metadataId + * @throws DataManagerException + */ + @Override + public void deleteMetadata(String metadataId) throws DataManagerException { + + } + + /** + * Retrieve metadata model + * + * @param metadataId + * @return + * @throws DataManagerException + */ + @Override + public MetadataModel getMetadata(String metadataId) throws DataManagerException { + return null; + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogServiceImpl.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogServiceImpl.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogServiceImpl.java new file mode 100644 index 0000000..9f29c92 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/MetadataCatalogServiceImpl.java @@ -0,0 +1,105 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import org.apache.airavata.data.manager.core.db.dao.MetadataDao; +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.apache.airavata.model.data.metadata.MetadataModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; + +public class MetadataCatalogServiceImpl extends MetadataCatalogService { + private final static Logger logger = LoggerFactory.getLogger(MetadataCatalogServiceImpl.class); + + private MetadataDao metadataDao; + + public MetadataCatalogServiceImpl() throws IOException { + this.metadataDao = new MetadataDao(); + } + + /** + * Create new metadata model + * + * @param metadataModel + * @return + * @throws DataManagerException + */ + @Override + public String createMetadata(MetadataModel metadataModel) throws DataManagerException { + try{ + return metadataDao.createMetadata(metadataModel); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + + /** + * Update exisiting metadata model + * + * @param metadataModel + * @throws DataManagerException + */ + @Override + public void updateMetadata(MetadataModel metadataModel) throws DataManagerException { + try{ + metadataDao.updateMetadata(metadataModel); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + + /** + * Delete existing metadata model + * + * @param metadataId + * @throws DataManagerException + */ + @Override + public void deleteMetadata(String metadataId) throws DataManagerException { + try{ + metadataDao.deleteMetadata(metadataId); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } + + /** + * Retrieve metadata model + * + * @param metadataId + * @return + * @throws DataManagerException + */ + @Override + public MetadataModel getMetadata(String metadataId) throws DataManagerException { + try{ + return metadataDao.getMetadata(metadataId); + }catch (Exception e){ + logger.error(e.getMessage(), e); + throw new DataManagerException(e); + } + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ReplicaCatalogServiceImpl.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ReplicaCatalogServiceImpl.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ReplicaCatalogServiceImpl.java new file mode 100644 index 0000000..e7bde66 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ReplicaCatalogServiceImpl.java @@ -0,0 +1,172 @@ +/* + * + * 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 org.apache.airavata.data.manager.core; + +import org.apache.airavata.data.manager.core.db.dao.FileCollectionDao; +import org.apache.airavata.data.manager.core.db.dao.FileDao; +import org.apache.airavata.data.manager.cpi.DataManagerException; +import org.apache.airavata.data.manager.cpi.ReplicaCatalogService; +import org.apache.airavata.model.data.replica.FileCollectionModel; +import org.apache.airavata.model.data.replica.FileModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; + +public class ReplicaCatalogServiceImpl implements ReplicaCatalogService { + private final static Logger logger = LoggerFactory.getLogger(ReplicaCatalogServiceImpl.class); + + private FileDao fileDao; + private FileCollectionDao fileCollectionDao; + + public ReplicaCatalogServiceImpl() throws IOException { + this.fileDao = new FileDao(); + this.fileCollectionDao = new FileCollectionDao(); + } + + /** + * Creates a new file entry in the replica catalog + * + * @param fileModel + * @return + */ + @Override + public String registerFileDetails(FileModel fileModel) throws DataManagerException { + try{ + return fileDao.createFile(fileModel); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Updates an existing file information + * + * @param fileModel + */ + @Override + public void updateFileDetails(FileModel fileModel) throws DataManagerException { + try{ + fileDao.updateFile(fileModel); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Deletes the specified file details entry + * + * @param fileId + */ + @Override + public void deleteFileDetails(String fileId) throws DataManagerException { + try{ + fileDao.deleteFile(fileId); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Retrieves file details for the specified file id + * + * @param fileId + * @return + */ + @Override + public FileModel getFileDetails(String fileId) throws DataManagerException { + try{ + return fileDao.getFile(fileId); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Create new file collection entry + * + * @param fileCollectionModel + * @return + * @throws DataManagerException + */ + @Override + public String registerFileCollection(FileCollectionModel fileCollectionModel) throws DataManagerException { + try{ + return fileCollectionDao.createFileCollection(fileCollectionModel); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Update existing file collection + * + * @param fileCollectionModel + * @throws DataManagerException + */ + @Override + public void updateFileCollection(FileCollectionModel fileCollectionModel) throws DataManagerException { + try{ + fileCollectionDao.updateFileCollection(fileCollectionModel); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Delete exisiting file collection + * + * @param collectionId + * @throws DataManagerException + */ + @Override + public void deleteFileCollection(String collectionId) throws DataManagerException { + try{ + fileCollectionDao.deleteFileCollection(collectionId); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } + + /** + * Retrieve file collection specifying the collection id + * + * @param collectionId + * @return + * @throws DataManagerException + */ + @Override + public FileCollectionModel getFileCollection(String collectionId) throws DataManagerException { + try{ + return fileCollectionDao.getFileCollection(collectionId); + }catch (Exception ex){ + logger.error(ex.getMessage(), ex); + throw new DataManagerException(ex); + } + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftDeserializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftDeserializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftDeserializer.java new file mode 100644 index 0000000..0841f45 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftDeserializer.java @@ -0,0 +1,151 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion; + +import com.fasterxml.jackson.core.JsonParser; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.*; +import com.fasterxml.jackson.databind.node.JsonNodeType; +import com.fasterxml.jackson.databind.node.ObjectNode; +import com.fasterxml.jackson.databind.type.TypeFactory; +import com.google.common.base.CaseFormat; +import org.apache.thrift.TBase; +import org.apache.thrift.TException; +import org.apache.thrift.TFieldIdEnum; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.lang.reflect.Field; +import java.lang.reflect.ParameterizedType; +import java.util.Iterator; +import java.util.Map; + +/** + * This abstract class represents a generic de-serializer for converting JSON to Thrift-based entities. + * + * @param <E> An implementation of the {@link org.apache.thrift.TFieldIdEnum} interface. + * @param <T> An implementation of the {@link org.apache.thrift.TBase} interface. + */ +public abstract class AbstractThriftDeserializer<E extends TFieldIdEnum, T extends TBase<T, E>> extends JsonDeserializer<T> { + + private static Logger log = LoggerFactory.getLogger(AbstractThriftDeserializer.class); + + @Override + public T deserialize(final JsonParser jp, final DeserializationContext ctxt) throws IOException, JsonProcessingException { + final T instance = newInstance(); + final ObjectMapper mapper = (ObjectMapper)jp.getCodec(); + final ObjectNode rootNode = (ObjectNode)mapper.readTree(jp); + final Iterator<Map.Entry<String, JsonNode>> iterator = rootNode.fields(); + + while(iterator.hasNext()) { + final Map.Entry<String, JsonNode> currentField = iterator.next(); + try { + /* + * If the current node is not a null value, process it. Otherwise, + * skip it. Jackson will treat the null as a 0 for primitive + * number types, which in turn will make Thrift think the field + * has been set. Also we ignore the MongoDB specific _id field + */ + if(currentField.getValue().getNodeType() != JsonNodeType.NULL) { + final E field = getField(CaseFormat.LOWER_UNDERSCORE.to(CaseFormat.UPPER_UNDERSCORE, currentField.getKey())); + final JsonParser parser = currentField.getValue().traverse(); + parser.setCodec(mapper); + final Object value = mapper.readValue(parser, generateValueType(instance, field)); + if(value != null) { + log.debug(String.format("Field %s produced value %s of type %s.", + currentField.getKey(), value, value.getClass().getName())); + instance.setFieldValue(field, value); + } else { + log.debug("Field {} contains a null value. Skipping...", currentField.getKey()); + } + } else { + log.debug("Field {} contains a null value. Skipping...", currentField.getKey()); + } + } catch (final NoSuchFieldException | IllegalArgumentException e) { + log.error("Unable to de-serialize field '{}'.", currentField.getKey(), e); + ctxt.mappingException(e.getMessage()); + } + } + + try { + // Validate that the instance contains all required fields. + validate(instance); + } catch (final TException e) { + log.error(String.format("Unable to deserialize JSON '%s' to type '%s'.", + jp.getValueAsString(), instance.getClass().getName(), e)); + ctxt.mappingException(e.getMessage()); + } + + return instance; + } + + /** + * Returns the {@code <E>} enumerated value that represents the target + * field in the Thrift entity referenced in the JSON document. + * @param fieldName The name of the Thrift entity target field. + * @return The {@code <E>} enumerated value that represents the target + * field in the Thrift entity referenced in the JSON document. + */ + protected abstract E getField(String fieldName); + + /** + * Creates a new instance of the Thrift entity class represented by this deserializer. + * @return A new instance of the Thrift entity class represented by this deserializer. + */ + protected abstract T newInstance(); + + /** + * Validates that the Thrift entity instance contains all required fields after deserialization. + * @param instance A Thrift entity instance. + * @throws org.apache.thrift.TException if unable to validate the instance. + */ + protected abstract void validate(T instance) throws TException; + + /** + * Generates a {@link JavaType} that matches the target Thrift field represented by the provided + * {@code <E>} enumerated value. If the field's type includes generics, the generics will + * be added to the generated {@link JavaType} to support proper conversion. + * @param thriftInstance The Thrift-generated class instance that will be converted to/from JSON. + * @param field A {@code <E>} enumerated value that represents a field in a Thrift-based entity. + * @return The {@link JavaType} representation of the type associated with the field. + * @throws NoSuchFieldException if unable to determine the field's type. + * @throws SecurityException if unable to determine the field's type. + */ + protected JavaType generateValueType(final T thriftInstance, final E field) throws NoSuchFieldException, SecurityException { + final TypeFactory typeFactory = TypeFactory.defaultInstance(); + + final Field declaredField = thriftInstance.getClass().getDeclaredField(field.getFieldName()); + if(declaredField.getType().equals(declaredField.getGenericType())) { + log.debug("Generating JavaType for type '{}'.", declaredField.getType()); + return typeFactory.constructType(declaredField.getType()); + } else { + final ParameterizedType type = (ParameterizedType)declaredField.getGenericType(); + final Class<?>[] parameterizedTypes = new Class<?>[type.getActualTypeArguments().length]; + for(int i=0; i<type.getActualTypeArguments().length; i++) { + parameterizedTypes[i] = (Class<?>)type.getActualTypeArguments()[i]; + } + log.debug("Generating JavaType for type '{}' with generics '{}'", declaredField.getType(), parameterizedTypes); + return typeFactory.constructParametricType(declaredField.getType(), parameterizedTypes); + } + } + +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftSerializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftSerializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftSerializer.java new file mode 100644 index 0000000..c469af6 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/AbstractThriftSerializer.java @@ -0,0 +1,122 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion; + +import com.fasterxml.jackson.core.JsonGenerator; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonSerializer; +import com.fasterxml.jackson.databind.SerializerProvider; +import com.google.common.base.CaseFormat; +import org.apache.thrift.TBase; +import org.apache.thrift.TFieldIdEnum; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.util.Collection; + +/** + * This abstract class represents a generic serializer for converting Thrift-based entities + * to JSON. + * + * @param <E> An implementation of the {@link org.apache.thrift.TFieldIdEnum} interface. + * @param <T> An implementation of the {@link org.apache.thrift.TBase} interface. + */ +public abstract class AbstractThriftSerializer<E extends TFieldIdEnum, T extends TBase<T, E>> + extends JsonSerializer<T> { + + private static final Logger log = LoggerFactory.getLogger(AbstractThriftSerializer.class); + + @Override + public Class<T> handledType() { + return getThriftClass(); + } + + @Override + public void serialize(final T value, final JsonGenerator jgen, final SerializerProvider provider) + throws IOException, JsonProcessingException { + jgen.writeStartObject(); + for(final E field : getFieldValues()) { + if(value.isSet(field)) { + final Object fieldValue = value.getFieldValue(field); + if(fieldValue != null) { + log.debug("Adding field {} to the JSON string...", + CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName()) + ); + + jgen.writeFieldName(CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName())); + if(fieldValue instanceof Short) { + jgen.writeNumber((Short)fieldValue); + } else if(fieldValue instanceof Integer) { + jgen.writeNumber((Integer)fieldValue); + } else if(fieldValue instanceof Long) { + jgen.writeNumber((Long)fieldValue); + } else if(fieldValue instanceof Double) { + jgen.writeNumber((Double)fieldValue); + } else if(fieldValue instanceof Float) { + jgen.writeNumber((Float)fieldValue); + } else if(fieldValue instanceof Boolean) { + jgen.writeBoolean((Boolean)fieldValue); + } else if(fieldValue instanceof String) { + jgen.writeString(fieldValue.toString()); + } else if(fieldValue instanceof Collection) { + log.debug("Array opened for field {}.", + CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName()) + ); + jgen.writeStartArray(); + for(final Object arrayObject : (Collection<?>)fieldValue) { + jgen.writeObject(arrayObject); + } + jgen.writeEndArray(); + log.debug("Array closed for field {}.", + CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName()) + ); + } else { + jgen.writeObject(fieldValue); + } + } else { + log.debug("Skipping converting field {} to JSON: value is null!", + CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName()) + ); + } + } else { + log.debug("Skipping converting field {} to JSON: field has not been set!", + CaseFormat.UPPER_CAMEL.to(CaseFormat.LOWER_UNDERSCORE,field.getFieldName()) + ); + } + } + jgen.writeEndObject(); + } + + /** + * Returns an array of {@code <E>} enumerated values that represent the fields present in the + * Thrift class associated with this serializer. + * @return The array of {@code <E>} enumerated values that represent the fields present in the + * Thrift class. + */ + protected abstract E[] getFieldValues(); + + /** + * Returns the {@code <T>} implementation class associated with this serializer. + * @return The {@code <T>} implementation class + */ + protected abstract Class<T> getThriftClass(); +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/ModelConversionHelper.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/ModelConversionHelper.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/ModelConversionHelper.java new file mode 100644 index 0000000..99dfbfc --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/ModelConversionHelper.java @@ -0,0 +1,102 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.Version; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.module.SimpleModule; +import org.apache.airavata.data.manager.core.db.conversion.metadata.MetadataDeserializer; +import org.apache.airavata.data.manager.core.db.conversion.metadata.MetadataSerializer; +import org.apache.airavata.data.manager.core.db.conversion.transfer.FileTransferRequestDeserializer; +import org.apache.airavata.data.manager.core.db.conversion.transfer.FileTransferRequestSerializer; +import org.apache.airavata.data.manager.core.db.conversion.replica.FileCollectionDeserializer; +import org.apache.airavata.data.manager.core.db.conversion.replica.FileCollectionSerializer; +import org.apache.airavata.data.manager.core.db.conversion.replica.FileDeserializer; +import org.apache.airavata.data.manager.core.db.conversion.replica.FileSerializer; +import org.apache.airavata.model.data.metadata.MetadataModel; +import org.apache.airavata.model.data.transfer.FileTransferRequestModel; +import org.apache.airavata.model.data.replica.FileCollectionModel; +import org.apache.airavata.model.data.replica.FileModel; +import org.apache.thrift.TBase; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; + + +/** + * This is utility class for model conversion of thrift to/from json + */ +public class ModelConversionHelper { + private final static Logger logger = LoggerFactory.getLogger(ModelConversionHelper.class); + + private ObjectMapper objectMapper; + + public ModelConversionHelper(){ + init(); + } + + /** + * Private method to register the custom serializers and deserializers + */ + private void init(){ + this.objectMapper = new ObjectMapper(); + SimpleModule module = new SimpleModule("DataManager", + new Version(1,0,0,null,null,null)); + + module.addSerializer(FileTransferRequestModel.class, new FileTransferRequestSerializer()); + module.addDeserializer(FileTransferRequestModel.class, new FileTransferRequestDeserializer()); + + module.addSerializer(FileModel.class, new FileSerializer()); + module.addDeserializer(FileModel.class, new FileDeserializer()); + + module.addSerializer(FileCollectionModel.class, new FileCollectionSerializer()); + module.addDeserializer(FileCollectionModel.class, new FileCollectionDeserializer()); + + module.addSerializer(MetadataModel.class, new MetadataSerializer()); + module.addDeserializer(MetadataModel.class, new MetadataDeserializer()); + + objectMapper.registerModule(module); + } + + /** + * Method to serialize a thrift object to json + * @param object + * @return + * @throws JsonProcessingException + */ + public String serializeObject(TBase object) throws JsonProcessingException { + String json = this.objectMapper.writeValueAsString(object); + return json; + } + + /** + * Method to deserialize a json to the thrift object + * @param clz + * @param json + * @return + * @throws IOException + */ + public TBase deserializeObject(Class<?> clz, String json) throws IOException { + return (TBase)this.objectMapper.readValue(json, clz); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataDeserializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataDeserializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataDeserializer.java new file mode 100644 index 0000000..a6ce1b4 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataDeserializer.java @@ -0,0 +1,44 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.metadata; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftDeserializer; +import org.apache.airavata.model.data.metadata.MetadataModel; +import org.apache.thrift.TException; + +public class MetadataDeserializer extends + AbstractThriftDeserializer<MetadataModel._Fields, MetadataModel> { + + @Override + protected MetadataModel._Fields getField(final String fieldName) { + return MetadataModel._Fields.valueOf(fieldName); + } + + @Override + protected MetadataModel newInstance() { + return new MetadataModel(); + } + + @Override + protected void validate(final MetadataModel instance) throws TException { + instance.validate(); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataSerializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataSerializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataSerializer.java new file mode 100644 index 0000000..c07484a --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/metadata/MetadataSerializer.java @@ -0,0 +1,41 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.metadata; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftSerializer; +import org.apache.airavata.model.data.metadata.MetadataModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class MetadataSerializer extends + AbstractThriftSerializer<MetadataModel._Fields, MetadataModel> { + private final static Logger logger = LoggerFactory.getLogger(MetadataSerializer.class); + + @Override + protected MetadataModel._Fields[] getFieldValues() { + return MetadataModel._Fields.values(); + } + + @Override + protected Class<MetadataModel> getThriftClass() { + return null; + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionDeserializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionDeserializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionDeserializer.java new file mode 100644 index 0000000..a34ab1b --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionDeserializer.java @@ -0,0 +1,44 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.replica; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftDeserializer; +import org.apache.airavata.model.data.replica.FileCollectionModel; +import org.apache.thrift.TException; + +public class FileCollectionDeserializer extends + AbstractThriftDeserializer<FileCollectionModel._Fields, FileCollectionModel> { + + @Override + protected FileCollectionModel._Fields getField(final String fieldName) { + return FileCollectionModel._Fields.valueOf(fieldName); + } + + @Override + protected FileCollectionModel newInstance() { + return new FileCollectionModel(); + } + + @Override + protected void validate(final FileCollectionModel instance) throws TException { + instance.validate(); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionSerializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionSerializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionSerializer.java new file mode 100644 index 0000000..56ed65e --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileCollectionSerializer.java @@ -0,0 +1,41 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.replica; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftSerializer; +import org.apache.airavata.model.data.replica.FileCollectionModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class FileCollectionSerializer extends + AbstractThriftSerializer<FileCollectionModel._Fields, FileCollectionModel> { + private final static Logger logger = LoggerFactory.getLogger(FileCollectionSerializer.class); + + @Override + protected FileCollectionModel._Fields[] getFieldValues() { + return FileCollectionModel._Fields.values(); + } + + @Override + protected Class<FileCollectionModel> getThriftClass() { + return null; + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileDeserializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileDeserializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileDeserializer.java new file mode 100644 index 0000000..d1e84d5 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileDeserializer.java @@ -0,0 +1,44 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.replica; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftDeserializer; +import org.apache.airavata.model.data.replica.FileModel; +import org.apache.thrift.TException; + +public class FileDeserializer extends + AbstractThriftDeserializer<FileModel._Fields, FileModel> { + + @Override + protected FileModel._Fields getField(final String fieldName) { + return FileModel._Fields.valueOf(fieldName); + } + + @Override + protected FileModel newInstance() { + return new FileModel(); + } + + @Override + protected void validate(final FileModel instance) throws TException { + instance.validate(); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileSerializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileSerializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileSerializer.java new file mode 100644 index 0000000..3a37645 --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/replica/FileSerializer.java @@ -0,0 +1,41 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.replica; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftSerializer; +import org.apache.airavata.model.data.replica.FileModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class FileSerializer extends + AbstractThriftSerializer<FileModel._Fields, FileModel> { + private final static Logger logger = LoggerFactory.getLogger(FileSerializer.class); + + @Override + protected FileModel._Fields[] getFieldValues() { + return FileModel._Fields.values(); + } + + @Override + protected Class<FileModel> getThriftClass() { + return null; + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestDeserializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestDeserializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestDeserializer.java new file mode 100644 index 0000000..e039d1c --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestDeserializer.java @@ -0,0 +1,44 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.transfer; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftDeserializer; +import org.apache.airavata.model.data.transfer.FileTransferRequestModel; +import org.apache.thrift.TException; + +public class FileTransferRequestDeserializer extends + AbstractThriftDeserializer<FileTransferRequestModel._Fields, FileTransferRequestModel> { + + @Override + protected FileTransferRequestModel._Fields getField(final String fieldName) { + return FileTransferRequestModel._Fields.valueOf(fieldName); + } + + @Override + protected FileTransferRequestModel newInstance() { + return new FileTransferRequestModel(); + } + + @Override + protected void validate(final FileTransferRequestModel instance) throws TException { + instance.validate(); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestSerializer.java ---------------------------------------------------------------------- diff --git a/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestSerializer.java b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestSerializer.java new file mode 100644 index 0000000..0c40d2c --- /dev/null +++ b/modules/data-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/db/conversion/transfer/FileTransferRequestSerializer.java @@ -0,0 +1,41 @@ +/* + * + * 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 org.apache.airavata.data.manager.core.db.conversion.transfer; + +import org.apache.airavata.data.manager.core.db.conversion.AbstractThriftSerializer; +import org.apache.airavata.model.data.transfer.FileTransferRequestModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class FileTransferRequestSerializer extends + AbstractThriftSerializer<FileTransferRequestModel._Fields, FileTransferRequestModel> { + private final static Logger logger = LoggerFactory.getLogger(FileTransferRequestSerializer.class); + + @Override + protected FileTransferRequestModel._Fields[] getFieldValues() { + return FileTransferRequestModel._Fields.values(); + } + + @Override + protected Class<FileTransferRequestModel> getThriftClass() { + return null; + } +} \ No newline at end of file
