http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java index 6c3e703..0b21d0e 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class ProcessStatus implements org.apache.thrift.TBase<ProcessStatus, ProcessStatus._Fields>, java.io.Serializable, Cloneable, Comparable<ProcessStatus> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("ProcessStatus");
http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java index b862fe5..ba34407 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class TaskStatus implements org.apache.thrift.TBase<TaskStatus, TaskStatus._Fields>, java.io.Serializable, Cloneable, Comparable<TaskStatus> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("TaskStatus"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java index 5ad7c2c..d509856 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class DataStagingTaskModel implements org.apache.thrift.TBase<DataStagingTaskModel, DataStagingTaskModel._Fields>, java.io.Serializable, Cloneable, Comparable<DataStagingTaskModel> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("DataStagingTaskModel"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java index 72e480d..3460741 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java @@ -55,7 +55,7 @@ import org.slf4j.LoggerFactory; * EnvironmentSetupTaskModel: A structure holding the environment creation task details * */ -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class EnvironmentSetupTaskModel implements org.apache.thrift.TBase<EnvironmentSetupTaskModel, EnvironmentSetupTaskModel._Fields>, java.io.Serializable, Cloneable, Comparable<EnvironmentSetupTaskModel> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("EnvironmentSetupTaskModel"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java index 936cbdf..0037cbf 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class JobSubmissionTaskModel implements org.apache.thrift.TBase<JobSubmissionTaskModel, JobSubmissionTaskModel._Fields>, java.io.Serializable, Cloneable, Comparable<JobSubmissionTaskModel> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("JobSubmissionTaskModel"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java index 74eac6d..4127d0e 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class MonitorTaskModel implements org.apache.thrift.TBase<MonitorTaskModel, MonitorTaskModel._Fields>, java.io.Serializable, Cloneable, Comparable<MonitorTaskModel> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("MonitorTaskModel"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java index eac5a11..def2e53 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java @@ -60,7 +60,7 @@ import org.slf4j.LoggerFactory; * subTaskModel: * A generic byte object for the Task developer to store internal serialized data into registry catalogs. */ -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class TaskModel implements org.apache.thrift.TBase<TaskModel, TaskModel._Fields>, java.io.Serializable, Cloneable, Comparable<TaskModel> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("TaskModel"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow_data_modelConstants.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow_data_modelConstants.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow_data_modelConstants.java deleted file mode 100644 index e74de28..0000000 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow_data_modelConstants.java +++ /dev/null @@ -1,58 +0,0 @@ -/** - * 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. - */ - -/** - * Autogenerated by Thrift Compiler (0.9.2) - * - * DO NOT EDIT UNLESS YOU ARE SURE THAT YOU KNOW WHAT YOU ARE DOING - * @generated - */ -package org.apache.airavata.model; - -import org.apache.thrift.scheme.IScheme; -import org.apache.thrift.scheme.SchemeFactory; -import org.apache.thrift.scheme.StandardScheme; - -import org.apache.thrift.scheme.TupleScheme; -import org.apache.thrift.protocol.TTupleProtocol; -import org.apache.thrift.protocol.TProtocolException; -import org.apache.thrift.EncodingUtils; -import org.apache.thrift.TException; -import org.apache.thrift.async.AsyncMethodCallback; -import org.apache.thrift.server.AbstractNonblockingServer.*; -import java.util.List; -import java.util.ArrayList; -import java.util.Map; -import java.util.HashMap; -import java.util.EnumMap; -import java.util.Set; -import java.util.HashSet; -import java.util.EnumSet; -import java.util.Collections; -import java.util.BitSet; -import java.nio.ByteBuffer; -import java.util.Arrays; -import javax.annotation.Generated; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -@SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -public class workflow_data_modelConstants { - - public static final String DEFAULT_ID = "DO_NOT_SET_AT_CLIENTS"; - -} http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java index ed97270..6b4bffe 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class Gateway implements org.apache.thrift.TBase<Gateway, Gateway._Fields>, java.io.Serializable, Cloneable, Comparable<Gateway> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("Gateway"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java index c8f1baf..01a1817 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class Group implements org.apache.thrift.TBase<Group, Group._Fields>, java.io.Serializable, Cloneable, Comparable<Group> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("Group"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java index 174882a..1a7918f 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class Project implements org.apache.thrift.TBase<Project, Project._Fields>, java.io.Serializable, Cloneable, Comparable<Project> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("Project"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java index 05bf930..87fbf72 100644 --- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java +++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java @@ -51,7 +51,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"}) -@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-22") +@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)", date = "2015-12-23") public class User implements org.apache.thrift.TBase<User, User._Fields>, java.io.Serializable, Cloneable, Comparable<User> { private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new org.apache.thrift.protocol.TStruct("User"); http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/pom.xml ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/pom.xml b/modules/file-manager/data-manager-core/pom.xml deleted file mode 100644 index e63bcf1..0000000 --- a/modules/file-manager/data-manager-core/pom.xml +++ /dev/null @@ -1,61 +0,0 @@ -<?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> - </dependencies> -</project> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerFactory.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerFactory.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerFactory.java deleted file mode 100644 index cd92146..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerFactory.java +++ /dev/null @@ -1,34 +0,0 @@ -/* - * - * 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 DataManagerFactory { - private final static Logger logger = LoggerFactory.getLogger(DataManagerFactory.class); - - public static DataManager getDataManager() throws DataManagerException { - return new DataManagerImpl(); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerImpl.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerImpl.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerImpl.java deleted file mode 100644 index 0cef6e0..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/DataManagerImpl.java +++ /dev/null @@ -1,444 +0,0 @@ -/* - * - * 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.jcraft.jsch.JSch; -import com.jcraft.jsch.JSchException; -import com.jcraft.jsch.Session; -import org.apache.airavata.common.exception.ApplicationSettingsException; -import org.apache.airavata.common.utils.ServerSettings; -import org.apache.airavata.credential.store.client.CredentialStoreClientFactory; -import org.apache.airavata.credential.store.cpi.CredentialStoreService; -import org.apache.airavata.credential.store.datamodel.SSHCredential; -import org.apache.airavata.credential.store.exception.CredentialStoreException; -import org.apache.airavata.data.manager.core.ssh.SSHUtils; -import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile; -import org.apache.airavata.model.appcatalog.gatewayprofile.StoragePreference; -import org.apache.airavata.model.appcatalog.storageresource.StorageResourceDescription; -import org.apache.airavata.model.data.movement.DataMovementInterface; -import org.apache.airavata.model.data.movement.DataMovementProtocol; -import org.apache.airavata.model.data.movement.SCPDataMovement; -import org.apache.airavata.model.data.resource.DataReplicaLocationModel; -import org.apache.airavata.model.data.resource.DataResourceModel; -import org.apache.airavata.model.data.resource.DataResourceType; -import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory; -import org.apache.airavata.registry.cpi.AppCatalog; -import org.apache.airavata.registry.cpi.AppCatalogException; -import org.apache.airavata.registry.cpi.DataCatalog; -import org.apache.airavata.registry.cpi.DataCatalogException; - -import org.apache.airavata.data.manager.cpi.DataManager; -import org.apache.airavata.data.manager.cpi.DataManagerException; -import org.apache.thrift.TException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.File; -import java.io.IOException; -import java.util.List; -import java.util.Optional; -import java.util.Properties; -import java.util.UUID; - -public class DataManagerImpl implements DataManager { - private final static Logger logger = LoggerFactory.getLogger(DataManagerImpl.class); - - private final AppCatalog appCatalog; - private final DataCatalog dataCatalog; - - public DataManagerImpl() throws DataManagerException { - try { - this.appCatalog = RegistryFactory.getAppCatalog(); - this.dataCatalog = RegistryFactory.getDataCatalog(); - } catch (Exception e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - public DataManagerImpl(AppCatalog appCatalog, DataCatalog dataCatalog){ - this.appCatalog = appCatalog; - this.dataCatalog = dataCatalog; - } - - /** - * To create a replica entry for an already existing file(s). This is how the system comes to know about already - * existing resources - * @param dataResourceModel - * @return - */ - @Override - public String registerResource(DataResourceModel dataResourceModel) throws DataManagerException { - try { - String resourceId = dataCatalog.registerResource(dataResourceModel); - return resourceId; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To remove a resource entry from the replica catalog - * @param resourceId - * @return - */ - @Override - public boolean removeResource(String resourceId) throws DataManagerException { - try { - boolean result = dataCatalog.removeResource(resourceId); - return result; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To update an existing data resource model - * @param dataResourceModel - * @return - * @throws DataCatalogException - */ - @Override - public boolean updateResource(DataResourceModel dataResourceModel) throws DataManagerException { - try { - boolean result = dataCatalog.updateResource(dataResourceModel); - return result; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To retrieve a resource object providing the resourceId - * @param resourceId - * @return - */ - @Override - public DataResourceModel getResource(String resourceId) throws DataManagerException { - try { - DataResourceModel dataResource = dataCatalog.getResource(resourceId); - return dataResource; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To create a new data replica location. This is how the system comes to know about already - * existing resources - * - * @param dataReplicaLocationModel - * @return - */ - @Override - public String registerReplicaLocation(DataReplicaLocationModel dataReplicaLocationModel) throws DataManagerException { - try { - String replicaId = dataCatalog.registerReplicaLocation(dataReplicaLocationModel); - return replicaId; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To remove a replica entry from the replica catalog - * - * @param replicaId - * @return - */ - @Override - public boolean removeReplicaLocation(String replicaId) throws DataManagerException { - try { - boolean result = dataCatalog.removeReplicaLocation(replicaId); - return result; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To update an existing data replica model - * - * @param dataReplicaLocationModel - * @return - * @throws DataCatalogException - */ - @Override - public boolean updateReplicaLocation(DataReplicaLocationModel dataReplicaLocationModel) throws DataManagerException { - try { - boolean result = dataCatalog.updateReplicaLocation(dataReplicaLocationModel); - return result; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To retrieve a replica object providing the replicaId - * - * @param replicaId - * @return - */ - @Override - public DataReplicaLocationModel getReplicaLocation(String replicaId) throws DataManagerException { - try { - DataReplicaLocationModel dataReplicaLocationModel = dataCatalog.getReplicaLocation(replicaId); - return dataReplicaLocationModel; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * To retrieve all the replica entries for a given resource id - * - * @param resourceId - * @return - * @throws DataCatalogException - */ - @Override - public List<DataReplicaLocationModel> getAllReplicaLocations(String resourceId) throws DataManagerException { - try { - List<DataReplicaLocationModel> dataReplicaLocationModelList = dataCatalog.getAllReplicaLocations(resourceId); - return dataReplicaLocationModelList; - } catch (DataCatalogException e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * API method to copy a resource to the provided destination storage resource. Only resources of type FILE can be - * copied using this API method. - * - * @param dataResourceId - * @param destStorageResourceId - * @param destinationParentPath - * @return - */ - @Override - public String copyResource(String dataResourceId, String destStorageResourceId, String destinationParentPath) throws DataManagerException { - try { - return copyReplica(dataResourceId, null, destStorageResourceId, destinationParentPath); - } catch (Exception e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * API method to copy the specified replica to the provided destination storage resource. Only resources of type FILE - * can be copied using this API method. Method returns the new replicaId - * - * @param dataResourceId - * @param replicaId - * @param destStorageResourceId - * @param destinationParentPath - * @return - * @throws DataManagerException - */ - @Override - public String copyReplica(String dataResourceId, String replicaId, String destStorageResourceId, String destinationParentPath) throws DataManagerException { - try{ - DataResourceModel dataResourceModel = dataCatalog.getResource(dataResourceId); - if(dataResourceModel.getDataResourceType() != DataResourceType.FILE) - throw new DataCatalogException("Only resources of type FILE can be transferred using this method"); - - StorageResourceDescription destinationStorageResource = appCatalog.getStorageResource() - .getStorageResource(destStorageResourceId); - if(destinationStorageResource == null) - throw new DataCatalogException("Invalid destination storage resource id"); - - List<DataReplicaLocationModel> replicaLocationModels = dataResourceModel.getReplicaLocations(); - if(replicaLocationModels == null || replicaLocationModels.size() == 0) - throw new DataCatalogException("No replicas available for the given data resource"); - - DataReplicaLocationModel sourceReplica = null; - if(replicaId == null || replicaId.isEmpty()) { - //FIXME This should be an intelligent selection - sourceReplica = replicaLocationModels.get(0); - }else{ - for(DataReplicaLocationModel rp : replicaLocationModels){ - if(rp.getReplicaId().equals(replicaId)){ - sourceReplica = rp; - } - } - } - if(sourceReplica == null) - throw new DataManagerException("No matching source replica found"); - - StorageResourceDescription sourceStorageResource = appCatalog.getStorageResource() - .getStorageResource(sourceReplica.getStorageResourceId()); - if(sourceStorageResource == null) - throw new DataCatalogException("Cannot find storage resource of the source replica"); - - //FIXME Currently we support only SCP data movement protocol - List<DataMovementInterface> sourceDataMovementInterfaces = sourceStorageResource.getDataMovementInterfaces(); - Optional<DataMovementInterface> sourceDataMovementInterface = sourceDataMovementInterfaces.stream() - .filter(dmi -> dmi.getDataMovementProtocol() == DataMovementProtocol.SCP).findFirst(); - if(!sourceDataMovementInterface.isPresent()) - throw new DataCatalogException("No matching DMI found for source storage resource"); - List<DataMovementInterface> destDataMovementInterfaces = destinationStorageResource.getDataMovementInterfaces(); - Optional<DataMovementInterface> destDataMovementInterface = destDataMovementInterfaces.stream() - .filter(dmi -> dmi.getDataMovementProtocol() == DataMovementProtocol.SCP).findFirst(); - if(!destDataMovementInterface.isPresent()) - throw new DataCatalogException("No matching DMI found for destination storage resource"); - - //Finding the gateway specific storage preferences for resources - GatewayResourceProfile gatewayProfile = appCatalog.getGatewayProfile().getGatewayProfile(dataResourceModel.getGatewayId()); - List<StoragePreference> storagePreferences = gatewayProfile.getStoragePreferences(); - StoragePreference sourceResourcePreference = null; - for(StoragePreference sp : storagePreferences) { - if (sp.getStorageResourceId().equals(sourceStorageResource.getStorageResourceId())) { - sourceResourcePreference = sp; - break; - } - } - if(sourceResourcePreference == null) - throw new DataCatalogException("Could not find storage preference for storage resource id:" - + sourceStorageResource.getStorageResourceId()); - StoragePreference destResourcePreference = null; - for(StoragePreference sp : storagePreferences) { - if (sp.getStorageResourceId().equals(destStorageResourceId)) { - destResourcePreference = sp; - break; - } - } - if(destResourcePreference == null) - throw new DataCatalogException("Could not find storage preference for storage resource id:" - + destinationStorageResource.getStorageResourceId()); - - String destFilePath = copyUsingScp(gatewayProfile, sourceStorageResource, sourceDataMovementInterface.get(), - sourceResourcePreference, sourceReplica, destinationStorageResource, destDataMovementInterface.get(), - destResourcePreference, destinationParentPath); - - DataReplicaLocationModel dataReplicaLocationModel = new DataReplicaLocationModel(); - dataReplicaLocationModel.setResourceId(dataResourceId); - dataReplicaLocationModel.setFileAbsolutePath(destFilePath); - String newReplicaId = this.registerReplicaLocation(dataReplicaLocationModel); - return newReplicaId; - }catch (Exception e) { - logger.error(e.getMessage(), e); - throw new DataManagerException(e); - } - } - - /** - * This method copies the provided source replica to the destination storage resource and returns the absolute file path - * of the destination file. This method uses the credential store service to fetch required credentials for talking to - * storage resources - * - * @param gatewayProfile - * @param sourceStorageResource - * @param sourceDataMovementInterface - * @param sourceResourcePreference - * @param sourceReplica - * @param destStorageResource - * @param destDataMovementInterface - * @param destResourcePreference - * @param destinationParentPath - * @return - * @throws TException - * @throws ApplicationSettingsException - * @throws AppCatalogException - * @throws JSchException - * @throws IOException - */ - private String copyUsingScp(GatewayResourceProfile gatewayProfile, StorageResourceDescription sourceStorageResource, - DataMovementInterface sourceDataMovementInterface, StoragePreference sourceResourcePreference, - DataReplicaLocationModel sourceReplica, StorageResourceDescription destStorageResource, - DataMovementInterface destDataMovementInterface, StoragePreference destResourcePreference, - String destinationParentPath) - throws Exception { - //Creating JSch sessions - //Source session - Properties config = new java.util.Properties(); - config.put("StrictHostKeyChecking", "no"); - - CredentialStoreService.Client credentialStoreServiceClient = getCredentialStoreServiceClient(); - String sourceHostName = sourceStorageResource.getHostName(); - SCPDataMovement sourceSCPDMI = appCatalog.getComputeResource().getSCPDataMovement(sourceDataMovementInterface.getDataMovementInterfaceId()); - int sourcePort = sourceSCPDMI.getSshPort(); - String sourceLoginUserName = sourceResourcePreference.getLoginUserName(); - JSch sourceJSch = new JSch(); - String sourceCredentialStoreToken; - if(sourceResourcePreference.getResourceSpecificCredentialStoreToken() != null - && !sourceResourcePreference.getResourceSpecificCredentialStoreToken().isEmpty()){ - sourceCredentialStoreToken = sourceResourcePreference.getResourceSpecificCredentialStoreToken(); - }else{ - sourceCredentialStoreToken = gatewayProfile.getCredentialStoreToken(); - } - SSHCredential sourceSshCredential = credentialStoreServiceClient.getSSHCredential(sourceCredentialStoreToken, - gatewayProfile.getGatewayID()); - sourceJSch.addIdentity(UUID.randomUUID().toString(), sourceSshCredential.getPrivateKey().getBytes(), - sourceSshCredential.getPublicKey().getBytes(), sourceSshCredential.getPassphrase().getBytes()); - Session sourceSession = sourceJSch.getSession(sourceLoginUserName, sourceHostName, sourcePort); - sourceSession.setConfig(config); - sourceSession.connect(); - String sourceFilePath = sourceReplica.getFileAbsolutePath(); - - //Destination session - String destHostName = destStorageResource.getHostName(); - SCPDataMovement destSCPDMI = appCatalog.getComputeResource().getSCPDataMovement(destDataMovementInterface - .getDataMovementInterfaceId()); - int destPort = destSCPDMI.getSshPort(); - String destLoginUserName = sourceResourcePreference.getLoginUserName(); - JSch destJSch = new JSch(); - String destCredentialStoreToken; - if(destResourcePreference.getResourceSpecificCredentialStoreToken() != null - && !destResourcePreference.getResourceSpecificCredentialStoreToken().isEmpty()){ - destCredentialStoreToken = destResourcePreference.getResourceSpecificCredentialStoreToken(); - }else{ - destCredentialStoreToken = gatewayProfile.getCredentialStoreToken(); - } - SSHCredential destSshCredential = credentialStoreServiceClient.getSSHCredential(destCredentialStoreToken, - gatewayProfile.getGatewayID()); - destJSch.addIdentity(UUID.randomUUID().toString(), destSshCredential.getPrivateKey().getBytes(), - destSshCredential.getPublicKey().getBytes(), destSshCredential.getPassphrase().getBytes()); - Session destSession = destJSch.getSession(destLoginUserName, destHostName, destPort); - destSession.setConfig(config); - destSession.connect(); - - SSHUtils.scpThirdParty(sourceFilePath, sourceSession, destinationParentPath, destSession); - if(!destinationParentPath.endsWith(File.separator)) - destinationParentPath += File.separator; - String destFilePath = destinationParentPath + (new File(sourceFilePath).getName()); - return destFilePath; - } - - private CredentialStoreService.Client getCredentialStoreServiceClient() throws TException, ApplicationSettingsException { - final int serverPort = Integer.parseInt(ServerSettings.getCredentialStoreServerPort()); - final String serverHost = ServerSettings.getCredentialStoreServerHost(); - try { - return CredentialStoreClientFactory.createAiravataCSClient(serverHost, serverPort); - } catch (CredentialStoreException e) { - throw new TException("Unable to create credential store client...", e); - } - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/CommandOutput.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/CommandOutput.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/CommandOutput.java deleted file mode 100644 index 0d8247a..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/CommandOutput.java +++ /dev/null @@ -1,34 +0,0 @@ -/* - * - * 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.ssh; - -import com.jcraft.jsch.Channel; -import java.io.OutputStream; - -public interface CommandOutput { - void onOutput(Channel var1); - - OutputStream getStandardError(); - - void exitCode(int var1); - - int getExitCode(); -} http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHApiException.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHApiException.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHApiException.java deleted file mode 100644 index 66678e5..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHApiException.java +++ /dev/null @@ -1,33 +0,0 @@ -/* - * - * 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.ssh; - -public class SSHApiException extends Exception { - - public SSHApiException(String message) { - super(message); - } - - public SSHApiException(String message, Exception e) { - super(message, e); - } - -} http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHUtils.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHUtils.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHUtils.java deleted file mode 100644 index 582cade..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/SSHUtils.java +++ /dev/null @@ -1,506 +0,0 @@ -/* - * - * 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.ssh; - -import com.jcraft.jsch.Channel; -import com.jcraft.jsch.ChannelExec; -import com.jcraft.jsch.JSchException; -import com.jcraft.jsch.Session; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.*; -import java.util.Arrays; -import java.util.List; - -/** - * Utility class to do all ssh and scp related things. - */ -public class SSHUtils { - private static final Logger log = LoggerFactory.getLogger(SSHUtils.class); - - - /** - * This will copy a local file to a remote location - * - * @param remoteFile remote location you want to transfer the file, this cannot be a directory, if user pass - * a dirctory we do copy it to that directory but we simply return the directory name - * todo handle the directory name as input and return the proper final output file name - * @param localFile Local file to transfer, this can be a directory - * @return returns the final remote file path, so that users can use the new file location - */ - public static String scpTo(String localFile, String remoteFile, Session session) throws IOException, - JSchException, SSHApiException { - FileInputStream fis = null; - String prefix = null; - if (new File(localFile).isDirectory()) { - prefix = localFile + File.separator; - } - boolean ptimestamp = true; - - // exec 'scp -t rfile' remotely - String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + remoteFile; - Channel channel = session.openChannel("exec"); - - StandardOutReader stdOutReader = new StandardOutReader(); - ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError()); - ((ChannelExec) channel).setCommand(command); - - // get I/O streams for remote scp - OutputStream out = channel.getOutputStream(); - InputStream in = channel.getInputStream(); - - channel.connect(); - - if (checkAck(in) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new SSHApiException(error); - } - - File _lfile = new File(localFile); - - if (ptimestamp) { - command = "T" + (_lfile.lastModified() / 1000) + " 0"; - // The access time should be sent here, - // but it is not accessible with JavaAPI ;-< - command += (" " + (_lfile.lastModified() / 1000) + " 0\n"); - out.write(command.getBytes()); - out.flush(); - if (checkAck(in) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new SSHApiException(error); - } - } - - // send "C0644 filesize filename", where filename should not include '/' - long filesize = _lfile.length(); - command = "C0644 " + filesize + " "; - if (localFile.lastIndexOf('/') > 0) { - command += localFile.substring(localFile.lastIndexOf('/') + 1); - } else { - command += localFile; - } - command += "\n"; - out.write(command.getBytes()); - out.flush(); - if (checkAck(in) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new SSHApiException(error); - } - - // send a content of localFile - fis = new FileInputStream(localFile); - byte[] buf = new byte[1024]; - while (true) { - int len = fis.read(buf, 0, buf.length); - if (len <= 0) break; - out.write(buf, 0, len); //out.flush(); - } - fis.close(); - fis = null; - // send '\0' - buf[0] = 0; - out.write(buf, 0, 1); - out.flush(); - if (checkAck(in) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new SSHApiException(error); - } - out.close(); - stdOutReader.onOutput(channel); - - - channel.disconnect(); - if (stdOutReader.getStdErrorString().contains("scp:")) { - throw new SSHApiException(stdOutReader.getStdErrorString()); - } - //since remote file is always a file we just return the file - return remoteFile; - } - - /** - * This method will copy a remote file to a local directory - * - * @param remoteFile remote file path, this has to be a full qualified path - * @param localFile This is the local file to copy, this can be a directory too - * @return returns the final local file path of the new file came from the remote resource - */ - public static void scpFrom(String remoteFile, String localFile, Session session) throws IOException, - JSchException, SSHApiException { - FileOutputStream fos = null; - try { - String prefix = null; - if (new File(localFile).isDirectory()) { - prefix = localFile + File.separator; - } - - // exec 'scp -f remotefile' remotely - String command = "scp -f " + remoteFile; - Channel channel = session.openChannel("exec"); - ((ChannelExec) channel).setCommand(command); - - StandardOutReader stdOutReader = new StandardOutReader(); - ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError()); - // get I/O streams for remote scp - OutputStream out = channel.getOutputStream(); - InputStream in = channel.getInputStream(); - - if (!channel.isClosed()){ - channel.connect(); - } - - byte[] buf = new byte[1024]; - - // send '\0' - buf[0] = 0; - out.write(buf, 0, 1); - out.flush(); - - while (true) { - int c = checkAck(in); - if (c != 'C') { - break; - } - - // read '0644 ' - in.read(buf, 0, 5); - - long filesize = 0L; - while (true) { - if (in.read(buf, 0, 1) < 0) { - // error - break; - } - if (buf[0] == ' ') break; - filesize = filesize * 10L + (long) (buf[0] - '0'); - } - - String file = null; - for (int i = 0; ; i++) { - in.read(buf, i, 1); - if (buf[i] == (byte) 0x0a) { - file = new String(buf, 0, i); - break; - } - } - - //System.out.println("filesize="+filesize+", file="+file); - - // send '\0' - buf[0] = 0; - out.write(buf, 0, 1); - out.flush(); - - // read a content of lfile - fos = new FileOutputStream(prefix == null ? localFile : prefix + file); - int foo; - while (true) { - if (buf.length < filesize) foo = buf.length; - else foo = (int) filesize; - foo = in.read(buf, 0, foo); - if (foo < 0) { - // error - break; - } - fos.write(buf, 0, foo); - filesize -= foo; - if (filesize == 0L) break; - } - fos.close(); - fos = null; - - if (checkAck(in) != 0) { - String error = "Error transfering the file content"; - log.error(error); - throw new SSHApiException(error); - } - - // send '\0' - buf[0] = 0; - out.write(buf, 0, 1); - out.flush(); - } - stdOutReader.onOutput(channel); - if (stdOutReader.getStdErrorString().contains("scp:")) { - throw new SSHApiException(stdOutReader.getStdErrorString()); - } - - } catch (Exception e) { - log.error(e.getMessage(), e); - } finally { - try { - if (fos != null) fos.close(); - } catch (Exception ee) { - } - } - } - - /** - * This method will copy a remote file to a local directory - * - * @param sourceFile remote file path, this has to be a full qualified path - * @param sourceSession JSch session for source - * @param destinationFile This is the local file to copy, this can be a directory too - * @param destinationSession JSch Session for target - * @return returns the final local file path of the new file came from the remote resource - */ - public static void scpThirdParty(String sourceFile, Session sourceSession, String destinationFile, Session destinationSession) throws - Exception{ - OutputStream sout = null; - InputStream sin = null; - OutputStream dout = null; - InputStream din = null; - try { - String prefix = null; - - // exec 'scp -f sourceFile' - String sourceCommand = "scp -f " + sourceFile; - Channel sourceChannel = sourceSession.openChannel("exec"); - ((ChannelExec) sourceChannel).setCommand(sourceCommand); - StandardOutReader sourceStdOutReader = new StandardOutReader(); - ((ChannelExec) sourceChannel).setErrStream(sourceStdOutReader.getStandardError()); - // get I/O streams for remote scp - sout = sourceChannel.getOutputStream(); - sin = sourceChannel.getInputStream(); - sourceChannel.connect(); - - - boolean ptimestamp = true; - // exec 'scp -t destinationFile' - String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + destinationFile; - Channel targetChannel = destinationSession.openChannel("exec"); - StandardOutReader targetStdOutReader = new StandardOutReader(); - ((ChannelExec) targetChannel).setErrStream(targetStdOutReader.getStandardError()); - ((ChannelExec) targetChannel).setCommand(command); - // get I/O streams for remote scp - dout = targetChannel.getOutputStream(); - din = targetChannel.getInputStream(); - targetChannel.connect(); - - if (checkAck(din) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new Exception(error); - } - - - byte[] buf = new byte[1024]; - - // send '\0' - buf[0] = 0; - sout.write(buf, 0, 1); - sout.flush(); - - while (true) { - int c = checkAck(sin); - if (c != 'C') { - break; - } - - // read '0644 ' - sin.read(buf, 0, 5); - - long fileSize = 0L; - while (true) { - if (sin.read(buf, 0, 1) < 0) { - // error - break; - } - if (buf[0] == ' ') break; - fileSize = fileSize * 10L + (long) (buf[0] - '0'); - } - - String fileName = null; - for (int i = 0; ; i++) { - sin.read(buf, i, 1); - if (buf[i] == (byte) 0x0a) { - fileName = new String(buf, 0, i); - break; - } - } - String initData = "C0644 " + fileSize + " " + fileName + "\n"; - assert dout != null; - dout.write(initData.getBytes()); - dout.flush(); - - // send '\0' to source - buf[0] = 0; - sout.write(buf, 0, 1); - sout.flush(); - - int rLength; - while (true) { - if (buf.length < fileSize) rLength = buf.length; - else rLength = (int) fileSize; - rLength = sin.read(buf, 0, rLength); // read content of the source File - if (rLength < 0) { - // error - break; - } - dout.write(buf, 0, rLength); // write to destination file - fileSize -= rLength; - if (fileSize == 0L) break; - } - - // send '\0' to target - buf[0] = 0; - dout.write(buf, 0, 1); - dout.flush(); - if (checkAck(din) != 0) { - String error = "Error Reading input Stream"; - log.error(error); - throw new Exception(error); - } - dout.close(); - dout = null; - - if (checkAck(sin) != 0) { - String error = "Error transfering the file content"; - log.error(error); - throw new Exception(error); - } - - // send '\0' - buf[0] = 0; - sout.write(buf, 0, 1); - sout.flush(); - } - - } catch (Exception e) { - log.error(e.getMessage(), e); - throw e; - } finally { - try { - if (dout != null) dout.close(); - } catch (Exception ee) { - log.error("", ee); - } - try { - if (din != null) din.close(); - } catch (Exception ee) { - log.error("", ee); - } - try { - if (sout != null) sout.close(); - } catch (Exception ee) { - log.error("", ee); - } - try { - if (din != null) din.close(); - } catch (Exception ee) { - log.error("", ee); - } - } - } - - public static void makeDirectory(String path, Session session) throws IOException, JSchException, SSHApiException { - - // exec 'scp -t rfile' remotely - String command = "mkdir -p " + path; - Channel channel = session.openChannel("exec"); - StandardOutReader stdOutReader = new StandardOutReader(); - - ((ChannelExec) channel).setCommand(command); - - - ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError()); - try { - channel.connect(); - } catch (JSchException e) { - - channel.disconnect(); -// session.disconnect(); - - throw new SSHApiException("Unable to retrieve command output. Command - " + command + - " on server - " + session.getHost() + ":" + session.getPort() + - " connecting user name - " - + session.getUserName(), e); - } - stdOutReader.onOutput(channel); - if (stdOutReader.getStdErrorString().contains("mkdir:")) { - throw new SSHApiException(stdOutReader.getStdErrorString()); - } - - channel.disconnect(); - } - - public static List<String> listDirectory(String path, Session session) throws IOException, JSchException, - SSHApiException { - - // exec 'scp -t rfile' remotely - String command = "ls " + path; - Channel channel = session.openChannel("exec"); - StandardOutReader stdOutReader = new StandardOutReader(); - - ((ChannelExec) channel).setCommand(command); - - - ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError()); - try { - channel.connect(); - } catch (JSchException e) { - - channel.disconnect(); -// session.disconnect(); - - throw new SSHApiException("Unable to retrieve command output. Command - " + command + - " on server - " + session.getHost() + ":" + session.getPort() + - " connecting user name - " - + session.getUserName(), e); - } - stdOutReader.onOutput(channel); - stdOutReader.getStdOutputString(); - if (stdOutReader.getStdErrorString().contains("ls:")) { - throw new SSHApiException(stdOutReader.getStdErrorString()); - } - channel.disconnect(); - return Arrays.asList(stdOutReader.getStdOutputString().split("\n")); - } - - - static int checkAck(InputStream in) throws IOException { - int b = in.read(); - if (b == 0) return b; - if (b == -1) return b; - - if (b == 1 || b == 2) { - StringBuffer sb = new StringBuffer(); - int c; - do { - c = in.read(); - sb.append((char) c); - } - while (c != '\n'); - if (b == 1) { // error - System.out.print(sb.toString()); - } - if (b == 2) { // fatal error - System.out.print(sb.toString()); - } - } - return b; - } - -} http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/StandardOutReader.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/StandardOutReader.java b/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/StandardOutReader.java deleted file mode 100644 index c03660b..0000000 --- a/modules/file-manager/data-manager-core/src/main/java/org/apache/airavata/data/manager/core/ssh/StandardOutReader.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * - * 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.ssh; - -import com.jcraft.jsch.Channel; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; - -public class StandardOutReader implements CommandOutput { - - private static final Logger logger = LoggerFactory.getLogger(StandardOutReader.class); - String stdOutputString = null; - ByteArrayOutputStream errorStream = new ByteArrayOutputStream(); - private int exitCode; - - public void onOutput(Channel channel) { - try { - StringBuffer pbsOutput = new StringBuffer(""); - InputStream inputStream = channel.getInputStream(); - byte[] tmp = new byte[1024]; - do { - while (inputStream.available() > 0) { - int i = inputStream.read(tmp, 0, 1024); - if (i < 0) break; - pbsOutput.append(new String(tmp, 0, i)); - } - } while (!channel.isClosed()) ; - String output = pbsOutput.toString(); - this.setStdOutputString(output); - } catch (IOException e) { - logger.error(e.getMessage(), e); - } - - } - - - public void exitCode(int code) { - System.out.println("Program exit code - " + code); - this.exitCode = code; - } - - @Override - public int getExitCode() { - return exitCode; - } - - public String getStdOutputString() { - return stdOutputString; - } - - public void setStdOutputString(String stdOutputString) { - this.stdOutputString = stdOutputString; - } - - public String getStdErrorString() { - return errorStream.toString(); - } - - public OutputStream getStandardError() { - return errorStream; - } -} http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerFactoryTest.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerFactoryTest.java b/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerFactoryTest.java deleted file mode 100644 index 359c286..0000000 --- a/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerFactoryTest.java +++ /dev/null @@ -1,45 +0,0 @@ -/* - * - * 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.aoache.airavata.data.manager.core; - -import junit.framework.Assert; -import org.apache.airavata.data.manager.core.DataManagerImpl; -import org.apache.airavata.data.manager.cpi.DataManager; -import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory; -import org.apache.airavata.registry.cpi.AppCatalog; -import org.apache.airavata.registry.cpi.AppCatalogException; -import org.apache.airavata.registry.cpi.DataCatalog; -import org.apache.airavata.registry.cpi.DataCatalogException; -import org.junit.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class DataManagerFactoryTest { - private final static Logger logger = LoggerFactory.getLogger(DataManagerFactoryTest.class); - - @Test - public void testCreateDataManager() throws DataCatalogException, DataCatalogException, AppCatalogException { - DataCatalog dataCatalog = RegistryFactory.getDataCatalog(); - AppCatalog appCatalog = RegistryFactory.getAppCatalog(); - DataManager dataManagerImpl = new DataManagerImpl(appCatalog, dataCatalog); - Assert.assertNotNull(dataManagerImpl); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/5881af94/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerImplTest.java ---------------------------------------------------------------------- diff --git a/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerImplTest.java b/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerImplTest.java deleted file mode 100644 index 42c4091..0000000 --- a/modules/file-manager/data-manager-core/src/test/java/org/aoache/airavata/data/manager/core/DataManagerImplTest.java +++ /dev/null @@ -1,208 +0,0 @@ -/* - * - * 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.aoache.airavata.data.manager.core; - -import org.apache.airavata.data.manager.core.DataManagerImpl; -import org.apache.airavata.data.manager.cpi.DataManagerException; -import org.aoache.airavata.data.manager.core.utils.AppCatInit; -import org.aoache.airavata.data.manager.core.utils.DataCatInit; -import org.apache.airavata.model.data.resource.DataReplicaLocationModel; -import org.apache.airavata.model.data.resource.DataResourceModel; -import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory; -import org.apache.airavata.registry.cpi.AppCatalog; -import org.apache.airavata.registry.cpi.DataCatalog; -import org.apache.airavata.data.manager.cpi.DataManager; -import org.junit.AfterClass; -import org.junit.Assert; -import org.junit.BeforeClass; -import org.junit.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.List; -import java.util.UUID; - -public class DataManagerImplTest { - private final static Logger logger = LoggerFactory.getLogger(DataManagerImplTest.class); - private static AppCatInit appCatInit; - private static DataCatInit dataCatInit; - private static DataManager dataManager; - private static DataResourceModel dataResourceModel; - private static DataReplicaLocationModel dataReplicaLocationModel; - - @BeforeClass - public static void setUp() { - try { - System.out.println("********** SET UP ************"); - appCatInit = new AppCatInit("appcatalog-derby.sql"); - appCatInit.initializeDB(); - dataCatInit = new DataCatInit("datacatalog-derby.sql"); - dataCatInit.initializeDB(); - AppCatalog appCatalog = RegistryFactory.getAppCatalog(); - DataCatalog dataCatalog = RegistryFactory.getDataCatalog(); - DataManagerImplTest.dataManager = new DataManagerImpl(appCatalog, dataCatalog); - dataResourceModel = new DataResourceModel(); - dataResourceModel.setResourceName("test-file.txt"); - dataReplicaLocationModel = new DataReplicaLocationModel(); - dataReplicaLocationModel.setReplicaName("1-st-replica"); - } catch (Exception e) { - logger.error(e.getMessage(), e); - } - } - - @AfterClass - public static void tearDown() throws Exception { - System.out.println("********** TEAR DOWN ************"); - dataCatInit.stopDerbyServer(); - } - - @Test - public void testPublishDataResource(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - org.junit.Assert.assertNotNull(resourceId); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testRemoveDataResource(){ - try { - boolean result = dataManager.removeResource("234234234"); - Assert.assertFalse(result); - String resourceId = dataManager.registerResource(dataResourceModel); - Assert.assertNotNull(resourceId); - result = dataManager.removeResource(resourceId); - Assert.assertTrue(result); - result = dataManager.removeResource(resourceId); - Assert.assertFalse(result); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testGetDataResource(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - Assert.assertNotNull(resourceId); - DataResourceModel persistedCopy = dataManager.getResource(resourceId); - Assert.assertNotNull(persistedCopy); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testUpdateDataResource(){ - try { - dataResourceModel.setResourceId(UUID.randomUUID().toString()); - boolean result = dataManager.updateResource(dataResourceModel); - Assert.assertFalse(result); - dataManager.registerResource(dataResourceModel); - dataResourceModel.setResourceName("updated-name"); - dataManager.updateResource(dataResourceModel); - dataResourceModel = dataManager.getResource(dataResourceModel.getResourceId()); - Assert.assertTrue(dataResourceModel.getResourceName().equals("updated-name")); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testPublishReplicaLocation(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - dataReplicaLocationModel.setResourceId(resourceId); - String replicaId = dataManager.registerReplicaLocation(dataReplicaLocationModel); - org.junit.Assert.assertNotNull(replicaId); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testRemoveReplicaLocation(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - dataReplicaLocationModel.setResourceId(resourceId); - String replicaId = dataManager.registerReplicaLocation(dataReplicaLocationModel); - boolean result = dataManager.removeReplicaLocation(replicaId); - Assert.assertTrue(result); - result = dataManager.removeReplicaLocation(dataReplicaLocationModel.getReplicaId()); - Assert.assertFalse(result); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testGetReplicaLocation(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - dataReplicaLocationModel.setResourceId(resourceId); - String replicaId = dataManager.registerReplicaLocation(dataReplicaLocationModel); - DataReplicaLocationModel persistedCopy = dataManager.getReplicaLocation(replicaId); - Assert.assertNotNull(persistedCopy); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testUpdateReplicaLocation(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - dataReplicaLocationModel.setResourceId(resourceId); - String replicaId = dataManager.registerReplicaLocation(dataReplicaLocationModel); - DataReplicaLocationModel persistedCopy = dataManager.getReplicaLocation(replicaId); - persistedCopy.setReplicaDescription("updated-description"); - dataManager.updateReplicaLocation(persistedCopy); - persistedCopy = dataManager.getReplicaLocation(replicaId); - Assert.assertTrue(persistedCopy.getReplicaDescription().equals("updated-description")); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } - - @Test - public void testGetAllReplicaLocations(){ - try { - String resourceId = dataManager.registerResource(dataResourceModel); - dataReplicaLocationModel.setResourceId(resourceId); - String replicaId = dataManager.registerReplicaLocation(dataReplicaLocationModel); - List<DataReplicaLocationModel> replicaLocationModelList = dataManager.getAllReplicaLocations(resourceId); - Assert.assertTrue(replicaLocationModelList.get(0).getReplicaId().equals(replicaId)); - } catch (DataManagerException e) { - e.printStackTrace(); - Assert.fail(); - } - } -} \ No newline at end of file
