This is an automated email from the ASF dual-hosted git repository. smarru pushed a commit to branch master in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit 676140dfcaaea634d03d33828cfa4daaa029f261 Author: Harsha Phulwani <[email protected]> AuthorDate: Fri Nov 17 18:30:32 2017 -0500 Revert "Added entities,repositories,utils and updated pom file" This reverts commit 9859fd79e659db94e86489cdb2611e84a3c398c4. --- .gitignore | 30 +- .../airavata-allocation-manager-server/pom.xml | 64 +--- .../manager/db/entities/DomainEntity.java | 116 ------- .../manager/db/entities/RequestStatusEntity.java | 78 ----- .../db/entities/UserAllocationDetailEntity.java | 205 ----------- .../db/entities/UserAllocationDetailEntityPK.java | 57 --- .../manager/db/entities/UserDetailEntity.java | 78 ----- .../db/repositories/AbstractRepository.java | 163 --------- .../manager/db/repositories/DomainRepository.java | 33 -- .../db/repositories/RequestStatusRepository.java | 14 - .../UserAllocationDetailPKRepository.java | 14 - .../UserAllocationDetailRepository.java | 14 - .../db/repositories/UserDetailRepository.java | 19 - .../allocation/manager/db/utils/Committer.java | 26 -- .../manager/db/utils/ConnectionPool.java | 381 --------------------- .../allocation/manager/db/utils/DBConstants.java | 106 ------ .../manager/db/utils/DatabaseCreator.java | 352 ------------------- .../allocation/manager/db/utils/JPAUtils.java | 215 ------------ .../allocation/manager/db/utils/JdbcStorage.java | 174 ---------- .../manager/db/utils/ObjectMapperSingleton.java | 38 -- .../airavata/allocation/manager/models/Domain.java | 5 - bin/README.txt | 16 - bin/build.xml | 53 --- bin/db.config | 24 -- .../airavata/jobsubmission/gram/errors.properties | 176 ---------- 25 files changed, 27 insertions(+), 2424 deletions(-) diff --git a/.gitignore b/.gitignore index db19882..d6e588b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,11 +1,5 @@ -# Compiled class file *.class - -# Log file -*.log - -# BlueJ files -*.ctxt +*id_rsa* # Mobile Tools for Java (J2ME) .mtj.tmp/ @@ -14,18 +8,18 @@ *.jar *.war *.ear -*.zip -*.tar.gz -*.rar -# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml -hs_err_pid* -# Ignore files ending with target -*target/ - -# Ignore files starting with dot -.* -!.gitignore +target/ +.idea/ +tmp/ +logs/ +gaussian_sample/ +*.ser +*.iml +*.gen +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* +solr-server/logs/solr.log diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/pom.xml b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/pom.xml index 8cb41b4..86dd4fc 100644 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/pom.xml +++ b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/pom.xml @@ -1,55 +1,21 @@ -<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";> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-allocation-manager</artifactId> - <version>0.0.1-SNAPSHOT</version> - </parent> - <artifactId>airavata-allocation-manager-server</artifactId> - <dependencies> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-allocation-manager-stubs</artifactId> - <version>0.0.1-SNAPSHOT</version> - </dependency> - <dependency> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-api</artifactId> - <version>1.7.10</version> - </dependency> - <dependency> - <groupId>net.sf.dozer</groupId> - <artifactId>dozer</artifactId> - <version>5.4.0</version> - <exclusions> - <exclusion> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-log4j12</artifactId> - </exclusion> - </exclusions> - </dependency> - <dependency> - <groupId>org.apache.openjpa</groupId> - <artifactId>openjpa-all</artifactId> - <version>2.2.0</version> - </dependency> - <!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java --> - <dependency> - <groupId>mysql</groupId> - <artifactId>mysql-connector-java</artifactId> - <version>5.1.34</version> - </dependency> - <!-- https://mvnrepository.com/artifact/org.apache.thrift/libthrift --> +<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";> + <modelVersion>4.0.0</modelVersion> + <parent> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-allocation-manager</artifactId> + <version>0.0.1-SNAPSHOT</version> + </parent> + <artifactId>airavata-allocation-manager-server</artifactId> + <dependencies> <dependency> <groupId>org.apache.thrift</groupId> <artifactId>libthrift</artifactId> <version>0.10.0</version> - <type>pom</type> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-allocation-manager-stubs</artifactId> + <version>0.0.1-SNAPSHOT</version> </dependency> </dependencies> - <properties> - <maven.compiler.source>1.8</maven.compiler.source> - <maven.compiler.target>1.8</maven.compiler.target> - </properties> -</project> \ No newline at end of file +</project> \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/DomainEntity.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/DomainEntity.java deleted file mode 100644 index 2aed6f9..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/DomainEntity.java +++ /dev/null @@ -1,116 +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.allocation.manager.db.entities; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.persistence.*; - -@Entity -@Table(name = "DOMAIN", schema = "" ) -public class DomainEntity { - private final static Logger logger = LoggerFactory.getLogger(DomainEntity.class); - private String domainId; - private String name; - private String description; - private Long createdTime; - private Long updatedTime; - - @Id - @Column(name = "DOMAIN_ID") - public String getDomainId() { - return domainId; - } - - public void setDomainId(String domainId) { - this.domainId = domainId; - } - - @Basic - @Column(name = "NAME") - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - @Basic - @Column(name = "DESCRIPTION") - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - @Basic - @Column(name = "CREATED_TIME") - public Long getCreatedTime() { - return createdTime; - } - - public void setCreatedTime(Long createdTime) { - this.createdTime = createdTime; - } - - @Basic - @Column(name = "UPDATED_TIME") - public Long getUpdatedTime() { - return updatedTime; - } - - public void setUpdatedTime(Long updatedTime) { - this.updatedTime = updatedTime; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - - DomainEntity that = (DomainEntity) o; - - if (getDomainId() != null ? !getDomainId().equals(that.getDomainId()) : that.getDomainId() != null) - return false; - if (getName() != null ? !getName().equals(that.getName()) : that.getName() != null) return false; - if (getDescription() != null ? !getDescription().equals(that.getDescription()) : that.getDescription() != null) - return false; - if (getCreatedTime() != null ? !getCreatedTime().equals(that.getCreatedTime()) : that.getCreatedTime() != null) - return false; - if (getUpdatedTime() != null ? !getUpdatedTime().equals(that.getUpdatedTime()) : that.getUpdatedTime() != null) - return false; - - return true; - } - - @Override - public int hashCode() { - int result = getDomainId() != null ? getDomainId().hashCode() : 0; - result = 31 * result + (getName() != null ? getName().hashCode() : 0); - result = 31 * result + (getDescription() != null ? getDescription().hashCode() : 0); - result = 31 * result + (getCreatedTime() != null ? getCreatedTime().hashCode() : 0); - result = 31 * result + (getUpdatedTime() != null ? getUpdatedTime().hashCode() : 0); - return result; - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/RequestStatusEntity.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/RequestStatusEntity.java deleted file mode 100644 index 42ccc4a..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/RequestStatusEntity.java +++ /dev/null @@ -1,78 +0,0 @@ -package org.apache.airavata.allocation.manager.db.entities; - -import java.io.Serializable; -import javax.persistence.*; -import java.math.BigInteger; - - -/** - * The persistent class for the REQUEST_STATUS database table. - * - */ -@Entity -@Table(name="REQUEST_STATUS") -@NamedQuery(name="RequestStatusEntity.findAll", query="SELECT r FROM RequestStatusEntity r") -public class RequestStatusEntity implements Serializable { - private static final long serialVersionUID = 1L; - - @Id - @Column(name="PROJECT_ID") - private String projectId; - - @Column(name="END_DATE") - private BigInteger endDate; - - @Lob - @Column(name="REVIEWERS") - private String reviewers; - - @Column(name="START_DATE") - private BigInteger startDate; - - @Column(name="STATUS") - private String status; - - public RequestStatusEntity() { - } - - public String getProjectId() { - return this.projectId; - } - - public void setProjectId(String projectId) { - this.projectId = projectId; - } - - public BigInteger getEndDate() { - return this.endDate; - } - - public void setEndDate(BigInteger endDate) { - this.endDate = endDate; - } - - public String getReviewers() { - return this.reviewers; - } - - public void setReviewers(String reviewers) { - this.reviewers = reviewers; - } - - public BigInteger getStartDate() { - return this.startDate; - } - - public void setStartDate(BigInteger startDate) { - this.startDate = startDate; - } - - public String getStatus() { - return this.status; - } - - public void setStatus(String status) { - this.status = status; - } - -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntity.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntity.java deleted file mode 100644 index 35ab18d..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntity.java +++ /dev/null @@ -1,205 +0,0 @@ -package org.apache.airavata.allocation.manager.db.entities; - -import java.io.Serializable; -import javax.persistence.*; -import java.math.BigInteger; - - -/** - * The persistent class for the USER_ALLOCATION_DETAILS database table. - * - */ -@Entity -@Table(name="USER_ALLOCATION_DETAILS") -@NamedQuery(name="UserAllocationDetailEntity.findAll", query="SELECT u FROM UserAllocationDetailEntity u") -public class UserAllocationDetailEntity implements Serializable { - private static final long serialVersionUID = 1L; - - @EmbeddedId - private UserAllocationDetailEntityPK id; - - @Lob - @Column(name="APPLICATIONS_TO_BE_USED") - private String applicationsToBeUsed; - - @Column(name="DISK_USAGE_RANGE_PER_JOB") - private BigInteger diskUsageRangePerJob; - - @Lob - @Column(name="DOCUMENTS") - private byte[] documents; - - @Lob - @Column(name="FIELD_OF_SCIENCE") - private String fieldOfScience; - - @Lob - @Column(name="KEYWORDS") - private String keywords; - - @Column(name="MAX_MEMORY_PER_CPU") - private BigInteger maxMemoryPerCpu; - - @Column(name="NUMBER_OF_CPU_PER_JOB") - private BigInteger numberOfCpuPerJob; - - @Lob - @Column(name="PROJECT_DESCRIPTION") - private String projectDescription; - - @Lob - @Column(name="PROJECT_REVIEWED_AND_FUNDED_BY") - private String projectReviewedAndFundedBy; - - @Column(name="REQ_DATE") - private BigInteger reqDate; - - @Column(name="SERVICE_UNITS") - private BigInteger serviceUnits; - - @Lob - @Column(name="SPECIFIC_RESOURCE_SELECTION") - private String specificResourceSelection; - - @Lob - @Column(name="TITLE") - private String title; - - @Column(name="TYPE_OF_ALLOCATION") - private String typeOfAllocation; - - @Column(name="TYPICAL_SU_PER_JOB") - private BigInteger typicalSuPerJob; - - public UserAllocationDetailEntity() { - } - - public UserAllocationDetailEntityPK getId() { - return this.id; - } - - public void setId(UserAllocationDetailEntityPK id) { - this.id = id; - } - - public String getApplicationsToBeUsed() { - return this.applicationsToBeUsed; - } - - public void setApplicationsToBeUsed(String applicationsToBeUsed) { - this.applicationsToBeUsed = applicationsToBeUsed; - } - - public BigInteger getDiskUsageRangePerJob() { - return this.diskUsageRangePerJob; - } - - public void setDiskUsageRangePerJob(BigInteger diskUsageRangePerJob) { - this.diskUsageRangePerJob = diskUsageRangePerJob; - } - - public byte[] getDocuments() { - return this.documents; - } - - public void setDocuments(byte[] documents) { - this.documents = documents; - } - - public String getFieldOfScience() { - return this.fieldOfScience; - } - - public void setFieldOfScience(String fieldOfScience) { - this.fieldOfScience = fieldOfScience; - } - - public String getKeywords() { - return this.keywords; - } - - public void setKeywords(String keywords) { - this.keywords = keywords; - } - - public BigInteger getMaxMemoryPerCpu() { - return this.maxMemoryPerCpu; - } - - public void setMaxMemoryPerCpu(BigInteger maxMemoryPerCpu) { - this.maxMemoryPerCpu = maxMemoryPerCpu; - } - - public BigInteger getNumberOfCpuPerJob() { - return this.numberOfCpuPerJob; - } - - public void setNumberOfCpuPerJob(BigInteger numberOfCpuPerJob) { - this.numberOfCpuPerJob = numberOfCpuPerJob; - } - - public String getProjectDescription() { - return this.projectDescription; - } - - public void setProjectDescription(String projectDescription) { - this.projectDescription = projectDescription; - } - - public String getProjectReviewedAndFundedBy() { - return this.projectReviewedAndFundedBy; - } - - public void setProjectReviewedAndFundedBy(String projectReviewedAndFundedBy) { - this.projectReviewedAndFundedBy = projectReviewedAndFundedBy; - } - - public BigInteger getReqDate() { - return this.reqDate; - } - - public void setReqDate(BigInteger reqDate) { - this.reqDate = reqDate; - } - - public BigInteger getServiceUnits() { - return this.serviceUnits; - } - - public void setServiceUnits(BigInteger serviceUnits) { - this.serviceUnits = serviceUnits; - } - - public String getSpecificResourceSelection() { - return this.specificResourceSelection; - } - - public void setSpecificResourceSelection(String specificResourceSelection) { - this.specificResourceSelection = specificResourceSelection; - } - - public String getTitle() { - return this.title; - } - - public void setTitle(String title) { - this.title = title; - } - - public String getTypeOfAllocation() { - return this.typeOfAllocation; - } - - public void setTypeOfAllocation(String typeOfAllocation) { - this.typeOfAllocation = typeOfAllocation; - } - - public BigInteger getTypicalSuPerJob() { - return this.typicalSuPerJob; - } - - public void setTypicalSuPerJob(BigInteger typicalSuPerJob) { - this.typicalSuPerJob = typicalSuPerJob; - } - -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntityPK.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntityPK.java deleted file mode 100644 index e768883..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserAllocationDetailEntityPK.java +++ /dev/null @@ -1,57 +0,0 @@ -package org.apache.airavata.allocation.manager.db.entities; - -import java.io.Serializable; -import javax.persistence.*; - -/** - * The primary key class for the USER_ALLOCATION_DETAILS database table. - * - */ -@Embeddable -public class UserAllocationDetailEntityPK implements Serializable { - //default serial version id, required for serializable classes. - private static final long serialVersionUID = 1L; - - @Column(name="PROJECT_ID") - private String projectId; - - @Column(name="USERNAME") - private String username; - - public UserAllocationDetailEntityPK() { - } - public String getProjectId() { - return this.projectId; - } - public void setProjectId(String projectId) { - this.projectId = projectId; - } - public String getUsername() { - return this.username; - } - public void setUsername(String username) { - this.username = username; - } - - public boolean equals(Object other) { - if (this == other) { - return true; - } - if (!(other instanceof UserAllocationDetailEntityPK)) { - return false; - } - UserAllocationDetailEntityPK castOther = (UserAllocationDetailEntityPK)other; - return - this.projectId.equals(castOther.projectId) - && this.username.equals(castOther.username); - } - - public int hashCode() { - final int prime = 31; - int hash = 17; - hash = hash * prime + this.projectId.hashCode(); - hash = hash * prime + this.username.hashCode(); - - return hash; - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserDetailEntity.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserDetailEntity.java deleted file mode 100644 index 9eb04fc..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/entities/UserDetailEntity.java +++ /dev/null @@ -1,78 +0,0 @@ -package org.apache.airavata.allocation.manager.db.entities; - -import java.io.Serializable; -import javax.persistence.*; - - -/** - * The persistent class for the USER_DETAILS database table. - * - */ -@Entity -@Table(name="USER_DETAILS") -@NamedQuery(name="UserDetailEntity.findAll", query="SELECT u FROM UserDetailEntity u") -public class UserDetailEntity implements Serializable { - private static final long serialVersionUID = 1L; - - @Id - @Column(name="USERNAME") - private String username; - - @Lob - @Column(name="EMAIL") - private String email; - - @Lob - @Column(name="FULL_NAME") - private String fullName; - - @Column(name="PASSWORD") - private String password; - - @Column(name="USER_TYPE") - private String userType; - - public UserDetailEntity() { - } - - public String getUsername() { - return this.username; - } - - public void setUsername(String username) { - this.username = username; - } - - public String getEmail() { - return this.email; - } - - public void setEmail(String email) { - this.email = email; - } - - public String getFullName() { - return this.fullName; - } - - public void setFullName(String fullName) { - this.fullName = fullName; - } - - public String getPassword() { - return this.password; - } - - public void setPassword(String password) { - this.password = password; - } - - public String getUserType() { - return this.userType; - } - - public void setUserType(String userType) { - this.userType = userType; - } - -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/AbstractRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/AbstractRepository.java deleted file mode 100644 index 6449b4a..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/AbstractRepository.java +++ /dev/null @@ -1,163 +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.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.utils.Committer; -import org.apache.airavata.allocation.manager.db.utils.DBConstants; -import org.apache.airavata.allocation.manager.db.utils.JPAUtils; -import org.apache.airavata.allocation.manager.db.utils.ObjectMapperSingleton; -import org.apache.airavata.allocation.manager.models.AllocationManagerException; -import org.dozer.Mapper; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.persistence.EntityManager; -import javax.persistence.Query; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; - -public abstract class AbstractRepository<T, E, Id> { - private final static Logger logger = LoggerFactory.getLogger(AbstractRepository.class); - - private Class<T> thriftGenericClass; - private Class<E> dbEntityGenericClass; - - public AbstractRepository(Class<T> thriftGenericClass, Class<E> dbEntityGenericClass){ - this.thriftGenericClass = thriftGenericClass; - this.dbEntityGenericClass = dbEntityGenericClass; - } - - public T create(T t) throws Exception { - return update(t); - } - - //FIXME do a bulk insert - public List<T> create(List<T> tList) throws Exception { - return update(tList); - } - - public T update(T t) throws Exception { - Mapper mapper = ObjectMapperSingleton.getInstance(); - E entity = mapper.map(t, dbEntityGenericClass); - E persistedCopy = execute(entityManager -> entityManager.merge(entity)); - return mapper.map(persistedCopy, thriftGenericClass); - } - - //FIXME do a bulk update - public List<T> update(List<T> tList) throws Exception { - List<T> returnList = new ArrayList<T>(); - for(T temp : tList) - returnList.add(update(temp)); - return returnList; - } - - public boolean delete(Id id) throws Exception { - execute(entityManager -> { - E entity = entityManager.find(dbEntityGenericClass, id); - entityManager.remove(entity); - return entity; - }); - return true; - } - - public boolean delete(List<Id> idList) throws Exception { - for(Id id : idList) - delete(id); - return true; - } - - public T get(Id id) throws Exception { - E entity = execute(entityManager -> entityManager - .find(dbEntityGenericClass, id)); - Mapper mapper = ObjectMapperSingleton.getInstance(); - if(entity == null) - return null; - return mapper.map(entity, thriftGenericClass); - } - - public boolean isExists(Id id) throws Exception { - return get(id) != null; - } - - public List<T> get(List<Id> idList) throws Exception { - List<T> returnList = new ArrayList<>(); - for(Id id : idList) - returnList.add(get(id)); - return returnList; - } - - public List<T> select(Map<String, String> filters, int offset, int limit) throws Exception { - String query = "SELECT DISTINCT p from " + dbEntityGenericClass.getSimpleName() + " as p"; - ArrayList<String> parameters = new ArrayList<>(); - int parameterCount = 1; - if (filters != null && filters.size() != 0) { - query += " WHERE "; - for (String k : filters.keySet()) { - query += "p." + k + " = ?" + parameterCount + " AND "; - parameters.add(filters.get(k)); - parameterCount++; - } - query = query.substring(0, query.length() - 5); - } - - query += " ORDER BY p.createdTime DESC"; - String queryString = query; - int newLimit = limit < 0 ? DBConstants.SELECT_MAX_ROWS: limit; - List resultSet = execute(entityManager -> { - javax.persistence.Query q = entityManager.createQuery(queryString); - for (int i = 0; i < parameters.size(); i++) { - q.setParameter(i + 1, parameters.get(i)); - } - return q.setFirstResult(offset).setMaxResults(newLimit).getResultList(); - }); - Mapper mapper = ObjectMapperSingleton.getInstance(); - List<T> gatewayList = new ArrayList<>(); - resultSet.stream().forEach(rs -> gatewayList.add(mapper.map(rs, thriftGenericClass))); - return gatewayList; - } - - public List<T> select(String queryString, Map<String,Object> queryParameters, int offset, int limit) throws Exception { - int newLimit = limit < 0 ? DBConstants.SELECT_MAX_ROWS: limit; - List resultSet = execute(entityManager -> { - Query q = entityManager.createQuery(queryString); - for(Map.Entry<String, Object> queryParam : queryParameters.entrySet()){ - q.setParameter(queryParam.getKey(), queryParam.getValue()); - } - return q.setFirstResult(offset).setMaxResults(newLimit).getResultList(); - }); - Mapper mapper = ObjectMapperSingleton.getInstance(); - List<T> gatewayList = new ArrayList<>(); - resultSet.stream().forEach(rs -> gatewayList.add(mapper.map(rs, thriftGenericClass))); - return gatewayList; - } - - public <R> R execute(Committer<EntityManager, R> committer) throws Exception { - EntityManager entityManager = JPAUtils.getEntityManager(); - try { - entityManager.getTransaction().begin(); - R r = committer.commit(entityManager); - entityManager.getTransaction().commit(); - return r; - } finally { - entityManager.close(); - } - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/DomainRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/DomainRepository.java deleted file mode 100644 index c86d85b..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/DomainRepository.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.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.entities.DomainEntity; -import org.apache.airavata.allocation.manager.models.Domain; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class DomainRepository extends AbstractRepository<Domain, DomainEntity, String> { - private final static Logger logger = LoggerFactory.getLogger(DomainRepository.class); - - public DomainRepository(){ - super(Domain.class, DomainEntity.class); - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/RequestStatusRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/RequestStatusRepository.java deleted file mode 100644 index 71cbba8..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/RequestStatusRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.apache.airavata.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.entities.RequestStatusEntity; -import org.apache.airavata.allocation.manager.models.RequestStatus; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class RequestStatusRepository extends AbstractRepository<RequestStatus, RequestStatusEntity,String> { - private final static Logger logger = LoggerFactory.getLogger(DomainRepository.class); - - public RequestStatusRepository(){ - super(RequestStatus.class, RequestStatusEntity.class); - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailPKRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailPKRepository.java deleted file mode 100644 index 265e063..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailPKRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.apache.airavata.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.entities.UserAllocationDetailEntityPK; -import org.apache.airavata.allocation.manager.models.UserAllocationDetailPK; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class UserAllocationDetailPKRepository extends AbstractRepository<UserAllocationDetailPK, UserAllocationDetailPK, String> { - private final static Logger logger = LoggerFactory.getLogger(DomainRepository.class); - - public UserAllocationDetailPKRepository(){ - super(UserAllocationDetailPK.class, UserAllocationDetailPK.class); - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailRepository.java deleted file mode 100644 index adfd6d2..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserAllocationDetailRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.apache.airavata.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.entities.UserAllocationDetailEntity; -import org.apache.airavata.allocation.manager.models.UserAllocationDetail; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class UserAllocationDetailRepository extends AbstractRepository<UserAllocationDetail, UserAllocationDetailEntity, String> { - private final static Logger logger = LoggerFactory.getLogger(DomainRepository.class); - - public UserAllocationDetailRepository(){ - super(UserAllocationDetail.class, UserAllocationDetailEntity.class); - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserDetailRepository.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserDetailRepository.java deleted file mode 100644 index c05ff5c..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/repositories/UserDetailRepository.java +++ /dev/null @@ -1,19 +0,0 @@ -package org.apache.airavata.allocation.manager.db.repositories; - -import org.apache.airavata.allocation.manager.db.entities.UserDetailEntity; -import org.apache.airavata.allocation.manager.models.UserDetail; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class UserDetailRepository extends AbstractRepository<UserDetail, UserDetailEntity, String> { - private final static Logger logger = LoggerFactory.getLogger(DomainRepository.class); - - public UserDetailRepository(){ - super(UserDetail.class, UserDetailEntity.class); - } - - public static void main(String args[]) - { - - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/Committer.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/Committer.java deleted file mode 100644 index 64e9abc..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/Committer.java +++ /dev/null @@ -1,26 +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.allocation.manager.db.utils; - -@FunctionalInterface -public interface Committer<T, R> { - - R commit(T t); -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ConnectionPool.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ConnectionPool.java deleted file mode 100644 index 2d3a64e..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ConnectionPool.java +++ /dev/null @@ -1,381 +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.allocation.manager.db.utils; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.sql.DataSource; -import java.sql.Connection; -import java.sql.DriverManager; -import java.sql.SQLException; -import java.util.HashMap; -import java.util.Iterator; -import java.util.Stack; -import java.util.concurrent.Semaphore; - - -/** - * A class for preallocating, recycling, and managing JDBC connections. - */ -public class ConnectionPool { - private static final Logger logger = LoggerFactory.getLogger(ConnectionPool.class); - - private long MAX_IDLE_TIME = 5 * 60 * 1000; // 5 minutes - - private String driver; - private String url; - private String username; - private String password; - private String jdbcUrl; - - private int maxConnections; - - private boolean autoCommit = true; - private boolean waitIfBusy; - - private Semaphore needConnection = new Semaphore(0); - private boolean stop; - - private Stack<Connection> availableConnections; - private Stack<Connection> busyConnections; - - private HashMap<Connection, Long> lastAccessTimeRecord = new HashMap<Connection, Long>(); - - private String urlType = ""; - - private DataSource datasource; - - private int transactionIsolation = Connection.TRANSACTION_NONE; - - private Thread clenupThread; - private Thread producerThread; - - public ConnectionPool(String driver, String url, String username, String password, int initialConnections, - int maxConnections, boolean waitIfBusy) throws SQLException { - this.driver = driver; - this.url = url; - this.username = username; - this.password = password; - this.urlType = "speratedURL"; - initialize(initialConnections, maxConnections, waitIfBusy); - } - - public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections, - boolean waitIfBusy, boolean autoCommit, int transactionIsolation) throws SQLException { - this.driver = driver; - this.jdbcUrl = jdbcUrl; - this.urlType = "simpleURL"; - this.autoCommit = autoCommit; - this.transactionIsolation = transactionIsolation; - initialize(initialConnections, maxConnections, waitIfBusy); - } - - public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections, boolean waitIfBusy) - throws SQLException { - this.driver = driver; - this.jdbcUrl = jdbcUrl; - this.urlType = "simpleURL"; - initialize(initialConnections, maxConnections, waitIfBusy); - } - - public ConnectionPool(DataSource dataSource, int initialConnections, int maxConnections, boolean waitIfBusy) - throws SQLException { - this.urlType = "dataSource"; - this.datasource = dataSource; - initialize(initialConnections, maxConnections, waitIfBusy); - } - - /** - * Check if this connection pool is auto commit or not - * - * @return - */ - public boolean isAutoCommit() { - return this.autoCommit; - } - - private void initialize(int initialConnections, int maxConnections, boolean waitIfBusy) throws SQLException { - this.maxConnections = maxConnections; - this.waitIfBusy = waitIfBusy; - - int sizeOfConnections = (initialConnections > maxConnections) ? maxConnections : initialConnections; - - availableConnections = new Stack<Connection>(); - busyConnections = new Stack<Connection>(); - - for (int i = 0; i < sizeOfConnections; i++) { - Connection con = makeNewConnection(); - setTimeStamp(con); - availableConnections.push(con); - - } - - producerThread = new Thread(new FillUpThread()); - producerThread.start(); - - clenupThread = new Thread(new CleanUpThread()); - clenupThread.start(); - } - - public synchronized Connection getConnection() throws SQLException { - if (!availableConnections.isEmpty()) { - Connection existingConnection = availableConnections.pop(); - - // If connection on available list is closed (e.g., - // it timed out), then remove it from available list - // and race for a connection again. - if (existingConnection.isClosed()) { - lastAccessTimeRecord.remove(existingConnection); - // notifyAll for fairness - notifyAll(); - } else { - busyConnections.push(existingConnection); - setTimeStamp(existingConnection); - return existingConnection; - } - } else if (!waitIfBusy && busyConnections.size() >= maxConnections) { - // You reached maxConnections limit and waitIfBusy flag is false. - // Throw SQLException in such a case. - throw new SQLException("Connection limit reached"); - } else { - - if (busyConnections.size() < maxConnections) { - // available connection is empty, but total number of connection - // doesn't reach maxConnection. Request for more connection - needConnection.release(); - } - - try { - // wait for free connection - wait(); - } catch (InterruptedException ie) { - } - } - // always race for connection forever - return getConnection(); - } - - // This explicitly makes a new connection. Called in - // the foreground when initializing the ConnectionPool, - // and called in the background when running. - private Connection makeNewConnection() throws SQLException { - try { - // Load database driver if not already loaded - Class.forName(driver); - Connection connection; - // Establish network connection to database - if (urlType.equals("speratedURL")) { - connection = DriverManager.getConnection(url, username, password); - } else if (urlType.equals("simpleURL")) { - connection = DriverManager.getConnection(jdbcUrl); - } else { // if(urlType.equals("dataSource")){ - connection = datasource.getConnection(); - } - connection.setTransactionIsolation(this.transactionIsolation); - connection.setAutoCommit(this.autoCommit); - return connection; - } catch (ClassNotFoundException cnfe) { - // Simplify try/catch blocks of people using this by - // throwing only one exception type. - throw new SQLException("Can't find class for driver: " + driver); - } - } - - private synchronized void fillUpConnection(Connection conn) { - setTimeStamp(conn); - availableConnections.push(conn); - - // notify all since new connection is created - notifyAll(); - } - - private void setTimeStamp(Connection connection) { - lastAccessTimeRecord.put(connection, System.currentTimeMillis()); - } - - // The database connection cannot be left idle for too long, otherwise TCP - // connection will be broken. - /** - * From http://forums.mysql.com/read.php?39,28450,57460#msg-57460 Okay, then it looks like wait_timeout on the - * server is killing your connection (it is set to 8 hours of idle time by default). Either set that value higher on - * your server, or configure your connection pool to not hold connections idle that long (I prefer the latter). Most - * folks I know that run MySQL with a connection pool in high-load production environments only let connections sit - * idle for a matter of minutes, since it only takes a few milliseconds to open a connection, and the longer one - * sits idle the more chance it will go "bad" because of a network hiccup or the MySQL server being restarted. - * - * @throws java.sql.SQLException - */ - private boolean isConnectionStale(Connection connection) { - long currentTime = System.currentTimeMillis(); - long lastAccess = lastAccessTimeRecord.get(connection); - if (currentTime - lastAccess > MAX_IDLE_TIME) { - return true; - } else - return false; - } - - private synchronized void closeStaleConnections() { - // close idle connections - Iterator<Connection> iter = availableConnections.iterator(); - while (iter.hasNext()) { - Connection existingConnection = iter.next(); - if (isConnectionStale(existingConnection)) { - try { - existingConnection.close(); - iter.remove(); - } catch (SQLException sql) { - logger.error(sql.getMessage(), sql); - } - } - } - // close busy connections that have been checked out for too long. - // This should not happen since this means program has bug for not - // releasing connections . - iter = busyConnections.iterator(); - while (iter.hasNext()) { - Connection busyConnection = iter.next(); - if (isConnectionStale(busyConnection)) { - try { - busyConnection.close(); - iter.remove(); - logger.warn("****Connection has checked out too long. Forced release. Check the program for calling release connection [free(Connection) method]"); - } catch (SQLException sql) { - logger.error(sql.getMessage(), sql); - } - } - } - } - - public synchronized void free(Connection connection) { - busyConnections.removeElement(connection); - availableConnections.addElement(connection); - // Wake up threads that are waiting for a connection - notifyAll(); - } - - /** - * Close all the connections. Use with caution: be sure no connections are in use before calling. Note that you are - * not <I>required</I> to call this when done with a ConnectionPool, since connections are guaranteed to be closed - * when garbage collected. But this method gives more control regarding when the connections are closed. - */ - public synchronized void dispose() { - logger.info("Connection Pool Shutting down"); - - // stop clean up thread - this.stop = true; - this.clenupThread.interrupt(); - - // stop producer up thread - this.producerThread.interrupt(); - - // close all connection - closeConnections(availableConnections); - availableConnections = new Stack<Connection>(); - closeConnections(busyConnections); - busyConnections = new Stack<Connection>(); - lastAccessTimeRecord.clear(); - - logger.info("All connection is closed"); - - try { - this.clenupThread.join(); - this.producerThread.join(); - } catch (Exception e) { - logger.error("Cannot shutdown cleanup thread", e); - } - - logger.info("Connection Pool Shutdown"); - } - - private void closeConnections(Stack<Connection> connections) { - while (!connections.isEmpty()) { - Connection connection = connections.pop(); - try { - if (!connection.isClosed()) { - connection.close(); - } - } catch (SQLException sqle) { - // Ignore errors; garbage collect anyhow - logger.warn(sqle.getMessage()); - } - } - } - - public synchronized String toString() { - String info = "ConnectionPool(" + url + "," + username + ")" + ", available=" + availableConnections.size() - + ", busy=" + busyConnections.size() + ", max=" + maxConnections; - return (info); - } - - class CleanUpThread implements Runnable { - public void run() { - while (!stop) { - try { - Thread.sleep(MAX_IDLE_TIME); - closeStaleConnections(); - } catch (InterruptedException e) { - logger.info("Clean up thread is interrupted to close"); - } - } - } - } - - class FillUpThread implements Runnable { - public void run() { - while (!stop) { - try { - // block until get - needConnection.acquire(); - - Connection conn = makeNewConnection(); - fillUpConnection(conn); - } catch (SQLException e) { - // cannot create connection (increase semaphore value back) - needConnection.release(); - logger.error(e.getMessage(), e); - } catch (InterruptedException e) { - logger.info("Fill up thread is interrupted to close"); - break; - } - } - } - } - - public void shutdown() throws SQLException{ - for (Connection c : availableConnections) { - try { - c.close(); - } catch (SQLException e) { - logger.error("Error while closing the connection", e); - throw new SQLException("Error while closing the connection", e); - } - } - - for (Connection c : busyConnections) { - try { - c.close(); - } catch (SQLException e) { - logger.error("Error while closing the connection", e); - throw new SQLException("Error while closing the connection", e); - } - } - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DBConstants.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DBConstants.java deleted file mode 100644 index 1de1363..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DBConstants.java +++ /dev/null @@ -1,106 +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.allocation.manager.db.utils; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class DBConstants { - private final static Logger logger = LoggerFactory.getLogger(DBConstants.class); - - public static int SELECT_MAX_ROWS = 1000; - - public static class DomainTable { - public static final String DOMAIN_ID = "domainId"; - public static final String NAME = "name"; - public static final String DESCRIPTION = "description"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class UserTable { - public static final String USER_ID = "userId"; - public static final String DOMAIN_ID = "domainId"; - public static final String USER_NAME = "userName"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class UserGroupTable { - public static final String GROUP_ID = "groupId"; - public static final String DOMAIN_ID = "domainId"; - public static final String NAME = "name"; - public static final String DESCRIPTION = "description"; - public static final String OWNER_ID = "ownerId"; - public static final String GROUP_TYPE = "groupType"; - public static final String GROUP_CARDINALITY = "groupCardinality"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class GroupMembershipTable { - public static final String PARENT_ID = "parentId"; - public static final String CHILD_ID = "childId"; - public static final String CHILD_TYPE = "childType"; - public static final String DOMAIN_ID = "domainId"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class EntityTypeTable { - public static final String ENTITY_TYPE_ID = "entityTypeId"; - public static final String DOMAIN_ID = "domainId"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class PermissionTypeTable { - public static final String ENTITY_TYPE_ID = "permissionTypeId"; - public static final String DOMAIN_ID = "domainId"; - public static final String NAME = "name"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } - - public static class EntityTable { - public static final String ENTITY_ID = "entityId"; - public static final String PARENT_ENTITY_ID = "parentEntityId"; - public static final String ENTITY_TYPE_ID = "entityTypeId"; - public static final String NAME = "name"; - public static final String DESCRIPTION = "description"; - public static final String FULL_TEXT = "fullText"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - public static final String DOMAIN_ID = "domainId"; - public static final String ORIGINAL_ENTITY_CREATION_TIME = "originalEntityCreationTime"; - public static final String SHARED = "shared"; - } - - public static class SharingTable { - public static final String DOMAIN_ID = "domainId"; - public static final String PERMISSION_TYPE_ID = "permissionTypeId"; - public static final String ENTITY_ID = "entityId"; - public static final String GROUP_ID = "groupId"; - public static final String INHERITED_PARENT_ID = "inheritedParentId"; - public static final String SHARING_TYPE = "sharingType"; - public static final String CREATED_TIME = "createdTime"; - public static final String UPDATED_TIME = "updatedTime"; - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DatabaseCreator.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DatabaseCreator.java deleted file mode 100644 index d8368f5..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/DatabaseCreator.java +++ /dev/null @@ -1,352 +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.allocation.manager.db.utils; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.sql.*; -import java.util.StringTokenizer; - -/** - * This class creates the database tables required for airavata with default configuration this - * class creates derby database in server mode. User can specify required database in appropriate - * properties files. - */ -public class DatabaseCreator { - private final static Logger logger = LoggerFactory.getLogger(DatabaseCreator.class); - - public enum DatabaseType { - derby("(?i).*derby.*"), mysql("(?i).*mysql.*"), other(""); - - private String pattern; - - private DatabaseType(String matchingPattern) { - this.pattern = matchingPattern; - } - - public String getMatchingPattern() { - return this.pattern; - } - } - - private static DatabaseType[] supportedDatabase = new DatabaseType[] { DatabaseType.derby, DatabaseType.mysql }; - - private static Logger log = LoggerFactory.getLogger(DatabaseCreator.class); - private static final String delimiter = ";"; - - /** - * Creates database - * - * @throws Exception - */ - public static void createRegistryDatabase(String prefix, Connection conn) throws Exception { - createDatabase(prefix, conn); - } - - - - /** - * Checks whether database tables are created by using select * on given table name - * - * @param tableName - * Table which should be existed - * @return <code>true</core> if checkSQL is success, else <code>false</code> . - */ - public static boolean isDatabaseStructureCreated(String tableName, Connection conn) { - try { - - log.debug("Running a query to test the database tables existence."); - - // check whether the tables are already created with a query - Statement statement = null; - try { - statement = conn.createStatement(); - ResultSet rs = statement.executeQuery("select * from " + tableName); - if (rs != null) { - rs.close(); - } - } finally { - try { - if (statement != null) { - statement.close(); - } - } catch (SQLException e) { - return false; - } - } - } catch (SQLException e) { - return false; - } - - return true; - } - - /** - * executes given sql - * - * @param sql - * @throws Exception - */ - private static void executeSQL(String sql, Connection conn) throws Exception { - // Check and ignore empty statements - if ("".equals(sql.trim())) { - return; - } - - Statement statement = null; - try { - log.debug("SQL : " + sql); - - boolean ret; - int updateCount = 0, updateCountTotal = 0; - statement = conn.createStatement(); - ret = statement.execute(sql); - updateCount = statement.getUpdateCount(); - do { - if (!ret) { - if (updateCount != -1) { - updateCountTotal += updateCount; - } - } - ret = statement.getMoreResults(); - if (ret) { - updateCount = statement.getUpdateCount(); - } - } while (ret); - - log.debug(sql + " : " + updateCountTotal + " rows affected"); - - SQLWarning warning = conn.getWarnings(); - while (warning != null) { - log.info(warning + " sql warning"); - warning = warning.getNextWarning(); - } - conn.clearWarnings(); - } catch (SQLException e) { - if (e.getSQLState().equals("X0Y32")) { - // eliminating the table already exception for the derby - // database - log.info("Table Already Exists", e); - } else { - throw new Exception("Error occurred while executing : " + sql, e); - } - } finally { - if (statement != null) { - try { - statement.close(); - } catch (SQLException e) { - log.error("Error occurred while closing result set.", e); - } - } - } - } - - /** - * computes relatational database type using database name - * - * @return DatabaseType - * @throws Exception - * - */ - public static DatabaseType getDatabaseType(Connection conn) throws Exception { - try { - if (conn != null && (!conn.isClosed())) { - DatabaseMetaData metaData = conn.getMetaData(); - String databaseProductName = metaData.getDatabaseProductName(); - return checkType(databaseProductName); - } - } catch (SQLException e) { - String msg = "Failed to create Airavata database." + e.getMessage(); - log.error(msg, e); - throw new Exception(msg, e); - } - return DatabaseType.other; - } - - /** - * Overloaded method with String input - * - * @return DatabaseType - * @throws Exception - * - */ - public static DatabaseType getDatabaseType(String dbUrl) throws Exception { - return checkType(dbUrl); - } - - private static DatabaseType checkType(String text) throws Exception { - try { - if (text != null) { - for (DatabaseType type : supportedDatabase) { - if (text.matches(type.getMatchingPattern())) - return type; - } - } - String msg = "Unsupported database: " + text - + ". Database will not be created automatically by the Airavata. " - + "Please create the database using appropriate database scripts for " + "the database."; - throw new Exception(msg); - - } catch (SQLException e) { - String msg = "Failed to create Airavatadatabase." + e.getMessage(); - log.error(msg, e); - throw new Exception(msg, e); - } - } - - /** - * Get scripts location which is prefix + "-" + databaseType + ".sql" - * - * @param prefix - * @param databaseType - * @return script location - */ - private static String getScriptLocation(String prefix, DatabaseType databaseType) { - String scriptName = prefix + "-" + databaseType + ".sql"; - log.debug("Loading database script from :" + scriptName); - return scriptName; - } - - private static void createDatabase(String prefix, Connection conn) throws Exception { - Statement statement = null; - try { - conn.setAutoCommit(false); - statement = conn.createStatement(); - executeSQLScript(getScriptLocation(prefix, DatabaseCreator.getDatabaseType(conn)), conn); - conn.commit(); - log.debug("Tables are created successfully."); - } catch (SQLException e) { - String msg = "Failed to create database tables for Airavata resource store. " + e.getMessage(); - log.error(msg, e); - conn.rollback(); - throw new Exception(msg, e); - } finally { - conn.setAutoCommit(true); - try { - if (statement != null) { - statement.close(); - } - } catch (SQLException e) { - log.error("Failed to close statement.", e); - } - } - } - - private static void executeSQLScript(String dbscriptName, Connection conn) throws Exception { - StringBuffer sql = new StringBuffer(); - BufferedReader reader = null; - - try { - InputStream is = DatabaseCreator.class.getClassLoader().getResourceAsStream(dbscriptName); - if(is == null) { - logger.info("Script file not found at " + dbscriptName + ". Uses default database script file"); - DatabaseType databaseType = DatabaseCreator.getDatabaseType(conn); - if(databaseType.equals(DatabaseType.derby)){ - is = DatabaseCreator.class.getClassLoader().getResourceAsStream("sharing-registry-derby.sql"); - }else if(databaseType.equals(DatabaseType.mysql)){ - is = DatabaseCreator.class.getClassLoader().getResourceAsStream("sharing-registry-mysql.sql"); - } - } - reader = new BufferedReader(new InputStreamReader(is)); - String line; - while ((line = reader.readLine()) != null) { - line = line.trim(); - if (line.startsWith("//")) { - continue; - } - if (line.startsWith("--")) { - continue; - } - StringTokenizer st = new StringTokenizer(line); - if (st.hasMoreTokens()) { - String token = st.nextToken(); - if ("REM".equalsIgnoreCase(token)) { - continue; - } - } - sql.append(" ").append(line); - - // SQL defines "--" as a comment to EOL - // and in Oracle it may contain a hint - // so we cannot just remove it, instead we must end it - if (line.indexOf("--") >= 0) { - sql.append("\n"); - } - if ((checkStringBufferEndsWith(sql, delimiter))) { - executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn); - sql.replace(0, sql.length(), ""); - } - } - // Catch any statements not followed by ; - if (sql.length() > 0) { - executeSQL(sql.toString(), conn); - } - } catch (IOException e) { - log.error("Error occurred while executing SQL script for creating Airavata database", e); - throw new Exception("Error occurred while executing SQL script for creating Airavata database", e); - - } finally { - if (reader != null) { - reader.close(); - } - } - } - - /** - * Checks that a string buffer ends up with a given string. It may sound trivial with the existing JDK API but the - * various implementation among JDKs can make those methods extremely resource intensive and perform poorly due to - * massive memory allocation and copying. See - * - * @param buffer - * the buffer to perform the check on - * @param suffix - * the suffix - * @return <code>true</code> if the character sequence represented by the argument is a suffix of the character - * sequence represented by the StringBuffer object; <code>false</code> otherwise. Note that the result will - * be <code>true</code> if the argument is the empty string. - */ - public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) { - if (suffix.length() > buffer.length()) { - return false; - } - // this loop is done on purpose to avoid memory allocation performance - // problems on various JDKs - // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and - // implementation is ok though does allocation/copying - // StringBuffer.toString().endsWith() does massive memory - // allocation/copying on JDK 1.5 - // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169 - int endIndex = suffix.length() - 1; - int bufferIndex = buffer.length() - 1; - while (endIndex >= 0) { - if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) { - return false; - } - bufferIndex--; - endIndex--; - } - return true; - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JPAUtils.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JPAUtils.java deleted file mode 100644 index 3781c4b..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JPAUtils.java +++ /dev/null @@ -1,215 +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.allocation.manager.db.utils; - -import org.apache.airavata.common.exception.ApplicationSettingsException; -import org.apache.airavata.common.utils.ServerSettings; -import org.apache.airavata.allocation.manager.models.AllocationManagerException; -import org.apache.derby.drda.NetworkServerControl; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.persistence.*; -import java.io.IOException; -import java.net.InetAddress; -import java.net.URI; -import java.sql.Connection; -import java.sql.SQLException; -import java.util.HashMap; -import java.util.Map; - -public class JPAUtils { - private final static Logger logger = LoggerFactory.getLogger(JPAUtils.class); - - public static final String PERSISTENCE_UNIT_NAME = "airavata-sharing-registry"; - public static final String SHARING_REG_JDBC_DRIVER = "sharingcatalog.jdbc.driver"; - public static final String SHARING_REG_JDBC_URL = "sharingcatalog.jdbc.url"; - public static final String SHARING_REG_JDBC_USER = "sharingcatalog.jdbc.user"; - public static final String SHARING_REG_JDBC_PWD = "sharingcatalog.jdbc.password"; - public static final String SHARING_REG_VALIDATION_QUERY = "sharingcatalog.validationQuery"; - public static final String JPA_CACHE_SIZE = "jpa.cache.size"; - public static final String JPA_CACHE_ENABLED = "cache.enable"; - - public static final String CONFIGURATION = "CONFIGURATION"; - public static final String START_DERBY_ENABLE = "start.derby.server.mode"; - public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer"; - private static NetworkServerControl server; - private static JdbcStorage db; - private static String jdbcURl; - private static String jdbcDriver; - private static String jdbcUser; - private static String jdbcPassword; - - @PersistenceUnit(unitName = PERSISTENCE_UNIT_NAME) - protected static EntityManagerFactory factory; - @PersistenceContext(unitName = PERSISTENCE_UNIT_NAME) - private static EntityManager entityManager; - - public synchronized static EntityManager getEntityManager() throws Exception { - if (factory == null) { - String connectionProperties = "DriverClassName=" + readServerProperties(SHARING_REG_JDBC_DRIVER) + "," + - "Url=" + readServerProperties(SHARING_REG_JDBC_URL) + "?autoReconnect=true," + - "Username=" + readServerProperties(SHARING_REG_JDBC_USER) + "," + - "Password=" + readServerProperties(SHARING_REG_JDBC_PWD) + - ",validationQuery=" + readServerProperties(SHARING_REG_VALIDATION_QUERY); - -// String connectionProperties = "DriverClassName=com.mysql.jdbc.Driver," + -// "Url=jdbc:mysql://localhost:3306/airavata_sharing_catalog?autoReconnect=true," + -// "Username=root," + -// "Password=," + -// ",validationQuery=SELECT 1 FROM CONFIGURATION"; - - Map<String, String> properties = new HashMap<String, String>(); - properties.put("openjpa.ConnectionDriverName", "org.apache.commons.dbcp.BasicDataSource"); - properties.put("openjpa.ConnectionProperties", connectionProperties); - properties.put("openjpa.DynamicEnhancementAgent", "true"); - properties.put("openjpa.RuntimeUnenhancedClasses", "unsupported"); - -// properties.put("openjpa.DataCache", "" + readServerProperties(JPA_CACHE_ENABLED) -// + "(CacheSize=" + Integer.valueOf(readServerProperties(JPA_CACHE_SIZE)) + ", SoftReferenceSize=0)"); -// properties.put("openjpa.QueryCache", "" + readServerProperties(JPA_CACHE_ENABLED) -// + "(CacheSize=" + Integer.valueOf(readServerProperties(JPA_CACHE_SIZE)) + ", SoftReferenceSize=0)"); - - properties.put("openjpa.RemoteCommitProvider", "sjvm"); - properties.put("openjpa.Log", "DefaultLevel=INFO, Runtime=INFO, Tool=INFO, SQL=INFO"); - properties.put("openjpa.jdbc.SynchronizeMappings", "buildSchema(ForeignKeys=true)"); - properties.put("openjpa.jdbc.QuerySQLCache", "false"); -// properties.put("openjpa.Multithreaded", "true"); - properties.put("openjpa.ConnectionFactoryProperties", "PrettyPrint=true, PrettyPrintLineLength=72," + - " PrintParameters=true, MaxActive=10, MaxIdle=5, MinIdle=2, MaxWait=31536000, autoReconnect=true"); - properties.put("openjpa.RuntimeUnenhancedClasses", "warn"); - factory = Persistence.createEntityManagerFactory(PERSISTENCE_UNIT_NAME, properties); - } - - entityManager = factory.createEntityManager(); - return entityManager; - } - - public static void initializeDB() throws Exception { - jdbcDriver = readServerProperties(SHARING_REG_JDBC_DRIVER); - jdbcURl = readServerProperties(SHARING_REG_JDBC_URL); - jdbcUser = readServerProperties(SHARING_REG_JDBC_USER); - jdbcPassword = readServerProperties(SHARING_REG_JDBC_PWD); - jdbcURl = jdbcURl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword; - - if (getDBType(jdbcURl).equals("derby") && isDerbyStartEnabled()) { - startDerbyInServerMode(); - } - db = new JdbcStorage(10, 50, jdbcURl, jdbcDriver, true); - - Connection conn = null; - try { - conn = db.connect(); - if (!DatabaseCreator.isDatabaseStructureCreated(CONFIGURATION, conn)) { - DatabaseCreator.createRegistryDatabase("database_scripts/sharing-registry", conn); - logger.info("New Database created for Sharing Catalog !!! "); - } else { - logger.info("Database already created for Sharing Catalog !!!"); - } - } catch (Exception e) { - logger.error(e.getMessage(), e); - throw new RuntimeException("Database failure", e); - } finally { - db.closeConnection(conn); - try { - if(conn != null){ - if (!conn.getAutoCommit()) { - conn.commit(); - } - conn.close(); - } - } catch (SQLException e) { - logger.error("Error while closing database connection...", e.getMessage(), e); - } - } - } - - public static String getDBType(String jdbcUrl){ - try{ - String cleanURI = jdbcUrl.substring(5); - URI uri = URI.create(cleanURI); - return uri.getScheme(); - } catch (Exception e) { - logger.error(e.getMessage(), e); - return null; - } - } - - public static boolean isDerbyStartEnabled(){ - try { - String s = ServerSettings.getSetting(START_DERBY_ENABLE); - if("true".equals(s)){ - return true; - } - } catch (ApplicationSettingsException e) { - logger.error("Unable to read airavata server properties", e.getMessage(), e); - return false; - } - return false; - } - - public static void startDerbyInServerMode() { - try { - System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true"); - server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"), - getPort(jdbcURl), - jdbcUser, jdbcPassword); - java.io.PrintWriter consoleWriter = new java.io.PrintWriter(System.out, true); - server.start(consoleWriter); - } catch (IOException e) { - logger.error("Unable to start Apache derby in the server mode! Check whether " + - "specified port is available"); - } catch (Exception e) { - logger.error("Unable to start Apache derby in the server mode! Check whether " + - "specified port is available"); - } - } - - public static void stopDerbyInServerMode() { - System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "false"); - if (server!=null){ - try { - server.shutdown(); - } catch (Exception e) { - logger.error("Error when stopping the derby server : "+e.getLocalizedMessage()); - } - } - } - - public static int getPort(String jdbcURL){ - try{ - String cleanURI = jdbcURL.substring(5); - URI uri = URI.create(cleanURI); - return uri.getPort(); - } catch (Exception e) { - logger.error(e.getMessage(), e); - return -1; - } - } - - public static String readServerProperties(String propertyName) throws Exception { - try { - return ServerSettings.getSetting(propertyName); - } catch (ApplicationSettingsException e) { - logger.error("Unable to read airavata-server.properties...", e); - throw new Exception("Unable to read airavata-server.properties..."); - } - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JdbcStorage.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JdbcStorage.java deleted file mode 100644 index ea3a360..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/JdbcStorage.java +++ /dev/null @@ -1,174 +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.allocation.manager.db.utils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.sql.*; - -public class JdbcStorage { - private static Logger log = LoggerFactory.getLogger(JdbcStorage.class); - - private ConnectionPool connectionPool; - - public JdbcStorage(String jdbcUrl, String jdbcDriver) { - // default init connection and max connection - this(3, 50, jdbcUrl, jdbcDriver, true); - } - - public JdbcStorage(int initCon, int maxCon, String url, String driver, boolean enableTransactions) { - try { - if (enableTransactions) { - connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true, false, - Connection.TRANSACTION_SERIALIZABLE); - } else { - connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true); - } - } catch (Exception e) { - throw new RuntimeException("Failed to create database connection pool.", e); - } - } - - /** - * Check if this connection pool is auto commit or not - * - * @return - */ - public boolean isAutoCommit() { - return connectionPool.isAutoCommit(); - } - - public void commit(Connection conn) { - try { - if (conn != null && !conn.getAutoCommit()) { - conn.commit(); - } - } catch (SQLException sqle) { - log.error("Cannot commit data", sqle); - } - } - - public void commitAndFree(Connection conn) { - commit(conn); - closeConnection(conn); - } - - public void rollback(Connection conn) { - try { - if (conn != null && !conn.getAutoCommit()) { - conn.rollback(); - } - } catch (SQLException sqle) { - log.error("Cannot Rollback data", sqle); - } - } - - public void rollbackAndFree(Connection conn) { - rollback(conn); - closeConnection(conn); - } - - public Connection connect() { - - Connection conn = null; - try { - conn = connectionPool.getConnection(); - } catch (SQLException e) { - log.error(e.getMessage(), e); - } - return conn; - } - - /** - * This method is provided so that you can have better control over the statement. For example: You can use - * stmt.setString to convert quotation mark automatically in an UPDATE statement - * - * NOTE: Statement is closed after execution - */ - public int executeUpdateAndClose(PreparedStatement stmt) throws SQLException { - int rows = 0; - try { - rows = stmt.executeUpdate(); - if (rows == 0) { - log.info("Problem: 0 rows affected by insert/update/delete statement."); - } - } finally { - stmt.close(); - } - return rows; - } - - public int countRow(String tableName, String columnName) throws SQLException { - String query = new String("SELECT COUNT(" + columnName + ") FROM " + tableName); - int count = -1; - Connection conn = null; - PreparedStatement stmt = null; - try { - conn = connectionPool.getConnection(); - stmt = conn.prepareStatement(query); - ResultSet rs = stmt.executeQuery(); - rs.next(); - count = rs.getInt(1); - commit(conn); - } catch (SQLException sql) { - rollback(conn); - throw sql; - } finally { - try { - if (stmt != null && !stmt.isClosed()) { - stmt.close(); - } - } finally { - closeConnection(conn); - } - } - return count; - } - - public void quietlyClose(Connection conn, Statement... stmts) { - if (stmts != null) { - for (Statement stmt : stmts) { - try { - if (stmt != null && !stmt.isClosed()) { - stmt.close(); - } - } catch (SQLException sql) { - log.error(sql.getMessage(), sql); - } - } - } - closeConnection(conn); - } - - public void closeConnection(Connection conn) { - if (conn != null) { - connectionPool.free(conn); - } - } - - public void closeAllConnections() { - if (connectionPool != null) - connectionPool.dispose(); - } - - public void shutdown() throws SQLException { - connectionPool.shutdown(); - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ObjectMapperSingleton.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ObjectMapperSingleton.java deleted file mode 100644 index b5f6c00..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-server/src/main/java/org/apache/airavata/allocation/manager/db/utils/ObjectMapperSingleton.java +++ /dev/null @@ -1,38 +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.allocation.manager.db.utils; - -import org.dozer.DozerBeanMapper; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class ObjectMapperSingleton extends DozerBeanMapper{ - private final static Logger logger = LoggerFactory.getLogger(ObjectMapperSingleton.class); - - private static ObjectMapperSingleton instance; - - private ObjectMapperSingleton(){} - - public static ObjectMapperSingleton getInstance(){ - if(instance == null) - instance = new ObjectMapperSingleton(); - return instance; - } -} \ No newline at end of file diff --git a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-stubs/src/main/java/org/apache/airavata/allocation/manager/models/Domain.java b/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-stubs/src/main/java/org/apache/airavata/allocation/manager/models/Domain.java deleted file mode 100644 index 2eccf05..0000000 --- a/allocation-manager/airavata-allocation-manager/airavata-allocation-manager-stubs/src/main/java/org/apache/airavata/allocation/manager/models/Domain.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.apache.airavata.allocation.manager.models; - -public class Domain { -// Placeholder file for Madrina to create -} diff --git a/bin/README.txt b/bin/README.txt deleted file mode 100644 index a5d51f6..0000000 --- a/bin/README.txt +++ /dev/null @@ -1,16 +0,0 @@ - - -## Temporarily using ANT compile the Aurora Management code. -## TODO: integrate with maven build system, instead of using ANT - -#In the following directory run the compilation command: -airavata/modules/cloud/AuroraIntegration/src - -#Compilation command -ant all - -#Run command -## TODO: add the command to run and test the code - -## Add sample output that shows the Aurora code working - diff --git a/bin/build.xml b/bin/build.xml deleted file mode 100644 index 5533336..0000000 --- a/bin/build.xml +++ /dev/null @@ -1,53 +0,0 @@ -<?xml version="1.0" encoding="utf-8"?> -<project name="aurora" default="compile_all" basedir=".."> - - <property name="BUILD.compiler" value="modern"/> - <property name="src" value="src"/> - <property name="BUILD" value="BUILD"/> - <property name="classes" value="${BUILD}/classes"/> - - - <target name="all" depends="compile_all"/> - - <target name="compile_all" - depends="org"/> - - <target name="clean"> - <delete dir="${BUILD}"/> - </target> - - <!-- Prepare target directories --> - <target name="prepare"> - <mkdir dir="${BUILD}"/> - <mkdir dir="${classes}"/> - </target> - - - <target name="jar"> - <mkdir dir="${BUILD}/jar"/> - <jar destfile="${BUILD}/jar/auroraDriverl.jar" basedir="${BUILD}/classes"> - <manifest> - <attribute name="Main-Class" value="org.apache.airavata.cloud.aurora.driver.AuroraAdminDriver"/> - </manifest> - </jar> - </target> - - - - <!-- ** means all subdirectories as well --> - <!-- * means all files in the current directory --> - <!-- for just java files use *.java --> - - <target name="org" depends="prepare"> - <javac srcdir="${src}" - includes="org/**" - excludes="**/package.html" - destdir="${classes}" - classpath="${classes}" - debug="on" - optimize="on" - deprecation="off"/> - </target> - - -</project> diff --git a/bin/db.config b/bin/db.config deleted file mode 100644 index b2c7b9d..0000000 --- a/bin/db.config +++ /dev/null @@ -1,24 +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. -# -#database connection string - -##mySQL -jdbcDriver=com.mysql.jdbc.Driver - -#jdbcUrl=jdbc:mysql://localhost:3306/wsnt?user=wsnt2&password=PASSWORD \ No newline at end of file diff --git a/bin/org/apache/airavata/jobsubmission/gram/errors.properties b/bin/org/apache/airavata/jobsubmission/gram/errors.properties deleted file mode 100644 index 3e4382b..0000000 --- a/bin/org/apache/airavata/jobsubmission/gram/errors.properties +++ /dev/null @@ -1,176 +0,0 @@ -1 = Parameter not supported -2 = The RSL length is greater than the maximum allowed -3 = No resources available -4 = Bad directory specified -5 = The executable does not exist -6 = Insufficient funds -7 = Authentication with the remote server failed -8 = Job cancelled by user -9 = Job cancelled by system - -10 = Data transfer to the server failed -11 = The stdin file does not exist -12 = The connection to the server failed (check host and port) -13 = The provided RSL 'maxtime' value is invalid (not an integer or must be greater than 0) -14 = The provided RSL 'count' value is invalid (not an integer or must be greater than 0) -15 = The job manager received an invalid RSL -16 = Could not connect to job manager -17 = The job failed when the job manager attempted to run it -18 = Paradyn error -19 = The provided RSL 'jobtype' value is invalid - -20 = The provided RSL 'myjob' value is invalid -21 = The job manager failed to locate an internal script argument file -22 = The job manager failed to create an internal script argument file -23 = The job manager detected an invalid job state -24 = The job manager detected an invalid script response -25 = The job manager detected an invalid job state -26 = The provided RSL 'jobtype' value is not supported by this job manager -27 = Unimplemented -28 = The job manager failed to create an internal script submission file -29 = The job manager cannot find the user proxy - -30 = The job manager failed to open the user proxy -31 = The job manager failed to cancel the job as requested -32 = System memory allocation failed -33 = The interprocess job communication initialization failed -34 = The interprocess job communication setup failed -35 = The provided RSL 'host count' value is invalid -36 = One of the provided RSL parameters is unsupported -37 = The provided RSL 'queue' parameter is invalid -38 = The provided RSL 'project' parameter is invalid -39 = The provided RSL string includes variables that could not be identified - -40 = The provided RSL 'environment' parameter is invalid -41 = The provided RSL 'dryrun' parameter is invalid -42 = The provided RSL is invalid (an empty string) -43 = The job manager failed to stage the executable -44 = The job manager failed to stage the stdin file -45 = The requested job manager type is invalid -46 = The provided RSL 'arguments' parameter is invalid -47 = The gatekeeper failed to run the job manager -48 = The provided RSL could not be properly parsed -49 = There is a version mismatch between GRAM components - -50 = The provided RSL 'arguments' parameter is invalid -51 = The provided RSL 'count' parameter is invalid -52 = The provided RSL 'directory' parameter is invalid -53 = The provided RSL 'dryrun' parameter is invalid -54 = The provided RSL 'environment' parameter is invalid -55 = The provided RSL 'executable' parameter is invalid -56 = The provided RSL 'host_count' parameter is invalid -57 = The provided RSL 'jobtype' parameter is invalid -58 = The provided RSL 'maxtime' parameter is invalid -59 = The provided RSL 'myjob' parameter is invalid - -60 = The provided RSL 'paradyn' parameter is invalid -61 = The provided RSL 'project' parameter is invalid -62 = The provided RSL 'queue' parameter is invalid -63 = The provided RSL 'stderr' parameter is invalid -64 = The provided RSL 'stdin' parameter is invalid -65 = The provided RSL 'stdout' parameter is invalid -66 = The job manager failed to locate an internal script -67 = The job manager failed on the system call pipe() -68 = The job manager failed on the system call fcntl() -69 = The job manager failed to create the temporary stdout filename - -70 = The job manager failed to create the temporary stderr filename -71 = The job manager failed on the system call fork() -72 = The executable file permissions do not allow execution -73 = The job manager failed to open stdout -74 = The job manager failed to open stderr -75 = The cache file could not be opened in order to relocate the user proxy -76 = Cannot access cache files in ~/.globus/.gass_cache, check permissions, quota, and disk space -77 = The job manager failed to insert the contact in the client contact list -78 = The contact was not found in the job manager's client contact list -79 = Connecting to the job manager failed. Possible reasons: job terminated, invalid job contact, network problems, ... - -80 = The syntax of the job contact is invalid -81 = The executable parameter in the RSL is undefined -82 = The job manager service is misconfigured. condor arch undefined -83 = The job manager service is misconfigured. condor os undefined -84 = The provided RSL 'min_memory' parameter is invalid -85 = The provided RSL 'max_memory' parameter is invalid -86 = The RSL 'min_memory' value is not zero or greater -87 = The RSL 'max_memory' value is not zero or greater -88 = The creation of a HTTP message failed -89 = Parsing incoming HTTP message failed - -90 = The packing of information into a HTTP message failed -91 = An incoming HTTP message did not contain the expected information -92 = The job manager does not support the service that the client requested -93 = The gatekeeper failed to find the requested service -94 = The jobmanager does not accept any new requests (shutting down) -95 = The client failed to close the listener associated with the callback URL -96 = The gatekeeper contact cannot be parsed -97 = The job manager could not find the 'poe' command -98 = The job manager could not find the 'mpirun' command -99 = The provided RSL 'start_time' parameter is invalid" -100 = The provided RSL 'reservation_handle' parameter is invalid - -101 = The provided RSL 'max_wall_time' parameter is invalid -102 = The RSL 'max_wall_time' value is not zero or greater -103 = The provided RSL 'max_cpu_time' parameter is invalid -104 = The RSL 'max_cpu_time' value is not zero or greater -105 = The job manager is misconfigured, a scheduler script is missing -106 = The job manager is misconfigured, a scheduler script has invalid permissions -107 = The job manager failed to signal the job -108 = The job manager did not recognize/support the signal type -109 = The job manager failed to get the job id from the local scheduler - -110 = The job manager is waiting for a commit signal -111 = The job manager timed out while waiting for a commit signal -112 = The provided RSL 'save_state' parameter is invalid -113 = The provided RSL 'restart' parameter is invalid -114 = The provided RSL 'two_phase' parameter is invalid -115 = The RSL 'two_phase' value is not zero or greater -116 = The provided RSL 'stdout_position' parameter is invalid -117 = The RSL 'stdout_position' value is not zero or greater -118 = The provided RSL 'stderr_position' parameter is invalid -119 = The RSL 'stderr_position' value is not zero or greater - -120 = The job manager restart attempt failed -121 = The job state file doesn't exist -122 = Could not read the job state file -123 = Could not write the job state file -124 = The old job manager is still alive -125 = The job manager state file TTL expired -126 = It is unknown if the job was submitted -127 = The provided RSL 'remote_io_url' parameter is invalid -128 = Could not write the remote io url file -129 = The standard output/error size is different - -130 = The job manager was sent a stop signal (job is still running) -131 = The user proxy expired (job is still running) -132 = The job was not submitted by original jobmanager -133 = The job manager is not waiting for that commit signal -134 = The provided RSL scheduler specific parameter is invalid -135 = The job manager could not stage in a file -136 = The scratch directory could not be created -137 = The provided 'gass_cache' parameter is invalid -138 = The RSL contains attributes which are not valid for job submission -139 = The RSL contains attributes which are not valid for stdio update - -140 = The RSL contains attributes which are not valid for job restart -141 = The provided RSL 'file_stage_in' parameter is invalid -142 = The provided RSL 'file_stage_in_shared' parameter is invalid -143 = The provided RSL 'file_stage_out' parameter is invalid -144 = The provided RSL 'gass_cache' parameter is invalid -145 = The provided RSL 'file_cleanup' parameter is invalid -146 = The provided RSL 'scratch_dir' parameter is invalid -147 = The provided scheduler-specific RSL parameter is invalid -148 = A required RSL attribute was not defined in the RSL spec -149 = The gass_cache attribute points to an invalid cache directory - -150 = The provided RSL 'save_state' parameter has an invalid value -151 = The job manager could not open the RSL attribute validation file -152 = The job manager could not read the RSL attribute validation file -153 = The provided RSL 'proxy_timeout' is invalid -154 = The RSL 'proxy_timeout' value is not greater than zero -155 = The job manager could not stage out a file -156 = The job contact string does not match any which the job manager is handling -157 = Proxy delegation failed -158 = The job manager could not lock the state lock file - -1000 = Failed to start up callback handler -1003 = Job contact not set -- To stop receiving notification emails like this one, please contact "[email protected]" <[email protected]>.
