diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml deleted file mode 100644 index 3d920e68..00000000 --- a/.github/workflows/build.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: Java Build SNAPSHOT and push to Maven Central -# - -on: - workflow_dispatch: - #push: - # branches: - # - develop - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - with: - ref: develop - - name: setup JDK 1.8 - uses: actions/setup-java@v1 - with: - java-version: 1.8 - server-id: ossrh - server-username: MAVEN_USERNAME - server-password: MAVEN_PASSWORD - gpg-private-key: ${{ secrets.OSSRH_GPG_SECRET_KEY}} - gpg-passphrase: MAVEN_GPG_PASSPHRASE - - - name: Cache Maven packages - uses: actions/cache@v2 - with: - path: ~/.m2 - key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} - restore-keys: ${{ runner.os }}-m2 -# - name: Set up Maven Central -# uses: actions/setup-java@v1 -# with: -# java-version: 1.8 -# server-id: ossrh -# server-username: MAVEN_USERNAME -# server-password: MAVEN_PASSWORD -# gpg-private-key: ${{ secrets.OSSRH_GPG_SECRET_KEY}} -# gpg-passphrase: MAVEN_GPG_PASSPHRASE - - name: Build and publish package - run: mvn -B package deploy - env: - MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }} - MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }} - MAVEN_GPG_PASSPHRASE: ${{ secrets.OSSRH_GPG_SECRET_KEY_PASSWORD }} - diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml new file mode 100644 index 00000000..eaae993e --- /dev/null +++ b/.github/workflows/maven.yml @@ -0,0 +1,36 @@ +# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Java CI with Maven + +on: + push: + branches: [ "main", "develop" ] + pull_request: + branches: [ "*" ] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v7 + - name: Set up JDK + uses: actions/setup-java@v5 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Build with Maven + run: mvn -B verify --file pom.xml + + # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive + # - name: Update dependency graph + # uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6 + diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml deleted file mode 100644 index 89db92ff..00000000 --- a/.github/workflows/publish.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: Publish package on release -# Triggered when a new release is created -# Build and publish to maven central -on: - workflow_dispatch: - # Disable auto publish on release. Trigger manually only. - #push: - # tags: - # - "v*" - #release: - # types: - # - created - # Temporary, for inital push to sonatype - #push: - # branches: - # - main - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: setup JDK 1.8 - uses: actions/setup-java@v1 - with: - java-version: 1.8 - - - name: Set up Maven Central - uses: actions/setup-java@v1 - with: - java-version: 1.8 - server-id: ossrh - server-username: MAVEN_USERNAME - server-password: MAVEN_PASSWORD - gpg-private-key: ${{ secrets.OSSRH_GPG_SECRET_KEY}} - gpg-passphrase: MAVEN_GPG_PASSPHRASE - - - name: Build and publish package - run: mvn -B package deploy - env: - MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }} - MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }} - MAVEN_GPG_PASSPHRASE: ${{ secrets.OSSRH_GPG_SECRET_KEY_PASSWORD }} diff --git a/.gitignore b/.gitignore index 379b2fef..99fcc9e8 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,5 @@ target .idea gpg.asc /d1_common_java.iml +.vscode +misc diff --git a/pom.xml b/pom.xml index 7a1c94dc..8b9156fc 100644 --- a/pom.xml +++ b/pom.xml @@ -1,425 +1,204 @@ - - 4.0.0 - org.dataone - d1_common_java - jar - 2.4.3-SNAPSHOT - DataONE_Common_Java - http://dataone.org - DataONE Common Code with Service Interface Definitions - - 2.3.1 - v1.23 - 1.7 - - - - DataONE - developers@dataone.org - DataONE - https://dataone.org/ - - - - target - src/main/java - src/test/java - target/main-target - target/test-target - - - src/main/resources - true - - buildInfo/buildInfo.properties - - - - src/main/resources - false - - **/*.* - - - - - - org.apache.maven.plugins - maven-compiler-plugin - - 1.7 - ${compiler.target.version} - - - - - com.googlecode.maven-download-plugin - download-maven-plugin - 1.6.0 - - - install-format-ids - validate - - wget - - - https://raw.githubusercontent.com/DataONEorg/object-formats/${d1_format_ids.revision}/objectFormatListV2.xml - false - ${project.basedir}/src/main/resources/org/dataone/service/resources/config/v2 - - - - - - - org.apache.maven.plugins - maven-antrun-plugin - - - validate - - run - - - - - - - - - - - org.codehaus.mojo - xml-maven-plugin - - - validate - - transform - - - - - - - ${project.basedir}/src/main/resources/org/dataone/service/resources/config/v2/ - objectFormatList.xml - ${project.basedir}/src/main/resources/org/dataone/service/resources/config/v1/ - ${project.basedir}/objectFormatListv2-to-v1.xsl - - - - - - net.sf.saxon - Saxon-HE - 10.3 - - - - - org.codehaus.mojo - buildnumber-maven-plugin - - - validate - - create - - - - - false - false - - - - org.apache.maven.plugins - maven-jar-plugin - - - - ${project.version} - ${buildNumber} - ${scmBranch} - ${timestamp} - - - - - - - - test-jar - - - - - - org.apache.maven.plugins - maven-source-plugin - 2.2.1 - - - attach-sources - package - - jar-no-fork - - - - - - maven-clean-plugin - - true - - - ${project.build.directory} - - **/*.jar - **/.* - **/.svn/* - - false - - - - - - com.mycila.maven-license-plugin - maven-license-plugin - -
src/license-header.txt
- - - - maven-javadoc-plugin - 2.9 - - - resource-bundles - package - - - resource-bundle - - - - attach-javadocs - - jar - - - - -Xdoclint:none - - - - - - false - - - - org.sonatype.plugins - nexus-staging-maven-plugin - 1.6.6 - true - - ossrh - https://oss.sonatype.org/ - true - - - - org.apache.maven.plugins - maven-gpg-plugin - 1.6 - - - sign-artifacts - verify - - sign - - - - --pinentry-mode - loopback - - - - - - - - - - - oss.sonatype.org-snapshot - http://oss.sonatype.org/content/repositories/snapshots - - false - - - true - - - - - - javax.mail - mail - 1.4.1 - jar - compile - - - - javax.xml.bind - jaxb-api - 2.2.3 - - - joda-time - joda-time - 2.9.9 - - - - - log4j - log4j - 1.2.17 - - - - - - - - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.1 - maven-plugin - compile - - - junit - junit - [4.13.1,) - jar - test - - - org.apache.maven.plugins - maven-jar-plugin - 2.3.1 - maven-plugin - compile - - - commons-lang - commons-lang - - - - - org.apache.maven.plugins - maven-clean-plugin - 2.4.1 - maven-plugin - compile - - - commons-fileupload - commons-fileupload - [1.3.3,) - - - org.apache.httpcomponents - httpmime - 4.3.3 - - - org.apache.commons - commons-collections4 - [4.1,) - - - org.apache.commons - commons-lang3 - 3.3.2 - - - commons-configuration - commons-configuration - 1.7 - - - - commons-io - commons-io - 2.4 - - - commons-beanutils - commons-beanutils - [1.9.4,) - - - javax.servlet - javax.servlet-api - 3.0.1 - jar - provided - - - - org.dataone - d1_test_resources - ${d1_test_resources.version} - jar - test - - - - - Apache License, Version 2.0 - LICENSE.txt - - - - https://github.com/DataONEorg/d1_common_java - scm:git:ssh://github.com:DataONEorg/d1_common_java.git - scm:git:ssh://git@github.com:DataONEorg/d1_common_java.git - HEAD - - - - ossrh - https://oss.sonatype.org/content/repositories/snapshots - - - ossrh - https://oss.sonatype.org/service/local/staging/deploy/maven2/ - - - - - - org.apache.maven.plugins - maven-javadoc-plugin - - - - \ No newline at end of file + + 4.0.0 + org.dataone + d1_common_java + jar + 2.4.3-SNAPSHOT + DataONE_Common_Java + https://dataone.org + DataONE Common Code with Service Interface Definitions + + 2.4.0 + v1.28 + 25 + + + + DataONE + developers@dataone.org + DataONE + https://dataone.org/ + + + + target + src/main/java + src/test/java + target/main-target + target/test-target + + + src/main/resources + true + + buildInfo/buildInfo.properties + + + + src/main/resources + false + + **/*.* + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.15.0 + + + org.apache.maven.plugins + maven-jar-plugin + 3.4.2 + + + + test-jar + + + + + + + + org.apache.maven.wagon + wagon-ssh-external + 3.5.3 + + + + + + maven.dataone.org + https://maven.dataone.org/ + + true + + + true + + + + + + javax.mail + mail + 1.4.1 + jar + compile + + + + jakarta.xml.bind + jakarta.xml.bind-api + 2.3.2 + + + + org.glassfish.jaxb + jaxb-runtime + 2.3.2 + + + joda-time + joda-time + 2.14.2 + + + org.apache.logging.log4j + log4j-api + 2.26.0 + + + junit + junit + [4.13.1,) + jar + test + + + commons-fileupload + commons-fileupload + [1.3.3,) + + + org.apache.httpcomponents + httpmime + 4.5.14 + + + org.apache.commons + commons-collections4 + [4.1,) + + + org.apache.commons + commons-lang3 + 3.20.0 + + + commons-configuration + commons-configuration + 1.7 + + + + commons-io + commons-io + 2.22.0 + + + commons-beanutils + commons-beanutils + [1.9.4,) + + + javax.servlet + javax.servlet-api + 4.0.1 + jar + provided + + + org.dataone + d1_test_resources + ${d1_test_resources.version} + jar + test + + + + + Apache License, Version 2.0 + LICENSE.txt + + + + https://github.com/DataONEorg/d1_common_java + scm:git:ssh://github.com:DataONEorg/d1_common_java.git + scm:git:ssh://git@github.com:DataONEorg/d1_common_java.git + HEAD + + + + false + maven.dataone.org + DataONE + scpexe://maven.dataone.org/var/www/maven + default + + + + + + org.apache.maven.plugins + maven-javadoc-plugin + + + + diff --git a/src/main/java/org/dataone/mimemultipart/MultipartRequest.java b/src/main/java/org/dataone/mimemultipart/MultipartRequest.java index 05123e17..c8290df1 100644 --- a/src/main/java/org/dataone/mimemultipart/MultipartRequest.java +++ b/src/main/java/org/dataone/mimemultipart/MultipartRequest.java @@ -44,6 +44,7 @@ import javax.servlet.http.Cookie; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; +import javax.servlet.http.HttpUpgradeHandler; import javax.servlet.http.HttpSession; import javax.servlet.http.Part; @@ -66,6 +67,7 @@ public class MultipartRequest implements HttpServletRequest { * @param mpParams Map of field name to form field String value */ public MultipartRequest(HttpServletRequest request, Map mpFiles, Map> mpParams) { + this.request = request; this.multipartFiles = mpFiles; this.multipartParameters = mpParams; } @@ -416,11 +418,6 @@ public void logout() throws ServletException { request.logout(); } - /* - * the following 3 methods are servlet-api v 3.1.0 methods, needing to be - * implemented when moving to tomcat 8.0. Uncomment them at that time. - */ -/* @Override public String changeSessionId() { return request.changeSessionId(); @@ -436,6 +433,6 @@ public T upgrade(Class arg0) throws IOException, ServletException { return request.upgrade(arg0); } -*/ + } diff --git a/src/main/java/org/dataone/mimemultipart/MultipartRequestResolver.java b/src/main/java/org/dataone/mimemultipart/MultipartRequestResolver.java index 2f48cb55..d0f23708 100644 --- a/src/main/java/org/dataone/mimemultipart/MultipartRequestResolver.java +++ b/src/main/java/org/dataone/mimemultipart/MultipartRequestResolver.java @@ -25,7 +25,7 @@ import java.io.*; import java.util.*; - +import javax.servlet.ServletContext; import javax.servlet.http.HttpServletRequest; import org.apache.commons.fileupload.FileItem; import org.apache.commons.fileupload.FileUpload; @@ -33,7 +33,9 @@ import org.apache.commons.fileupload.disk.DiskFileItem; import org.apache.commons.fileupload.disk.DiskFileItemFactory; import org.apache.commons.fileupload.servlet.ServletFileUpload; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; + /* * Copyright 2002-2010 the original author or authors. @@ -74,7 +76,8 @@ */ public class MultipartRequestResolver { - Logger logger = Logger.getLogger(MultipartRequestResolver.class.getName()); + private static final Logger logger = LogManager.getLogger(MultipartRequestResolver.class.getName()); + private DiskFileItemFactory factory; private org.apache.commons.fileupload.servlet.ServletFileUpload upload; final static int SIZE = 16384; diff --git a/src/main/java/org/dataone/service/exceptions/BaseException.java b/src/main/java/org/dataone/service/exceptions/BaseException.java index 33f59536..f226b3f0 100644 --- a/src/main/java/org/dataone/service/exceptions/BaseException.java +++ b/src/main/java/org/dataone/service/exceptions/BaseException.java @@ -34,7 +34,9 @@ import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; + import org.w3c.dom.Document; import org.w3c.dom.Element; @@ -50,7 +52,8 @@ */ public class BaseException extends Exception { - static Logger logger = Logger.getLogger(BaseException.class.getName()); + private static final Logger logger = LogManager.getLogger(BaseException.class.getName()); + /** The major error code associated with this exception. */ private int code; diff --git a/src/main/java/org/dataone/service/types/v1/ObjectFormatList.java b/src/main/java/org/dataone/service/types/v1/ObjectFormatList.java index 9a1989fe..410c42c8 100644 --- a/src/main/java/org/dataone/service/types/v1/ObjectFormatList.java +++ b/src/main/java/org/dataone/service/types/v1/ObjectFormatList.java @@ -1,7 +1,6 @@ package org.dataone.service.types.v1; -import java.io.Serializable; import java.util.ArrayList; import java.util.List; import javax.xml.bind.annotation.XmlAccessType; @@ -36,7 +35,7 @@ "objectFormat" }) @XmlRootElement(name = "objectFormatList") -public class ObjectFormatList extends Slice implements Serializable +public class ObjectFormatList extends Slice { @XmlElement(required = true) protected List objectFormat = new ArrayList(); diff --git a/src/main/java/org/dataone/service/types/v1/Permission.java b/src/main/java/org/dataone/service/types/v1/Permission.java index c51d290d..9b90d1e6 100644 --- a/src/main/java/org/dataone/service/types/v1/Permission.java +++ b/src/main/java/org/dataone/service/types/v1/Permission.java @@ -1,8 +1,6 @@ package org.dataone.service.types.v1; -import java.io.Serializable; - import javax.xml.bind.annotation.XmlEnum; import javax.xml.bind.annotation.XmlEnumValue; import javax.xml.bind.annotation.XmlType; @@ -35,7 +33,7 @@ */ @XmlType(name = "Permission") @XmlEnum -public enum Permission implements Serializable { +public enum Permission { @XmlEnumValue("read") READ("read"), @XmlEnumValue("write") diff --git a/src/main/java/org/dataone/service/types/v1/ReplicationStatus.java b/src/main/java/org/dataone/service/types/v1/ReplicationStatus.java index a77a1bcd..6c157ad5 100644 --- a/src/main/java/org/dataone/service/types/v1/ReplicationStatus.java +++ b/src/main/java/org/dataone/service/types/v1/ReplicationStatus.java @@ -1,8 +1,6 @@ package org.dataone.service.types.v1; -import java.io.Serializable; - import javax.xml.bind.annotation.XmlEnum; import javax.xml.bind.annotation.XmlEnumValue; import javax.xml.bind.annotation.XmlType; @@ -37,7 +35,7 @@ both available and valid (matching checksum with original), and if it is */ @XmlType(name = "ReplicationStatus") @XmlEnum -public enum ReplicationStatus implements Serializable { +public enum ReplicationStatus { @XmlEnumValue("queued") QUEUED("queued"), diff --git a/src/main/java/org/dataone/service/types/v1/ServiceMethodRestriction.java b/src/main/java/org/dataone/service/types/v1/ServiceMethodRestriction.java index 95dc2616..4a601e5a 100644 --- a/src/main/java/org/dataone/service/types/v1/ServiceMethodRestriction.java +++ b/src/main/java/org/dataone/service/types/v1/ServiceMethodRestriction.java @@ -1,7 +1,6 @@ package org.dataone.service.types.v1; -import java.io.Serializable; import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; @@ -28,7 +27,7 @@ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "ServiceMethodRestriction") @XmlRootElement(name = "serviceMethodRestriction") -public class ServiceMethodRestriction extends SubjectList implements Serializable +public class ServiceMethodRestriction extends SubjectList { @XmlAttribute(name = "methodName", required = true) diff --git a/src/main/java/org/dataone/service/types/v1/TypeFactory.java b/src/main/java/org/dataone/service/types/v1/TypeFactory.java index b793c8fb..d9300cb8 100644 --- a/src/main/java/org/dataone/service/types/v1/TypeFactory.java +++ b/src/main/java/org/dataone/service/types/v1/TypeFactory.java @@ -32,7 +32,8 @@ import org.apache.commons.io.input.CountingInputStream; import org.dataone.exceptions.MarshallingException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.exceptions.NotFound; import org.dataone.service.exceptions.ServiceFailure; import org.dataone.service.types.v1.util.ChecksumUtil; @@ -49,7 +50,7 @@ */ public class TypeFactory { - protected static Logger logger = Logger.getLogger(TypeFactory.class.getName()); + protected static Logger logger = LogManager.getLogger(TypeFactory.class.getName()); /** * Factory method for creating an ObjectFormatIdentifier. Does not enforce business rules. diff --git a/src/main/java/org/dataone/service/types/v1/util/AuthUtils.java b/src/main/java/org/dataone/service/types/v1/util/AuthUtils.java index b843b160..79f3551f 100644 --- a/src/main/java/org/dataone/service/types/v1/util/AuthUtils.java +++ b/src/main/java/org/dataone/service/types/v1/util/AuthUtils.java @@ -6,15 +6,12 @@ import java.util.Set; import org.apache.commons.collections4.CollectionUtils; -import org.apache.log4j.Logger; -import org.dataone.service.exceptions.InvalidSystemMetadata; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.types.v1.AccessRule; import org.dataone.service.types.v1.Group; -import org.dataone.service.types.v1.Node; -import org.dataone.service.types.v1.NodeList; import org.dataone.service.types.v1.Permission; import org.dataone.service.types.v1.Person; -import org.dataone.service.types.v1.Service; import org.dataone.service.types.v1.Session; import org.dataone.service.types.v1.Subject; import org.dataone.service.types.v1.SubjectInfo; @@ -23,7 +20,7 @@ public class AuthUtils { - private static final Logger logger = Logger.getLogger(AuthUtils.class); + private static final Logger logger = LogManager.getLogger(AuthUtils.class.getName()); private static Subject buildSubject(String value) { diff --git a/src/main/java/org/dataone/service/types/v1/util/ServiceMethodRestrictionUtil.java b/src/main/java/org/dataone/service/types/v1/util/ServiceMethodRestrictionUtil.java index 7190c2b1..2a73ad42 100644 --- a/src/main/java/org/dataone/service/types/v1/util/ServiceMethodRestrictionUtil.java +++ b/src/main/java/org/dataone/service/types/v1/util/ServiceMethodRestrictionUtil.java @@ -25,7 +25,8 @@ import java.util.ArrayList; import java.util.List; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.configuration.Settings; import org.dataone.service.types.v1.Node; import org.dataone.service.types.v1.NodeState; @@ -43,7 +44,7 @@ */ public class ServiceMethodRestrictionUtil { - private static final Logger logger = Logger.getLogger(ServiceMethodRestrictionUtil.class); + private static final Logger logger = LogManager.getLogger(ServiceMethodRestrictionUtil.class.getName()); /** * Interprets the CN's ServiceMethodRestriction for a given Subject+serviceName+methodName diff --git a/src/main/java/org/dataone/service/types/v1/util/TypeCompareUtil.java b/src/main/java/org/dataone/service/types/v1/util/TypeCompareUtil.java index d7a49a40..358f5925 100644 --- a/src/main/java/org/dataone/service/types/v1/util/TypeCompareUtil.java +++ b/src/main/java/org/dataone/service/types/v1/util/TypeCompareUtil.java @@ -38,7 +38,8 @@ import java.util.Set; import java.util.TreeSet; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.types.v1.AccessRule; import org.dataone.service.types.v1.Identifier; import org.dataone.service.types.v1.NodeReference; @@ -63,7 +64,7 @@ */ public class TypeCompareUtil { - static Logger logger = Logger.getLogger(TypeCompareUtil.class.getName()); + static Logger logger = LogManager.getLogger(TypeCompareUtil.class.getName()); // TODO: compare with https://github.com/SQiShER/java-object-diff/ wrt/ long-term implementation diff --git a/src/main/java/org/dataone/service/types/v1_1/QueryEngineList.java b/src/main/java/org/dataone/service/types/v1_1/QueryEngineList.java index 16484fc9..2db023d9 100644 --- a/src/main/java/org/dataone/service/types/v1_1/QueryEngineList.java +++ b/src/main/java/org/dataone/service/types/v1_1/QueryEngineList.java @@ -6,7 +6,6 @@ import java.util.List; import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; -import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; /** diff --git a/src/main/java/org/dataone/service/types/v2/Node.java b/src/main/java/org/dataone/service/types/v2/Node.java index 316975f8..1b7e098f 100644 --- a/src/main/java/org/dataone/service/types/v2/Node.java +++ b/src/main/java/org/dataone/service/types/v2/Node.java @@ -1,7 +1,6 @@ package org.dataone.service.types.v2; -import java.io.Serializable; import java.util.ArrayList; import java.util.List; import javax.xml.bind.annotation.XmlAccessType; @@ -31,8 +30,7 @@ "property" }) @XmlRootElement(name = "node") -public class Node extends org.dataone.service.types.v1.Node implements - Serializable +public class Node extends org.dataone.service.types.v1.Node { private static final long serialVersionUID = 10000001; protected List property = new ArrayList(); diff --git a/src/main/java/org/dataone/service/types/v2/OptionList.java b/src/main/java/org/dataone/service/types/v2/OptionList.java index b456ae26..d5ccfed5 100644 --- a/src/main/java/org/dataone/service/types/v2/OptionList.java +++ b/src/main/java/org/dataone/service/types/v2/OptionList.java @@ -9,7 +9,6 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -import javax.xml.bind.annotation.XmlValue; /** * A list of options that indicate the possible values for a DataONE service. Each option that can be validly sent to a service is diff --git a/src/main/java/org/dataone/service/types/v2/SystemMetadata.java b/src/main/java/org/dataone/service/types/v2/SystemMetadata.java index 11d03c3b..4641774a 100644 --- a/src/main/java/org/dataone/service/types/v2/SystemMetadata.java +++ b/src/main/java/org/dataone/service/types/v2/SystemMetadata.java @@ -1,7 +1,6 @@ package org.dataone.service.types.v2; -import java.io.Serializable; import org.dataone.service.types.v1.Identifier; import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; @@ -40,7 +39,6 @@ }) @XmlRootElement( name = "systemMetadata") public class SystemMetadata extends org.dataone.service.types.v1.SystemMetadata - implements Serializable { private static final long serialVersionUID = 10000001; diff --git a/src/main/java/org/dataone/service/types/v2/TypeFactory.java b/src/main/java/org/dataone/service/types/v2/TypeFactory.java index 8afa4939..97007e47 100644 --- a/src/main/java/org/dataone/service/types/v2/TypeFactory.java +++ b/src/main/java/org/dataone/service/types/v2/TypeFactory.java @@ -131,7 +131,7 @@ public static T convertTypeFromType(Object original, Class destinationCla original.toString())); } - T destInstance = destinationClass.newInstance(); + T destInstance = destinationClass.getDeclaredConstructor().newInstance(); Map propMap = BeanUtils.describe(original); if (logger.isDebugEnabled()) @@ -201,7 +201,7 @@ public static T convertTypeFromType(Object original, Class destinationCla if (origType == boolean.class) readMethodName = readMethodName.replaceFirst("get", "is"); - Method m = original.getClass().getMethod(readMethodName, (Class[])null); + original.getClass().getMethod(readMethodName, (Class[])null); if (destType == origType) BeanUtils.copyProperty(destInstance, propName, PropertyUtils.getSimpleProperty(original, propName)); diff --git a/src/main/java/org/dataone/service/types/v2/util/ObjectFormatServiceImpl.java b/src/main/java/org/dataone/service/types/v2/util/ObjectFormatServiceImpl.java index 0db3d0e2..ff508f83 100644 --- a/src/main/java/org/dataone/service/types/v2/util/ObjectFormatServiceImpl.java +++ b/src/main/java/org/dataone/service/types/v2/util/ObjectFormatServiceImpl.java @@ -25,7 +25,8 @@ import java.util.HashMap; import org.dataone.exceptions.MarshallingException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.exceptions.NotFound; import org.dataone.service.exceptions.NotImplemented; import org.dataone.service.exceptions.ServiceFailure; @@ -58,7 +59,7 @@ public class ObjectFormatServiceImpl { */ protected ObjectFormatServiceImpl() throws ServiceFailure { - logger = Logger.getLogger(ObjectFormatServiceImpl.class); + logger = LogManager.getLogger(ObjectFormatServiceImpl.class.getName()); objectFormatMap = new HashMap(); try { diff --git a/src/main/java/org/dataone/service/types/v2/util/ServiceMethodRestrictionUtil.java b/src/main/java/org/dataone/service/types/v2/util/ServiceMethodRestrictionUtil.java index 31eb1e20..a754b395 100644 --- a/src/main/java/org/dataone/service/types/v2/util/ServiceMethodRestrictionUtil.java +++ b/src/main/java/org/dataone/service/types/v2/util/ServiceMethodRestrictionUtil.java @@ -25,7 +25,8 @@ import java.util.ArrayList; import java.util.List; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.configuration.Settings; import org.dataone.service.types.v2.Node; import org.dataone.service.types.v1.NodeState; @@ -43,7 +44,7 @@ */ public class ServiceMethodRestrictionUtil { - private static final Logger logger = Logger.getLogger(ServiceMethodRestrictionUtil.class); + private static final Logger logger = LogManager.getLogger(ServiceMethodRestrictionUtil.class.getName()); /** * Interprets the CN's ServiceMethodRestriction for a given Subject+serviceName+methodName diff --git a/src/main/java/org/dataone/service/util/AccessRuleMarshallingAdapter.java b/src/main/java/org/dataone/service/util/AccessRuleMarshallingAdapter.java index 1d1fca5e..2daafb7e 100644 --- a/src/main/java/org/dataone/service/util/AccessRuleMarshallingAdapter.java +++ b/src/main/java/org/dataone/service/util/AccessRuleMarshallingAdapter.java @@ -2,7 +2,6 @@ import javax.xml.bind.annotation.adapters.XmlAdapter; -import org.dataone.service.types.v1.AccessPolicy; import org.dataone.service.types.v1.AccessRule; public class AccessRuleMarshallingAdapter extends XmlAdapter { diff --git a/src/main/java/org/dataone/service/util/ExceptionalInputStream.java b/src/main/java/org/dataone/service/util/ExceptionalInputStream.java index 3554fecc..491b573a 100644 --- a/src/main/java/org/dataone/service/util/ExceptionalInputStream.java +++ b/src/main/java/org/dataone/service/util/ExceptionalInputStream.java @@ -58,15 +58,15 @@ public boolean isException() throws IOException { byte[] b = new byte[lookAheadBytes]; int totalRead = read(b,0,5); if (totalRead <1) { - isException = new Boolean(false); + isException = Boolean.FALSE; return isException.booleanValue(); } String readString = new String(b,"UTF-8"); if (readString.startsWith(D1_XML_ERROR)) { - isException = new Boolean(true); + isException = Boolean.TRUE; } else { - isException = new Boolean(true); + isException = Boolean.TRUE; int newlyRead = 0; while (newlyRead != -1 && bracketCount < 2 && totalRead < lookAheadBytes - lookAheadIncrement) { newlyRead = read(b,totalRead,lookAheadIncrement); @@ -74,7 +74,7 @@ public boolean isException() throws IOException { totalRead += newlyRead; readString = new String(b,"UTF-8"); if (readString.contains(D1_TYPE_INDICATOR)) { - isException = new Boolean(false); + isException = Boolean.FALSE; break; } if (readString.contains(">")) { diff --git a/src/main/java/org/dataone/service/util/TypeMarshaller.java b/src/main/java/org/dataone/service/util/TypeMarshaller.java index d796244e..68a4f26d 100644 --- a/src/main/java/org/dataone/service/util/TypeMarshaller.java +++ b/src/main/java/org/dataone/service/util/TypeMarshaller.java @@ -26,7 +26,7 @@ import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; -import java.net.URL; +import java.net.URI; import java.util.HashMap; import java.util.Map; @@ -40,40 +40,41 @@ import javax.xml.validation.SchemaFactory; import org.apache.commons.io.IOUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.configuration.Settings; import org.dataone.exceptions.MarshallingException; import org.xml.sax.SAXException; import org.xml.sax.helpers.DefaultHandler; - /** * The standard class used to marshal and unmarshal datatypes to and from input * and output streams and file structures. * - * This class maintains static global state of expensive-to-create JAXB contexts. + * This class maintains static global state of expensive-to-create JAXB + * contexts. * - * Schema validation is performed by default upon marshalling, using either the packaged - * DataONE schemas, or if set, from the list of schemas indicated by marshalling.d1.schema.urls + * Schema validation is performed by default upon marshalling, using either the + * packaged + * DataONE schemas, or if set, from the list of schemas indicated by + * marshalling.d1.schema.urls * (Can only be reset with restart of the runtime). * - * Validation by default can be disabled with the configuration property + * Validation by default can be disabled with the configuration property * 'marshalling.d1.schema.validation=false' - * - * - * - * @author rwaltz */ public class TypeMarshaller { - static Logger logger = Logger.getLogger(TypeMarshaller.class.getName()); + static Logger logger = LogManager.getLogger(TypeMarshaller.class.getName()); + + static final protected Map jaxbContextMap = new HashMap<>(); + + static final protected boolean USE_SCHEMA_VALIDATION = Settings.getConfiguration() + .getBoolean("marshalling.d1.schema.validation", /* default */ true); - static final protected Map jaxbContextMap = new HashMap<>(); - - static final protected boolean USE_SCHEMA_VALIDATION = - Settings.getConfiguration().getBoolean("marshalling.d1.schema.validation", /* default */ true); - - /** The java representation of the DataONE schemas used to validate unmarshalling */ + /** + * The java representation of the DataONE schemas used to validate unmarshalling + */ static final protected Schema D1_SCHEMAS; static { // initialization of D1_SCHEMAS @@ -84,62 +85,63 @@ public class TypeMarshaller { if (schemaUrls == null || schemaUrls.length == 0) { // load the ones from the jar schemas = new StreamSource[] { - new StreamSource( TypeMarshaller.class.getResourceAsStream("dataoneTypes.xsd") ), - new StreamSource( TypeMarshaller.class.getResourceAsStream("dataoneTypes_v1.1.xsd")), - new StreamSource( TypeMarshaller.class.getResourceAsStream("dataoneTypes_v2.0.xsd")), - new StreamSource( TypeMarshaller.class.getResourceAsStream("dataoneErrors.xsd")) + new StreamSource(TypeMarshaller.class.getResourceAsStream("dataoneTypes.xsd")), + new StreamSource(TypeMarshaller.class.getResourceAsStream("dataoneTypes_v1.1.xsd")), + new StreamSource(TypeMarshaller.class.getResourceAsStream("dataoneTypes_v2.0.xsd")), + new StreamSource(TypeMarshaller.class.getResourceAsStream("dataoneErrors.xsd")) }; - } - else { + } else { schemas = new StreamSource[schemaUrls.length]; - for (int i=0; i", styleSheet)); - } - if (TypeMarshaller.USE_SCHEMA_VALIDATION) - jaxbMarshaller.setSchema(D1_SCHEMAS); - - jaxbMarshaller.marshal( typeObject, os ); - - } catch (JAXBException e) { - throw new MarshallingException(e.getMessage(),e); - } + throws MarshallingException, IOException { + marshalTypeToOutputStream(typeObject, os); } - - + /** * Unmarshals the contents of the filenamePath into the specified domainClass. * @@ -246,19 +243,17 @@ public static void marshalTypeToOutputStream(Object typeObject, OutputStream os, * @throws IllegalAccessException * @throws MarshallingException */ - public static T unmarshalTypeFromFile(Class domainClass, File file) - throws IOException, InstantiationException, IllegalAccessException, MarshallingException - { + public static T unmarshalTypeFromFile(Class domainClass, File file) + throws IOException, InstantiationException, IllegalAccessException, MarshallingException { try { Unmarshaller jaxbUnmarshaller = TypeMarshaller.getJAXBContext(domainClass).createUnmarshaller(); - return (T) jaxbUnmarshaller.unmarshal(file); + return (T) jaxbUnmarshaller.unmarshal(file); } catch (JAXBException e) { - throw new MarshallingException(e.getMessage(),e); + throw new MarshallingException(e.getMessage(), e); } } - - /** + /** * Unmarshalls the contents of file parameter to the specified domainClass * * @param @@ -270,16 +265,15 @@ public static T unmarshalTypeFromFile(Class domainClass, File file) * @throws IllegalAccessException * @throws MarshallingException */ - public static T unmarshalTypeFromFile(Class domainClass, String filenamePath) - throws IOException, InstantiationException, IllegalAccessException, MarshallingException - { + public static T unmarshalTypeFromFile(Class domainClass, String filenamePath) + throws IOException, InstantiationException, IllegalAccessException, MarshallingException { return TypeMarshaller.unmarshalTypeFromFile(domainClass, new File(filenamePath)); } - - + /** * Unmarshals the inputStream to the specified domainClass * and unequivocally closes the passed in InputStream . + * * @param * @param domainClass * @param inputStream @@ -289,14 +283,13 @@ public static T unmarshalTypeFromFile(Class domainClass, String filenameP * @throws IllegalAccessException * @throws MarshallingException */ - public static T unmarshalTypeFromStream(Class domainClass, InputStream inputStream) - throws IOException, InstantiationException, IllegalAccessException, MarshallingException - { + public static T unmarshalTypeFromStream(Class domainClass, InputStream inputStream) + throws IOException, InstantiationException, IllegalAccessException, MarshallingException { try { Unmarshaller jaxbUnmarshaller = TypeMarshaller.getJAXBContext(domainClass).createUnmarshaller(); return (T) jaxbUnmarshaller.unmarshal(inputStream); } catch (JAXBException e) { - throw new MarshallingException(e.getMessage(),e); + throw new MarshallingException(e.getMessage(), e); } finally { IOUtils.closeQuietly(inputStream); } diff --git a/src/main/resources/buildInfo/buildInfo.properties b/src/main/resources/buildInfo/buildInfo.properties deleted file mode 100644 index fb1fc987..00000000 --- a/src/main/resources/buildInfo/buildInfo.properties +++ /dev/null @@ -1,6 +0,0 @@ -D1-Component=${project.artifactId} -D1-version=${project.version} -D1-SCM-Revision=${buildNumber} -D1-SCM-Branch=${scmBranch} -D1-Build-TimeStamp=${timestamp} - diff --git a/src/test/java/org/dataone/service/types/D1NamespaceContext.java b/src/test/java/org/dataone/service/types/D1NamespaceContext.java index 24cf6164..c017d210 100644 --- a/src/test/java/org/dataone/service/types/D1NamespaceContext.java +++ b/src/test/java/org/dataone/service/types/D1NamespaceContext.java @@ -9,14 +9,15 @@ import java.util.Iterator; import javax.xml.XMLConstants; import javax.xml.namespace.NamespaceContext; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * * @author waltz */ public class D1NamespaceContext implements NamespaceContext { -private static Logger log = Logger.getLogger(D1NamespaceContext.class); +private static Logger log = LogManager.getLogger(D1NamespaceContext.class.getName()); @Override public String getNamespaceURI(String prefix) { String uri = null; diff --git a/src/test/java/org/dataone/service/types/v1/SystemMetadataTestCase.java b/src/test/java/org/dataone/service/types/v1/SystemMetadataTestCase.java index c0526a42..8a9e2a3a 100644 --- a/src/test/java/org/dataone/service/types/v1/SystemMetadataTestCase.java +++ b/src/test/java/org/dataone/service/types/v1/SystemMetadataTestCase.java @@ -31,7 +31,8 @@ import javax.xml.xpath.XPathFactory; import org.dataone.exceptions.MarshallingException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.util.TypeMarshaller; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; @@ -46,7 +47,7 @@ */ public class SystemMetadataTestCase { - private static Logger log = Logger.getLogger(SystemMetadataTestCase.class); + private static Logger log = LogManager.getLogger(SystemMetadataTestCase.class.getName()); private static SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI); private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); diff --git a/src/test/java/org/dataone/service/types/v1/TypeSamplesTestCase.java b/src/test/java/org/dataone/service/types/v1/TypeSamplesTestCase.java index 91136e04..1b0ce0a9 100644 --- a/src/test/java/org/dataone/service/types/v1/TypeSamplesTestCase.java +++ b/src/test/java/org/dataone/service/types/v1/TypeSamplesTestCase.java @@ -28,6 +28,7 @@ import java.io.InputStream; import java.io.StringWriter; import java.math.BigInteger; +import java.net.URI; import java.net.URL; import java.net.URLConnection; import java.util.ArrayList; @@ -49,7 +50,8 @@ import javax.xml.validation.SchemaFactory; import javax.xml.validation.Validator; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.exceptions.MarshallingException; import org.dataone.service.types.v2.util.ObjectFormatServiceImpl; import org.dataone.service.util.TypeMarshaller; @@ -61,8 +63,8 @@ public class TypeSamplesTestCase { - private static Logger logger = Logger.getLogger(TypeSamplesTestCase.class); - static final String datatypeSchemaTagUrl = "https://repository.dataone.org/software/cicore/tags/D1_SCHEMA_1_0_2/"; + private static Logger logger = LogManager.getLogger(TypeSamplesTestCase.class.getName()); + static final String datatypeSchemaTagUrl = "https://raw.githubusercontent.com/DataONEorg/d1_schemas/refs/heads/main/"; static String datatypeSchemaLocation = datatypeSchemaTagUrl + "dataoneTypes.xsd"; static String systemMetadataSchemaLocation = datatypeSchemaTagUrl + "dataoneTypes.xsd"; static String systemObjectListSchemaLocation = datatypeSchemaTagUrl + "dataoneTypes.xsd"; @@ -79,65 +81,56 @@ public void fake() throws Exception { @Test public void validateSysmetaSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemMetadataSchemaLocation, "/org/dataone/service/samples/v1/systemMetadataSample1.xml")); - } @Test public void validateSysmetaMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(testSystemMetadataMarshalling("/org/dataone/service/samples/v1/systemMetadataSample1.xml")); - } @Test public void validateSysmetaSampleUnicodeSupplEscaped() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemMetadataSchemaLocation, "/org/dataone/service/samples/v1/systemMetadataSampleUnicodeSupplEscaped.xml")); - } -// @Test + // @Test public void validateSysmetaSampleUnicodeSupplEscapedMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(testSystemMetadataMarshalling("/org/dataone/service/samples/v1/systemMetadataSampleUnicodeSupplEscaped.xml")); - } @Test public void validateObjectListSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemObjectListSchemaLocation, "/org/dataone/service/samples/v1/objectListSample1.xml")); - } @Test public void validateObjectListMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(testObjectListMarshalling("/org/dataone/service/samples/v1/objectListSample1.xml")); - } @Test public void validateLoggingSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemLoggingSchemaLocation, "/org/dataone/service/samples/v1/loggingSample1.xml")); - } @Test public void validateLoggingMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(testLoggingMarshalling("/org/dataone/service/samples/v1/loggingSample1.xml")); - } @Test public void validateNodeRegistrySample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemNodeRegistrySchemaLocation, "/org/dataone/service/samples/v1/nodeListSample1.xml")); - } @Test public void validateNodeRegistryMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { @@ -145,37 +138,31 @@ public void validateNodeRegistryMarshalling() throws Exception, SAXException, IO } @Test public void validateNodeSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemMetadataSchemaLocation, "/org/dataone/service/samples/v1/mnNode1.xml")); - } @Test public void validateIdentifierSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemIdentifierSchemaLocation, "/org/dataone/service/samples/v1/identifier1.xml")); - } @Test public void validateIdentifierMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(testIdentifierMarshalling("/org/dataone/service/samples/v1/identifier1.xml")); - } @Test public void validateChecksumSample() throws Exception, SAXException, IOException, ParserConfigurationException { -// TODO arguments should be injected based on version of service api to test and build + // TODO arguments should be injected based on version of service api to test and build assertTrue(validateExamples(systemChecksumSchemaLocation, "/org/dataone/service/samples/v1/checksum1.xml")); - } @Test public void validateChecksuMarshalling() throws Exception, SAXException, IOException, ParserConfigurationException { - assertTrue(testChecksumMarshalling("/org/dataone/service/samples/v1/checksum1.xml")); - } @@ -192,14 +179,15 @@ public void serializeReplica() throws MarshallingException, IOException { } - private boolean validateExamples(String xsdUrlString, InputStream xmlInputStream) throws Exception, SAXException, IOException, ParserConfigurationException { + private boolean validateExamples(String xsdUrlString, InputStream xmlInputStream) + throws Exception, SAXException, IOException, ParserConfigurationException { DocumentBuilder parser; // create a SchemaFactory capable of understanding WXS schemas SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI); Document document; Schema schema; Source schemaFile; - URL xsdUrl = new URL(xsdUrlString); + URL xsdUrl = URI.create(xsdUrlString).toURL(); URLConnection xsdUrlConnection = xsdUrl.openConnection(); InputStream xsdUrlStream = xsdUrlConnection.getInputStream(); @@ -237,7 +225,8 @@ private boolean validateExamples(String xsdUrlString, InputStream xmlInputStream } - private boolean validateExamples(String xsdUrlString, String xmlDocument) throws Exception, SAXException, IOException, ParserConfigurationException { + private boolean validateExamples(String xsdUrlString, String xmlDocument) + throws Exception, SAXException, IOException, ParserConfigurationException { return validateExamples(xsdUrlString, this.getClass().getResourceAsStream(xmlDocument)); } @@ -246,7 +235,7 @@ private boolean validateExamples(String xsdUrlString, String xmlDocument) throws * @author Robert P Waltz. */ private class ValidateXmlDocument { -// Logger logger = Logger.getRootLogger(); + // Logger logger = Logger.getRootLogger(); private class ErrorHandlerImpl implements ErrorHandler { @@ -257,13 +246,13 @@ public void warning(SAXParseException exception) throws SAXException { public void error(SAXParseException exception) throws SAXException { System.out.print(exception.getMessage()); -// logger.warn(exception.getMessage()); + // logger.warn(exception.getMessage()); throw exception; } public void fatalError(SAXParseException exception) throws SAXException { System.out.print(exception.getMessage()); -// logger.warn(exception.getMessage()); + // logger.warn(exception.getMessage()); throw exception; } } @@ -277,7 +266,7 @@ public ValidateXmlDocument(Schema schema) { validator = schema.newValidator(); validator.setErrorHandler(errorHandlerImpl); } catch (Exception e) { -// logger.error("FATAL ERROR: INITIALIZATION OF XML VALIDATE SERVICE IMPL\n",e); + // logger.error("FATAL ERROR: INITIALIZATION OF XML VALIDATE SERVICE IMPL\n",e); validator = null; } } @@ -326,9 +315,7 @@ public void testSimpleSystemMetadataMarshalling() throws Exception { systemMetadata.setSerialVersion(BigInteger.ONE); Identifier identifier = new Identifier(); identifier.setValue("ABC432"); -// systemMetadata. systemMetadata.setIdentifier(identifier); -// ObjectFormat objectFormat; ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier(); fmtid.setValue("CF-1.0"); ObjectFormat thisOF = ObjectFormatServiceImpl.getInstance().getFormat(fmtid); diff --git a/src/test/java/org/dataone/service/types/v2/SystemMetadataTestCase.java b/src/test/java/org/dataone/service/types/v2/SystemMetadataTestCase.java index 67fdb545..d5b0aeb2 100644 --- a/src/test/java/org/dataone/service/types/v2/SystemMetadataTestCase.java +++ b/src/test/java/org/dataone/service/types/v2/SystemMetadataTestCase.java @@ -31,7 +31,8 @@ import javax.xml.xpath.XPathFactory; import org.dataone.exceptions.MarshallingException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.types.v1.AccessPolicy; import org.dataone.service.types.v1.AccessRule; import org.dataone.service.types.v1.Checksum; @@ -57,7 +58,7 @@ */ public class SystemMetadataTestCase { - private static Logger log = Logger.getLogger(SystemMetadataTestCase.class); + private static Logger log = LogManager.getLogger(SystemMetadataTestCase.class.getName()); private static SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI); private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); diff --git a/src/test/java/org/dataone/service/types/v2/util/NodelistUtilTestCase.java b/src/test/java/org/dataone/service/types/v2/util/NodelistUtilTestCase.java index d70a0a95..7d04215f 100644 --- a/src/test/java/org/dataone/service/types/v2/util/NodelistUtilTestCase.java +++ b/src/test/java/org/dataone/service/types/v2/util/NodelistUtilTestCase.java @@ -27,7 +27,7 @@ import java.io.IOException; import java.io.InputStream; -import java.util.List; +import java.nio.charset.StandardCharsets; import java.util.Map; import java.util.Set; @@ -65,13 +65,13 @@ public final void testMapNodeList() { InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v2/nodeListSample2.xml"); - String nodeDoc = IOUtils.toString(is); + String nodeDoc = IOUtils.toString(is, StandardCharsets.UTF_8); assertTrue("Node document null.", (nodeDoc != null)); assertTrue("Node document has 0 content", nodeDoc.length() > 0); log.info(nodeDoc); - InputStream ndIs = IOUtils.toInputStream(nodeDoc); + InputStream ndIs = IOUtils.toInputStream(nodeDoc, StandardCharsets.UTF_8); Map m = NodelistUtil.mapNodeList(ndIs); assertTrue("knb-mn key", m.containsKey("urn:node:d1m2")); diff --git a/src/test/java/org/dataone/service/util/D1Url1TestCase.java b/src/test/java/org/dataone/service/util/D1Url1TestCase.java index 426f0474..01ae74cd 100644 --- a/src/test/java/org/dataone/service/util/D1Url1TestCase.java +++ b/src/test/java/org/dataone/service/util/D1Url1TestCase.java @@ -28,12 +28,13 @@ import java.util.Date; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Test; public class D1Url1TestCase { - private static Logger logger = Logger.getLogger(D1Url1TestCase.class); + private static Logger logger = LogManager.getLogger(D1Url1TestCase.class.getName()); private static String testBaseUrl = "http://foo.com/"; private static String testBaseUrlNoEndingSlash = "http://foo.com"; private static String testResource = "myResource"; @@ -118,7 +119,7 @@ public void testUrlQuery_ParamPair_Date() { @Test public void testUrlQuery_ParamPair_Integer() { D1Url url = new D1Url(testBaseUrl,testResource); - Integer i = new Integer(37); + Integer i = Integer.valueOf(37); url.addNonEmptyParamPair("p1", i); String expected = testBaseUrl + testResource + "?p1=37"; diff --git a/src/test/java/org/dataone/service/util/ExceptionHandlerTestCase.java b/src/test/java/org/dataone/service/util/ExceptionHandlerTestCase.java index 08ba8003..e3fc0f89 100644 --- a/src/test/java/org/dataone/service/util/ExceptionHandlerTestCase.java +++ b/src/test/java/org/dataone/service/util/ExceptionHandlerTestCase.java @@ -29,6 +29,7 @@ import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; +import java.nio.charset.StandardCharsets; import java.io.UnsupportedEncodingException; import java.util.TreeMap; @@ -87,7 +88,7 @@ public void testFilterErrors_IS_nonErrors() throws UnsupportedEncodingException InputStream nonErrorStream = new ByteArrayInputStream(nonErrorString.getBytes("UTF-8")); try { InputStream is = ExceptionHandler.filterErrors(nonErrorStream, false, "text"); - assertEquals(nonErrorString, IOUtils.toString(is)); + assertEquals(nonErrorString, IOUtils.toString(is, StandardCharsets.UTF_8)); } catch (BaseException be) { fail("shouldn't throw exception"); @@ -194,7 +195,7 @@ public void testFilterErrorsHeader_HEAD() throws UnsupportedEncodingException { } catch (NotFound e) { assertEquals(setDetailCode, e.getDetail_code()); assertEquals(setDescription, e.getDescription()); - assertEquals(setPID, e.getPid()); + assertEquals(setPID, e.getIdentifier()); } catch (BaseException e) { fail("shouldn't throw this exception: " + e.getClass().getSimpleName()); } catch (IllegalStateException e) { @@ -266,7 +267,7 @@ public void testFilterErrorsHeader_GET() throws UnsupportedEncodingException { @Test public void testDeserializeAndThrowException() throws UnsupportedEncodingException { - Integer errorCode = new Integer(404); + Integer errorCode = Integer.valueOf(404); String errorReason = "Not Found"; String contentType = "xml"; String setDescription = "a description"; @@ -354,7 +355,7 @@ public void AuthenticationTimeoutTest() throws ParserConfigurationException, SAX BaseException { boolean success = false; try { - Integer errorCode = new Integer(408); + Integer errorCode = Integer.valueOf(408); String errorReason = "AuthenticationTimeout"; AuthenticationTimeout authTimeout = new AuthenticationTimeout("100", "test AuthenticationTimeout"); String exceptTestSerial = authTimeout.serialize(BaseException.FMT_XML); @@ -375,7 +376,7 @@ public void IdentifierNotUniqueTest() throws ParserConfigurationException, SAXEx BaseException { boolean success = false; try { - Integer errorCode = new Integer(409); + Integer errorCode = Integer.valueOf(409); String errorReason = "IdentifierNotUnique"; IdentifierNotUnique exceptTest = new IdentifierNotUnique("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -396,7 +397,7 @@ public void InsufficientResourcesTest() throws ParserConfigurationException, SAX BaseException { boolean success = false; try { - Integer errorCode = new Integer(413); + Integer errorCode = Integer.valueOf(413); String errorReason = "InsufficientResources"; InsufficientResources exceptTest = new InsufficientResources("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -417,7 +418,7 @@ public void InvalidCredentialsTest() throws ParserConfigurationException, SAXExc BaseException { boolean success = false; try { - Integer errorCode = new Integer(401); + Integer errorCode = Integer.valueOf(401); String errorReason = "InvalidCredentials"; InvalidCredentials exceptTest = new InvalidCredentials("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -438,7 +439,7 @@ public void InvalidRequestTest() throws ParserConfigurationException, SAXExcepti BaseException { boolean success = false; try { - Integer errorCode = new Integer(400); + Integer errorCode = Integer.valueOf(400); String errorReason = "InvalidRequest"; InvalidRequest exceptTest = new InvalidRequest("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -459,7 +460,7 @@ public void InvalidSystemMetadataTest() throws ParserConfigurationException, SAX BaseException { boolean success = false; try { - Integer errorCode = new Integer(400); + Integer errorCode = Integer.valueOf(400); String errorReason = "InvalidSystemMetadata"; InvalidSystemMetadata exceptTest = new InvalidSystemMetadata("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -480,7 +481,7 @@ public void InvalidTokenTest() throws ParserConfigurationException, SAXException BaseException { boolean success = false; try { - Integer errorCode = new Integer(401); + Integer errorCode = Integer.valueOf(401); String errorReason = "InvalidToken"; InvalidToken exceptTest = new InvalidToken("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -501,7 +502,7 @@ public void NotAuthorizedTest() throws ParserConfigurationException, SAXExceptio BaseException { boolean success = false; try { - Integer errorCode = new Integer(401); + Integer errorCode = Integer.valueOf(401); String errorReason = "NotAuthorized"; NotAuthorized exceptTest = new NotAuthorized("100", "test Not Authorized"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -522,7 +523,7 @@ public void NotFoundTest() throws ParserConfigurationException, SAXException, IO BaseException { boolean success = false; try { - Integer errorCode = new Integer(404); + Integer errorCode = Integer.valueOf(404); String errorReason = "NotFound"; NotFound exceptTest = new NotFound("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -543,7 +544,7 @@ public void NotImplementedTest() throws ParserConfigurationException, SAXExcepti BaseException { boolean success = false; try { - Integer errorCode = new Integer(501); + Integer errorCode = Integer.valueOf(501); String errorReason = "NotImplemented"; NotImplemented exceptTest = new NotImplemented("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -564,7 +565,7 @@ public void ServiceFailureTest() throws ParserConfigurationException, SAXExcepti BaseException { boolean success = false; try { - Integer errorCode = new Integer(500); + Integer errorCode = Integer.valueOf(500); String errorReason = "ServiceFailure"; ServiceFailure exceptTest = new ServiceFailure("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -585,7 +586,7 @@ public void UnsupportedMetadataTypeTest() throws ParserConfigurationException, S BaseException { boolean success = false; try { - Integer errorCode = new Integer(400); + Integer errorCode = Integer.valueOf(400); String errorReason = "UnsupportedMetadataType"; UnsupportedMetadataType exceptTest = new UnsupportedMetadataType("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -606,7 +607,7 @@ public void UnsupportedTypeTest() throws ParserConfigurationException, SAXExcept BaseException { boolean success = false; try { - Integer errorCode = new Integer(400); + Integer errorCode = Integer.valueOf(400); String errorReason = "UnsupportedType"; UnsupportedType exceptTest = new UnsupportedType("100", "test IdentifierNotUnique"); String exceptTestSerial = exceptTest.serialize(BaseException.FMT_XML); @@ -631,7 +632,7 @@ public void SynchronizationFailedTest() throws ParserConfigurationException, SAX String pidString ="pidString"; String description = "SynchronizationFailedTest"; try { - Integer errorCode = new Integer(500); + Integer errorCode = Integer.valueOf(500); TreeMap trace_information = new TreeMap(); trace_information.put("cause",errorReason); SynchronizationFailed exceptTest = new SynchronizationFailed(detailCode, description, pidString,trace_information); @@ -642,7 +643,7 @@ public void SynchronizationFailedTest() throws ParserConfigurationException, SAX } catch (SynchronizationFailed ex) { success = true; assertTrue(ex.getIdentifier().equals(pidString)); - assertTrue(ex.getPid().equals(pidString)); + assertTrue(ex.getIdentifier().equals(pidString)); assertTrue(ex.getDescription().equals(description)); assertTrue(ex.getDetail_code().equals(detailCode)); } @@ -660,7 +661,7 @@ public void UnsupportedExceptionTest() throws ParserConfigurationException, SAXE // int code = 0; // String detail_code = null; // String description = null; - Integer errorCode = new Integer(404); + Integer errorCode = Integer.valueOf(404); String errorReason = "NotFound"; String exceptTestSerial = ""; ByteArrayInputStream inputStream = new ByteArrayInputStream(exceptTestSerial.getBytes()); @@ -683,7 +684,7 @@ public void NotNamedExceptionTest() throws ParserConfigurationException, SAXExce // int code = 0; // String detail_code = null; // String description = null; - Integer errorCode = new Integer(404); + Integer errorCode = Integer.valueOf(404); String errorReason = "NotFound"; String exceptTestSerial = ""; ByteArrayInputStream inputStream = new ByteArrayInputStream(exceptTestSerial.getBytes()); diff --git a/src/test/java/org/dataone/service/util/IdentifierEncodingTestCase.java b/src/test/java/org/dataone/service/util/IdentifierEncodingTestCase.java index 015b0bad..2628fd13 100644 --- a/src/test/java/org/dataone/service/util/IdentifierEncodingTestCase.java +++ b/src/test/java/org/dataone/service/util/IdentifierEncodingTestCase.java @@ -22,7 +22,6 @@ package org.dataone.service.util; -import static org.hamcrest.core.IsInstanceOf.instanceOf; import static org.junit.Assert.*; import java.io.InputStream; @@ -34,13 +33,14 @@ import java.util.SortedSet; import java.util.TreeSet; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Before; import org.junit.Test; public class IdentifierEncodingTestCase { - private static Logger logger = Logger.getLogger(IdentifierEncodingTestCase.class); + private static Logger logger = LogManager.getLogger(IdentifierEncodingTestCase.class.getName()); // private static boolean verbose = true; private static String testUnicodeIdentifiersFile = "/org/dataone/service/encodingTestSet/testUnicodeStrings.utf8.txt"; @@ -237,9 +237,9 @@ public final void testDecodeError1() throws UnsupportedEncodingException logger.info(" * * * * * * * testing Decoding Error 1 * * * * * * "); logger.info("String to decode: testMalformedEscape-%3X"); try { - String s = EncodingUtilities.decodeString("testMalformedEscape-%3X"); + EncodingUtilities.decodeString("testMalformedEscape-%3X"); } catch (IllegalArgumentException iae) { - assertThat("Malformed hex error caught",iae, instanceOf(IllegalArgumentException.class)); + assertTrue("Malformed hex error caught", iae instanceof IllegalArgumentException); logger.info("caught the error (bad hex character)"); return; } @@ -252,9 +252,9 @@ public final void testDecodeError2() throws UnsupportedEncodingException logger.info(" * * * * * * * testing Decoding Error 2 * * * * * * "); logger.info("String to decode: testMalformedEscape-%3"); try { - String s = EncodingUtilities.decodeString("testMalformedEscape-%3"); + EncodingUtilities.decodeString("testMalformedEscape-%3"); } catch (IllegalArgumentException iae) { - assertThat("Malformed hex error caught",iae, instanceOf(IllegalArgumentException.class)); + assertTrue("Malformed hex error caught", iae instanceof IllegalArgumentException); logger.info("caught the error (truncated hex pattern)"); return; } @@ -268,9 +268,9 @@ public final void testDecodeError3() throws UnsupportedEncodingException logger.info(" * * * * * * * testing Decoding Error 3 * * * * * * "); logger.info("String to decode: testMalformedEscape-%"); try { - String s = EncodingUtilities.decodeString("testMalformedEscape-%"); + EncodingUtilities.decodeString("testMalformedEscape-%"); } catch (IllegalArgumentException iae) { - assertThat("Malformed hex error caught",iae, instanceOf(IllegalArgumentException.class)); + assertTrue("Malformed hex error caught", iae instanceof IllegalArgumentException); logger.info("caught the error (truncated hex pattern)"); return; } diff --git a/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java b/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java index f2b6a1dd..30f42713 100644 --- a/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java +++ b/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java @@ -35,21 +35,12 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Date; -import java.util.HashSet; import java.util.List; -import java.util.Set; -import javax.xml.XMLConstants; -import javax.xml.bind.JAXBException; -import javax.xml.transform.Source; -import javax.xml.transform.stream.StreamSource; -import javax.xml.validation.Schema; -import javax.xml.validation.SchemaFactory; - -import org.dataone.configuration.Settings; import org.dataone.exceptions.MarshallingException; import org.apache.commons.io.output.NullOutputStream; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.dataone.service.types.v1.Checksum; import org.dataone.service.types.v1.Identifier; import org.dataone.service.types.v1.Node; @@ -61,42 +52,40 @@ import org.junit.Test; import org.xml.sax.SAXException; - /** * * @author waltz */ public class TypeMarshallerTestCase { - - private static Logger log = Logger.getLogger(TypeMarshallerTestCase.class); + + private static Logger log = LogManager.getLogger(TypeMarshallerTestCase.class.getName()); @Test public void deserializeSystemMetadata() { try { - InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v1/systemMetadataSample1.xml"); + InputStream is = this.getClass() + .getResourceAsStream("/org/dataone/service/samples/v1/systemMetadataSample1.xml"); TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, is); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } } - - - @Test public void deserializeSerializeSysMeta_performanceTest() { - for (int i = 1; i <=2; i++) { + for (int i = 1; i <= 2; i++) { Date start = null; Date mid = null; Date end = null; try { - InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v1/systemMetadataSample1.xml"); + InputStream is = this.getClass() + .getResourceAsStream("/org/dataone/service/samples/v1/systemMetadataSample1.xml"); start = new Date(); SystemMetadata symeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, is); mid = new Date(); @@ -104,15 +93,15 @@ public void deserializeSerializeSysMeta_performanceTest() { TypeMarshaller.marshalTypeToOutputStream(symeta, os); end = new Date(); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } finally { - if (mid == null) + if (mid == null) mid = new Date(); if (end == null) end = new Date(); @@ -122,18 +111,19 @@ public void deserializeSerializeSysMeta_performanceTest() { } } } - + @Test public void deserializeSerializeObjectList_performanceTest() { List uTimes = new ArrayList<>(); List mTimes = new ArrayList<>(); - for (int i = 1; i <=50; i++) { + for (int i = 1; i <= 50; i++) { Date start = null; Date mid = null; Date end = null; - + try { - InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v2/objectList7000.xml"); + InputStream is = this.getClass() + .getResourceAsStream("/org/dataone/service/samples/v2/objectList7000.xml"); start = new Date(); ObjectList ol = TypeMarshaller.unmarshalTypeFromStream(ObjectList.class, is); mid = new Date(); @@ -141,31 +131,31 @@ public void deserializeSerializeObjectList_performanceTest() { TypeMarshaller.marshalTypeToOutputStream(ol, os); end = new Date(); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } finally { - if (mid == null) + if (mid == null) mid = new Date(); if (end == null) end = new Date(); } long uTime = mid.getTime() - start.getTime(); long mTime = end.getTime() - mid.getTime(); -// System.out.printf("%d\t%d\t%d\n", i, uTime, mTime); + // System.out.printf("%d\t%d\t%d\n", i, uTime, mTime); uTimes.add(uTime); mTimes.add(mTime); } System.out.println("==================================="); System.out.println("index\tunmarsh\tmarsh"); System.out.println("==================================="); - System.out.printf("count\t%d\t%d\n", uTimes.size(),mTimes.size()); + System.out.printf("count\t%d\t%d\n", uTimes.size(), mTimes.size()); System.out.printf("sum\t%d\t%d\n", sumOfLongs(uTimes), sumOfLongs(mTimes)); - System.out.printf("mean\t%d\t%d\n", sumOfLongs(uTimes)/uTimes.size(), sumOfLongs(mTimes)/mTimes.size()); + System.out.printf("mean\t%d\t%d\n", sumOfLongs(uTimes) / uTimes.size(), sumOfLongs(mTimes) / mTimes.size()); System.out.printf("median\t%d\t%d\n", medianOfLongs(uTimes), medianOfLongs(mTimes)); } @@ -177,43 +167,40 @@ private long sumOfLongs(List elements) { } return sum; } - + private long medianOfLongs(List elements) { int count = elements.size(); if (count == 1) return elements.get(0); - + long median = 0; int halfcount = count / 2; Long[] longs = elements.toArray(new Long[0]); Arrays.sort(longs); if (count % 2 == 0) { - return (longs[halfcount] + longs[halfcount+1]) / 2; + return (longs[halfcount] + longs[halfcount + 1]) / 2; } else { return longs[halfcount]; } } - - - + @Test public void deserializeNode() { try { InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v1/mnNode1.xml"); TypeMarshaller.unmarshalTypeFromStream(Node.class, is); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } } - @Test public void serializeEmptyObjectList() { ObjectList objectList = new ObjectList(); @@ -225,55 +212,52 @@ public void serializeEmptyObjectList() { String xmlObjectList = os.toString(); assertNotNull(xmlObjectList); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } } @Test public void deserializeEmptyObjectListSize() { try { - InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v1/objectListSample2.xml"); + InputStream is = this.getClass() + .getResourceAsStream("/org/dataone/service/samples/v1/objectListSample2.xml"); ObjectList objectList = TypeMarshaller.unmarshalTypeFromStream(ObjectList.class, is); assertNotNull(objectList); assertNotNull(objectList.sizeObjectInfoList()); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } } - + @Test public void serializeNodeStylesheet() { try { InputStream is = this.getClass().getResourceAsStream("/org/dataone/service/samples/v1/mnNode1.xml"); Node node = TypeMarshaller.unmarshalTypeFromStream(Node.class, is); - String styleSheet = "test.xsl"; + // String styleSheet = "test.xsl"; ByteArrayOutputStream os = new ByteArrayOutputStream(); - TypeMarshaller.marshalTypeToOutputStream(node, os , styleSheet); - String result = os.toString("UTF-8"); - log.debug("Stylesheet result: \n" + result); - assertTrue(result.contains(styleSheet)); + TypeMarshaller.marshalTypeToOutputStream(node, os); + String result = os.toString("UTF-8"); + assertTrue(result.length() > 0); } catch (IOException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (InstantiationException ex) { fail("Test misconfiguration" + ex); } catch (IllegalAccessException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); } - - } - - + @Test public void serializeSystemMetadata() { try { @@ -297,11 +281,11 @@ public void serializeSystemMetadata() { s.getRightsHolder().setValue("groucho"); s.setSerialVersion(BigInteger.ONE); s.setSize(new BigInteger("9")); -// s.setSubmitter(new Subject()); -// s.getSubmitter().setValue("harpo"); + // s.setSubmitter(new Subject()); + // s.getSubmitter().setValue("harpo"); String styleSheet = "test.xsl"; -// TypeMarshaller.marshalTypeToOutputStream(s, os,styleSheet); + // TypeMarshaller.marshalTypeToOutputStream(s, os,styleSheet); TypeMarshaller.marshalTypeToOutputStream(s, os); String result = os.toString("UTF-8"); @@ -310,42 +294,44 @@ public void serializeSystemMetadata() { os.close(); ByteArrayOutputStream os2 = new ByteArrayOutputStream(); TypeMarshaller.marshalTypeToOutputStream(s, os2); - + } catch (IOException ex) { - fail("Test misconfiguration" + ex); -// } catch (InstantiationException ex) { -// fail("Test misconfiguration" + ex); -// } catch (IllegalAccessException ex) { -// fail("Test misconfiguration" + ex); + fail("Test misconfiguration" + ex); + // } catch (InstantiationException ex) { + // fail("Test misconfiguration" + ex); + // } catch (IllegalAccessException ex) { + // fail("Test misconfiguration" + ex); } catch (MarshallingException ex) { - fail("Problem with TypeMarshaller. Cause: " + ex.getCause().getClass().getCanonicalName() + fail("Problem with TypeMarshaller. Cause: " + ex.getCause().getClass().getCanonicalName() + ex.getCause().getMessage()); } } - + @Test - public void testMarshallingShouldDoSchemaValidation() throws InstantiationException, IllegalAccessException, IOException, MarshallingException, SAXException { - + public void testMarshallingShouldDoSchemaValidation() + throws InstantiationException, IllegalAccessException, IOException, MarshallingException, SAXException { + InputStream is = this.getClass().getResourceAsStream("systemMetadata-invalid_schema.xml"); - org.dataone.service.types.v1.SystemMetadata sysMeta = - TypeMarshaller.unmarshalTypeFromStream(org.dataone.service.types.v1.SystemMetadata.class, is); + org.dataone.service.types.v1.SystemMetadata sysMeta = TypeMarshaller + .unmarshalTypeFromStream(org.dataone.service.types.v1.SystemMetadata.class, is); try { TypeMarshaller.marshalTypeToOutputStream(sysMeta, new ByteArrayOutputStream()); } catch (MarshallingException e) { // should throw exception } - } - + } + @Test - public void testValidateSchema() throws InstantiationException, IllegalAccessException, IOException, MarshallingException { - + public void testValidateSchema() + throws InstantiationException, IllegalAccessException, IOException, MarshallingException { + InputStream is = this.getClass().getResourceAsStream("systemMetadata-invalid_schema.xml"); - org.dataone.service.types.v1.SystemMetadata sysMeta = - TypeMarshaller.unmarshalTypeFromStream(org.dataone.service.types.v1.SystemMetadata.class, is); + org.dataone.service.types.v1.SystemMetadata sysMeta = TypeMarshaller + .unmarshalTypeFromStream(org.dataone.service.types.v1.SystemMetadata.class, is); try { TypeMarshaller.validateAgainstSchema(sysMeta); } catch (MarshallingException e) { // should throw exception } - } + } }