diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml new file mode 100644 index 00000000..0638de7a --- /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@v4 + - name: Set up JDK + uses: actions/setup-java@v4 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Build with Maven + run: mvn -B package --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/pom.xml b/pom.xml index 7a1c94dc..d370d7f9 100644 --- a/pom.xml +++ b/pom.xml @@ -6,12 +6,12 @@ jar 2.4.3-SNAPSHOT DataONE_Common_Java - http://dataone.org + https://dataone.org DataONE Common Code with Service Interface Definitions 2.3.1 v1.23 - 1.7 + 25 @@ -47,182 +47,6 @@ 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 @@ -235,33 +59,13 @@ 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 + https://oss.sonatype.org/content/repositories/snapshots false @@ -278,11 +82,17 @@ jar compile - + + + jakarta.xml.bind + jakarta.xml.bind-api + 2.3.2 + + - javax.xml.bind - jaxb-api - 2.2.3 + org.glassfish.jaxb + jaxb-runtime + 2.3.2 joda-time @@ -296,16 +106,6 @@ log4j 1.2.17 - - - - - - - - - - org.apache.maven.plugins maven-compiler-plugin @@ -333,13 +133,6 @@ - - org.apache.maven.plugins - maven-clean-plugin - 2.4.1 - maven-plugin - compile - commons-fileupload commons-fileupload @@ -383,7 +176,6 @@ jar provided - org.dataone d1_test_resources @@ -422,4 +214,4 @@ - \ No newline at end of file + diff --git a/src/main/java/org/dataone/service/util/TypeMarshaller.java b/src/main/java/org/dataone/service/util/TypeMarshaller.java index d796244e..d8118f33 100644 --- a/src/main/java/org/dataone/service/util/TypeMarshaller.java +++ b/src/main/java/org/dataone/service/util/TypeMarshaller.java @@ -46,34 +46,34 @@ 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 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 */ + 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 + */ static final protected Schema D1_SCHEMAS; static { // initialization of D1_SCHEMAS @@ -84,62 +84,63 @@ 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 +242,17 @@ 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 +264,15 @@ 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 +282,13 @@ 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/util/TypeMarshallerTestCase.java b/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java index f2b6a1dd..9a0e53ce 100644 --- a/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java +++ b/src/test/java/org/dataone/service/util/TypeMarshallerTestCase.java @@ -35,18 +35,8 @@ 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; @@ -61,42 +51,40 @@ 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 = Logger.getLogger(TypeMarshallerTestCase.class); @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 +92,15 @@ 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 +110,19 @@ 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 +130,31 @@ 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 +166,40 @@ 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 +211,52 @@ 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 +280,11 @@ 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 +293,44 @@ 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 } - } + } }