OCFL 2.1.0 and Update CI (#60)

* Update jackson * Use an updated version of logback-classic * Remove unused test dependencies * Update to ocfl 2.1.0 * Update version display * Update github actions to be in line with fcrepo * Add windows to the build matrix * Encode object ids to allow ids with colons on windows * Close the stream when getting object reports * Add gitattributes * Use correct class * Minor styling/formatting tweaks * Minor updates to assertions
fcrepo-exts · Jul 2, 2024 · ebbe7d0 · ebbe7d0
1 parent 0a2f63d
commit ebbe7d0
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,22 @@
+* text
+*.json text
+*.java text diff=java
+
+# Keep the line endings for some test files by setting to binary
+# This is to allow tests to pass in windows and *nix
+*.0 binary
+ADMINMD binary
+BIB0 binary
+props binary
+TECH0 binary
+TECH1 binary
+
+# Images
+*REF binary
+*THUMB binary
+*MASTER0 binary
+
+# Fedora 6
+*.nt eol=lf
+*.json eol=lf
+*.sha512 eol=lf
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -16,22 +16,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows-latest]
+        java: ['11']
+        experimental: [false]
+        include:
+          - java: 17
+            os: ubuntu-latest
+            experimental: true
     steps:
     - name: Git support longpaths
       run: git config --global core.longpaths true
     - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up JDK 11
-      uses: actions/setup-java@v1
+      uses: actions/checkout@v4
+    - name: Set up JDK ${{ matrix.java }}
+      uses: actions/setup-java@v4
       with:
-        java-version: 11
-    - name: Cache Maven packages
-      uses: actions/cache@v2
-      with:
-        path: ~/.m2
-        key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
-        restore-keys: ${{ runner.os }}-m2
+        distribution: 'temurin'
+        java-version: ${{ matrix.java }}
+        cache: 'maven'
     - name: Build with Maven
       run: mvn -B -U clean install
 
@@ -43,10 +45,11 @@ jobs:
       - name: Git support longpaths
         run: git config --global core.longpaths true
       - name: Checkout fcrepo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v4
         with:
+          distribution: 'temurin'
           java-version: 11
           server-id: sonatype-nexus-snapshots
           server-username: MAVEN_USERNAME

diff --git a/pom.xml b/pom.xml
@@ -17,11 +17,11 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <compiler.plugin.version>3.8.0</compiler.plugin.version>
         <fcrepo-build-tools.version>6.0.0</fcrepo-build-tools.version>
-        <fcrepo-migration-utils.version>6.3.0</fcrepo-migration-utils.version>
-        <fcrepo.storage.ocfl.version>6.3.0</fcrepo.storage.ocfl.version>
-        <ocfl-java.version>1.5.0</ocfl-java.version>
+        <fcrepo-migration-utils.version>6.6.0-SNAPSHOT</fcrepo-migration-utils.version>
+        <fcrepo.storage.ocfl.version>6.4.0-SNAPSHOT</fcrepo.storage.ocfl.version>
+        <ocfl-java.version>2.1.0</ocfl-java.version>
         <gpg.plugin.version>1.6</gpg.plugin.version>
-        <jackson.version>2.11.1</jackson.version>
+        <jackson.version>2.17.1</jackson.version>
         <checkstyle.plugin.version>3.1.1</checkstyle.plugin.version>
         <license.plugin.version>3.0</license.plugin.version>
         <project.java.source>11</project.java.source>
@@ -223,7 +223,7 @@
         </dependency>
 
         <dependency>
-            <groupId>edu.wisc.library.ocfl</groupId>
+            <groupId>io.ocfl</groupId>
             <artifactId>ocfl-java-aws</artifactId>
             <version>${ocfl-java.version}</version>
             <!--
@@ -248,7 +248,7 @@
         <dependency>
             <groupId>org.freemarker</groupId>
             <artifactId>freemarker</artifactId>
-            <version>2.3.30</version>
+            <version>2.3.32</version>
         </dependency>
 
         <dependency>
@@ -280,59 +280,52 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>30.0-jre</version>
+            <version>33.2.1-jre</version>
         </dependency>
 
         <dependency>
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>
-            <version>4.5.2</version>
+            <version>4.7.6</version>
         </dependency>
 
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>2.8.0</version>
+            <version>2.16.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.11</version>
+            <version>3.14.0</version>
         </dependency>
         <dependency>
             <groupId>commons-codec</groupId>
             <artifactId>commons-codec</artifactId>
-            <version>1.14</version>
+            <version>1.17.0</version>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
-            <version>1.7.30</version>
+            <version>2.0.12</version>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <version>1.5.6</version>
         </dependency>
 
         <!-- Test -->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.13</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest</artifactId>
-            <version>2.2</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.assertj</groupId>
             <artifactId>assertj-core</artifactId>
-            <version>3.19.0</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-core</artifactId>
-            <version>2.22.0</version>
+            <version>3.26.0</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

diff --git a/src/main/java/org/fcrepo/migration/validator/Driver.java b/src/main/java/org/fcrepo/migration/validator/Driver.java
@@ -34,7 +34,7 @@
  * @author dbernstein
  */
 @CommandLine.Command(name = "fcrepo-migration-validator", mixinStandardHelpOptions = true, sortOptions = false,
-        version = "0.1.0-SNAPSHOT")
+        version = "Fedora Migration Validator 1.3.0")
 public class Driver implements Callable<Integer> {
 
     private static final Logger LOGGER = getLogger(Driver.class);

diff --git a/src/main/java/org/fcrepo/migration/validator/api/ObjectValidationConfig.java b/src/main/java/org/fcrepo/migration/validator/api/ObjectValidationConfig.java
@@ -8,7 +8,7 @@
 import java.io.File;
 import java.nio.file.Path;
 
-import edu.wisc.library.ocfl.api.OcflRepository;
+import io.ocfl.api.OcflRepository;
 import org.fcrepo.migration.validator.impl.F6DigestAlgorithm;
 
 /**

diff --git a/src/main/java/org/fcrepo/migration/validator/api/ObjectValidationResults.java b/src/main/java/org/fcrepo/migration/validator/api/ObjectValidationResults.java
@@ -5,6 +5,8 @@
  */
 package org.fcrepo.migration.validator.api;
 
+import java.net.URLEncoder;
+import java.nio.charset.Charset;
 import java.util.List;
 import java.util.stream.Collectors;
 
@@ -42,6 +44,21 @@ public String getObjectId() {
         return results.stream().findFirst().map(ValidationResult::getSourceObjectId).orElse("unknown");
     }
 
+    /**
+     * This method returns an encoded version of the object id for use as a filesystem path
+     * @return the encoded object-id
+     */
+    public String getEncodedObjectId() {
+        if (results == null || results.isEmpty()) {
+            return "unknown";
+        }
+
+        return results.stream().findFirst()
+                      .map(ValidationResult::getSourceObjectId)
+                      .map(objectId -> URLEncoder.encode(objectId, Charset.defaultCharset()))
+                      .orElse("unknown");
+    }
+
     /**
      * This method indicates if the result set has any errors
      * @return true if there are validation errors

diff --git a/src/main/java/org/fcrepo/migration/validator/api/RepositoryValidator.java b/src/main/java/org/fcrepo/migration/validator/api/RepositoryValidator.java
@@ -5,7 +5,7 @@
  */
 package org.fcrepo.migration.validator.api;
 
-import edu.wisc.library.ocfl.api.OcflRepository;
+import io.ocfl.api.OcflRepository;
 
 /**
  * An interface for performing validations across the repository.

diff --git a/src/main/java/org/fcrepo/migration/validator/api/ValidationHandler.java b/src/main/java/org/fcrepo/migration/validator/api/ValidationHandler.java
@@ -29,7 +29,7 @@
 import com.google.common.hash.Funnels;
 import com.google.common.hash.HashCode;
 import com.google.common.io.ByteStreams;
-import edu.wisc.library.ocfl.api.model.OcflObjectVersion;
+import io.ocfl.api.model.OcflObjectVersion;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.RDFNode;

diff --git a/src/main/java/org/fcrepo/migration/validator/api/ValidationTask.java b/src/main/java/org/fcrepo/migration/validator/api/ValidationTask.java
@@ -15,5 +15,5 @@
  */
 public abstract class ValidationTask implements Supplier<ValidationTask> {
 
-    abstract public Optional<String> getPid();
+    public abstract Optional<String> getPid();
 }
diff --git a/src/main/java/org/fcrepo/migration/validator/impl/ApplicationConfigurationHelper.java b/src/main/java/org/fcrepo/migration/validator/impl/ApplicationConfigurationHelper.java
@@ -10,12 +10,12 @@
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import com.github.benmanes.caffeine.cache.Caffeine;
 import com.google.common.base.Suppliers;
-import edu.wisc.library.ocfl.api.MutableOcflRepository;
-import edu.wisc.library.ocfl.api.OcflRepository;
-import edu.wisc.library.ocfl.core.OcflRepositoryBuilder;
-import edu.wisc.library.ocfl.core.extension.storage.layout.config.HashedNTupleLayoutConfig;
-import edu.wisc.library.ocfl.core.path.mapper.LogicalPathMappers;
-import edu.wisc.library.ocfl.core.storage.OcflStorageBuilder;
+import io.ocfl.api.MutableOcflRepository;
+import io.ocfl.api.OcflRepository;
+import io.ocfl.core.OcflRepositoryBuilder;
+import io.ocfl.core.extension.storage.layout.config.HashedNTupleLayoutConfig;
+import io.ocfl.core.path.mapper.LogicalPathMappers;
+import io.ocfl.core.storage.OcflStorageBuilder;
 import org.apache.commons.lang3.SystemUtils;
 import org.fcrepo.migration.ObjectSource;
 import org.fcrepo.migration.foxml.AkubraFSIDResolver;
@@ -40,8 +40,8 @@
 import java.util.function.Supplier;
 
 import static com.fasterxml.jackson.databind.SerializationFeature.WRITE_DATES_AS_TIMESTAMPS;
-import static edu.wisc.library.ocfl.api.util.Enforce.expressionTrue;
-import static edu.wisc.library.ocfl.api.util.Enforce.notNull;
+import static io.ocfl.api.util.Enforce.expressionTrue;
+import static io.ocfl.api.util.Enforce.notNull;
 
 /**
  * A helper class for configuring and creating application components.
@@ -124,16 +124,17 @@ private ObjectSource doObjectSource() throws IOException {
 
     private MutableOcflRepository repository(final Fedora3ValidationConfig config, final Path workDir) {
         final var storage = OcflStorageBuilder.builder()
-                .fileSystem(config.getOcflRepositoryRootDirectory().toPath())
-                .build();
+                                              .fileSystem(config.getOcflRepositoryRootDirectory().toPath())
+                                              .build();
         final var logicalPathMapper = SystemUtils.IS_OS_WINDOWS ?
-                LogicalPathMappers.percentEncodingWindowsMapper() : LogicalPathMappers.percentEncodingLinuxMapper();
+                                      LogicalPathMappers.percentEncodingWindowsMapper() :
+                                      LogicalPathMappers.percentEncodingLinuxMapper();
 
         return new OcflRepositoryBuilder().storage(storage)
-                .defaultLayoutConfig(new HashedNTupleLayoutConfig())
-                .logicalPathMapper(logicalPathMapper)
-                .workDir(workDir)
-                .buildMutable();
+                                          .defaultLayoutConfig(new HashedNTupleLayoutConfig())
+                                          .logicalPathMapper(logicalPathMapper)
+                                          .workDir(workDir)
+                                          .buildMutable();
     }
 
     /**
@@ -164,7 +165,7 @@ public OcflObjectSessionFactory ocflObjectSessionFactory() {
                 .maximumSize(512)
                 .expireAfterAccess(Duration.ofMinutes(10))
                 .build();
-        // https://jira.lyrasis.org/browse/FCREPO-3632:
+
         return new DefaultOcflObjectSessionFactory(repositorySupplier.get(),
                 workDirectory,
                 objectMapper,

diff --git a/src/main/java/org/fcrepo/migration/validator/impl/F3RepositoryValidator.java b/src/main/java/org/fcrepo/migration/validator/impl/F3RepositoryValidator.java
@@ -15,7 +15,7 @@
 import java.util.regex.Pattern;
 import java.util.stream.Stream;
 
-import edu.wisc.library.ocfl.api.OcflRepository;
+import io.ocfl.api.OcflRepository;
 import org.fcrepo.migration.FedoraObjectProcessor;
 import org.fcrepo.migration.ObjectSource;
 import org.fcrepo.migration.validator.api.RepositoryValidator;

diff --git a/src/main/java/org/fcrepo/migration/validator/impl/F6DigestAlgorithm.java b/src/main/java/org/fcrepo/migration/validator/impl/F6DigestAlgorithm.java
@@ -8,7 +8,7 @@
 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hasher;
 import com.google.common.hash.Hashing;
-import edu.wisc.library.ocfl.api.model.DigestAlgorithm;
+import io.ocfl.api.model.DigestAlgorithm;
 
 /**
  * Supported digest algorithms for ocfl

diff --git a/src/main/java/org/fcrepo/migration/validator/impl/FileSystemValidationResultWriter.java b/src/main/java/org/fcrepo/migration/validator/impl/FileSystemValidationResultWriter.java
@@ -12,8 +12,11 @@
 
 import java.io.FileWriter;
 import java.io.IOException;
+import java.net.URLEncoder;
+import java.nio.charset.Charset;
 import java.nio.file.Path;
 import java.util.List;
+import java.util.function.UnaryOperator;
 
 import static org.fcrepo.migration.validator.api.ValidationResult.Status.OK;
 import static org.fcrepo.migration.validator.impl.ValidationResultUtils.resolvePathToJsonResult;
@@ -30,6 +33,7 @@ public class FileSystemValidationResultWriter implements ValidationResultWriter
 
     private final Path validationRoot;
     private final boolean writeFailureOnly;
+    private final UnaryOperator<String> pathEncoder;
 
     /**
      * Constructor
@@ -41,6 +45,8 @@ public FileSystemValidationResultWriter(final Path validationRoot, final boolean
         this.validationRoot = validationRoot;
         this.writeFailureOnly = writeFailureOnly;
         validationRoot.toFile().mkdirs();
+
+        pathEncoder = original -> URLEncoder.encode(original, Charset.defaultCharset());
     }
 
     @Override
@@ -51,8 +57,8 @@ public void write(final List<ValidationResult> results) {
                 continue;
             }
 
-            LOGGER.debug("Writing of results here: {}", result);
-            final var jsonFilePath = this.validationRoot.resolve(resolvePathToJsonResult(result));
+            final var jsonFilePath = this.validationRoot.resolve(resolvePathToJsonResult(result, pathEncoder));
+            LOGGER.debug("Writing of results here: {}", jsonFilePath);
             final var file = jsonFilePath.toFile();
             file.getParentFile().mkdirs();
             try (final var writer = new FileWriter(file)) {

diff --git a/src/main/java/org/fcrepo/migration/validator/impl/HeadOnlyValidationHandler.java b/src/main/java/org/fcrepo/migration/validator/impl/HeadOnlyValidationHandler.java
@@ -18,8 +18,8 @@
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import edu.wisc.library.ocfl.api.OcflRepository;
-import edu.wisc.library.ocfl.api.model.ObjectVersionId;
+import io.ocfl.api.OcflRepository;
+import io.ocfl.api.model.ObjectVersionId;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.jena.riot.RDFFormat;