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Avalon overrides #1

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Avalon overrides #1

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8b45bb5
Don't include ebucore:filename predicate in server managed triples be…
cjcolvar Dec 10, 2024
ccf323d
Don't attempt to migrate ACLs because we don't have any
cjcolvar Dec 10, 2024
b903f5f
Look for rdf files with extensions that match the configured src rdf …
cjcolvar Dec 10, 2024
db929d0
Write rdf in same format as source since filename extensions are base…
cjcolvar Dec 10, 2024
07f8dea
Make avalon specific fork version from 6.3.0
cjcolvar Jan 8, 2025
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2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
</parent>

<groupId>org.fcrepo</groupId>
<version>6.4.0-SNAPSHOT</version>
<version>6.3.0-AVALON</version>
<artifactId>fcrepo-upgrade-utils</artifactId>
<name>Fedora Repository Utilities</name>
<description>The Fedora Commons repository upgrade utilities: Provides tools for maintaining the Fedora Commons
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7 changes: 7 additions & 0 deletions src/main/java/org/fcrepo/upgrade/utils/Config.java
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Expand Up @@ -218,6 +218,13 @@ public Lang getSrcRdfLang() {
return srcRdfLang;
}

/**
* @return the extension of the rdf lang of the export
*/
public String getSrcRdfExt() {
return srcRdfLang.getFileExtensions().get(0);
}

/**
* Sets the rdf lang of the export
* @param srcRdfLang the rdf lang of the export
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49 changes: 24 additions & 25 deletions src/main/java/org/fcrepo/upgrade/utils/F47ToF5UpgradeManager.java
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Expand Up @@ -90,7 +90,6 @@ class F47ToF5UpgradeManager extends UpgradeManagerBase implements UpgradeManager
private static final String FCR_VERSIONS_PATH_SEGMENT = "fcr%3Aversions";
private static final String FCR_ACL_PATH_SEGMENT = "fcr%3Aacl";
private static final String TYPE_RELATION = "type";
private static final String TURTLE_EXTENSION = ".ttl";
private static final String HEADERS_SUFFIX = ".headers";
public static final String APPLICATION_OCTET_STREAM_MIMETYPE = "application/octet-stream";
/**
Expand Down Expand Up @@ -120,7 +119,7 @@ private void processDirectory(final File dir) {
private void processFile(final Path path) {

//skip versions container
if (path.endsWith(FCR_VERSIONS_PATH_SEGMENT + TURTLE_EXTENSION)) {
if (path.endsWith(FCR_VERSIONS_PATH_SEGMENT + "." + config.getSrcRdfExt())) {
LOGGER.debug("version containers are not required for import. Skipping {}...", path);
return;
}
Expand All @@ -145,7 +144,7 @@ private void processFile(final Path path) {
Files.createDirectories(newLocation.getParent());
LOGGER.debug("copy file {} to {}", path, newLocation);
FileUtils.copyFile(path.toFile(), newLocation.toFile());
if (newLocation.toString().endsWith(TURTLE_EXTENSION)) {
if (newLocation.toString().endsWith(config.getSrcRdfExt())) {
upgradeRdfAndCreateHeaders(versionTimestamp, newLocation);
}
LOGGER.info("Resource upgraded: {}", path);
Expand All @@ -161,7 +160,7 @@ private void upgradeRdfAndCreateHeaders(final TemporalAccessor versionTimestamp,
//parse the file
final Model model = ModelFactory.createDefaultModel();
try (final InputStream is = new BufferedInputStream(new FileInputStream(newLocation.toFile()))) {
RDFDataMgr.read(model, is, Lang.TTL);
RDFDataMgr.read(model, is, config.getSrcRdfLang());
}

final Map<String, List<String>> metadataHeaders = new HashMap<>();
Expand All @@ -182,10 +181,10 @@ private void upgradeRdfAndCreateHeaders(final TemporalAccessor versionTimestamp,

//skip if ACL or Authorization: these files are upgraded through a separate code path
// see convertAcl() below.
if (rdfTypes.contains(ACL) || rdfTypes.contains(AUTHORIZATION)) {
newLocation.toFile().delete();
return;
}
//if (rdfTypes.contains(ACL) || rdfTypes.contains(AUTHORIZATION)) {
// newLocation.toFile().delete();
// return;
//}

rdfTypes.retainAll(LDP_CONTAINER_TYPES);
final var isConcreteContainerDefined = !rdfTypes.isEmpty();
Expand Down Expand Up @@ -251,17 +250,17 @@ private void upgradeRdfAndCreateHeaders(final TemporalAccessor versionTimestamp,
}
}
binaryHeaders.put(CONTENT_TYPE_HEADER, Collections.singletonList(mimetype));
} else if (statement.getPredicate().equals(ACCESS_CONTROL)) {
//} else if (statement.getPredicate().equals(ACCESS_CONTROL)) {
//remove the current statement across both past versions and latest version
model.remove(currentStatement);
rewriteModel.set(true);
//model.remove(currentStatement);
//rewriteModel.set(true);

//on the latest version
if(versionTimestamp == null) {
//convert the acl
convertAcl(newLocation, currentStatement.getSubject().getURI(),
currentStatement.getObject().asResource().getURI());
}
//if(versionTimestamp == null) {
// //convert the acl
// convertAcl(newLocation, currentStatement.getSubject().getURI(),
// currentStatement.getObject().asResource().getURI());
//}
}
});

Expand All @@ -284,7 +283,7 @@ private void upgradeRdfAndCreateHeaders(final TemporalAccessor versionTimestamp,
// rewrite only if the model has changed.
if (rewriteModel.get()) {
try {
RDFDataMgr.write(new BufferedOutputStream(new FileOutputStream(newLocation.toFile())), model, Lang.TTL);
RDFDataMgr.write(new BufferedOutputStream(new FileOutputStream(newLocation.toFile())), model, config.getSrcRdfLang());
} catch (IOException e) {
throw new RuntimeException(e);
}
Expand Down Expand Up @@ -321,7 +320,7 @@ private void convertAcl(final Path convertedProtectedResourceLocation, String pr
//locate the exported acl rdf on disk based on aclURI
final var relativeAclPath = create(aclUri).getPath();
final var aclDirectory = Path.of(this.config.getInputDir().toPath().toString(), relativeAclPath);
final var aclRdfFilePath = aclDirectory + TURTLE_EXTENSION;
final var aclRdfFilePath = aclDirectory + "." + config.getSrcRdfExt();
final var newAclResource = ResourceFactory.createResource(protectedResource + "/fcr:acl");
final var aclModel = createModelFromFile(Path.of(aclRdfFilePath));
final var aclTriples = new ArrayList<Statement>();
Expand All @@ -338,7 +337,7 @@ private void convertAcl(final Path convertedProtectedResourceLocation, String pr

final var newAclFilePath = Path
.of(FilenameUtils.removeExtension(convertedProtectedResourceLocation.toString()),
FCR_ACL_PATH_SEGMENT + TURTLE_EXTENSION);
FCR_ACL_PATH_SEGMENT + "." + config.getSrcRdfExt());
newAclFilePath.getParent().toFile().mkdirs();

//determine the location of new acl
Expand Down Expand Up @@ -385,7 +384,7 @@ private void convertAcl(final Path convertedProtectedResourceLocation, String pr

//save to new acl to file
try (final OutputStream os = new BufferedOutputStream(new FileOutputStream(newAclFilePath.toFile()))) {
RDFDataMgr.write(os, newModel, Lang.TTL);
RDFDataMgr.write(os, newModel, config.getSrcRdfLang());
} catch (IOException e) {
throw new RuntimeException(e);
}
Expand Down Expand Up @@ -422,7 +421,7 @@ private Path resolveVersionsContainer(final Path path) {
while (currentPath != path.getRoot()) {
final var parent = currentPath.getParent();
if (parent.endsWith(FCR_VERSIONS_PATH_SEGMENT)) {
return Path.of(parent.toString() + TURTLE_EXTENSION);
return Path.of(parent.toString() + "." + config.getSrcRdfExt());
}

currentPath = parent;
Expand All @@ -432,10 +431,10 @@ private Path resolveVersionsContainer(final Path path) {

private TemporalAccessor resolveMementoTimestamp(final Path path) {
var metadataPath = path;
if (!path.toString().endsWith(TURTLE_EXTENSION)) {
if (!path.toString().endsWith(config.getSrcRdfExt())) {
final var metadataPathStr = metadataPath.toString();
final var newMetadataPathStr = FilenameUtils.removeExtension(metadataPathStr) + File.separator +
FCR_METADATA_PATH_SEGMENT + TURTLE_EXTENSION;
FCR_METADATA_PATH_SEGMENT + "." + config.getSrcRdfExt();
metadataPath = Path.of(newMetadataPathStr);
}

Expand All @@ -456,7 +455,7 @@ private TemporalAccessor resolveMementoTimestamp(final Path path) {
private Model createModelFromFile(final Path path) {
final Model model = ModelFactory.createDefaultModel();
try (final InputStream is = new BufferedInputStream(new FileInputStream(path.toFile()))) {
RDFDataMgr.read(model, is, Lang.TTL);
RDFDataMgr.read(model, is, config.getSrcRdfLang());
} catch (IOException ex) {
throw new RuntimeException(ex);
}
Expand All @@ -466,7 +465,7 @@ private Model createModelFromFile(final Path path) {
private Path resolveNewVersionedResourceLocation(final Path path, final TemporalAccessor mementoTimestamp) {
final var mementoId = MEMENTO_FORMATTER.format(mementoTimestamp);
//create a new location compatible with an F5 export.
final var isDescription = path.endsWith(FCR_METADATA_PATH_SEGMENT + TURTLE_EXTENSION);
final var isDescription = path.endsWith(FCR_METADATA_PATH_SEGMENT + "." + config.getSrcRdfExt());
final var inputPath = this.config.getInputDir().toPath();
final var relativePath = inputPath.relativize(path);
final var relativePathStr = relativePath.toString();
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3 changes: 2 additions & 1 deletion src/main/java/org/fcrepo/upgrade/utils/RdfConstants.java
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Expand Up @@ -96,7 +96,8 @@ private RdfConstants() {
private static final Set<Property> serverManagedProperties;
static {
final ImmutableSet.Builder<Property> b = ImmutableSet.builder();
b.addAll(fixityProperties).addAll(ldpManagedProperties).addAll(binaryProperties);
//b.addAll(fixityProperties).addAll(ldpManagedProperties).addAll(binaryProperties);
b.addAll(fixityProperties).addAll(ldpManagedProperties);
serverManagedProperties = b.build();
}

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2 changes: 1 addition & 1 deletion src/main/java/org/fcrepo/upgrade/utils/f6/ResourceMigrator.java
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Expand Up @@ -90,7 +90,7 @@ public ResourceMigrator(final Config config,

this.baseUri = stripTrailingSlash(config.getBaseUri());
this.srcRdfLang = config.getSrcRdfLang();
this.srcRdfExt = "." + srcRdfLang.getFileExtensions().get(0);
this.srcRdfExt = "." + config.getSrcRdfExt();

// Currently, this is all F6 supports
this.dstRdfLang = Lang.NT;
Expand Down