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diff --git a/src/main/java/org/purl/wf4ever/robundle/Bundle.java b/src/main/java/org/purl/wf4ever/robundle/Bundle.java
index 9b23cfe..dd34433 100644
--- a/src/main/java/org/purl/wf4ever/robundle/Bundle.java
+++ b/src/main/java/org/purl/wf4ever/robundle/Bundle.java
@@ -59,6 +59,17 @@
return getRoot().getFileSystem();
}
+ public Manifest getManifest() throws IOException {
+ if (manifest == null) {
+ synchronized (this) {
+ if (manifest == null) {
+ manifest = readOrPopulateManifest();
+ }
+ }
+ }
+ return manifest;
+ }
+
public Path getPath(String path) {
return getRoot().resolve(path);
}
@@ -76,21 +87,6 @@
return deleteOnClose;
}
- public void setDeleteOnClose(boolean deleteOnClose) {
- this.deleteOnClose = deleteOnClose;
- }
-
- public Manifest getManifest() throws IOException {
- if (manifest == null) {
- synchronized (this) {
- if (manifest == null) {
- manifest = readOrPopulateManifest();
- }
- }
- }
- return manifest;
- }
-
protected Manifest readOrPopulateManifest() throws IOException {
Manifest newManifest = new Manifest(this);
Path manifestPath = Bundles.getManifestPath(this);
@@ -113,4 +109,8 @@
return newManifest;
}
+ public void setDeleteOnClose(boolean deleteOnClose) {
+ this.deleteOnClose = deleteOnClose;
+ }
+
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/Bundles.java b/src/main/java/org/purl/wf4ever/robundle/Bundles.java
index 52cc055..4068ee3 100644
--- a/src/main/java/org/purl/wf4ever/robundle/Bundles.java
+++ b/src/main/java/org/purl/wf4ever/robundle/Bundles.java
@@ -102,6 +102,26 @@
return fileName.substring(0, lastDot);
}
+ public static Path getAnnotations(Bundle bundle) throws IOException {
+ Path dir = bundle.getFileSystem().getPath(DOT_RO, ANNOTATIONS);
+ Files.createDirectories(dir);
+ return dir;
+ }
+
+ public static Path getManifestPath(Bundle bundle) {
+ return bundle.getRoot().resolve(DOT_RO).resolve(MANIFEST_JSON);
+ }
+
+ public static String getMimeType(Bundle bundle) throws IOException {
+ Path mimetypePath = bundle.getRoot().resolve(
+ BundleFileSystemProvider.MIMETYPE_FILE);
+ String mimetype = getStringValue(mimetypePath);
+ if (mimetype == null || mimetype.isEmpty()) {
+ return BundleFileSystemProvider.APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP;
+ }
+ return mimetype.trim();
+ }
+
public static URI getReference(Path path) throws IOException {
if (path == null || isMissing(path)) {
return null;
@@ -151,20 +171,6 @@
return !isReference(path) && Files.isRegularFile(path);
}
- public static Bundle openBundle(URL url) throws IOException {
- if ("file.".equals(url.getProtocol())) {
- try {
- return openBundle(Paths.get(url.toURI()));
- } catch (URISyntaxException e) {
- throw new IllegalArgumentException("Invalid URL " + url, e);
- }
- } else {
- try (InputStream in = url.openStream()) {
- return openBundle(in);
- }
- }
- }
-
public static Bundle openBundle(InputStream in) throws IOException {
Path path = TemporaryFiles.temporaryBundle();
Files.copy(in, path);
@@ -179,6 +185,20 @@
return new Bundle(fs.getRootDirectory(), false);
}
+ public static Bundle openBundle(URL url) throws IOException {
+ if ("file.".equals(url.getProtocol())) {
+ try {
+ return openBundle(Paths.get(url.toURI()));
+ } catch (URISyntaxException e) {
+ throw new IllegalArgumentException("Invalid URL " + url, e);
+ }
+ } else {
+ try (InputStream in = url.openStream()) {
+ return openBundle(in);
+ }
+ }
+ }
+
public static Bundle openBundleReadOnly(Path zip) throws IOException {
Path tmpBundle = TemporaryFiles.temporaryBundle();
// BundleFileSystemProvider requires write-access, so we'll have to copy
@@ -271,6 +291,33 @@
}
}
+ public static void setMimeType(Bundle bundle, String mimetype)
+ throws IOException {
+ if (!ASCII.newEncoder().canEncode(mimetype)) {
+ throw new IllegalArgumentException("mimetype must be ASCII, not "
+ + mimetype);
+ }
+ if (mimetype.contains("\n") || mimetype.contains("\r")) {
+ throw new IllegalArgumentException(
+ "mimetype can't contain newlines");
+ }
+ if (!mimetype.contains("/")) {
+ throw new IllegalArgumentException("Invalid mimetype: " + mimetype);
+ }
+ Path root = bundle.getRoot();
+
+ Path mimetypePath = bundle.getRoot().resolve(
+ BundleFileSystemProvider.MIMETYPE_FILE);
+ if (!Files.isRegularFile(mimetypePath)) {
+ // It would require low-level zip-modification to properly add
+ // 'mimetype' now
+ throw new IOException("Special file '"
+ + BundleFileSystemProvider.MIMETYPE_FILE
+ + "' missing from bundle, can't set mimetype");
+ }
+ setStringValue(mimetypePath, mimetype);
+ }
+
public static Path setReference(Path path, URI ref) throws IOException {
path = withExtension(path, DOT_URL);
@@ -317,6 +364,15 @@
StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE);
}
+ public static Path uriToBundlePath(Bundle bundle, URI uri) {
+ URI rootUri = bundle.getRoot().toUri();
+ uri = relativizeFromBase(uri, rootUri);
+ if (uri.isAbsolute() || uri.getFragment() != null) {
+ return null;
+ }
+ return bundle.getFileSystem().provider().getPath(rootUri.resolve(uri));
+ }
+
protected static Path withExtension(Path path, String extension) {
if (!extension.isEmpty() && !extension.startsWith(".")) {
throw new IllegalArgumentException(
@@ -332,60 +388,4 @@
return path.resolveSibling(newP);
}
- public static Path getAnnotations(Bundle bundle) throws IOException {
- Path dir = bundle.getFileSystem().getPath(DOT_RO, ANNOTATIONS);
- Files.createDirectories(dir);
- return dir;
- }
-
- public static Path getManifestPath(Bundle bundle) {
- return bundle.getRoot().resolve(DOT_RO).resolve(MANIFEST_JSON);
- }
-
- public static String getMimeType(Bundle bundle) throws IOException {
- Path mimetypePath = bundle.getRoot().resolve(
- BundleFileSystemProvider.MIMETYPE_FILE);
- String mimetype = getStringValue(mimetypePath);
- if (mimetype == null || mimetype.isEmpty()) {
- return BundleFileSystemProvider.APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP;
- }
- return mimetype.trim();
- }
-
- public static void setMimeType(Bundle bundle, String mimetype)
- throws IOException {
- if (!ASCII.newEncoder().canEncode(mimetype)) {
- throw new IllegalArgumentException("mimetype must be ASCII, not "
- + mimetype);
- }
- if (mimetype.contains("\n") || mimetype.contains("\r")) {
- throw new IllegalArgumentException(
- "mimetype can't contain newlines");
- }
- if (!mimetype.contains("/")) {
- throw new IllegalArgumentException("Invalid mimetype: " + mimetype);
- }
- Path root = bundle.getRoot();
-
- Path mimetypePath = bundle.getRoot().resolve(
- BundleFileSystemProvider.MIMETYPE_FILE);
- if (!Files.isRegularFile(mimetypePath)) {
- // It would require low-level zip-modification to properly add
- // 'mimetype' now
- throw new IOException("Special file '"
- + BundleFileSystemProvider.MIMETYPE_FILE
- + "' missing from bundle, can't set mimetype");
- }
- setStringValue(mimetypePath, mimetype);
- }
-
- public static Path uriToBundlePath(Bundle bundle, URI uri) {
- URI rootUri = bundle.getRoot().toUri();
- uri = relativizeFromBase(uri, rootUri);
- if (uri.isAbsolute() || uri.getFragment() != null) {
- return null;
- }
- return bundle.getFileSystem().provider().getPath(rootUri.resolve(uri));
- }
-
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/fs/BundleFileSystemProvider.java b/src/main/java/org/purl/wf4ever/robundle/fs/BundleFileSystemProvider.java
index 3aa0586..d8d5f76 100644
--- a/src/main/java/org/purl/wf4ever/robundle/fs/BundleFileSystemProvider.java
+++ b/src/main/java/org/purl/wf4ever/robundle/fs/BundleFileSystemProvider.java
@@ -49,8 +49,6 @@
import org.purl.wf4ever.robundle.utils.TemporaryFiles;
public class BundleFileSystemProvider extends FileSystemProvider {
- public static final String MIMETYPE_FILE = "mimetype";
-
public class BundleFileChannel extends FileChannel {
@SuppressWarnings("unused")
@@ -153,6 +151,8 @@
private static final BundleFileSystemProvider INSTANCE = new BundleFileSystemProvider();
}
+ public static final String MIMETYPE_FILE = "mimetype";
+
public static final String APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP = "application/vnd.wf4ever.robundle+zip";
/**
* The list of open file systems. This is static so that it is shared across
@@ -262,6 +262,8 @@
return fs;
}
+ private Boolean jarDoubleEscaping;
+
/**
* Public constructor provided for FileSystemProvider.installedProviders().
* Use #getInstance() instead.
@@ -272,56 +274,14 @@
public BundleFileSystemProvider() {
}
- private Boolean jarDoubleEscaping;
-
- protected boolean getJarDoubleEscaping() {
- if (jarDoubleEscaping != null) {
- return jarDoubleEscaping;
+ private boolean asBoolean(Object object, boolean defaultValue) {
+ if (object instanceof Boolean) {
+ return (Boolean) object;
}
- // https://bugs.openjdk.java.net/browse/JDK-8001178 introduced an
- // inconsistent
- // URI syntax. Before 7u40, jar: URIs to ZipFileSystemProvided had to
- // have
- // double-escaped the URI for the ZIP file, after 7u40 it is only
- // escaped once.
- // E.g.
- // to open before 7u40 you needed
- // jar:file:///file%2520with%2520spaces.zip, now you need
- // jar:file:///file%20with%20spaces.zip
- //
- // The new format is now consistent with URL.openStream() and
- // URLClassLoader's traditional jar: syntax, but somehow
- // zippath.toUri() still returns the double-escaped one, which
- // should only affects BundleFileSystem.findSource(). To help
- // findSource()
- // if this new bug is later fixed, we here detect which escaping style
- // is used.
-
- String name = "jar test";
- try {
- Path tmp = Files.createTempFile(name, ".zip");
- if (!tmp.toUri().toASCIIString().contains("jar%20test")) {
- // Hmm.. spaces not allowed in tmp? As we don't know, we'll
- // assume Java 7 behaviour
- jarDoubleEscaping = false;
- return jarDoubleEscaping;
- }
- createBundleAsZip(tmp, null);
- try (FileSystem fs = FileSystems.newFileSystem(tmp, null)) {
- URI root = fs.getRootDirectories().iterator().next().toUri();
- if (root.toASCIIString().contains("jar%2520test")) {
- jarDoubleEscaping = true;
- } else {
- jarDoubleEscaping = false;
- }
- }
- Files.delete(tmp);
- } catch (IOException e) {
- // Unknown error.. we'll assume Java 7 behaviour
- jarDoubleEscaping = true;
+ if (object instanceof String) {
+ return Boolean.valueOf((String) object);
}
- return jarDoubleEscaping;
-
+ return defaultValue;
}
protected URI baseURIFor(URI uri) {
@@ -426,6 +386,56 @@
}
}
+ protected boolean getJarDoubleEscaping() {
+ if (jarDoubleEscaping != null) {
+ return jarDoubleEscaping;
+ }
+ // https://bugs.openjdk.java.net/browse/JDK-8001178 introduced an
+ // inconsistent
+ // URI syntax. Before 7u40, jar: URIs to ZipFileSystemProvided had to
+ // have
+ // double-escaped the URI for the ZIP file, after 7u40 it is only
+ // escaped once.
+ // E.g.
+ // to open before 7u40 you needed
+ // jar:file:///file%2520with%2520spaces.zip, now you need
+ // jar:file:///file%20with%20spaces.zip
+ //
+ // The new format is now consistent with URL.openStream() and
+ // URLClassLoader's traditional jar: syntax, but somehow
+ // zippath.toUri() still returns the double-escaped one, which
+ // should only affects BundleFileSystem.findSource(). To help
+ // findSource()
+ // if this new bug is later fixed, we here detect which escaping style
+ // is used.
+
+ String name = "jar test";
+ try {
+ Path tmp = Files.createTempFile(name, ".zip");
+ if (!tmp.toUri().toASCIIString().contains("jar%20test")) {
+ // Hmm.. spaces not allowed in tmp? As we don't know, we'll
+ // assume Java 7 behaviour
+ jarDoubleEscaping = false;
+ return jarDoubleEscaping;
+ }
+ createBundleAsZip(tmp, null);
+ try (FileSystem fs = FileSystems.newFileSystem(tmp, null)) {
+ URI root = fs.getRootDirectories().iterator().next().toUri();
+ if (root.toASCIIString().contains("jar%2520test")) {
+ jarDoubleEscaping = true;
+ } else {
+ jarDoubleEscaping = false;
+ }
+ }
+ Files.delete(tmp);
+ } catch (IOException e) {
+ // Unknown error.. we'll assume Java 7 behaviour
+ jarDoubleEscaping = true;
+ }
+ return jarDoubleEscaping;
+
+ }
+
@Override
public Path getPath(URI uri) {
BundleFileSystem fs = getFileSystem(uri);
@@ -597,16 +607,6 @@
return fs;
}
- private boolean asBoolean(Object object, boolean defaultValue) {
- if (object instanceof Boolean) {
- return (Boolean) object;
- }
- if (object instanceof String) {
- return Boolean.valueOf((String) object);
- }
- return defaultValue;
- }
-
@Override
public InputStream newInputStream(Path path, OpenOption... options)
throws IOException {
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/Manifest.java b/src/main/java/org/purl/wf4ever/robundle/manifest/Manifest.java
index ac180ab..d5891ab 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/Manifest.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/Manifest.java
@@ -40,22 +40,22 @@
"aggregates", "annotations", "@graph" })
public class Manifest {
- private static final String MANIFEST_JSON = "manifest.json";
-
- private static Logger logger = Logger.getLogger(Manifest.class
- .getCanonicalName());
-
- private static URI ROOT = URI.create("/");
+ public abstract class FileTimeMixin {
+ @JsonValue
+ public abstract String toString();
+ }
public abstract class PathMixin {
@JsonValue
public abstract String toString();
}
- public abstract class FileTimeMixin {
- @JsonValue
- public abstract String toString();
- }
+ private static final String MANIFEST_JSON = "manifest.json";
+
+ private static Logger logger = Logger.getLogger(Manifest.class
+ .getCanonicalName());
+
+ private static URI ROOT = URI.create("/");
private static final String META_INF = "/META-INF";
private static final String MIMETYPE = "/mimetype";
@@ -103,6 +103,28 @@
return new ArrayList<>(aggregates.values());
}
+ public PathMetadata getAggregation(Path file) {
+ URI fileUri = file.toUri();
+ return getAggregation(fileUri);
+ }
+
+ public PathMetadata getAggregation(URI uri) {
+ uri = relativeToBundleRoot(uri);
+ PathMetadata metadata = aggregates.get(uri);
+ if (metadata == null) {
+ metadata = new PathMetadata();
+ if (!uri.isAbsolute() && uri.getFragment() == null) {
+ Path path = Bundles.uriToBundlePath(bundle, uri);
+ metadata.setFile(path);
+ metadata.setMediatype(guessMediaType(path));
+ } else {
+ metadata.setUri(uri);
+ }
+ aggregates.put(uri, metadata);
+ }
+ return metadata;
+ }
+
public List<PathAnnotation> getAnnotations() {
return annotations;
}
@@ -116,6 +138,11 @@
}
@JsonIgnore
+ public URI getBaseURI() {
+ return getBundle().getRoot().toUri();
+ }
+
+ @JsonIgnore
public Bundle getBundle() {
return bundle;
}
@@ -130,11 +157,6 @@
return context;
}
- @JsonIgnore
- public URI getBaseURI() {
- return getBundle().getRoot().toUri();
- }
-
public Agent getCreatedBy() {
return createdBy;
}
@@ -292,6 +314,11 @@
}
}
+ public URI relativeToBundleRoot(URI uri) {
+ uri = ROOT.resolve(bundle.getRoot().toUri().relativize(uri));
+ return uri;
+ }
+
public void setAggregates(List<PathMetadata> aggregates) {
this.aggregates.clear();
@@ -359,6 +386,10 @@
this.manifest = manifest;
}
+ public void writeAsCombineManifest() throws IOException {
+ new CombineManifest(this).createManifestXML();
+ }
+
/**
* Write as an RO Bundle JSON-LD manifest
*
@@ -403,35 +434,4 @@
public Path writeAsODFManifest() throws IOException {
return new ODFManifest(this).createManifestXML();
}
-
- public PathMetadata getAggregation(Path file) {
- URI fileUri = file.toUri();
- return getAggregation(fileUri);
- }
-
- public PathMetadata getAggregation(URI uri) {
- uri = relativeToBundleRoot(uri);
- PathMetadata metadata = aggregates.get(uri);
- if (metadata == null) {
- metadata = new PathMetadata();
- if (!uri.isAbsolute() && uri.getFragment() == null) {
- Path path = Bundles.uriToBundlePath(bundle, uri);
- metadata.setFile(path);
- metadata.setMediatype(guessMediaType(path));
- } else {
- metadata.setUri(uri);
- }
- aggregates.put(uri, metadata);
- }
- return metadata;
- }
-
- public URI relativeToBundleRoot(URI uri) {
- uri = ROOT.resolve(bundle.getRoot().toUri().relativize(uri));
- return uri;
- }
-
- public void writeAsCombineManifest() throws IOException {
- new CombineManifest(this).createManifestXML();
- }
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/PathAnnotation.java b/src/main/java/org/purl/wf4ever/robundle/manifest/PathAnnotation.java
index 3a255ed..53828f6 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/PathAnnotation.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/PathAnnotation.java
@@ -16,6 +16,10 @@
private URI uri;
private URI content;
+ public void generateAnnotationId() {
+ setUri(URI.create("urn:uuid:" + UUID.randomUUID()));
+ }
+
@JsonIgnore
public URI getAbout() {
if (about.isEmpty()) {
@@ -47,19 +51,17 @@
return getUri();
}
- public URI getUri() {
- return uri;
- }
-
public URI getContent() {
return content;
}
- public void setAbout(URI about) {
- this.about.clear();
- if (about != null) {
- this.about.add(about);
- }
+ public URI getUri() {
+ return uri;
+ }
+
+ private URI relativizePath(Path path) {
+ return URI.create("/.ro/").relativize(
+ URI.create(path.toUri().getRawPath()));
}
public void setAbout(List<URI> about) {
@@ -69,8 +71,15 @@
this.about = about;
}
- public void setUri(URI uri) {
- this.uri = uri;
+ public void setAbout(Path path) {
+ setAbout(relativizePath(path));
+ }
+
+ public void setAbout(URI about) {
+ this.about.clear();
+ if (about != null) {
+ this.about.add(about);
+ }
}
@Deprecated
@@ -78,25 +87,16 @@
setUri(annotation);
}
+ public void setContent(Path path) {
+ this.content = relativizePath(path);
+ }
+
public void setContent(URI content) {
this.content = content;
}
- public void generateAnnotationId() {
- setUri(URI.create("urn:uuid:" + UUID.randomUUID()));
- }
-
- public void setAbout(Path path) {
- setAbout(relativizePath(path));
- }
-
- private URI relativizePath(Path path) {
- return URI.create("/.ro/").relativize(
- URI.create(path.toUri().getRawPath()));
- }
-
- public void setContent(Path path) {
- this.content = relativizePath(path);
+ public void setUri(URI uri) {
+ this.uri = uri;
}
@Override
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/PathMetadata.java b/src/main/java/org/purl/wf4ever/robundle/manifest/PathMetadata.java
index 378f940..22c380c 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/PathMetadata.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/PathMetadata.java
@@ -38,6 +38,18 @@
setUri(URI.create(uriStr));
}
+ public List<Agent> getAuthoredBy() {
+ return authoredBy;
+ }
+
+ public FileTime getAuthoredOn() {
+ return authoredOn;
+ }
+
+ public Proxy getBundledAs() {
+ return bundledAs;
+ }
+
public URI getConformsTo() {
return conformsTo;
}
@@ -70,6 +82,15 @@
}
@JsonIgnore
+ public Proxy getOrCreateBundledAs() {
+ if (bundledAs == null) {
+ bundledAs = new Proxy();
+ setProxy();
+ }
+ return bundledAs;
+ }
+
+ @JsonIgnore
@Deprecated
public URI getProxy() {
Proxy bundledAs = getBundledAs();
@@ -83,6 +104,25 @@
return uri;
}
+ public void setAuthoredBy(List<Agent> authoredBy) {
+ if (authoredBy == null) {
+ throw new NullPointerException("authoredBy list can't be empty");
+ }
+ this.authoredBy = authoredBy;
+ }
+
+ public void setAuthoredOn(FileTime authoredOn) {
+ this.authoredOn = authoredOn;
+ }
+
+ public void setBundledAs(Proxy bundledAs) {
+ if (bundledAs == null) {
+ throw new NullPointerException(
+ "bundledAs can't be empty (try a new Proxy instance)");
+ }
+ this.bundledAs = bundledAs;
+ }
+
public void setConformsTo(URI conformsTo) {
this.conformsTo = conformsTo;
}
@@ -144,44 +184,4 @@
return "PathMetadata <null>";
}
- public List<Agent> getAuthoredBy() {
- return authoredBy;
- }
-
- public void setAuthoredBy(List<Agent> authoredBy) {
- if (authoredBy == null) {
- throw new NullPointerException("authoredBy list can't be empty");
- }
- this.authoredBy = authoredBy;
- }
-
- public FileTime getAuthoredOn() {
- return authoredOn;
- }
-
- public void setAuthoredOn(FileTime authoredOn) {
- this.authoredOn = authoredOn;
- }
-
- @JsonIgnore
- public Proxy getOrCreateBundledAs() {
- if (bundledAs == null) {
- bundledAs = new Proxy();
- setProxy();
- }
- return bundledAs;
- }
-
- public Proxy getBundledAs() {
- return bundledAs;
- }
-
- public void setBundledAs(Proxy bundledAs) {
- if (bundledAs == null) {
- throw new NullPointerException(
- "bundledAs can't be empty (try a new Proxy instance)");
- }
- this.bundledAs = bundledAs;
- }
-
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/Proxy.java b/src/main/java/org/purl/wf4ever/robundle/manifest/Proxy.java
index b146fc7..88b279d 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/Proxy.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/Proxy.java
@@ -53,11 +53,11 @@
this.folder = folder;
}
- public void setURI(URI uri) {
- this.uri = uri;
- }
-
public void setURI() {
setURI(URI.create("urn:uuid:" + UUID.randomUUID()));
}
+
+ public void setURI(URI uri) {
+ this.uri = uri;
+ }
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/RDFToManifest.java b/src/main/java/org/purl/wf4ever/robundle/manifest/RDFToManifest.java
index 3df1795..fe1687d 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/RDFToManifest.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/RDFToManifest.java
@@ -33,18 +33,37 @@
public class RDFToManifest {
+ public static class ClosableIterable<T> implements AutoCloseable,
+ Iterable<T> {
+
+ private ExtendedIterator<T> iterator;
+
+ public ClosableIterable(ExtendedIterator<T> iterator) {
+ this.iterator = iterator;
+ }
+
+ @Override
+ public void close() {
+ iterator.close();
+ }
+
+ @Override
+ public ExtendedIterator<T> iterator() {
+ return iterator;
+ }
+ }
+
private static Logger logger = Logger.getLogger(RDFToManifest.class
.getCanonicalName());
static {
setCachedHttpClientInJsonLD();
}
-
private static final String PROV = "http://www.w3.org/ns/prov#";
private static final String PROV_O = "http://www.w3.org/ns/prov-o#";
private static final String FOAF_0_1 = "http://xmlns.com/foaf/0.1/";
- private static final String PAV = "http://purl.org/pav/";
+ private static final String PAV = "http://purl.org/pav/";
private static final String DCT = "http://purl.org/dc/terms/";
private static final String RO = "http://purl.org/wf4ever/ro#";
private static final String BUNDLE = "http://purl.org/wf4ever/bundle#";
@@ -56,11 +75,51 @@
private static final String PAV_RDF = "/ontologies/pav.rdf";
private static final String PROV_O_RDF = "/ontologies/prov-o.rdf";
private static final String PROV_AQ_RDF = "/ontologies/prov-aq.rdf";
+ public static <T> ClosableIterable<T> iterate(ExtendedIterator<T> iterator) {
+ return new ClosableIterable<T>(iterator);
+ }
+ protected static Model jsonLdAsJenaModel(InputStream jsonIn, URI base)
+ throws IOException, RiotException {
+ Model model = ModelFactory.createDefaultModel();
+ RDFDataMgr.read(model, jsonIn, base.toASCIIString(), Lang.JSONLD);
+ return model;
+
+ //
+ // Object input = JSONUtils.fromInputStream(jsonIn);
+ // JSONLDTripleCallback callback = new JenaTripleCallback();
+ // Model model = (Model)JSONLD.toRDF(input, callback, new
+ // Options(base.toASCIIString()));
+ // return model;
+ }
+ protected static URI makeBaseURI() throws URISyntaxException {
+ return new URI("app", UUID.randomUUID().toString(), "/", (String) null);
+ }
+
+ /**
+ * Use a JarCacheStorage so that our JSON-LD @context can be loaded from our
+ * classpath and not require network connectivity
+ *
+ */
+ protected static void setCachedHttpClientInJsonLD() {
+ // JarCacheStorage cacheStorage = new JarCacheStorage(
+ // RDFToManifest.class.getClassLoader());
+ // synchronized (DocumentLoader.class) {
+ // HttpClient oldHttpClient = DocumentLoader.getHttpClient();
+ // CachingHttpClient wrappedHttpClient = new CachingHttpClient(
+ // oldHttpClient, cacheStorage, cacheStorage.getCacheConfig());
+ // DocumentLoader.setHttpClient(wrappedHttpClient);
+ // }
+ // synchronized (JSONUtils.class) {
+ // HttpClient oldHttpClient = JSONUtilsSub.getHttpClient();
+ // CachingHttpClient wrappedHttpClient = new CachingHttpClient(
+ // oldHttpClient, cacheStorage, cacheStorage.getCacheConfig());
+ // JSONUtilsSub.setHttpClient(wrappedHttpClient);
+ // }
+ }
private OntModel ore;
private ObjectProperty aggregates;
private ObjectProperty proxyFor;
private ObjectProperty proxyIn;
-
private OntClass aggregation;
private OntModel foaf;
private DatatypeProperty foafName;
@@ -70,29 +129,164 @@
private OntModel provaq;
private ObjectProperty hasProvenance;
private OntModel dct;
+
private ObjectProperty conformsTo;
+
private OntClass standard;
+
private ObjectProperty authoredBy;
+
private DatatypeProperty createdOn;
private DatatypeProperty authoredOn;
-
private DatatypeProperty format;
-
private OntModel oa;
-
private ObjectProperty hasBody;
-
private ObjectProperty hasTarget;
+
private ObjectProperty isDescribedBy;
+
private OntModel bundle;
+
private ObjectProperty hasProxy;
+
private ObjectProperty inFolder;
+
private ObjectProperty hasAnnotation;
public RDFToManifest() {
loadOntologies();
}
+ private void checkNotNull(Object... possiblyNulls) {
+ int i = 0;
+ for (Object check : possiblyNulls) {
+ if (check == null) {
+ throw new IllegalStateException("Could not load item #" + i);
+ }
+ i++;
+ }
+
+ }
+
+ private Individual findRO(OntModel model, URI base) {
+ try (ClosableIterable<? extends OntResource> instances = iterate(aggregation
+ .listInstances())) {
+ for (OntResource o : instances) {
+ // System.out.println("Woo " + o);
+ return o.asIndividual();
+ }
+ }
+ // Fallback - resolve as "/"
+ // TODO: Ensure it's an Aggregation?
+ return model.getIndividual(base.toString());
+ }
+
+ private List<Agent> getAgents(URI base, Individual in,
+ ObjectProperty property) {
+ List<Agent> creators = new ArrayList<>();
+ for (Individual agent : listObjectProperties(in, property)) {
+ Agent a = new Agent();
+ if (agent.getURI() != null) {
+ a.setUri(relativizeFromBase(agent.getURI(), base));
+ }
+
+ RDFNode name = agent.getPropertyValue(foafName);
+ if (name != null && name.isLiteral()) {
+ a.setName(name.asLiteral().getLexicalForm());
+ }
+ creators.add(a);
+ }
+ return creators;
+ }
+
+ protected OntModel getOntModel() {
+ OntModel ontModel = ModelFactory
+ .createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF);
+ ontModel.setNsPrefix("foaf", FOAF_0_1);
+ ontModel.setNsPrefix("prov", PROV);
+ ontModel.setNsPrefix("ore", ORE);
+ ontModel.setNsPrefix("pav", PAV);
+ ontModel.setNsPrefix("dct", DCT);
+ // ontModel.getDocumentManager().loadImports(foaf.getOntModel());
+ return ontModel;
+ }
+
+ private Set<Individual> listObjectProperties(OntResource ontResource,
+ ObjectProperty prop) {
+ LinkedHashSet<Individual> results = new LinkedHashSet<>();
+ try (ClosableIterable<RDFNode> props = iterate(ontResource
+ .listPropertyValues(prop))) {
+ for (RDFNode node : props) {
+ if (!node.isResource() || !node.canAs(Individual.class)) {
+ continue;
+ }
+ results.add(node.as(Individual.class));
+ }
+ }
+ return results;
+ }
+
+ protected synchronized void loadBundle() {
+ if (bundle != null) {
+ return;
+ }
+ OntModel ontModel = loadOntologyFromClasspath(BUNDLE_RDF, BUNDLE);
+ hasProxy = ontModel.getObjectProperty(BUNDLE + "hasProxy");
+ hasAnnotation = ontModel.getObjectProperty(BUNDLE + "hasAnnotation");
+ inFolder = ontModel.getObjectProperty(BUNDLE + "inFolder");
+ checkNotNull(hasProxy, hasAnnotation, inFolder);
+ bundle = ontModel;
+ }
+
+ protected synchronized void loadDCT() {
+ if (dct != null) {
+ return;
+ }
+
+ OntModel ontModel = loadOntologyFromClasspath(
+ "/ontologies/dcterms_od.owl",
+ "http://purl.org/wf4ever/dcterms_od");
+
+ // properties from dct
+ standard = ontModel.getOntClass(DCT + "Standard");
+ conformsTo = ontModel.getObjectProperty(DCT + "conformsTo");
+
+ // We'll cheat dc:format in
+ format = ontModel
+ .createDatatypeProperty("http://purl.org/dc/elements/1.1/"
+ + "format");
+ checkNotNull(standard, conformsTo, format);
+
+ dct = ontModel;
+
+ }
+
+ //
+ protected synchronized void loadFOAF() {
+ if (foaf != null) {
+ return;
+ }
+
+ OntModel ontModel = loadOntologyFromClasspath(FOAF_RDF, FOAF_0_1);
+
+ // properties from foaf
+ foafName = ontModel.getDatatypeProperty(FOAF_0_1 + "name");
+ checkNotNull(foafName);
+
+ foaf = ontModel;
+ }
+
+ protected synchronized void loadOA() {
+ if (oa != null) {
+ return;
+ }
+ OntModel ontModel = loadOntologyFromClasspath(OA_RDF, OA);
+ hasTarget = ontModel.getObjectProperty(OA + "hasTarget");
+ hasBody = ontModel.getObjectProperty(OA + "hasBody");
+ checkNotNull(hasTarget, hasBody);
+ oa = ontModel;
+ }
+
protected void loadOntologies() {
loadDCT();
loadORE();
@@ -117,166 +311,6 @@
return ontModel;
}
- protected static Model jsonLdAsJenaModel(InputStream jsonIn, URI base)
- throws IOException, RiotException {
- Model model = ModelFactory.createDefaultModel();
- RDFDataMgr.read(model, jsonIn, base.toASCIIString(), Lang.JSONLD);
- return model;
-
- //
- // Object input = JSONUtils.fromInputStream(jsonIn);
- // JSONLDTripleCallback callback = new JenaTripleCallback();
- // Model model = (Model)JSONLD.toRDF(input, callback, new
- // Options(base.toASCIIString()));
- // return model;
- }
-
- /**
- * Use a JarCacheStorage so that our JSON-LD @context can be loaded from our
- * classpath and not require network connectivity
- *
- */
- protected static void setCachedHttpClientInJsonLD() {
- // JarCacheStorage cacheStorage = new JarCacheStorage(
- // RDFToManifest.class.getClassLoader());
- // synchronized (DocumentLoader.class) {
- // HttpClient oldHttpClient = DocumentLoader.getHttpClient();
- // CachingHttpClient wrappedHttpClient = new CachingHttpClient(
- // oldHttpClient, cacheStorage, cacheStorage.getCacheConfig());
- // DocumentLoader.setHttpClient(wrappedHttpClient);
- // }
- // synchronized (JSONUtils.class) {
- // HttpClient oldHttpClient = JSONUtilsSub.getHttpClient();
- // CachingHttpClient wrappedHttpClient = new CachingHttpClient(
- // oldHttpClient, cacheStorage, cacheStorage.getCacheConfig());
- // JSONUtilsSub.setHttpClient(wrappedHttpClient);
- // }
- }
-
- private void checkNotNull(Object... possiblyNulls) {
- int i = 0;
- for (Object check : possiblyNulls) {
- if (check == null) {
- throw new IllegalStateException("Could not load item #" + i);
- }
- i++;
- }
-
- }
-
- protected OntModel getOntModel() {
- OntModel ontModel = ModelFactory
- .createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF);
- ontModel.setNsPrefix("foaf", FOAF_0_1);
- ontModel.setNsPrefix("prov", PROV);
- ontModel.setNsPrefix("ore", ORE);
- ontModel.setNsPrefix("pav", PAV);
- ontModel.setNsPrefix("dct", DCT);
- // ontModel.getDocumentManager().loadImports(foaf.getOntModel());
- return ontModel;
- }
-
- //
- protected synchronized void loadFOAF() {
- if (foaf != null) {
- return;
- }
-
- OntModel ontModel = loadOntologyFromClasspath(FOAF_RDF, FOAF_0_1);
-
- // properties from foaf
- foafName = ontModel.getDatatypeProperty(FOAF_0_1 + "name");
- checkNotNull(foafName);
-
- foaf = ontModel;
- }
-
- protected synchronized void loadPAV() {
- if (pav != null) {
- return;
- }
-
- OntModel ontModel = loadOntologyFromClasspath(PAV_RDF, PAV);
- // properties from foaf
- createdBy = ontModel.getObjectProperty(PAV + "createdBy");
- createdOn = ontModel.getDatatypeProperty(PAV + "createdOn");
- authoredBy = ontModel.getObjectProperty(PAV + "authoredBy");
- authoredOn = ontModel.getDatatypeProperty(PAV + "authoredOn");
- checkNotNull(createdBy, createdOn, authoredBy, authoredOn);
-
- pav = ontModel;
- }
-
- protected synchronized void loadPROVO() {
- if (prov != null) {
- return;
- }
- OntModel ontModel = loadOntologyFromClasspath(PROV_O_RDF, PROV_O);
-
- checkNotNull(ontModel);
-
- prov = ontModel;
- }
-
- protected synchronized void loadPROVAQ() {
- if (provaq != null) {
- return;
- }
- OntModel ontModel = loadOntologyFromClasspath(PROV_AQ_RDF, PAV);
-
- // properties from foaf
- hasProvenance = ontModel.getObjectProperty(PROV + "has_provenance");
- checkNotNull(hasProvenance);
-
- provaq = ontModel;
- }
-
- protected synchronized void loadDCT() {
- if (dct != null) {
- return;
- }
-
- OntModel ontModel = loadOntologyFromClasspath(
- "/ontologies/dcterms_od.owl",
- "http://purl.org/wf4ever/dcterms_od");
-
- // properties from dct
- standard = ontModel.getOntClass(DCT + "Standard");
- conformsTo = ontModel.getObjectProperty(DCT + "conformsTo");
-
- // We'll cheat dc:format in
- format = ontModel
- .createDatatypeProperty("http://purl.org/dc/elements/1.1/"
- + "format");
- checkNotNull(standard, conformsTo, format);
-
- dct = ontModel;
-
- }
-
- protected synchronized void loadOA() {
- if (oa != null) {
- return;
- }
- OntModel ontModel = loadOntologyFromClasspath(OA_RDF, OA);
- hasTarget = ontModel.getObjectProperty(OA + "hasTarget");
- hasBody = ontModel.getObjectProperty(OA + "hasBody");
- checkNotNull(hasTarget, hasBody);
- oa = ontModel;
- }
-
- protected synchronized void loadBundle() {
- if (bundle != null) {
- return;
- }
- OntModel ontModel = loadOntologyFromClasspath(BUNDLE_RDF, BUNDLE);
- hasProxy = ontModel.getObjectProperty(BUNDLE + "hasProxy");
- hasAnnotation = ontModel.getObjectProperty(BUNDLE + "hasAnnotation");
- inFolder = ontModel.getObjectProperty(BUNDLE + "inFolder");
- checkNotNull(hasProxy, hasAnnotation, inFolder);
- bundle = ontModel;
- }
-
protected synchronized void loadORE() {
if (ore != null) {
return;
@@ -295,28 +329,44 @@
ore = ontModel;
}
- public static <T> ClosableIterable<T> iterate(ExtendedIterator<T> iterator) {
- return new ClosableIterable<T>(iterator);
+ protected synchronized void loadPAV() {
+ if (pav != null) {
+ return;
+ }
+
+ OntModel ontModel = loadOntologyFromClasspath(PAV_RDF, PAV);
+ // properties from foaf
+ createdBy = ontModel.getObjectProperty(PAV + "createdBy");
+ createdOn = ontModel.getDatatypeProperty(PAV + "createdOn");
+ authoredBy = ontModel.getObjectProperty(PAV + "authoredBy");
+ authoredOn = ontModel.getDatatypeProperty(PAV + "authoredOn");
+ checkNotNull(createdBy, createdOn, authoredBy, authoredOn);
+
+ pav = ontModel;
}
- public static class ClosableIterable<T> implements AutoCloseable,
- Iterable<T> {
-
- private ExtendedIterator<T> iterator;
-
- public ClosableIterable(ExtendedIterator<T> iterator) {
- this.iterator = iterator;
+ protected synchronized void loadPROVAQ() {
+ if (provaq != null) {
+ return;
}
+ OntModel ontModel = loadOntologyFromClasspath(PROV_AQ_RDF, PAV);
- @Override
- public void close() {
- iterator.close();
- }
+ // properties from foaf
+ hasProvenance = ontModel.getObjectProperty(PROV + "has_provenance");
+ checkNotNull(hasProvenance);
- @Override
- public ExtendedIterator<T> iterator() {
- return iterator;
+ provaq = ontModel;
+ }
+
+ protected synchronized void loadPROVO() {
+ if (prov != null) {
+ return;
}
+ OntModel ontModel = loadOntologyFromClasspath(PROV_O_RDF, PROV_O);
+
+ checkNotNull(ontModel);
+
+ prov = ontModel;
}
public void readTo(InputStream manifestResourceAsStream, Manifest manifest,
@@ -461,54 +511,4 @@
}
- private List<Agent> getAgents(URI base, Individual in,
- ObjectProperty property) {
- List<Agent> creators = new ArrayList<>();
- for (Individual agent : listObjectProperties(in, property)) {
- Agent a = new Agent();
- if (agent.getURI() != null) {
- a.setUri(relativizeFromBase(agent.getURI(), base));
- }
-
- RDFNode name = agent.getPropertyValue(foafName);
- if (name != null && name.isLiteral()) {
- a.setName(name.asLiteral().getLexicalForm());
- }
- creators.add(a);
- }
- return creators;
- }
-
- protected static URI makeBaseURI() throws URISyntaxException {
- return new URI("app", UUID.randomUUID().toString(), "/", (String) null);
- }
-
- private Set<Individual> listObjectProperties(OntResource ontResource,
- ObjectProperty prop) {
- LinkedHashSet<Individual> results = new LinkedHashSet<>();
- try (ClosableIterable<RDFNode> props = iterate(ontResource
- .listPropertyValues(prop))) {
- for (RDFNode node : props) {
- if (!node.isResource() || !node.canAs(Individual.class)) {
- continue;
- }
- results.add(node.as(Individual.class));
- }
- }
- return results;
- }
-
- private Individual findRO(OntModel model, URI base) {
- try (ClosableIterable<? extends OntResource> instances = iterate(aggregation
- .listInstances())) {
- for (OntResource o : instances) {
- // System.out.println("Woo " + o);
- return o.asIndividual();
- }
- }
- // Fallback - resolve as "/"
- // TODO: Ensure it's an Aggregation?
- return model.getIndividual(base.toString());
- }
-
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/combine/CombineManifest.java b/src/main/java/org/purl/wf4ever/robundle/manifest/combine/CombineManifest.java
index ed0a58c..f1871e1 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/combine/CombineManifest.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/combine/CombineManifest.java
@@ -58,14 +58,14 @@
*/
public class CombineManifest {
- private static final URI OMEX_METADATA = URI
- .create("http://identifiers.org/combine.specifications/omex-metadata");
-
- private static final String MANIFEST_XML = "manifest.xml";
-
public static class ManifestNamespacePrefixMapperJAXB_RI extends
NamespacePrefixMapper {
@Override
+ public String[] getPreDeclaredNamespaceUris() {
+ return new String[] { OMEX_METADATA.toString() };
+ }
+
+ @Override
public String getPreferredPrefix(String namespaceUri,
String suggestion, boolean requirePrefix) {
if (namespaceUri.equals(OMEX_METADATA.toString())) {
@@ -74,151 +74,159 @@
return suggestion;
}
- @Override
- public String[] getPreDeclaredNamespaceUris() {
- return new String[] { OMEX_METADATA.toString() };
- }
-
}
+ private static final URI OMEX_METADATA = URI
+ .create("http://identifiers.org/combine.specifications/omex-metadata");
+
+ private static final String MANIFEST_XML = "manifest.xml";
+
private static Logger logger = Logger.getLogger(CombineManifest.class
.getCanonicalName());
+ public static boolean containsManifest(Bundle bundle) {
+ return Files.isRegularFile(manifestXmlPath(bundle));
+ }
private org.purl.wf4ever.robundle.manifest.Manifest manifest;
private Bundle bundle;
+
private static boolean warnedPrefixMapper;
private static ObjectFactory objectFactory = new ObjectFactory();
private static JAXBContext jaxbContext;
- public CombineManifest(org.purl.wf4ever.robundle.manifest.Manifest manifest) {
- this.manifest = manifest;
- this.bundle = manifest.getBundle();
+ private static final String sparqlPrefixes = "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
+ + "PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> \n"
+ + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
+ + "PREFIX dct: <http://purl.org/dc/terms/> \n";
+
+ protected static synchronized Marshaller createMarshaller()
+ throws JAXBException {
+ Marshaller marshaller = getJaxbContext().createMarshaller();
+ setPrefixMapper(marshaller);
+ return marshaller;
}
- private OmexManifest makeOmexManifest() {
- Path manifestXml = bundle.getRoot().resolve("manifest.xml");
- OmexManifest omexManifest = objectFactory.createOmexManifest();
-
- PathMetadata aggr = manifest.getAggregation(manifestXml);
- if (aggr.getConformsTo() == null) {
- // Add the manifest itself
- aggr.setConformsTo(URI
- .create("http://identifiers.org/combine.specifications/omex-manifest"));
- }
-
- for (PathMetadata metadata : manifest.getAggregates()) {
- Content content = objectFactory.createContent();
- Path file = metadata.getFile();
-
- if (file == null) {
- content.setLocation(metadata.getUri().toString());
- } else {
- Path relPath = metadata.getFile().relativize(bundle.getRoot());
- content.setLocation("./" + relPath);
- }
- if (metadata.getMediatype() != null
- && !metadata.getMediatype().isEmpty()) {
- content.setFormat(metadata.getMediatype());
- } else if (metadata.getConformsTo() != null) {
- content.setFormat(metadata.getConformsTo().toString());
- } else {
- // Binary fallback as 'format' is required attribute
- content.setFormat("application/octet-stream");
- }
-
- // TODO: Handle 'master' attribute
-
- omexManifest.getContent().add(content);
-
- }
- // TODO: Should we add .ro/manifest.json and .ro/* ?
- return omexManifest;
+ protected static synchronized Unmarshaller createUnMarshaller()
+ throws JAXBException {
+ Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
+ return unmarshaller;
}
- public Path createManifestXML() throws IOException {
- OmexManifest omexManifest = makeOmexManifest();
+ private static List<RDFNode> creatingAgentsFor(Resource r) {
+ logger.fine("Finding creator of " + r);
+ String queryStr = sparqlPrefixes + "SELECT ?agent WHERE { \n" + " { \n"
+ + " ?r dct:creator [ \n" + " rdfs:member ?agent \n"
+ + " ] \n" + " } UNION { \n" + " ?r dct:creator ?agent .\n "
+ + " FILTER NOT EXISTS { ?agent rdfs:member ?member } \n"
+ + " } \n" + "} \n";
+ logger.finer(QueryFactory.create(queryStr).toString());
+ QueryExecution qexec = QueryExecutionFactory.create(queryStr,
+ r.getModel());
+ QuerySolutionMap binding = new QuerySolutionMap();
+ binding.add("r", r);
+ qexec.setInitialBinding(binding);
+ ResultSet select = qexec.execSelect();
+ List<RDFNode> agents = new ArrayList<>();
- Path manifestXml = manifestXmlPath(bundle);
- Files.createDirectories(manifestXml.getParent());
- try (OutputStream outStream = Files.newOutputStream(manifestXml)) {
- try {
- createMarshaller().marshal(omexManifest, outStream);
- } catch (JAXBException e) {
- throw new RuntimeException("Could not serialize OMEX Manifest",
- e);
- }
+ while (select.hasNext()) {
+ RDFNode agent = select.next().get("agent");
+ logger.fine("Found: " + agent);
+ agents.add(agent);
}
- return manifestXml;
+ return agents;
}
- public void readCombineArchive() throws IOException {
- readManifestXML();
- findAnnotations();
-
- }
-
- public void readManifestXML() throws IOException {
- Path manifestXml = manifestXmlPath(bundle);
- OmexManifest omexManifest;
- try (InputStream inStream = Files.newInputStream(manifestXml)) {
- InputSource src = new InputSource(inStream);
- Source source = new SAXSource(src);
- omexManifest = createUnMarshaller().unmarshal(source,
- OmexManifest.class).getValue();
- // omexManifest = (OmexManifest)
- // createUnMarshaller().unmarshal(inStream);
- } catch (JAXBException | ClassCastException e) {
- // logger.warning("Could not parse " + manifestXml);
- throw new IOException("Could not parse " + manifestXml, e);
+ protected static synchronized JAXBContext getJaxbContext()
+ throws JAXBException {
+ if (jaxbContext == null) {
+ jaxbContext = JAXBContext
+ .newInstance(org.identifiers.combine_specifications.omex_manifest.ObjectFactory.class);
}
- if (!manifest.getManifest().contains(manifestXml)) {
- manifest.getManifest().add(manifestXml);
- }
- for (Content c : omexManifest.getContent()) {
- PathMetadata metadata;
- if (c.getLocation().contains(":")) {
- try {
- URI uri = new URI(c.getLocation());
- if (uri.isAbsolute()) {
- metadata = manifest.getAggregation(uri);
- } else {
- logger.warning("Not an absolute URI, but contains :"
- + c.getLocation());
- continue;
- }
- } catch (URISyntaxException e) {
- logger.warning("Invalid URI " + c.getLocation());
- continue;
- }
- } else {
- Path path = bundle.getRoot().resolve(c.getLocation());
- if (Files.exists(path)) {
- metadata = manifest.getAggregation(path);
- } else {
- logger.warning(MANIFEST_XML + " listed relative path "
- + path + ", but it does not exist in bundle");
- continue;
- }
- }
-
- // Format - is it an URI or media type?
- if (c.getFormat().contains(":")) {
- metadata.setConformsTo(URI.create(c.getFormat()));
- } else if (!c.getFormat().isEmpty()) {
- metadata.setMediatype(c.getFormat());
- } else if (metadata.getFile() != null) {
- metadata.setMediatype(manifest.guessMediaType(metadata
- .getFile()));
- } // else: Not needed for URIs
- }
+ return jaxbContext;
}
private static Path manifestXmlPath(Bundle bundle) {
return bundle.getRoot().resolve(MANIFEST_XML);
}
+ private static Resource mboxForAgent(Resource agentResource) {
+ logger.fine("Finding mbox of " + agentResource);
+ String queryStr = sparqlPrefixes + "SELECT ?mbox WHERE { \n"
+ + " { ?agent foaf:mbox ?mbox } \n" + " UNION \n"
+ + " { ?agent vcard:hasEmail ?mbox } \n" + " UNION \n"
+ + " { ?agent vcard:email ?email . \n"
+ + " BIND(IRI(CONCAT(\"mbox:\", ?email)) AS ?mbox) \n" // legacy
+ + " } \n" + "} \n";
+ logger.finer(QueryFactory.create(queryStr).toString());
+ QueryExecution qexec = QueryExecutionFactory.create(queryStr,
+ agentResource.getModel());
+ QuerySolutionMap binding = new QuerySolutionMap();
+ binding.add("agent", agentResource);
+ qexec.setInitialBinding(binding);
+ ResultSet select = qexec.execSelect();
+ if (select.hasNext()) {
+ Resource mbox = select.next().getResource("mbox");
+ logger.fine("Found mbox: " + mbox);
+ return mbox;
+ }
+ logger.fine("mbox not found");
+ return null;
+ }
+
+ private static String nameForAgent(Resource agentResource) {
+ logger.fine("Finding name of " + agentResource);
+ String queryStr = sparqlPrefixes
+ + "SELECT ?name WHERE { \n"
+ + " { ?agent foaf:name ?name } \n"
+ + " UNION \n"
+ + " { ?agent vcard:fn ?name } \n"
+ + " UNION \n"
+ + " { ?agent vcard:FN ?name } \n"
+ + // legacy
+ " UNION \n"
+ + " { ?agent rdfs:label ?name } \n"
+ + " UNION \n"
+ + " { \n"
+ + " { ?agent vcard:n ?n } UNION { ?agent vcard:hasName ?n } \n"
+ + " ?n vcard:family-name ?family ; \n"
+ + " vcard:given-name ?given . \n"
+ + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
+ + " } \n" + " UNION \n" + " { "
+ + " ?agent foaf:givenName ?given ; \n"
+ + " foaf:familyName ?family \n"
+ + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
+ + " } \n" + " UNION \n" + " { "
+ + " ?agent foaf:firstName ?given ; \n"
+ + " foaf:surname ?family \n"
+ + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
+ + " } \n" + " } \n";
+ logger.finer(QueryFactory.create(queryStr).toString());
+ QueryExecution qexec = QueryExecutionFactory.create(queryStr,
+ agentResource.getModel());
+ QuerySolutionMap binding = new QuerySolutionMap();
+ binding.add("agent", agentResource);
+ qexec.setInitialBinding(binding);
+ ResultSet select = qexec.execSelect();
+ if (select.hasNext()) {
+ String name = select.next().getLiteral("name").getString();
+ logger.fine(name);
+ return name;
+ }
+ logger.fine("(null)");
+ return null;
+ }
+
+ private static Model parseRDF(Path metadata) throws IOException {
+ Model model = ModelFactory.createDefaultModel();
+ try (InputStream in = Files.newInputStream(metadata)) {
+ RDFDataMgr.read(model, in, metadata.toUri().toASCIIString(),
+ RDFLanguages.RDFXML);
+ }
+ return model;
+ }
+
protected static void setPrefixMapper(Marshaller marshaller) {
boolean setPrefixMapper = false;
@@ -244,30 +252,45 @@
}
}
- protected static synchronized Marshaller createMarshaller()
- throws JAXBException {
- Marshaller marshaller = getJaxbContext().createMarshaller();
- setPrefixMapper(marshaller);
- return marshaller;
+ public CombineManifest(org.purl.wf4ever.robundle.manifest.Manifest manifest) {
+ this.manifest = manifest;
+ this.bundle = manifest.getBundle();
}
- protected static synchronized Unmarshaller createUnMarshaller()
- throws JAXBException {
- Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
- return unmarshaller;
- }
-
- protected static synchronized JAXBContext getJaxbContext()
- throws JAXBException {
- if (jaxbContext == null) {
- jaxbContext = JAXBContext
- .newInstance(org.identifiers.combine_specifications.omex_manifest.ObjectFactory.class);
+ private Collection<URI> bundleSubjects() throws IOException {
+ Set<URI> subjects = new HashSet<>();
+ subjects.add(bundle.getRoot().toUri());
+ for (PathMetadata pathMetadata : manifest.getAggregates()) {
+ subjects.add(pathMetadata.getUri());
+ if (pathMetadata.getFile() != null) {
+ subjects.add(pathMetadata.getFile().toUri());
+ }
+ if (pathMetadata.getFolder() != null) {
+ subjects.add(pathMetadata.getFolder().toUri());
+ }
+ // subjects.add(pathMetadata.getProxy());
}
- return jaxbContext;
+ for (PathAnnotation a : manifest.getAnnotations()) {
+ subjects.add(a.getUri());
+ }
+ subjects.remove(null);
+ return subjects;
}
- public static boolean containsManifest(Bundle bundle) {
- return Files.isRegularFile(manifestXmlPath(bundle));
+ public Path createManifestXML() throws IOException {
+ OmexManifest omexManifest = makeOmexManifest();
+
+ Path manifestXml = manifestXmlPath(bundle);
+ Files.createDirectories(manifestXml.getParent());
+ try (OutputStream outStream = Files.newOutputStream(manifestXml)) {
+ try {
+ createMarshaller().marshal(omexManifest, outStream);
+ } catch (JAXBException e) {
+ throw new RuntimeException("Could not serialize OMEX Manifest",
+ e);
+ }
+ }
+ return manifestXml;
}
private void findAnnotations() throws IOException {
@@ -385,129 +408,106 @@
}
}
- private static List<RDFNode> creatingAgentsFor(Resource r) {
- logger.fine("Finding creator of " + r);
- String queryStr = sparqlPrefixes + "SELECT ?agent WHERE { \n" + " { \n"
- + " ?r dct:creator [ \n" + " rdfs:member ?agent \n"
- + " ] \n" + " } UNION { \n" + " ?r dct:creator ?agent .\n "
- + " FILTER NOT EXISTS { ?agent rdfs:member ?member } \n"
- + " } \n" + "} \n";
- logger.finer(QueryFactory.create(queryStr).toString());
- QueryExecution qexec = QueryExecutionFactory.create(queryStr,
- r.getModel());
- QuerySolutionMap binding = new QuerySolutionMap();
- binding.add("r", r);
- qexec.setInitialBinding(binding);
- ResultSet select = qexec.execSelect();
- List<RDFNode> agents = new ArrayList<>();
+ private OmexManifest makeOmexManifest() {
+ Path manifestXml = bundle.getRoot().resolve("manifest.xml");
+ OmexManifest omexManifest = objectFactory.createOmexManifest();
- while (select.hasNext()) {
- RDFNode agent = select.next().get("agent");
- logger.fine("Found: " + agent);
- agents.add(agent);
+ PathMetadata aggr = manifest.getAggregation(manifestXml);
+ if (aggr.getConformsTo() == null) {
+ // Add the manifest itself
+ aggr.setConformsTo(URI
+ .create("http://identifiers.org/combine.specifications/omex-manifest"));
}
- return agents;
- }
- private static String nameForAgent(Resource agentResource) {
- logger.fine("Finding name of " + agentResource);
- String queryStr = sparqlPrefixes
- + "SELECT ?name WHERE { \n"
- + " { ?agent foaf:name ?name } \n"
- + " UNION \n"
- + " { ?agent vcard:fn ?name } \n"
- + " UNION \n"
- + " { ?agent vcard:FN ?name } \n"
- + // legacy
- " UNION \n"
- + " { ?agent rdfs:label ?name } \n"
- + " UNION \n"
- + " { \n"
- + " { ?agent vcard:n ?n } UNION { ?agent vcard:hasName ?n } \n"
- + " ?n vcard:family-name ?family ; \n"
- + " vcard:given-name ?given . \n"
- + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
- + " } \n" + " UNION \n" + " { "
- + " ?agent foaf:givenName ?given ; \n"
- + " foaf:familyName ?family \n"
- + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
- + " } \n" + " UNION \n" + " { "
- + " ?agent foaf:firstName ?given ; \n"
- + " foaf:surname ?family \n"
- + " BIND(CONCAT(?given, \" \", ?family) AS ?name) \n"
- + " } \n" + " } \n";
- logger.finer(QueryFactory.create(queryStr).toString());
- QueryExecution qexec = QueryExecutionFactory.create(queryStr,
- agentResource.getModel());
- QuerySolutionMap binding = new QuerySolutionMap();
- binding.add("agent", agentResource);
- qexec.setInitialBinding(binding);
- ResultSet select = qexec.execSelect();
- if (select.hasNext()) {
- String name = select.next().getLiteral("name").getString();
- logger.fine(name);
- return name;
- }
- logger.fine("(null)");
- return null;
- }
+ for (PathMetadata metadata : manifest.getAggregates()) {
+ Content content = objectFactory.createContent();
+ Path file = metadata.getFile();
- private static Resource mboxForAgent(Resource agentResource) {
- logger.fine("Finding mbox of " + agentResource);
- String queryStr = sparqlPrefixes + "SELECT ?mbox WHERE { \n"
- + " { ?agent foaf:mbox ?mbox } \n" + " UNION \n"
- + " { ?agent vcard:hasEmail ?mbox } \n" + " UNION \n"
- + " { ?agent vcard:email ?email . \n"
- + " BIND(IRI(CONCAT(\"mbox:\", ?email)) AS ?mbox) \n" // legacy
- + " } \n" + "} \n";
- logger.finer(QueryFactory.create(queryStr).toString());
- QueryExecution qexec = QueryExecutionFactory.create(queryStr,
- agentResource.getModel());
- QuerySolutionMap binding = new QuerySolutionMap();
- binding.add("agent", agentResource);
- qexec.setInitialBinding(binding);
- ResultSet select = qexec.execSelect();
- if (select.hasNext()) {
- Resource mbox = select.next().getResource("mbox");
- logger.fine("Found mbox: " + mbox);
- return mbox;
- }
- logger.fine("mbox not found");
- return null;
- }
-
- private static final String sparqlPrefixes = "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
- + "PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> \n"
- + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
- + "PREFIX dct: <http://purl.org/dc/terms/> \n";
-
- private Collection<URI> bundleSubjects() throws IOException {
- Set<URI> subjects = new HashSet<>();
- subjects.add(bundle.getRoot().toUri());
- for (PathMetadata pathMetadata : manifest.getAggregates()) {
- subjects.add(pathMetadata.getUri());
- if (pathMetadata.getFile() != null) {
- subjects.add(pathMetadata.getFile().toUri());
+ if (file == null) {
+ content.setLocation(metadata.getUri().toString());
+ } else {
+ Path relPath = metadata.getFile().relativize(bundle.getRoot());
+ content.setLocation("./" + relPath);
}
- if (pathMetadata.getFolder() != null) {
- subjects.add(pathMetadata.getFolder().toUri());
+ if (metadata.getMediatype() != null
+ && !metadata.getMediatype().isEmpty()) {
+ content.setFormat(metadata.getMediatype());
+ } else if (metadata.getConformsTo() != null) {
+ content.setFormat(metadata.getConformsTo().toString());
+ } else {
+ // Binary fallback as 'format' is required attribute
+ content.setFormat("application/octet-stream");
}
- // subjects.add(pathMetadata.getProxy());
+
+ // TODO: Handle 'master' attribute
+
+ omexManifest.getContent().add(content);
+
}
- for (PathAnnotation a : manifest.getAnnotations()) {
- subjects.add(a.getUri());
- }
- subjects.remove(null);
- return subjects;
+ // TODO: Should we add .ro/manifest.json and .ro/* ?
+ return omexManifest;
}
- private static Model parseRDF(Path metadata) throws IOException {
- Model model = ModelFactory.createDefaultModel();
- try (InputStream in = Files.newInputStream(metadata)) {
- RDFDataMgr.read(model, in, metadata.toUri().toASCIIString(),
- RDFLanguages.RDFXML);
+ public void readCombineArchive() throws IOException {
+ readManifestXML();
+ findAnnotations();
+
+ }
+
+ public void readManifestXML() throws IOException {
+ Path manifestXml = manifestXmlPath(bundle);
+ OmexManifest omexManifest;
+ try (InputStream inStream = Files.newInputStream(manifestXml)) {
+ InputSource src = new InputSource(inStream);
+ Source source = new SAXSource(src);
+ omexManifest = createUnMarshaller().unmarshal(source,
+ OmexManifest.class).getValue();
+ // omexManifest = (OmexManifest)
+ // createUnMarshaller().unmarshal(inStream);
+ } catch (JAXBException | ClassCastException e) {
+ // logger.warning("Could not parse " + manifestXml);
+ throw new IOException("Could not parse " + manifestXml, e);
}
- return model;
+ if (!manifest.getManifest().contains(manifestXml)) {
+ manifest.getManifest().add(manifestXml);
+ }
+ for (Content c : omexManifest.getContent()) {
+ PathMetadata metadata;
+ if (c.getLocation().contains(":")) {
+ try {
+ URI uri = new URI(c.getLocation());
+ if (uri.isAbsolute()) {
+ metadata = manifest.getAggregation(uri);
+ } else {
+ logger.warning("Not an absolute URI, but contains :"
+ + c.getLocation());
+ continue;
+ }
+ } catch (URISyntaxException e) {
+ logger.warning("Invalid URI " + c.getLocation());
+ continue;
+ }
+ } else {
+ Path path = bundle.getRoot().resolve(c.getLocation());
+ if (Files.exists(path)) {
+ metadata = manifest.getAggregation(path);
+ } else {
+ logger.warning(MANIFEST_XML + " listed relative path "
+ + path + ", but it does not exist in bundle");
+ continue;
+ }
+ }
+
+ // Format - is it an URI or media type?
+ if (c.getFormat().contains(":")) {
+ metadata.setConformsTo(URI.create(c.getFormat()));
+ } else if (!c.getFormat().isEmpty()) {
+ metadata.setMediatype(c.getFormat());
+ } else if (metadata.getFile() != null) {
+ metadata.setMediatype(manifest.guessMediaType(metadata
+ .getFile()));
+ } // else: Not needed for URIs
+ }
}
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/manifest/odf/ODFManifest.java b/src/main/java/org/purl/wf4ever/robundle/manifest/odf/ODFManifest.java
index e688fa4..adbe3d7 100644
--- a/src/main/java/org/purl/wf4ever/robundle/manifest/odf/ODFManifest.java
+++ b/src/main/java/org/purl/wf4ever/robundle/manifest/odf/ODFManifest.java
@@ -30,6 +30,12 @@
public static class ManifestNamespacePrefixMapperJAXB_RI extends
NamespacePrefixMapper {
@Override
+ public String[] getPreDeclaredNamespaceUris() {
+ // TODO Auto-generated method stub
+ return super.getPreDeclaredNamespaceUris();
+ }
+
+ @Override
public String getPreferredPrefix(String namespaceUri,
String suggestion, boolean requirePrefix) {
if (namespaceUri
@@ -39,12 +45,6 @@
return suggestion;
}
- @Override
- public String[] getPreDeclaredNamespaceUris() {
- // TODO Auto-generated method stub
- return super.getPreDeclaredNamespaceUris();
- }
-
}
private static final String ODF_MANIFEST_VERSION = "1.2";
@@ -55,9 +55,151 @@
.getCanonicalName());
private static JAXBContext jaxbContext;
+ public static boolean containsManifest(Bundle bundle) {
+ return Files.isRegularFile(manifestXmlPath(bundle));
+ }
+ protected static synchronized Marshaller createMarshaller()
+ throws JAXBException {
+ Marshaller marshaller = getJaxbContext().createMarshaller();
+ setPrefixMapper(marshaller);
+ return marshaller;
+ }
+ protected static synchronized Unmarshaller createUnMarshaller()
+ throws JAXBException {
+ Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
+ return unmarshaller;
+ }
+ protected static synchronized JAXBContext getJaxbContext()
+ throws JAXBException {
+ if (jaxbContext == null) {
+ jaxbContext = JAXBContext
+ .newInstance(oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory.class
+ // ,
+ // org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory.class,
+ // org.w3._2000._09.xmldsig_.ObjectFactory.class,
+ // org.w3._2001._04.xmlenc_.ObjectFactory.class
+ );
+ }
+ return jaxbContext;
+ }
+
+ private static Path manifestXmlPath(Bundle bundle) {
+ return bundle.getRoot().resolve(MANIFEST_XML);
+ }
+
+ protected static void setPrefixMapper(Marshaller marshaller) {
+ boolean setPrefixMapper = false;
+
+ try {
+ // This only works with JAXB RI, in which case we can set the
+ // namespace prefix mapper
+ Class.forName("com.sun.xml.bind.marshaller.NamespacePrefixMapper");
+ marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper",
+ new ManifestNamespacePrefixMapperJAXB_RI());
+ // Note: A similar mapper for the built-in java
+ // (com.sun.xml.bind.internal.namespacePrefixMapper)
+ // is no longer included here, as it will not (easily) compile with
+ // Maven.
+ setPrefixMapper = true;
+ } catch (Exception e) {
+ logger.log(Level.FINE, "Can't find NamespacePrefixMapper", e);
+ }
+
+ if (!setPrefixMapper && !warnedPrefixMapper) {
+ logger.info("Could not set prefix mapper (missing or incompatible JAXB) "
+ + "- will use prefixes ns0, ns1, ..");
+ warnedPrefixMapper = true;
+ }
+ }
+
private org.purl.wf4ever.robundle.manifest.Manifest manifest;
+
private Bundle bundle;
+
+ // protected void prepareContainerXML() throws IOException {
+ //
+ //
+ // /* Check if we should prune <rootFiles> */
+ // Iterator<Object> iterator = containerXml.getValue().getRootFilesOrAny()
+ // .iterator();
+ // boolean foundAlready = false;
+ // while (iterator.hasNext()) {
+ // Object anyOrRoot = iterator.next();
+ // if (!(anyOrRoot instanceof JAXBElement)) {
+ // continue;
+ // }
+ // @SuppressWarnings("rawtypes")
+ // JAXBElement elem = (JAXBElement) anyOrRoot;
+ // if (!elem.getDeclaredType().equals(RootFiles.class)) {
+ // continue;
+ // }
+ // RootFiles rootFiles = (RootFiles) elem.getValue();
+ // if (foundAlready
+ // || (rootFiles.getOtherAttributes().isEmpty() && rootFiles
+ // .getAnyOrRootFile().isEmpty())) {
+ // // Delete it!
+ // System.err.println("Deleting unneccessary <rootFiles>");
+ // iterator.remove();
+ // }
+ // foundAlready = true;
+ // }
+ //
+ // Marshaller marshaller;
+ // OutputStream outStream = null;
+ // try {
+ // marshaller = createMarshaller();
+ // // XMLStreamWriter xmlStreamWriter = XMLOutputFactory
+ // // .newInstance().createXMLStreamWriter(outStream);
+ // // xmlStreamWriter.setDefaultNamespace(containerElem.getName()
+ // // .getNamespaceURI());
+ // //
+ // // xmlStreamWriter.setPrefix("dsig",
+ // // "http://www.w3.org/2000/09/xmldsig#");
+ // // xmlStreamWriter.setPrefix("xmlenc",
+ // // "http://www.w3.org/2001/04/xmlenc#");
+ // outStream = odfPackage.insertOutputStream(CONTAINER_XML);
+ //
+ // // FIXME: Set namespace prefixes and default namespace
+ //
+ // marshaller.setProperty("jaxb.formatted.output", true);
+ //
+ // // TODO: Ensure using default namespace
+ // marshaller.marshal(containerXml, outStream);
+ //
+ // } catch (IOException e) {
+ // throw e;
+ // } catch (Exception e) {
+ // throw new IOException("Could not parse " + CONTAINER_XML, e);
+ // } finally {
+ // if (outStream != null) {
+ // outStream.close();
+ // }
+ // }
+ // }
+ //
+ // @SuppressWarnings("unchecked")
+ // protected void parseContainerXML() throws IOException {
+ // createdContainerXml = false;
+ // InputStream containerStream = getResourceAsInputStream(CONTAINER_XML);
+ // if (containerStream == null) {
+ // // Make an empty containerXml
+ // Container container = containerFactory.createContainer();
+ // containerXml = containerFactory.createContainer(container);
+ // createdContainerXml = true;
+ // return;
+ // }
+ // try {
+ // Unmarshaller unMarshaller = createUnMarshaller();
+ // containerXml = (JAXBElement<Container>) unMarshaller
+ // .unmarshal(containerStream);
+ // } catch (JAXBException e) {
+ // throw new IOException("Could not parse " + CONTAINER_XML, e);
+ // }
+ //
+ // }
+
private ObjectFactory manifestFactory = new oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory();
+
private static boolean warnedPrefixMapper;
public ODFManifest(org.purl.wf4ever.robundle.manifest.Manifest manifest) {
@@ -158,146 +300,4 @@
}
}
- private static Path manifestXmlPath(Bundle bundle) {
- return bundle.getRoot().resolve(MANIFEST_XML);
- }
-
- // protected void prepareContainerXML() throws IOException {
- //
- //
- // /* Check if we should prune <rootFiles> */
- // Iterator<Object> iterator = containerXml.getValue().getRootFilesOrAny()
- // .iterator();
- // boolean foundAlready = false;
- // while (iterator.hasNext()) {
- // Object anyOrRoot = iterator.next();
- // if (!(anyOrRoot instanceof JAXBElement)) {
- // continue;
- // }
- // @SuppressWarnings("rawtypes")
- // JAXBElement elem = (JAXBElement) anyOrRoot;
- // if (!elem.getDeclaredType().equals(RootFiles.class)) {
- // continue;
- // }
- // RootFiles rootFiles = (RootFiles) elem.getValue();
- // if (foundAlready
- // || (rootFiles.getOtherAttributes().isEmpty() && rootFiles
- // .getAnyOrRootFile().isEmpty())) {
- // // Delete it!
- // System.err.println("Deleting unneccessary <rootFiles>");
- // iterator.remove();
- // }
- // foundAlready = true;
- // }
- //
- // Marshaller marshaller;
- // OutputStream outStream = null;
- // try {
- // marshaller = createMarshaller();
- // // XMLStreamWriter xmlStreamWriter = XMLOutputFactory
- // // .newInstance().createXMLStreamWriter(outStream);
- // // xmlStreamWriter.setDefaultNamespace(containerElem.getName()
- // // .getNamespaceURI());
- // //
- // // xmlStreamWriter.setPrefix("dsig",
- // // "http://www.w3.org/2000/09/xmldsig#");
- // // xmlStreamWriter.setPrefix("xmlenc",
- // // "http://www.w3.org/2001/04/xmlenc#");
- // outStream = odfPackage.insertOutputStream(CONTAINER_XML);
- //
- // // FIXME: Set namespace prefixes and default namespace
- //
- // marshaller.setProperty("jaxb.formatted.output", true);
- //
- // // TODO: Ensure using default namespace
- // marshaller.marshal(containerXml, outStream);
- //
- // } catch (IOException e) {
- // throw e;
- // } catch (Exception e) {
- // throw new IOException("Could not parse " + CONTAINER_XML, e);
- // } finally {
- // if (outStream != null) {
- // outStream.close();
- // }
- // }
- // }
- //
- // @SuppressWarnings("unchecked")
- // protected void parseContainerXML() throws IOException {
- // createdContainerXml = false;
- // InputStream containerStream = getResourceAsInputStream(CONTAINER_XML);
- // if (containerStream == null) {
- // // Make an empty containerXml
- // Container container = containerFactory.createContainer();
- // containerXml = containerFactory.createContainer(container);
- // createdContainerXml = true;
- // return;
- // }
- // try {
- // Unmarshaller unMarshaller = createUnMarshaller();
- // containerXml = (JAXBElement<Container>) unMarshaller
- // .unmarshal(containerStream);
- // } catch (JAXBException e) {
- // throw new IOException("Could not parse " + CONTAINER_XML, e);
- // }
- //
- // }
-
- protected static void setPrefixMapper(Marshaller marshaller) {
- boolean setPrefixMapper = false;
-
- try {
- // This only works with JAXB RI, in which case we can set the
- // namespace prefix mapper
- Class.forName("com.sun.xml.bind.marshaller.NamespacePrefixMapper");
- marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper",
- new ManifestNamespacePrefixMapperJAXB_RI());
- // Note: A similar mapper for the built-in java
- // (com.sun.xml.bind.internal.namespacePrefixMapper)
- // is no longer included here, as it will not (easily) compile with
- // Maven.
- setPrefixMapper = true;
- } catch (Exception e) {
- logger.log(Level.FINE, "Can't find NamespacePrefixMapper", e);
- }
-
- if (!setPrefixMapper && !warnedPrefixMapper) {
- logger.info("Could not set prefix mapper (missing or incompatible JAXB) "
- + "- will use prefixes ns0, ns1, ..");
- warnedPrefixMapper = true;
- }
- }
-
- protected static synchronized Marshaller createMarshaller()
- throws JAXBException {
- Marshaller marshaller = getJaxbContext().createMarshaller();
- setPrefixMapper(marshaller);
- return marshaller;
- }
-
- protected static synchronized Unmarshaller createUnMarshaller()
- throws JAXBException {
- Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
- return unmarshaller;
- }
-
- protected static synchronized JAXBContext getJaxbContext()
- throws JAXBException {
- if (jaxbContext == null) {
- jaxbContext = JAXBContext
- .newInstance(oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory.class
- // ,
- // org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory.class,
- // org.w3._2000._09.xmldsig_.ObjectFactory.class,
- // org.w3._2001._04.xmlenc_.ObjectFactory.class
- );
- }
- return jaxbContext;
- }
-
- public static boolean containsManifest(Bundle bundle) {
- return Files.isRegularFile(manifestXmlPath(bundle));
- }
-
}
diff --git a/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveCopyFileVisitor.java b/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveCopyFileVisitor.java
index c05451a..5489e04 100644
--- a/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveCopyFileVisitor.java
+++ b/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveCopyFileVisitor.java
@@ -22,6 +22,15 @@
public class RecursiveCopyFileVisitor extends SimpleFileVisitor<Path> {
+ public enum RecursiveCopyOption implements CopyOption {
+ /**
+ * Ignore any errors, copy as much as possible. The default is to stop
+ * on the first IOException.
+ *
+ */
+ IGNORE_ERRORS,
+ }
+
public static void copyRecursively(final Path source,
final Path destination, final CopyOption... copyOptions)
throws IOException {
@@ -52,15 +61,6 @@
Files.walkFileTree(source, walkOptions, Integer.MAX_VALUE, visitor);
}
- public enum RecursiveCopyOption implements CopyOption {
- /**
- * Ignore any errors, copy as much as possible. The default is to stop
- * on the first IOException.
- *
- */
- IGNORE_ERRORS,
- }
-
private final CopyOption[] copyOptions;
private final Set<CopyOption> copyOptionsSet;
private final Path destination;
@@ -94,6 +94,36 @@
.size())]);
}
+ private URI pathOnly(URI uri) {
+ if (!uri.isAbsolute()) {
+ return uri;
+ }
+ String path = uri.getRawPath();
+ // if (! uri.isOpaque()) {
+ // path = uri.getPath();
+ // }
+ if (uri.getScheme().equals("jar")) {
+ String part = uri.getSchemeSpecificPart();
+ int slashPos = part.indexOf("!/");
+ path = part.substring(slashPos + 1, part.length());
+ }
+ if (path == null) {
+ throw new IllegalArgumentException("Can't extract path from URI "
+ + uri);
+ }
+
+ if (!path.startsWith("/")) {
+ path = "/" + path;
+ }
+ try {
+ return new URI(null, null, path, null);
+ } catch (URISyntaxException e) {
+ throw new IllegalArgumentException("Can't extract path from URI "
+ + uri, e);
+ }
+
+ }
+
@Override
public FileVisitResult postVisitDirectory(Path dir, IOException exc)
throws IOException {
@@ -155,36 +185,6 @@
return destination.getFileSystem().provider().getPath(dest);
}
- private URI pathOnly(URI uri) {
- if (!uri.isAbsolute()) {
- return uri;
- }
- String path = uri.getRawPath();
- // if (! uri.isOpaque()) {
- // path = uri.getPath();
- // }
- if (uri.getScheme().equals("jar")) {
- String part = uri.getSchemeSpecificPart();
- int slashPos = part.indexOf("!/");
- path = part.substring(slashPos + 1, part.length());
- }
- if (path == null) {
- throw new IllegalArgumentException("Can't extract path from URI "
- + uri);
- }
-
- if (!path.startsWith("/")) {
- path = "/" + path;
- }
- try {
- return new URI(null, null, path, null);
- } catch (URISyntaxException e) {
- throw new IllegalArgumentException("Can't extract path from URI "
- + uri, e);
- }
-
- }
-
private URI uriWithSlash(Path dir) {
URI uri = dir.toUri();
if (!uri.toString().endsWith("/")) {
diff --git a/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveDeleteVisitor.java b/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveDeleteVisitor.java
index b13d5fb..fe9a3fe 100644
--- a/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveDeleteVisitor.java
+++ b/src/main/java/org/purl/wf4ever/robundle/utils/RecursiveDeleteVisitor.java
@@ -8,6 +8,14 @@
import java.nio.file.attribute.BasicFileAttributes;
public class RecursiveDeleteVisitor extends SimpleFileVisitor<Path> {
+ public static void deleteRecursively(Path p) throws IOException {
+ if (Files.isDirectory(p)) {
+ Files.walkFileTree(p, new RecursiveDeleteVisitor());
+ } else {
+ Files.delete(p);
+ }
+ }
+
@Override
public FileVisitResult postVisitDirectory(Path dir, IOException exc)
throws IOException {
@@ -22,12 +30,4 @@
Files.delete(file);
return FileVisitResult.CONTINUE;
}
-
- public static void deleteRecursively(Path p) throws IOException {
- if (Files.isDirectory(p)) {
- Files.walkFileTree(p, new RecursiveDeleteVisitor());
- } else {
- Files.delete(p);
- }
- }
}
\ No newline at end of file
