Merge branch 'rels-ingest-update'

src/main/java/org/purl/sword/server/fedora/fileHandlers/METSContainer.java

@@ -0,0 +1,277 @@
+/*
+ * Copyright 2015 Saxon State and University Library Dresden (SLUB)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.purl.sword.server.fedora.fileHandlers;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+import org.purl.sword.base.SWORDException;
+import org.purl.sword.server.fedora.fedoraObjects.*;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.security.DigestInputStream;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.LinkedList;
+import java.util.List;
+
+import static org.purl.sword.server.fedora.fedoraObjects.State.INACTIVE;
+
+public class METSContainer {
+
+    private static final String DS_ID_SLUBINFO = "SLUB-INFO";
+    private static final String DS_ID_SLUBINFO_LABEL = "SLUB Administrative Metadata";
+
+    private static final String DS_ID_QUCOSAXML = "QUCOSA-XML";
+    private static final String DS_ID_QUCOSAXML_LABEL = "Pristine Qucosa XML Metadata";
+
+    private static final String DS_MODS_MIME_TYPE = "application/mods+xml";
+    private static final String DS_ID_MODS = "MODS";
+    private static final String DS_ID_MODS_LABEL = "Object Bibliographic Metadata";
+
+    private static final String METS_DMDSEC_PREFIX = "/mets:mets/mets:dmdSec";
+    private static final String MODS_PREFIX = METS_DMDSEC_PREFIX + "/mets:mdWrap[@MDTYPE='MODS']/mets:xmlData/mods:mods";
+
+    private final XPathQuery XPATH_FILES = new XPathQuery("/mets:mets/mets:fileSec/mets:fileGrp[@USE='ORIGINAL']/mets:file");
+    private final XPathQuery XPATH_IDENTIFIERS = new XPathQuery(MODS_PREFIX + "/mods:identifier");
+    private final XPathQuery XPATH_MODS = new XPathQuery(MODS_PREFIX);
+    private final XPathQuery XPATH_QUCOSA = new XPathQuery(METS_DMDSEC_PREFIX + "/mets:mdWrap[@MDTYPE='OTHER' and @OTHERMDTYPE='QUCOSA-XML']/mets:xmlData/Opus");
+    private final XPathQuery XPATH_RELATEDITEMS = new XPathQuery(MODS_PREFIX + "/mods:relatedItem");
+    private final XPathQuery XPATH_SLUB = new XPathQuery("/mets:mets/mets:amdSec/mets:rightsMD" + "/mets:mdWrap[@MDTYPE='OTHER' and @OTHERMDTYPE='SLUBRIGHTS']/mets:xmlData/slub:info");
+    private final XPathQuery XPATH_TITLE = new XPathQuery(MODS_PREFIX + "/mods:titleInfo/mods:title[1]");
+    private final String md5;
+    private final Document metsDocument;
+
+    public METSContainer(InputStream in) throws NoSuchAlgorithmException, JDOMException, IOException {
+        DigestInputStream din = new DigestInputStream(in, MessageDigest.getInstance("MD5"));
+        metsDocument = new SAXBuilder().build(din);
+        md5 = digestToString(din.getMessageDigest());
+    }
+
+    public String getMd5() {
+        return md5;
+    }
+
+    public Datastream getModsDatastream() {
+        try {
+            return getDatastream(XPATH_MODS, DS_ID_MODS, DS_ID_MODS_LABEL, DS_MODS_MIME_TYPE);
+        } catch (SWORDException e) {
+            return null;
+        }
+    }
+
+    public Datastream getSlubInfoDatastream() {
+        try {
+            return getDatastream(XPATH_SLUB, DS_ID_SLUBINFO, DS_ID_SLUBINFO_LABEL);
+        } catch (SWORDException e) {
+            return null;
+        }
+    }
+
+    public Datastream getQucosaXmlDatastream() {
+        try {
+            final Datastream datastream = getDatastream(XPATH_QUCOSA, DS_ID_QUCOSAXML, DS_ID_QUCOSAXML_LABEL);
+            if (datastream != null) {
+                datastream.setState(INACTIVE);
+            }
+            return datastream;
+        } catch (SWORDException e) {
+            return null;
+        }
+    }
+
+    public List<Datastream> getDatastreams() throws SWORDException {
+        LinkedList<Datastream> resultList = new LinkedList<>();
+        addIfNotNull(resultList, getSlubInfoDatastream());
+        addIfNotNull(resultList, getQucosaXmlDatastream());
+        addIfNotNull(resultList, getModsDatastream());
+        addIfNotNull(resultList, getFileDatastreams());
+        return resultList;
+    }
+
+    public DublinCore getDublinCore() {
+        DublinCore dc = new DublinCore();
+        addIfNotNull(dc.getTitle(), getPrimaryTitle());
+        addIfNotNull(dc.getIdentifier(), getIdentifiers());
+        return dc;
+    }
+
+
+    public List<Datastream> getFileDatastreams() throws SWORDException {
+        List<Datastream> datastreamList = new LinkedList<>();
+        try {
+            final List<Element> fileElements = XPATH_FILES.selectNodes(metsDocument);
+            for (Element e : fileElements) {
+                final String id = validateAndReturn("file ID", e.getAttributeValue("ID"));
+
+                if (isADeleteRequest(e)) {
+                    datastreamList.add(new VoidDatastream(id));
+                } else {
+                    final Element fLocat = validateAndReturn("FLocat element", e.getChild("FLocat", Namespaces.METS));
+                    final String href = validateAndReturn("file content URL", fLocat.getAttributeValue("href", Namespaces.XLINK));
+                    final URI uri = new URI(href);
+                    final boolean isFile = uri.getScheme().equals("file");
+                    final String mimetype = validateAndReturn("mime type", e.getAttributeValue("MIMETYPE"));
+
+                    Datastream ds = buildDatastream(id, fLocat, href, mimetype, isFile);
+
+                    String digestType = emptyIfNull(e.getAttributeValue("CHECKSUMTYPE"));
+                    String digest = emptyIfNull(e.getAttributeValue("CHECKSUM"));
+                    if (!(digestType.isEmpty() || digest.isEmpty())) {
+                        ds.setDigestType(digestType);
+                        ds.setDigest(digest);
+                    }
+
+                    datastreamList.add(ds);
+                }
+            }
+
+        } catch (JDOMException e) {
+            throw new SWORDException("Cannot obtain file datastreams", e);
+        } catch (URISyntaxException e) {
+            throw new SWORDException("Invalid URL", e);
+        }
+        return datastreamList;
+    }
+
+    public List<File> getTemporayFiles() throws SWORDException {
+        final List<File> filesMarkedForRemoval = new LinkedList<>();
+        final List<Element> fileElements;
+        try {
+            fileElements = XPATH_FILES.selectNodes(metsDocument);
+            for (Element e : fileElements) {
+                if (!isADeleteRequest(e)) {
+                    final Element fLocat = validateAndReturn("FLocat element", e.getChild("FLocat", Namespaces.METS));
+                    final String href = validateAndReturn("file content URL", fLocat.getAttributeValue("href", Namespaces.XLINK));
+                    final URI uri = new URI(href);
+                    final boolean isFile = uri.getScheme().equals("file");
+                    final boolean isTemporary = emptyIfNull(fLocat.getAttributeValue("USE")).equals("TEMPORARY");
+                    if (isFile && isTemporary) {
+                        filesMarkedForRemoval.add(new File(uri));
+                    }
+                }
+            }
+        } catch (JDOMException e) {
+            throw new SWORDException("Cannot obtain file datastreams", e);
+        } catch (URISyntaxException ex) {
+            throw new SWORDException("Invalid URL", ex);
+        }
+        return filesMarkedForRemoval;
+    }
+
+    public List<Element> getModsRelatedItems() {
+        try {
+            return XPATH_RELATEDITEMS.selectNodes(metsDocument);
+        } catch (JDOMException e) {
+            return null;
+        }
+    }
+
+    private String getPrimaryTitle() {
+        try {
+            return XPATH_TITLE.selectValue(metsDocument);
+        } catch (JDOMException e) {
+            return null;
+        }
+    }
+
+    private List<String> getIdentifiers() {
+        try {
+            return XPATH_IDENTIFIERS.selectValues(metsDocument);
+        } catch (JDOMException e) {
+            return null;
+        }
+    }
+
+    private Datastream getDatastream(XPathQuery query, String datastreamID, String datastreamLabel) throws SWORDException {
+        return getDatastream(query, datastreamID, datastreamLabel, null);
+    }
+
+    private Datastream getDatastream(XPathQuery query, String datastreamID, String datastreamLabel, String overrideMimetype)
+            throws SWORDException {
+        Datastream result = null;
+        try {
+            Element el = query.selectNode(metsDocument);
+            if (el != null) {
+                Document d = new Document((Element) el.clone());
+                result = new XMLInlineDatastream(datastreamID, d);
+                result.setLabel(datastreamLabel);
+                if (overrideMimetype != null) {
+                    result.setMimeType(overrideMimetype);
+                } else {
+                    result.setMimeType(el.getParentElement().getParentElement().getAttributeValue("MIMETYPE"));
+                }
+                String versioning = System.getProperty("datastream.versioning", "false");
+                result.setVersionable(Boolean.parseBoolean(versioning));
+            }
+        } catch (JDOMException e) {
+            throw new SWORDException("Cannot obtain datastream: " + datastreamID, e);
+        }
+        return result;
+    }
+
+    private String digestToString(MessageDigest digest) {
+        StringBuilder sb = new StringBuilder();
+        for (byte b : digest.digest()) {
+            sb.append(String.format("%02x", b));
+        }
+        return sb.toString();
+    }
+
+    private <E> E validateAndReturn(String description, E value) throws SWORDException {
+        if (value != null) {
+            return value;
+        } else {
+            throw new SWORDException("Cannot obtain " + description);
+        }
+    }
+
+    private boolean isADeleteRequest(Element e) {
+        return e.getAttributeValue("USE") != null && e.getAttributeValue("USE").equals("DELETE");
+    }
+
+    private String emptyIfNull(String s) {
+        return (s == null) ? "" : s;
+    }
+
+    private Datastream buildDatastream(String id, Element fLocat, String href, String mimetype, boolean isFile) {
+        Datastream datastream;
+        if (isFile) {
+            LocalDatastream lds = new LocalDatastream(id, mimetype, href);
+            lds.setCleanup(false); // no automatic cleanup
+            datastream = lds;
+        } else {
+            datastream = new ManagedDatastream(id, mimetype, href);
+        }
+        datastream.setLabel(fLocat.getAttributeValue("title", Namespaces.XLINK));
+        return datastream;
+    }
+
+    private <E> void addIfNotNull(List<E> list, E e) {
+        if (e != null) list.add(e);
+    }
+
+    private <E> void addIfNotNull(List<E> list, List<E> es) {
+        if (es != null) list.addAll(es);
+    }
+
+}

src/main/java/org/purl/sword/server/fedora/fileHandlers/Namespaces.java

@@ -0,0 +1,31 @@
+/*
+ * Copyright 2015 Saxon State and University Library Dresden (SLUB)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.purl.sword.server.fedora.fileHandlers;
+
+import org.jdom.Namespace;
+
+public final class Namespaces {
+
+    public static final Namespace METS = Namespace.getNamespace("mets", "http://www.loc.gov/METS/");
+    public static final Namespace SLUB = Namespace.getNamespace("slub", "http://slub-dresden.de/");
+    public static final Namespace XLINK = Namespace.getNamespace("xlink", "http://www.w3.org/1999/xlink");
+    public static final Namespace MODS = Namespace.getNamespace("mods", "http://www.loc.gov/mods/v3");
+
+    private Namespaces() {
+    }
+
+}