merge 2023.06.x into 2024.06.x

mycore-base/src/main/java/org/mycore/common/content/MCRContent.java

@@ -33,11 +33,18 @@
 import java.nio.channels.ReadableByteChannel;
 import java.nio.file.AtomicMoveNotSupportedException;
 import java.nio.file.CopyOption;
+import java.nio.file.FileStore;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
 import java.nio.file.StandardOpenOption;
+import java.nio.file.attribute.AclEntry;
+import java.nio.file.attribute.AclFileAttributeView;
+import java.nio.file.attribute.PosixFileAttributeView;
+import java.nio.file.attribute.PosixFilePermission;
 import java.util.Base64;
+import java.util.List;
+import java.util.Set;
 
 import javax.xml.transform.Source;
 
@@ -245,7 +252,33 @@ public void sendSafelyTo(Path target) throws IOException {
         if (!Files.isWritable(dir)) {
             throw new IOException("Target directory is not writable: " + dir);
         }
+
+        // store current permissions of target file
+        // usually: ACLs for Windows and POSIX permissions for UNIX
+        List<AclEntry> aclEntries = null;
+        Set<PosixFilePermission> posixPermissions = null;
+        FileStore fileStore = Files.getFileStore(target);
+        if (fileStore.supportsFileAttributeView(AclFileAttributeView.class)) {
+            aclEntries = Files.getFileAttributeView(target, AclFileAttributeView.class).getAcl();
+        }
+        if (fileStore.supportsFileAttributeView(PosixFileAttributeView.class)) {
+            posixPermissions = Files.getPosixFilePermissions(target);
+        }
+        if (LOGGER.isWarnEnabled() && (aclEntries == null && posixPermissions == null)) {
+            LOGGER.warn("No supported file permissions (ACLs, POSIX) were found when recrating {} with new content;"
+                + " new version of file will have default file permissions", target::toAbsolutePath);
+        }
+
         Path tmp = Files.createTempFile(dir, target.getFileName().toString(), ".tmp");
+
+        // apply stored permissions to tmp file; will be preserved during the move operation below
+        if (aclEntries != null) {
+            Files.getFileAttributeView(tmp, AclFileAttributeView.class).setAcl(aclEntries);
+        }
+        if (posixPermissions != null) {
+            Files.setPosixFilePermissions(tmp, posixPermissions);
+        }
+
         try {
             final int chunkSize = 128 * 1024;
             try (InputStream in = getInputStream();
@@ -272,6 +305,7 @@ public void sendSafelyTo(Path target) throws IOException {
                 LOGGER.error("Failed to delete temporary file at {}", tmp, e);
             }
         }
+
     }
 
     /**

mycore-orcid2/src/main/java/org/mycore/orcid2/v3/work/MCRORCIDWorkEventHandlerImpl.java

@@ -18,6 +18,7 @@
 
 package org.mycore.orcid2.v3.work;
 
+import java.util.List;
 import java.util.Set;
 
 import org.mycore.common.content.MCRJDOMContent;
@@ -73,4 +74,12 @@ protected Set<String> findMatchingORCIDs(Set<MCRIdentifier> identifiers) {
     protected Work transformObject(MCRJDOMContent object) {
         return MCRORCIDWorkTransformerHelper.transformContent(object);
     }
+
+    @Override
+    protected List<String> listRelatedOrcidIdentifiers(Work work) {
+        return work.getWorkContributors().getContributor().stream().filter(c -> c.getContributorOrcid() != null)
+            .filter(c -> c.getContributorAttributes() != null)
+            .filter(c -> c.getContributorAttributes().getContributorRole() != null)
+            .map(c -> c.getContributorOrcid().getPath()).toList();
+    }
 }

mycore-orcid2/src/main/java/org/mycore/orcid2/work/MCRORCIDWorkEventHandler.java

@@ -148,13 +148,14 @@ private void handlePublication(MCRObject object) {
         final Map<String, MCRORCIDUser> toPublish = new HashMap<>(userOrcidPairFromFlag);
         toPublish.putAll(userOrcidPairFromObject);
         toPublish.keySet().removeAll(toDelete.keySet());
+        final T work = transformObject(new MCRJDOMContent(filteredObject.createXML()));
+        toPublish.keySet().removeAll(listRelatedOrcidIdentifiers(work));
         if (toDelete.isEmpty() && toPublish.isEmpty()) {
             LOGGER.info("Nothing to delete or publish. Skipping {}...", objectID);
             tryCollectAndSaveExternalPutCodes(filteredObject);
             return;
         }
         try {
-            final T work = transformObject(new MCRJDOMContent(filteredObject.createXML()));
             final Set<MCRIdentifier> identifiers = listTrustedIdentifiers(work);
             if (!toDelete.isEmpty()) {
                 deleteWorks(toDelete, identifiers, flagContent);
@@ -376,15 +377,15 @@ private List<MCRIdentifier> listTrustedNameIdentifiers(Element nameElement) {
 
     /**
      * Lists trusted identifiers as Set of MCRIdentifier.
-     * 
+     *
      * @param work the Work
      * @return Set of MCRIdentifier
      */
     abstract protected Set<MCRIdentifier> listTrustedIdentifiers(T work);
 
     /**
      * Lists matching ORCID iDs based on search via MCRIdentifier
-     * 
+     *
      * @param identifiers the MCRIdentifiers
      * @return Set of ORCID iDs as String
      * @throws MCRORCIDException if request fails
@@ -393,7 +394,7 @@ private List<MCRIdentifier> listTrustedNameIdentifiers(Element nameElement) {
 
     /**
      * Removes Work in ORCID profile and updates MCRORCIDPutCodeInfo.
-     * 
+     *
      * @param workInfo the MCRORCIDPutCodeInfo
      * @param orcid the ORCID iD
      * @param credential the MCRORCIDCredential
@@ -405,7 +406,7 @@ private List<MCRIdentifier> listTrustedNameIdentifiers(Element nameElement) {
 
     /**
      * Updates Work in ORCID profile.
-     * 
+     *
      * @param putCode the put code
      * @param work the Work
      * @param orcid the ORCID iD
@@ -418,7 +419,7 @@ private List<MCRIdentifier> listTrustedNameIdentifiers(Element nameElement) {
 
     /**
      * Creates Work in ORCID profile and updates MCRORCIDPutCodeInfo.
-     * 
+     *
      * @param work the Work
      * @param workInfo the MCRORCIDPutCodeInfo
      * @param orcid the ORCID iD
@@ -431,7 +432,7 @@ abstract protected void createWork(T work, MCRORCIDPutCodeInfo workInfo, String
 
     /**
      * Updates work info based on MCRIdentifier.
-     * 
+     *
      * @param identifiers the MCRIdentifier
      * @param workInfo the MCRORCIDPutCodeInfo
      * @param orcid the ORCID iD
@@ -443,7 +444,7 @@ abstract protected void updateWorkInfo(Set<MCRIdentifier> identifiers, MCRORCIDP
 
     /**
      * Updates work info based on MCRIdentifier.
-     * 
+     *
      * @param identifiers the MCRIdentifier
      * @param workInfo the MCRORCIDPutCodeInfo
      * @param orcid the ORCID iD
@@ -453,10 +454,18 @@ abstract protected void updateWorkInfo(Set<MCRIdentifier> identifiers, MCRORCIDP
 
     /**
      * Transforms MCRObject as MCRJDOMContent to Work.
-     * 
+     *
      * @param object the MCRObject
      * @return the Work
      */
     @SuppressWarnings("TypeParameterUnusedInFormals")
     abstract protected <T> T transformObject(MCRJDOMContent object);
+
+    /**
+     * Returns all ORCID iDs of related persons for work.
+     *
+     * @param work the work
+     * @return list over ORCID iD elements
+     */
+    abstract protected List<String> listRelatedOrcidIdentifiers(T work);
 }

mycore-pi/src/main/java/org/mycore/pi/urn/MCRURNUtils.java

@@ -19,9 +19,8 @@
 package org.mycore.pi.urn;
 
 import java.text.ParseException;
-import java.text.SimpleDateFormat;
+import java.time.Instant;
 import java.util.Date;
-import java.util.Locale;
 import java.util.Optional;
 
 import org.apache.logging.log4j.LogManager;
@@ -53,11 +52,14 @@ public static Date getDNBRegisterDate(String identifier) throws ParseException {
             .map(JsonElement::getAsString)
             .orElse(null);
 
+        return parseDNBRegisterDate(date);
+    }
+
+    static Date parseDNBRegisterDate(String date) {
         if (date == null) {
             return null;
         }
-
-        return new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSXXX", Locale.GERMAN).parse(date);
+        return Date.from(Instant.parse(date));
     }
 
 }

mycore-pi/src/test/java/org/mycore/pi/urn/MCRURNUtilsTest.java

@@ -0,0 +1,59 @@
+/*
+ * This file is part of ***  M y C o R e  ***
+ * See http://www.mycore.de/ for details.
+ *
+ * MyCoRe is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * MyCoRe is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with MyCoRe.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.mycore.pi.urn;
+
+import java.time.Instant;
+import java.time.format.DateTimeParseException;
+import java.util.Date;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class MCRURNUtilsTest {
+
+    private static final String[] VALID_DATES = {
+        "2025-11-07T15:00:21.000Z",
+        "2025-11-07T15:00:21Z",
+        "2025-11-07T15:00:21.1Z",
+        "2025-11-07T15:00:21-12:00",
+        "2025-11-07T15:00:21+01:00",
+        "2025-11-07T15:00:21.123456Z",
+    };
+
+    @Test
+    public void parseValidDates() {
+        for (String date : VALID_DATES) {
+            Date result = MCRURNUtils.parseDNBRegisterDate(date);
+            Assert.assertNotNull("should parse: " + date, result);
+            Assert.assertEquals("parsed date should match Instant.parse for: " + date,
+                Date.from(Instant.parse(date)), result);
+        }
+    }
+
+    @Test
+    public void parseNullReturnsNull() {
+        Assert.assertNull(MCRURNUtils.parseDNBRegisterDate(null));
+    }
+
+    @Test(expected = DateTimeParseException.class)
+    public void parseInvalidThrows() {
+        MCRURNUtils.parseDNBRegisterDate("invalidDate");
+    }
+
+}

mycore-user2/src/main/resources/xsl/users-subselect.xsl

@@ -21,6 +21,7 @@
   </xsl:variable>
 
   <xsl:template match="/users" mode="searchFormAdditional" priority="10">
+    <input type="hidden" name="XSL.Style" value="subselect" />
     <input type="hidden" name="_xed_subselect_session" value="{$xedSession}" />
   </xsl:template>
 

mycore-user2/src/main/resources/xslt/users-subselect.xsl

@@ -15,6 +15,7 @@
   <xsl:variable name="xedSession" select="mcrurl:get-param($RequestURL, '_xed_subselect_session')" />
 
   <xsl:template match="/users" mode="searchFormAdditional" priority="10">
+    <input type="hidden" name="XSL.Style" value="subselect" />
     <input type="hidden" name="_xed_subselect_session" value="{$xedSession}" />
   </xsl:template>