Merge pull request #1136 from ufal/dataquest/dtq-dev

merging dataquest-dev/dtq dev
ufal · Nov 21, 2024 · 79fb64d · 79fb64d
2 parents 0dcd935 + 1bd8967
commit 79fb64d
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Showing 50 changed files with 10,129 additions and 389 deletions.
diff --git a/dspace-api/src/main/java/org/dspace/app/util/DCInput.java b/dspace-api/src/main/java/org/dspace/app/util/DCInput.java
@@ -164,6 +164,11 @@ public class DCInput {
      */
     private ComplexDefinition complexDefinition = null;
 
+    /**
+     * give suggestions from this specific autocomplete solr index/file
+     */
+    private String autocompleteCustom = null;
+
     /**
      * the dropdown input type could have defined a default value
      */
@@ -235,6 +240,9 @@ public DCInput(Map<String, String> fieldMap, Map<String, List<String>> listMap,
         if ("complex".equals(inputType)) {
             complexDefinition = complexDefinitions.getByName((fieldMap.get(DCInputsReader.COMPLEX_DEFINITION_REF)));
         }
+        if ("autocomplete".equals(inputType)) {
+            autocompleteCustom = fieldMap.get(DCInputsReader.AUTOCOMPLETE_CUSTOM);
+        }
         hint = fieldMap.get("hint");
         warning = fieldMap.get("required");
         required = warning != null && warning.length() > 0;
@@ -725,6 +733,14 @@ public boolean isMetadataField() {
         return isMetadataField;
     }
 
+    public String getAutocompleteCustom() {
+        return autocompleteCustom;
+    }
+
+    public void setAutocompleteCustom(String autocompleteCustom) {
+        this.autocompleteCustom = autocompleteCustom;
+    }
+
     /**
      * Class representing a Map of the ComplexDefinition object
      * Class is copied from UFAL/CLARIN-DSPACE (https://github.com/ufal/clarin-dspace) and modified by

diff --git a/dspace-api/src/main/java/org/dspace/app/util/DCInputsReader.java b/dspace-api/src/main/java/org/dspace/app/util/DCInputsReader.java
@@ -76,6 +76,11 @@ public class DCInputsReader {
     static final String COMPLEX_DEFINITION_REF = "complex-definition-ref";
     public static final String TYPE_BIND_FIELD_ATTRIBUTE = "field";
 
+    /**
+     * Keyname for storing the name of the custom autocomplete input type
+     */
+    static final String AUTOCOMPLETE_CUSTOM = "autocomplete-custom";
+
 
     /**
      * Reference to the forms definitions map, computed from the forms
@@ -552,6 +557,11 @@ private void handleInputTypeTagName(String formName, Map<String, String> field,
             } else {
                 field.put(COMPLEX_DEFINITION_REF, definitionName);
             }
+        } else if (value.equals("autocomplete")) {
+            String definitionName = getAttribute(nd, AUTOCOMPLETE_CUSTOM);
+            if (definitionName != null) {
+                field.put(AUTOCOMPLETE_CUSTOM, definitionName);
+            }
         }
     }
 

diff --git a/dspace-api/src/main/java/org/dspace/authenticate/clarin/ClarinShibAuthentication.java b/dspace-api/src/main/java/org/dspace/authenticate/clarin/ClarinShibAuthentication.java
@@ -238,17 +238,25 @@ public int authenticate(Context context, String username, String password,
 
         // The user e-mail is not stored in the `shibheaders` but in the `clarinVerificationToken`.
         // The email was added to the `clarinVerificationToken` in the ClarinShibbolethFilter.
-        String netidHeader = configurationService.getProperty("authentication-shibboleth.netid-header");
-        clarinVerificationToken = clarinVerificationTokenService.findByNetID(context,
-                shibheaders.get_single(netidHeader));
+        String[] netidHeaders = configurationService.getArrayProperty("authentication-shibboleth.netid-header");
+
+        // Load the verification token from the request header or from the request parameter.
+        // This is only set if the user is trying to authenticate with the `verification-token`.
+        String VERIFICATION_TOKEN = "verification-token";
+        String verificationTokenFromRequest = StringUtils.defaultIfBlank(request.getHeader(VERIFICATION_TOKEN),
+                        request.getParameter(VERIFICATION_TOKEN));
+        if (StringUtils.isNotEmpty(verificationTokenFromRequest)) {
+            log.info("Verification token from request header `{}`: {}", VERIFICATION_TOKEN,
+                    verificationTokenFromRequest);
+            clarinVerificationToken = clarinVerificationTokenService.findByToken(context, verificationTokenFromRequest);
+        }
         // CLARIN
 
         // Initialize the additional EPerson metadata.
         initialize(context);
 
         // Should we auto register new users.
         boolean autoRegister = configurationService.getBooleanProperty("authentication-shibboleth.autoregister", true);
-        String[] netidHeaders = configurationService.getArrayProperty("authentication-shibboleth.netid-header");
 
         // Four steps to authenticate a user
         try {

diff --git a/dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java b/dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java
@@ -73,6 +73,9 @@ public class WorkspaceItem
     @Column(name = "page_reached")
     private Integer pageReached = -1;
 
+    @Column(name = "share_token")
+    private String shareToken = null;
+
     /**
      * Protected constructor, create object using:
      * {@link org.dspace.content.service.WorkspaceItemService#create(Context, Collection, boolean)}
@@ -131,6 +134,14 @@ public void setPageReached(int v) {
         pageReached = v;
     }
 
+    public String getShareToken() {
+        return shareToken;
+    }
+
+    public void setShareToken(String shareToken) {
+        this.shareToken = shareToken;
+    }
+
     /**
      * Decide if this WorkspaceItem is equal to another
      *

diff --git a/dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java b/dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java
@@ -243,6 +243,11 @@ public WorkspaceItem findByItem(Context context, Item item) throws SQLException
         return workspaceItemDAO.findByItem(context, item);
     }
 
+    @Override
+    public List<WorkspaceItem> findByShareToken(Context context, String shareToken) throws SQLException {
+        return workspaceItemDAO.findByShareToken(context, shareToken);
+    }
+
     @Override
     public List<WorkspaceItem> findAll(Context context) throws SQLException {
         return workspaceItemDAO.findAll(context);

diff --git a/dspace-api/src/main/java/org/dspace/content/clarin/ClarinVerificationTokenServiceImpl.java b/dspace-api/src/main/java/org/dspace/content/clarin/ClarinVerificationTokenServiceImpl.java
@@ -12,6 +12,7 @@
 import java.util.Objects;
 
 import org.apache.commons.lang.NullArgumentException;
+import org.dspace.authenticate.clarin.ShibHeaders;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.clarin.ClarinVerificationTokenDAO;
@@ -75,6 +76,19 @@ public ClarinVerificationToken findByNetID(Context context, String netID) throws
         return clarinVerificationTokenDAO.findByNetID(context, netID);
     }
 
+    @Override
+    public ClarinVerificationToken findByNetID(Context context, String[] netIdHeaders, ShibHeaders shibHeaders)
+            throws SQLException {
+        for (String netidHeader : netIdHeaders) {
+            String netID = shibHeaders.get_single(netidHeader);
+            ClarinVerificationToken clarinVerificationToken = clarinVerificationTokenDAO.findByNetID(context, netID);
+            if (Objects.nonNull(clarinVerificationToken)) {
+                return clarinVerificationToken;
+            }
+        }
+        return null;
+    }
+
     @Override
     public void delete(Context context, ClarinVerificationToken clarinVerificationToken)
             throws SQLException {

diff --git a/dspace-api/src/main/java/org/dspace/content/dao/WorkspaceItemDAO.java b/dspace-api/src/main/java/org/dspace/content/dao/WorkspaceItemDAO.java
@@ -37,6 +37,8 @@ public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer li
 
     public WorkspaceItem findByItem(Context context, Item i) throws SQLException;
 
+    public List<WorkspaceItem> findByShareToken(Context context, String shareToken) throws SQLException;
+
     public List<WorkspaceItem> findAll(Context context) throws SQLException;
 
     public List<WorkspaceItem> findAll(Context context, Integer limit, Integer offset) throws SQLException;

diff --git a/dspace-api/src/main/java/org/dspace/content/dao/impl/WorkspaceItemDAOImpl.java b/dspace-api/src/main/java/org/dspace/content/dao/impl/WorkspaceItemDAOImpl.java
@@ -81,6 +81,14 @@ public WorkspaceItem findByItem(Context context, Item i) throws SQLException {
         return uniqueResult(context, criteriaQuery, false, WorkspaceItem.class);
     }
 
+    @Override
+    public List<WorkspaceItem> findByShareToken(Context context, String shareToken) throws SQLException {
+        Query query = createQuery(context,
+                "from WorkspaceItem ws where ws.shareToken = :shareToken");
+        query.setParameter("shareToken", shareToken);
+        return list(query);
+    }
+
     @Override
     public List<WorkspaceItem> findAll(Context context) throws SQLException {
         CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);

diff --git a/dspace-api/src/main/java/org/dspace/content/service/WorkspaceItemService.java b/dspace-api/src/main/java/org/dspace/content/service/WorkspaceItemService.java
@@ -127,6 +127,16 @@ public List<WorkspaceItem> findByCollection(Context context, Collection collecti
     public WorkspaceItem findByItem(Context context, Item item)
         throws SQLException;
 
+    /**
+     * Find the workspace item by the share token.
+     * @param context       the DSpace context object
+     * @param shareToken    the share token
+     * @return              the List of workspace items or null
+     * @throws SQLException if database error
+     */
+    public List<WorkspaceItem> findByShareToken(Context context, String shareToken)
+            throws SQLException;
+
     /**
      * Get all workspace items in the whole system
      *

diff --git a/...e-api/src/main/java/org/dspace/content/service/clarin/ClarinVerificationTokenService.java b/...e-api/src/main/java/org/dspace/content/service/clarin/ClarinVerificationTokenService.java
@@ -10,6 +10,7 @@
 import java.sql.SQLException;
 import java.util.List;
 
+import org.dspace.authenticate.clarin.ShibHeaders;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.clarin.ClarinVerificationToken;
 import org.dspace.core.Context;
@@ -69,6 +70,18 @@ public interface ClarinVerificationTokenService {
      */
     ClarinVerificationToken findByNetID(Context context, String netID) throws SQLException;
 
+    /**
+     * Find the clarin verification token object from the shibboleth headers trying every netId header
+     * until the object is found
+     * @param context DSpace context object
+     * @param netIdHeaders array of the netId headers - values from the configuration
+     * @param shibHeaders object with the shibboleth headers
+     * @return found clarin verification token object or null
+     * @throws SQLException if database error
+     */
+    ClarinVerificationToken findByNetID(Context context, String[] netIdHeaders, ShibHeaders shibHeaders)
+            throws SQLException;
+
     /**
      * Remove the clarin verification token from DB
      * @param context DSpace context object

diff --git a/dspace-api/src/main/java/org/dspace/core/Utils.java b/dspace-api/src/main/java/org/dspace/core/Utils.java
@@ -506,4 +506,21 @@ public static String interpolateConfigsInString(String string) {
         ConfigurationService config = DSpaceServicesFactory.getInstance().getConfigurationService();
         return StringSubstitutor.replace(string, config.getProperties());
     }
+
+    /**
+     * Replace the last occurrence of a substring within a string.
+     *
+     * @param input The input string
+     * @param toReplace The substring to replace
+     * @param replacement The replacement substring
+     * @return Replaced input string or the original input string if the substring to replace is not found
+     */
+    public static String replaceLast(String input, String toReplace, String replacement) {
+        int lastIndex = input.lastIndexOf(toReplace);
+        if (lastIndex == -1) {
+            return input; // No replacement if not found
+        }
+
+        return input.substring(0, lastIndex) + replacement + input.substring(lastIndex + toReplace.length());
+    }
 }
diff --git a/dspace-api/src/main/java/org/dspace/discovery/indexobject/ItemIndexFactoryImpl.java b/dspace-api/src/main/java/org/dspace/discovery/indexobject/ItemIndexFactoryImpl.java
@@ -605,6 +605,28 @@ public void addDiscoveryFields(SolrInputDocument doc, Context context, Item item
         }
 
 
+
+        // process item metadata
+        // just add _comp to local*
+        List<MetadataValue> mds = itemService.getMetadata(item, "local", Item.ANY, Item.ANY, Item.ANY);
+        for (MetadataValue meta : mds) {
+            String field = "local" + "." + meta.getMetadataField().getElement();
+            String value = meta.getValue();
+            if (value == null) {
+                continue;
+            }
+            String qualifier = meta.getMetadataField().getQualifier();
+            if (qualifier != null && !qualifier.isEmpty()) {
+                field += "." + qualifier;
+            }
+            doc.addField(field + "_comp", value);
+        }
+
+        // create handle_title_ac field
+        String title = item.getName();
+        String handle = item.getHandle();
+        doc.addField("handle_title_ac", handle + ":" + title);
+
         log.debug("  Added Metadata");
 
         try {