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storagehub
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This commit is contained in:
lucio 2020-03-16 16:55:26 +01:00
parent 9d895f0adf
commit 133d71f14f
14 changed files with 167 additions and 44 deletions
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9
pom.xml
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@ -12,7 +12,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.gcube.data.access</groupId>
<artifactId>storagehub</artifactId>
<version>1.1.0</version>
<version>1.1.0-SNAPSHOT</version>
<name>storagehub</name>
<scm>
@ -70,7 +70,12 @@
<groupId>org.gcube.core</groupId>
<artifactId>common-smartgears</artifactId>
</dependency>
<dependency>
<groupId>org.gcube.core</groupId>
<artifactId>common-smartgears-app</artifactId>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>authorization-control-library</artifactId>

10
src/main/java/org/gcube/data/access/storagehub/RepositoryInitializerImpl.java
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@ -5,6 +5,7 @@ import javax.jcr.Repository;
import javax.naming.Context;
import javax.naming.InitialContext;
import org.apache.jackrabbit.api.JackrabbitRepository;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
@Singleton
@ -12,19 +13,22 @@ public class RepositoryInitializerImpl implements RepositoryInitializer{
private Repository repository;
@Override
public Repository getRepository(){
public synchronized Repository getRepository(){
return repository;
}
public RepositoryInitializerImpl() throws Exception{
protected RepositoryInitializerImpl() throws Exception{
InitialContext context = new InitialContext();
Context environment = (Context) context.lookup("java:comp/env");
repository = (Repository) environment.lookup("jcr/repository");
}
public void shutdown() {
((JackrabbitRepository)repository).shutdown();
}

41
src/main/java/org/gcube/data/access/storagehub/StorageHubAppllicationManager.java Normal file
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@ -0,0 +1,41 @@
package org.gcube.data.access.storagehub;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.smartgears.ApplicationManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class StorageHubAppllicationManager implements ApplicationManager {
private static Logger logger = LoggerFactory.getLogger(StorageHubAppllicationManager.class);
private boolean alreadyShutDown = false;
public static RepositoryInitializer repository;
@Override
public synchronized void onInit() {
logger.info("jackrabbit initialization started");
try {
repository = new RepositoryInitializerImpl();
} catch (Exception e) {
logger.error("ERROR INITIALIZING REPOSITORY",e);
}
repository.getRepository();
}
@Override
public synchronized void onShutdown() {
if (!alreadyShutDown)
try {
logger.info("jackrabbit is shutting down");
repository.shutdown();
alreadyShutDown= true;
} catch (Exception e) {
logger.warn("the database was not shutdown properly",e);
}
}
}

35
src/main/java/org/gcube/data/access/storagehub/Utils.java
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@ -110,7 +110,7 @@ public class Utils {
}
public static <T extends Item> List<T> serachByNameOnFolder(Session ses, Node parent, List<String> excludes, Range range, boolean showHidden, Class<? extends Item> nodeTypeToInclude, String nameParam) throws RepositoryException, BackendGenericError{
public static <T extends Item> List<T> serachByNameOnFolder(Session ses, Node parent, List<String> excludes, Range range, boolean showHidden, boolean excludeTrashed, Class<? extends Item> nodeTypeToInclude, String nameParam) throws RepositoryException, BackendGenericError{
String xpath = String.format("/jcr:root%s//element(*,nthl:workspaceItem)[jcr:like(fn:lower-case(@jcr:title), '%s')]",ISO9075.encodePath(parent.getPath()), nameParam.toLowerCase());
//String query = String.format("SELECT * FROM [nthl:workspaceLeafItem] AS node WHERE ISDESCENDANTNODE('%s') ORDER BY node.[jcr:lastModified] DESC ",vreFolder.getPath());
@ -119,7 +119,7 @@ public class Utils {
Query jcrQuery = ses.getWorkspace().getQueryManager().createQuery(xpath, Query.XPATH);
NodeIterator it = jcrQuery.execute().getNodes();
return getItemListFromNodeIterator(it, excludes, range, showHidden, nodeTypeToInclude);
return getItemListFromNodeIterator(parent, it, excludes, range, showHidden, excludeTrashed, nodeTypeToInclude);
}
@ -128,10 +128,10 @@ public class Utils {
long start = System.currentTimeMillis();
NodeIterator iterator = parent.getNodes();
logger.trace("time to get iterator {}",(System.currentTimeMillis()-start));
return getItemListFromNodeIterator(iterator, excludes, range, showHidden, nodeTypeToInclude);
return getItemListFromNodeIterator(null, iterator, excludes, range, showHidden, false, nodeTypeToInclude);
}
private static <T extends Item> List<T> getItemListFromNodeIterator(NodeIterator iterator, List<String> excludes, Range range, boolean showHidden, Class<? extends Item> nodeTypeToInclude) throws RepositoryException, BackendGenericError{
private static <T extends Item> List<T> getItemListFromNodeIterator(Node parent, NodeIterator iterator, List<String> excludes, Range range, boolean showHidden, boolean excludeTrashed, Class<? extends Item> nodeTypeToInclude) throws RepositoryException, BackendGenericError{
List<T> returnList = new ArrayList<T>();
logger.trace("nodeType is {}",nodeTypeToInclude);
@ -140,7 +140,10 @@ public class Utils {
Node2ItemConverter node2Item= new Node2ItemConverter();
while (iterator.hasNext()){
Node current = iterator.nextNode();
if (parent!=null && !current.getPath().startsWith(parent.getPath()))
continue;
logger.trace("current node "+current.getName());
if (isToExclude(current, showHidden))
@ -150,7 +153,7 @@ public class Utils {
if (range==null || (count>=range.getStart() && returnList.size()<range.getLimit())) {
T item = node2Item.getFilteredItem(current, excludes, nodeTypeToInclude);
if (item==null) continue;
if (item==null || (item.isTrashed() && excludeTrashed)) continue;
returnList.add(item);
}
count++;
@ -330,16 +333,19 @@ public class Utils {
item.setTitle(uniqueName);
item.setDescription(description);
//item.setCreationTime(now);
item.setHidden(hidden);
boolean hiddenDestNode= false;
try {
hiddenDestNode = destinationNode.getProperty(NodeProperty.HIDDEN.toString()).getBoolean();
}catch (Throwable e) {}
item.setHidden(hidden || hiddenDestNode);
item.setLastAction(ItemAction.CREATED);
item.setLastModificationTime(now);
item.setLastModifiedBy(login);
item.setOwner(login);
item.setPublicItem(false);
//to inherit hidden property
//item.setHidden(destinationItem.isHidden());
Node newNode = new Item2NodeConverter().getNode(destinationNode, item);
if (accountingHandler!=null) {
accountingHandler.createFolderAddObj(name, item.getClass().getSimpleName(), null, ses, destinationNode, false);
@ -364,9 +370,14 @@ public class Utils {
item.setOwner(login);
item.setPublicItem(false);
item.setValue(value);
try {
item.setHidden(destinationNode.getProperty(NodeProperty.HIDDEN.toString()).getBoolean());
} catch (Throwable e) {
item.setHidden(false);
}
//to inherit hidden property
//item.setHidden(destinationItem.isHidden());
Node newNode = new Item2NodeConverter().getNode(destinationNode, item);
if (accountingHandler!=null) {

6
src/main/java/org/gcube/data/access/storagehub/handlers/Item2NodeConverter.java
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@ -216,11 +216,15 @@ public class Item2NodeConverter {
}
public void updateHidden(Node node, Boolean hidden,String login) throws RepositoryException {
Utils.setPropertyOnChangeNode(node, login, ItemAction.UPDATED);
node.setProperty(NodeProperty.HIDDEN.toString(), hidden);
}
public <I extends Item> void updateMetadataNode(Node node, Map<String, Object> meta, String login){
try {
//TODO: make a method to update item not only metadata, check if the new metadata has an intersection with the old one to remove properties not needed
Utils.setPropertyOnChangeNode(node, login, ItemAction.UPDATED);
Node metadataNode;

9
src/main/java/org/gcube/data/access/storagehub/services/ACLManager.java
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@ -25,10 +25,7 @@ import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.apache.jackrabbit.api.security.JackrabbitAccessControlList;
import org.apache.jackrabbit.api.security.user.Group;
import org.apache.jackrabbit.api.security.user.User;
import org.apache.jackrabbit.commons.jackrabbit.authorization.AccessControlUtils;
import org.gcube.common.gxrest.response.outbound.GXOutboundErrorResponse;
import org.gcube.common.storagehub.model.Excludes;
@ -45,21 +42,23 @@ import org.gcube.common.storagehub.model.items.SharedFolder;
import org.gcube.common.storagehub.model.items.VreFolder;
import org.gcube.common.storagehub.model.types.ACLList;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
import org.gcube.data.access.storagehub.handlers.Node2ItemConverter;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.glassfish.jersey.media.multipart.FormDataParam;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
public class ACLManager {
private static final Logger log = LoggerFactory.getLogger(ACLManager.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@RequestScoped
@PathParam("id")

6
src/main/java/org/gcube/data/access/storagehub/services/GroupManager.java
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@ -54,6 +54,7 @@ import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.common.storagehub.model.types.PrimaryNodeType;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.exception.MyAuthException;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
@ -61,12 +62,14 @@ import org.gcube.data.access.storagehub.handlers.Node2ItemConverter;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.VRE;
import org.gcube.data.access.storagehub.handlers.VREManager;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.glassfish.jersey.media.multipart.FormDataParam;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@Path("groups")
@ManagedBy(StorageHubAppllicationManager.class)
public class GroupManager {
@Context ServletContext context;
@ -79,8 +82,7 @@ public class GroupManager {
private static final Logger log = LoggerFactory.getLogger(GroupManager.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
VREManager vreManager;

5
src/main/java/org/gcube/data/access/storagehub/services/ItemSharing.java
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@ -15,7 +15,6 @@ import javax.ws.rs.Consumes;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
@ -39,6 +38,7 @@ import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.common.storagehub.model.types.PrimaryNodeType;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
@ -55,8 +55,7 @@ public class ItemSharing {
private static final Logger log = LoggerFactory.getLogger(ItemSharing.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
AccountingHandler accountingHandler;

15
src/main/java/org/gcube/data/access/storagehub/services/ItemsCreator.java
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@ -54,8 +54,10 @@ import org.gcube.common.storagehub.model.items.FolderItem;
import org.gcube.common.storagehub.model.items.GCubeItem;
import org.gcube.common.storagehub.model.storages.MetaInfo;
import org.gcube.common.storagehub.model.types.ItemAction;
import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.MultipleOutputStream;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
@ -65,6 +67,7 @@ import org.gcube.data.access.storagehub.handlers.StorageBackendHandler;
import org.gcube.data.access.storagehub.handlers.VersionHandler;
import org.gcube.data.access.storagehub.handlers.content.ContentHandler;
import org.gcube.data.access.storagehub.handlers.content.ContentHandlerFactory;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;
@ -73,6 +76,7 @@ import org.slf4j.LoggerFactory;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
public class ItemsCreator {
private static final Logger log = LoggerFactory.getLogger(ItemsCreator.class);
@ -81,8 +85,7 @@ public class ItemsCreator {
@Context ServletContext context;
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
ContentHandlerFactory contenthandlerFactory;
@ -317,15 +320,15 @@ public class ItemsCreator {
private Node createFileItemInternally(Session ses, Node destinationNode, InputStream stream, String name, String description, String login, boolean withLock) throws RepositoryException, UserNotAuthorizedException, ItemLockedException, BackendGenericError{
//to inherit hidden property
//item.setHidden(destinationItem.isHidden());
Node newNode;
try {
newNode = ses.getNode(org.gcube.common.storagehub.model.Paths.append(org.gcube.common.storagehub.model.Paths.getPath(destinationNode.getPath()), name).toPath());
authChecker.checkWriteAuthorizationControl(ses, newNode.getIdentifier(), false);
AbstractFileItem item = fillItemWithContent(stream, name, description, destinationNode.getPath(), login);
item.setHidden(destinationNode.getProperty(NodeProperty.HIDDEN.toString()).getBoolean());
if (withLock) {
try {
ses.getWorkspace().getLockManager().lock(newNode.getPath(), true, true, 0,login);

57
src/main/java/org/gcube/data/access/storagehub/services/ItemsManager.java
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@ -73,6 +73,7 @@ import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.Range;
import org.gcube.data.access.storagehub.SingleFileStreamingOutput;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.exception.MyAuthException;
@ -83,18 +84,19 @@ import org.gcube.data.access.storagehub.handlers.Node2ItemConverter;
import org.gcube.data.access.storagehub.handlers.StorageBackendHandler;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.VersionHandler;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
public class ItemsManager {
private static final Logger log = LoggerFactory.getLogger(ItemsManager.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
AccountingHandler accountingHandler;
@ -314,14 +316,15 @@ public class ItemsManager {
@GET
@Path("{id}/search")
@Produces(MediaType.APPLICATION_JSON)
public ItemList searchItems(@QueryParam("showHidden") Boolean showHidden, @QueryParam("exclude") List<String> excludes, @QueryParam("onlyType") String nodeType,@QueryParam("name") String name ){
public ItemList searchItems(@QueryParam("showHidden") Boolean showHidden, @QueryParam("excludeTrashed") Boolean excludeTrashed, @QueryParam("exclude") List<String> excludes, @QueryParam("onlyType") String nodeType,@QueryParam("name") String name ){
InnerMethodName.instance.set("search");
Session ses = null;
List<? extends Item> toReturn = null;
try{
log.debug("search for node {}",name);
ses = repository.getRepository().login(CredentialHandler.getAdminCredentials(context));
authChecker.checkReadAuthorizationControl(ses, id);
toReturn = Utils.serachByNameOnFolder(ses, ses.getNodeByIdentifier(id), excludes, null, showHidden==null?false:showHidden, nodeType!=null ? ClassHandler.instance().get(nodeType) : null, name);
toReturn = Utils.serachByNameOnFolder(ses, ses.getNodeByIdentifier(id), excludes, null, showHidden==null?false:showHidden,excludeTrashed==true?false:excludeTrashed , nodeType!=null ? ClassHandler.instance().get(nodeType) : null, name);
log.debug("search retrieved {} elements",toReturn.size());
}catch (ItemNotFoundException e) {
log.error("id {} not found",id,e);
@ -1044,6 +1047,52 @@ public class ItemsManager {
return Response.ok(id).build();
}
//TODO: transform this and setMetadata in a generic method for all properties
@PUT
@Consumes(MediaType.APPLICATION_JSON)
@Path("/{id}/hidden")
public Response setItemAsHidden(Boolean hidden){
InnerMethodName.instance.set("setHidden");
Session ses = null;
try{
final String login = AuthorizationProvider.instance.get().getClient().getId();
ses = repository.getRepository().login(CredentialHandler.getAdminCredentials(context));
authChecker.checkWriteAuthorizationControl(ses, id, false);
final Node nodeToUpdate = ses.getNodeByIdentifier(id);
try {
ses.getWorkspace().getLockManager().lock(nodeToUpdate.getPath(), false, true, 0,login);
}catch (LockException e) {
throw new ItemLockedException(e);
}
try {
item2Node.updateHidden(nodeToUpdate, hidden, login);
ses.save();
}finally {
ses.getWorkspace().getLockManager().unlock(nodeToUpdate.getPath());
}
//TODO: UPDATE accounting
}catch(RepositoryException re ){
log.error("jcr error moving item", re);
GXOutboundErrorResponse.throwException(new BackendGenericError(re));
}catch(StorageHubException she ){
log.error(she.getErrorMessage(), she);
GXOutboundErrorResponse.throwException(she, Response.Status.fromStatusCode(she.getStatus()));
}finally{
if (ses!=null) {
ses.logout();
}
}
return Response.ok(id).build();
}
@PUT
@Consumes(MediaType.APPLICATION_JSON)
@Path("/{id}/metadata")

2
src/main/java/org/gcube/data/access/storagehub/services/RepositoryInitializer.java
View File

@ -5,4 +5,6 @@ import javax.jcr.Repository;
public interface RepositoryInitializer {
Repository getRepository();
void shutdown();
}

6
src/main/java/org/gcube/data/access/storagehub/services/UserManager.java
View File

@ -38,16 +38,19 @@ import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.items.Item;
import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.exception.MyAuthException;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.UnshareHandler;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@Path("users")
@ManagedBy(StorageHubAppllicationManager.class)
public class UserManager {
private static final String INFRASTRUCTURE_MANAGER_ROLE = "Infrastructure-Manager";
@ -56,8 +59,7 @@ public class UserManager {
private static final Logger log = LoggerFactory.getLogger(UserManager.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
UnshareHandler unshareHandler;

8
src/main/java/org/gcube/data/access/storagehub/services/WorkspaceManager.java
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@ -42,6 +42,7 @@ import org.gcube.common.storagehub.model.service.ItemWrapper;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.Range;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.handlers.CredentialHandler;
import org.gcube.data.access.storagehub.handlers.Item2NodeConverter;
@ -51,6 +52,7 @@ import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.VRE;
import org.gcube.data.access.storagehub.handlers.VREManager;
import org.gcube.data.access.storagehub.query.sql2.evaluators.Evaluators;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -59,13 +61,13 @@ import com.fasterxml.jackson.databind.ObjectMapper;
@Path("")
@ManagedBy(StorageHubAppllicationManager.class)
public class WorkspaceManager {
private static final Logger log = LoggerFactory.getLogger(WorkspaceManager.class);
@Inject
RepositoryInitializer repository;
RepositoryInitializer repository = StorageHubAppllicationManager.repository;
@Inject
Evaluators evaluator;

2
src/main/webapp/WEB-INF/README
View File

@ -25,7 +25,7 @@ The projects leading to this software have received funding from a series of
Version
--------------------------------------------------
1.1.0-SNAPSHOT (2020-03-11)
1.1.0-SNAPSHOT (2020-03-16)
Please see the file named "changelog.xml" in this directory for the release notes.