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solved issue on export

This commit is contained in:
lucio 2024-07-10 13:14:31 +02:00
parent 38874c9529
commit 76639ed5f1
19 changed files with 68 additions and 67 deletions
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4
Dockerfile
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@ -1,4 +1,4 @@
FROM d4science/smartgears-distribution:4.0.0-SNAPSHOT-java17-tomcat10.1.19
FROM d4science/smartgears-distribution:4.0.1-SNAPSHOT-java17-tomcat10.1.19
COPY ./target/storagehub.war /tomcat/webapps/
COPY ./docker/jackrabbit/bootstrap.properties /app/jackrabbit/
#COPY ./docker/jackrabbit/bootstrap.properties /app/jackrabbit/
COPY ./docker/storagehub.xml /tomcat/conf/Catalina/localhost/

6
Dockerfile-standalone
View File

@ -1,8 +1,8 @@
FROM d4science/smartgears-distribution:4.0.0-SNAPSHOT-java17-tomcat10.1.19
FROM smartgears-distribution:4.0.1-SNAPSHOT-java17-tomcat10.1.19
COPY ./target/storagehub.war /tomcat/webapps/
COPY ./docker/jackrabbit /app/jackrabbit
COPY ./docker/storagehub.xml /tomcat/conf/Catalina/localhost/
COPY ./docker/logback.xml /etc/
COPY ./docker/container.ini /etc/
RUN mkdir -p /etc/config/StorageHub
COPY ./docker/storage-settings.properties /etc/config/StorageHub/
RUN mkdir -p /etc/config/storagehub
COPY ./docker/storage-settings.properties /etc/config/storagehub/

2
docker-compose.yml
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@ -1,7 +1,7 @@
version: '3.7'
services:
storagehub:
image: d4science/staragehub:latest
image: d4science/storagehub:latest
ports:
- '${APP_PORT}:8080'
volumes:

2
docker/container.ini
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@ -17,7 +17,7 @@ location = pisa
[authorization]
factory = org.gcube.smartgears.security.defaults.DefaultAuthorizationProviderFactory
factory.endpoint = https://accounts.dev.d4science.org/auth/realms/d4science/protocol/openid-connect/token
factory.endpoint = https://accounts.cloud-dev.d4science.org/auth/realms/d4science/protocol/openid-connect/token
credentials.class = org.gcube.smartgears.security.SimpleCredentials
credentials.clientID = node-whn-test-uno-d-d4s.d4science.org
credentials.secret = 979bd3bc-5cc4-11ec-bf63-0242ac130002

1
docker/jackrabbit/repository.xml
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@ -40,6 +40,7 @@
<AccessManager class="org.apache.jackrabbit.core.security.DefaultAccessManager" />
<LoginModule class="org.apache.jackrabbit.core.security.authentication.DefaultLoginModule">
<param name="adminId" value="admin" />
<param name="adminPassword" value="admin" />
</LoginModule>
</Security>
<!-- location of workspaces root directory and name of default workspace -->

4
gcube/extra-resources/WEB-INF/web.xml
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@ -4,10 +4,6 @@
<param-name>admin-username</param-name>
<param-value>admin</param-value>
</context-param>
<context-param>
<param-name>admin-pwd</param-name>
<param-value>admin</param-value>
</context-param>
<context-param>
<param-name>resolver-basepath</param-name>
<param-value>https://data-d.d4science.org/shub</param-value>

17
pom.xml
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@ -22,7 +22,7 @@
<packaging>war</packaging>
<properties>
<webappDirectory>${project.basedir}/src/main/webapp/WEB-INF</webappDirectory>
<jackrabbit.version>2.20.7</jackrabbit.version>
<jackrabbit.version>2.22.0</jackrabbit.version>
<jackson.version>2.15.3</jackson.version>
<slf4j.version>2.0.12</slf4j.version>
<tika.version>2.6.0</tika.version>
@ -130,6 +130,8 @@
<artifactId>jackrabbit-core</artifactId>
<version>${jackrabbit.version}</version>
</dependency>
<!-- <dependency> <groupId>org.apache.jackrabbit</groupId>
<artifactId>jackrabbit-jcr-server</artifactId>
<version>${jackrabbit.version}</version> </dependency> -->
@ -222,10 +224,11 @@
<groupId>org.glassfish.jersey.ext.cdi</groupId>
<artifactId>jersey-cdi1x-servlet</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.jboss.weld.se/weld-se-core -->
<!--
https://mvnrepository.com/artifact/org.jboss.weld.servlet/weld-servlet-core -->
<dependency>
<groupId>org.jboss.weld.se</groupId>
<artifactId>weld-se-core</artifactId>
<groupId>org.jboss.weld.servlet</groupId>
<artifactId>weld-servlet-core</artifactId>
<version>5.1.2.Final</version>
</dependency>
@ -339,11 +342,7 @@
<artifactId>aws-java-sdk-s3</artifactId>
<version>1.12.683</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.minio/minio
<dependency>
<groupId>io.minio</groupId>

4
src/main/java/org/gcube/data/access/storagehub/StorageHubApplicationManager.java
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@ -55,12 +55,12 @@ public class StorageHubApplicationManager implements ApplicationManager {
Path importPath = Paths.get(shubSpecificConf.toString(), "import");
Path mainFileImportPath = Paths.get(importPath.toString(), "data.json");
if (importPath.toFile().exists() && mainFileImportPath.toFile().exists()) {
Session session = null;
JackrabbitSession session = null;
try {
ObjectMapper mapper = new ObjectMapper();
DumpData data = mapper.readValue(mainFileImportPath.toFile(), DumpData.class);
session = repository.getRepository().login();
session = (JackrabbitSession) repository.getRepository().login(Constants.JCR_CREDENTIALS);
dh.importData((JackrabbitSession) session, data);
session.save();

1
src/main/java/org/gcube/data/access/storagehub/Utils.java
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@ -261,6 +261,7 @@ public class Utils {
destinationNode = params.getSession().getNodeByIdentifier(params.getParentId());
destinationItem = (FolderItem) new Node2ItemConverter().getItem(destinationNode, Excludes.ALL);
}catch (RepositoryException e) {
logger.error("id not found",e);
throw new IdNotFoundException(params.getParentId());
}
String uniqueName = Utils.checkExistanceAndGetUniqueName(params.getSession(), destinationNode, params.getName());

8
src/main/java/org/gcube/data/access/storagehub/handlers/DataHandler.java
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@ -50,9 +50,13 @@ public class DataHandler {
List<String> groups = groupHandler.getGroups(session);
logger.debug("found users {} ",usersData);
logger.debug("found groups {} ",groups);
List<GroupData> groupsData = new ArrayList<GroupData>(groups.size());
for (String group : groups) {
Item vreFolderItem = vreManager.getVRE(group).getVreFolder();
logger.debug("serching for group {}",group);
Item vreFolderItem = vreManager.getVreFolderItemByGroupName(session, group, null).getVreFolder();
String owner = vreFolderItem.getOwner();
List<ACL> acls = aclHandler.get(vreFolderItem, session);
@ -91,7 +95,7 @@ public class DataHandler {
logger.warn("error adding user {} to group {}", member, g.getName(), t);
}
Item vreFolderItem = vreManager.getVRE(g.getName()).getVreFolder();
Item vreFolderItem = vreManager.getVreFolderItemByGroupName(session, g.getName(), null).getVreFolder();
for (ACL acl : g.getAcls()) {
aclHandler.update(acl.getPricipal(), (Node)vreFolderItem.getRelatedNode(), acl.getAccessTypes().get(0), session);

2
src/main/java/org/gcube/data/access/storagehub/handlers/items/Item2NodeConverter.java
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@ -55,7 +55,7 @@ public class Item2NodeConverter {
String primaryType= ClassHandler.instance().getNodeType(item.getClass());
Node newNode = null;
if (uuid==null)
parentNode.addNode(Text.escapeIllegalJcrChars(item.getName()), primaryType);
newNode = parentNode.addNode(Text.escapeIllegalJcrChars(item.getName()), primaryType);
else ((NodeImpl)parentNode).addNodeWithUuid(item.getName(), primaryType, uuid);
fillNode(newNode, item);
return newNode;

27
src/main/java/org/gcube/data/access/storagehub/handlers/vres/VREManager.java
View File

@ -10,15 +10,9 @@ import javax.jcr.Node;
import javax.jcr.RepositoryException;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.apache.jackrabbit.api.security.user.Group;
import org.apache.jackrabbit.api.security.user.User;
import org.apache.jackrabbit.api.security.user.UserManager;
import org.gcube.common.security.ContextBean;
import org.gcube.common.security.ContextBean.Type;
import org.gcube.common.security.providers.SecretManagerProvider;
import org.gcube.common.security.secrets.Secret;
import org.gcube.common.storagehub.model.exceptions.BackendGenericError;
import org.gcube.common.storagehub.model.exceptions.InvalidCallParameters;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.items.Item;
import org.gcube.data.access.storagehub.Constants;
@ -53,7 +47,7 @@ public class VREManager {
ExecutorService executor = Executors.newFixedThreadPool(5);
public synchronized VRE getVRE(String completeName) {
private synchronized VRE getVRE(String completeName) {
logger.trace("requesting VRE {}",completeName);
if (vreMap.containsKey(completeName))
return vreMap.get(completeName);
@ -73,30 +67,19 @@ public class VREManager {
}
public synchronized VRE getVreFolderItem(JackrabbitSession ses, String userId, List<String> excludes ) throws RepositoryException, StorageHubException{
Secret secret = SecretManagerProvider.get();
ContextBean bean = new ContextBean(secret.getContext());
public String retrieveGroupNameFromContext(String context) throws StorageHubException{
ContextBean bean = new ContextBean(context);
if (!bean.is(Type.VRE)) throw new BackendGenericError("the current scope is not a VRE");
String entireScopeName= bean.toString().replaceAll("^/(.*)/?$", "$1").replaceAll("/", "-");
return getVreFolderItemByGroupName(ses, entireScopeName, userId, excludes);
return entireScopeName;
}
public synchronized VRE getVreFolderItemByGroupName(JackrabbitSession ses, String groupName, String userId, List<String> excludes ) throws RepositoryException, StorageHubException{
UserManager um = ses.getUserManager();
Group groupAuth = um.getAuthorizable(groupName, Group.class);
User userAuth = um.getAuthorizable(userId, User.class);
if (groupAuth == null || userAuth == null || !groupAuth.isMember(userAuth))
throw new InvalidCallParameters("error getting VRE with user "+userId+" for group "+groupName);
public synchronized VRE getVreFolderItemByGroupName(JackrabbitSession ses, String groupName, List<String> excludes ) throws RepositoryException, StorageHubException{
VRE vre = this.getVRE(groupName);
if (vre!=null) return vre;
else {
Node vreFolderNode = groupHandler.getFolderNodeRelatedToGroup(ses, groupName);
Item vreFolder = node2Item.getItem(vreFolderNode, excludes);
return this.putVRE(vreFolder);
}

4
src/main/java/org/gcube/data/access/storagehub/health/JCRRepositoryCheck.java
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@ -12,7 +12,7 @@ import org.gcube.data.access.storagehub.repository.StoragehubRepository;
public class JCRRepositoryCheck implements HealthCheck{
StoragehubRepository repository = StoragehubRepository.repository;
@Override
public String getName() {
@ -22,7 +22,7 @@ public class JCRRepositoryCheck implements HealthCheck{
@Override
public HealthCheckResponse check() {
try {
Session session = repository.getRepository().login();
Session session = StoragehubRepository.repository.getRepository().login();
if (session != null) session.logout();
return HealthCheckResponse.builder(getName()).up().build();
}catch (LoginException e) { }

3
src/main/java/org/gcube/data/access/storagehub/repository/JackrabbitRepositoryImpl.java
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@ -19,9 +19,6 @@ import org.gcube.data.access.storagehub.Constants;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import jakarta.enterprise.context.ApplicationScoped;
@ApplicationScoped
public class JackrabbitRepositoryImpl implements StoragehubRepository {
private static final Logger log = LoggerFactory.getLogger(JackrabbitRepositoryImpl.class);

1
src/main/java/org/gcube/data/access/storagehub/services/ItemsCreator.java
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@ -206,7 +206,6 @@ public class ItemsCreator extends Impersonable{
log.debug("UPLOAD: call started");
ses = repository.getRepository().login(Constants.JCR_CREDENTIALS);
URLConnection connectionURL = new URI(url).toURL().openConnection();
long fileLength = connectionURL.getContentLengthLong();

4
src/main/java/org/gcube/data/access/storagehub/services/UserManager.java
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@ -176,8 +176,8 @@ public class UserManager {
log.error(she.getErrorMessage(), she);
GXOutboundErrorResponse.throwException(she, Response.Status.fromStatusCode(she.getStatus()));
} catch (RepositoryException re) {
log.error("jcr error creating item", re);
GXOutboundErrorResponse.throwException(new BackendGenericError("jcr error creating item", re));
log.error("jcr error removing item", re);
GXOutboundErrorResponse.throwException(new BackendGenericError("jcr error removing item", re));
} finally {
if (session != null)
session.logout();

26
src/main/java/org/gcube/data/access/storagehub/services/WorkspaceManager.java
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@ -10,6 +10,8 @@ import javax.jcr.Session;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.gcube.common.gxrest.response.outbound.GXOutboundErrorResponse;
import org.gcube.common.security.providers.SecretManagerProvider;
import org.gcube.common.security.secrets.Secret;
import org.gcube.common.storagehub.model.Excludes;
import org.gcube.common.storagehub.model.Paths;
import org.gcube.common.storagehub.model.exceptions.BackendGenericError;
@ -43,6 +45,7 @@ import org.gcube.data.access.storagehub.handlers.vres.VRE;
import org.gcube.data.access.storagehub.handlers.vres.VREManager;
import org.gcube.data.access.storagehub.query.sql2.evaluators.Evaluators;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.delegates.UserManagerDelegate;
import org.gcube.data.access.storagehub.storage.backend.impl.GCubeVolatileStorageBackendFactory;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -104,6 +107,9 @@ public class WorkspaceManager extends Impersonable {
@Inject
PublicLinkHandler publicLinkHandler;
@Inject
UserManagerDelegate userHandler;
@RequestScoped
@QueryParam("exclude")
private List<String> excludes = Collections.emptyList();
@ -209,7 +215,15 @@ public class WorkspaceManager extends Impersonable {
Item vreItem = null;
try {
ses = (JackrabbitSession) repository.getRepository().login(Constants.JCR_CREDENTIALS);
vreItem = vreManager.getVreFolderItem(ses, currentUser, excludes).getVreFolder();
Secret secret = SecretManagerProvider.get();
String groupName= vreManager.retrieveGroupNameFromContext(secret.getContext());
if (!userHandler.getGroupsPerUser(ses, currentUser).contains(groupName))
throw new InvalidCallParameters("error getting VRE with user "+currentUser+" for group "+groupName);
vreItem = vreManager.getVreFolderItemByGroupName(ses, groupName, excludes).getVreFolder();
} catch (RepositoryException re) {
log.error("jcr error getting vrefolder", re);
GXOutboundErrorResponse.throwException(new BackendGenericError(re));
@ -233,7 +247,15 @@ public class WorkspaceManager extends Impersonable {
try {
ses = (JackrabbitSession) repository.getRepository().login(Constants.JCR_CREDENTIALS);
VRE vre = vreManager.getVreFolderItem(ses, currentUser, excludes);
Secret secret = SecretManagerProvider.get();
String groupName= vreManager.retrieveGroupNameFromContext(secret.getContext());
if (!userHandler.getGroupsPerUser(ses, currentUser).contains(groupName))
throw new InvalidCallParameters("error getting VRE with user "+currentUser+" for group "+groupName);
VRE vre = vreManager.getVreFolderItemByGroupName(ses, groupName, excludes);
log.trace("VRE retrieved {}", vre.getVreFolder().getTitle());
recentItems = vre.getRecents();
log.trace("recents retrieved {}", vre.getVreFolder().getTitle());

11
src/main/java/org/gcube/data/access/storagehub/services/admin/ScriptManager.java
View File

@ -73,6 +73,10 @@ public class ScriptManager {
@Inject
ItemHandler itemHandler;
@Inject
DataHandler dataHandler;
@Inject
PathUtil pathUtil;
@ -116,10 +120,9 @@ public class ScriptManager {
return status;
}
@POST
@GET
@Path("export")
@AuthorizationControl(allowedRoles = {INFRASTRUCTURE_MANAGER_ROLE})
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public ScriptStatus export() {
InnerMethodName.set("export");
@ -135,8 +138,8 @@ public class ScriptManager {
JackrabbitSession session = null;
try {
session = (JackrabbitSession) repository.getRepository().login();
DumpData dd = new DataHandler().exportData(session);
session = (JackrabbitSession) repository.getRepository().login(Constants.JCR_CREDENTIALS);
DumpData dd = dataHandler.exportData(session);
ObjectMapper om = new ObjectMapper();
status.setSuccess(om.writeValueAsString(dd));
log.info("""

4
src/main/java/org/gcube/data/access/storagehub/services/delegates/GroupManagerDelegate.java
View File

@ -40,7 +40,6 @@ import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.items.builders.FolderCreationParameters;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.GroupManager;
import org.gcube.data.access.storagehub.services.interfaces.ACLManagerInterface;
import org.slf4j.Logger;
@ -63,11 +62,8 @@ public class GroupManagerDelegate {
@Inject
ACLManagerInterface aclManagerDelegate;
private final StoragehubRepository repository = StoragehubRepository.repository;
public List<String> getGroups(JackrabbitSession session) throws RepositoryException {
List<String> groups = new ArrayList<>();
session = (JackrabbitSession) repository.getRepository().login(Constants.JCR_CREDENTIALS);
Iterator<Authorizable> result = session.getUserManager().findAuthorizables(new Query() {
@Override