From bc4c1415ebbd7079a61e3097464c7efbe86e8e6c Mon Sep 17 00:00:00 2001
From: pkupczyk <piotr.kupczyk@id.ethz.ch>
Date: Fri, 19 Apr 2024 10:49:09 +0200
Subject: [PATCH] BIS-741 : AFS uses DSS store - AFS changes
---
.../java/ch/ethz/sis/shared/io/IOUtils.java | 53 +++++++++
server-data-store/build.gradle | 4 +-
.../AtomicFileSystemServerParameter.java | 1 +
.../sis/afsserver/worker/WorkerFactory.java | 2 +-
.../OpenBISAuthorizationInfoProvider.java | 59 +++++-----
.../afsserver/worker/proxy/ExecutorProxy.java | 109 +++++++++++++++---
.../sis/afsserver/worker/proxy/ProxyUtil.java | 109 ++++++++++++++++++
7 files changed, 290 insertions(+), 47 deletions(-)
create mode 100644 server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ProxyUtil.java
diff --git a/lib-transactional-file-system/src/main/java/ch/ethz/sis/shared/io/IOUtils.java b/lib-transactional-file-system/src/main/java/ch/ethz/sis/shared/io/IOUtils.java
index 627a0c3edad..e2fd2439149 100644
--- a/lib-transactional-file-system/src/main/java/ch/ethz/sis/shared/io/IOUtils.java
+++ b/lib-transactional-file-system/src/main/java/ch/ethz/sis/shared/io/IOUtils.java
@@ -20,6 +20,7 @@ import ch.ethz.sis.afs.api.dto.File;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
+import java.nio.charset.StandardCharsets;
import java.nio.file.AtomicMoveNotSupportedException;
import java.nio.file.DirectoryStream;
import java.nio.file.FileStore;
@@ -47,6 +48,7 @@ import java.security.MessageDigest;
import java.time.OffsetDateTime;
import java.time.ZoneId;
import java.util.*;
+import java.util.stream.Collectors;
public class IOUtils {
@@ -630,6 +632,57 @@ public class IOUtils {
}
}
+ public static String[] getShares(String folder){
+ try
+ {
+ return Files.list(Paths.get(folder)).filter(file ->
+ {
+ if (!Files.isDirectory(file))
+ {
+ return false;
+ }
+ try
+ {
+ Integer.parseInt(file.getFileName().toString());
+ return true;
+ } catch (NumberFormatException e)
+ {
+ return false;
+ }
+ }).map(file -> file.getFileName().toString()).toArray(String[]::new);
+ } catch (IOException e)
+ {
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static String[] getShards(String str) {
+ byte[] md5 = getMD5(str.getBytes(StandardCharsets.UTF_8));
+ String hex = asHex(md5);
+ return new String[]{
+ hex.substring(0, 2),
+ hex.substring(2,4),
+ hex.substring(4,6)
+ };
+ }
+
+ private static final char[] HEX_ARRAY = "0123456789ABCDEF".toCharArray();
+
+ public static String asHex(byte[] bytes) {
+ char[] hex = new char[bytes.length * 2];
+
+ int bytesIndex = 0;
+ int hexIndex = 0;
+
+ while(bytesIndex < bytes.length) {
+ hex[hexIndex++] = HEX_ARRAY[bytes[bytesIndex] >>> 4 & 0x0F];
+ hex[hexIndex++] = HEX_ARRAY[bytes[bytesIndex] & 0x0F];
+ bytesIndex++;
+ }
+
+ return new String(hex);
+ }
+
public static String encodeBase64(byte[] input) {
return Base64.getEncoder().encodeToString(input);
}
diff --git a/server-data-store/build.gradle b/server-data-store/build.gradle
index 45908299720..47b932d13dd 100644
--- a/server-data-store/build.gradle
+++ b/server-data-store/build.gradle
@@ -23,12 +23,12 @@ dependencies {
annotationProcessor 'lombok:lombok:1.18.22'
implementation project(':lib-transactional-file-system'),
project(':api-data-store-server-java'),
+ project(':api-openbis-java'),
project(':lib-json'),
'lombok:lombok:1.18.22',
'io.netty:netty-all:4.1.68.Final',
'log4j:log4j-api:2.10.0',
- 'log4j:log4j-core:2.10.0',
- 'openbis:openbis-v3-api-batteries-included:20.10.5';
+ 'log4j:log4j-core:2.10.0'
testImplementation 'junit:junit:4.10',
'hamcrest:hamcrest-core:1.3'
}
diff --git a/server-data-store/src/main/java/ch/ethz/sis/afsserver/startup/AtomicFileSystemServerParameter.java b/server-data-store/src/main/java/ch/ethz/sis/afsserver/startup/AtomicFileSystemServerParameter.java
index 4c85918d48d..7e540481a25 100644
--- a/server-data-store/src/main/java/ch/ethz/sis/afsserver/startup/AtomicFileSystemServerParameter.java
+++ b/server-data-store/src/main/java/ch/ethz/sis/afsserver/startup/AtomicFileSystemServerParameter.java
@@ -27,6 +27,7 @@ public enum AtomicFileSystemServerParameter {
jsonObjectMapperClass,
writeAheadLogRoot,
storageRoot,
+ storageUuid,
//
// Parameters for the HTTP server
//
diff --git a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/WorkerFactory.java b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/WorkerFactory.java
index 007f4511187..4fc1f94960f 100755
--- a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/WorkerFactory.java
+++ b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/WorkerFactory.java
@@ -29,7 +29,7 @@ public class WorkerFactory extends AbstractFactory<Configuration, Configuration,
public Worker create(Configuration configuration) throws Exception {
// 5. Execute the operation
- AuditorProxy executorProxy = new AuditorProxy(new ExecutorProxy());
+ AuditorProxy executorProxy = new AuditorProxy(new ExecutorProxy(configuration));
// 4. Check that the user have rights to do the operation
AuthorizationInfoProvider authorizationInfoProvider = configuration.getInstance(AtomicFileSystemServerParameter.authorizationInfoProviderClass);
diff --git a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/providers/impl/OpenBISAuthorizationInfoProvider.java b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/providers/impl/OpenBISAuthorizationInfoProvider.java
index 1f92d5a503c..e5abec89a88 100644
--- a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/providers/impl/OpenBISAuthorizationInfoProvider.java
+++ b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/providers/impl/OpenBISAuthorizationInfoProvider.java
@@ -15,61 +15,64 @@
*/
package ch.ethz.sis.afsserver.worker.providers.impl;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
import ch.ethz.sis.afsserver.startup.AtomicFileSystemServerParameter;
import ch.ethz.sis.afsserver.worker.providers.AuthorizationInfoProvider;
+import ch.ethz.sis.afsserver.worker.proxy.ProxyUtil;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPermIdHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.rights.Right;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.rights.Rights;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.rights.fetchoptions.RightsFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
import ch.ethz.sis.shared.io.FilePermission;
import ch.ethz.sis.shared.startup.Configuration;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-public class OpenBISAuthorizationInfoProvider implements AuthorizationInfoProvider {
+public class OpenBISAuthorizationInfoProvider implements AuthorizationInfoProvider
+{
private IApplicationServerApi v3 = null;
@Override
- public void init(Configuration initParameter) throws Exception {
+ public void init(Configuration initParameter) throws Exception
+ {
String openBISUrl = initParameter.getStringProperty(AtomicFileSystemServerParameter.openBISUrl);
int openBISTimeout = initParameter.getIntegerProperty(AtomicFileSystemServerParameter.openBISTimeout);
v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, openBISUrl, openBISTimeout);
}
@Override
- public boolean doesSessionHaveRights(String sessionToken, String owner, Set<FilePermission> permissions) {
- Set<FilePermission> found = new HashSet<>();
+ public boolean doesSessionHaveRights(String sessionToken, String owner, Set<FilePermission> permissions)
+ {
+ IPermIdHolder foundOwner = ProxyUtil.findOwner(v3, sessionToken, owner);
- ISampleId identifier = null;
- if (owner.contains("/")) { // Is Identifier
- identifier = new SampleIdentifier(owner);
- } else { // Is permId
- identifier = new SamplePermId(owner);
- }
- Map<ISampleId, Sample> samples = v3.getSamples(sessionToken, List.of(identifier), new SampleFetchOptions());
- if (!samples.isEmpty()) {
- found.add(FilePermission.Read);
+ if (foundOwner == null)
+ {
+ return false;
}
- Rights rights = v3.getRights(sessionToken, List.of(identifier), new RightsFetchOptions()).get(identifier);
- if (rights.getRights().contains(Right.UPDATE)) {
- found.add(FilePermission.Write);
+
+ Set<FilePermission> foundPermissions = new HashSet<>();
+ foundPermissions.add(FilePermission.Read);
+
+ Rights rights = v3.getRights(sessionToken, List.of(foundOwner.getPermId()), new RightsFetchOptions()).get(foundOwner.getPermId());
+
+ if (rights.getRights().contains(Right.UPDATE))
+ {
+ foundPermissions.add(FilePermission.Write);
}
- for (FilePermission permission:permissions) {
- if (!found.contains(permission)) {
+ for (FilePermission permission : permissions)
+ {
+ if (!foundPermissions.contains(permission))
+ {
return false;
}
}
+
return true;
}
+
}
diff --git a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ExecutorProxy.java b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ExecutorProxy.java
index 2b4b5e71ecf..21e208255da 100644
--- a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ExecutorProxy.java
+++ b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ExecutorProxy.java
@@ -15,20 +15,42 @@
*/
package ch.ethz.sis.afsserver.worker.proxy;
+import java.nio.file.Files;
+import java.nio.file.Paths;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
+import ch.ethz.sis.afs.exception.AFSExceptions;
import ch.ethz.sis.afsapi.dto.File;
import ch.ethz.sis.afsapi.dto.FreeSpace;
+import ch.ethz.sis.afsserver.startup.AtomicFileSystemServerParameter;
import ch.ethz.sis.afsserver.worker.AbstractProxy;
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPermIdHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
import ch.ethz.sis.shared.io.IOUtils;
+import ch.ethz.sis.shared.startup.Configuration;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import lombok.NonNull;
-public class ExecutorProxy extends AbstractProxy {
+public class ExecutorProxy extends AbstractProxy
+{
- public ExecutorProxy() {
+ private final IApplicationServerApi v3;
+
+ private final String storageRoot;
+
+ private final String storageUuid;
+
+ public ExecutorProxy(final Configuration configuration)
+ {
super(null);
+ String openBISUrl = configuration.getStringProperty(AtomicFileSystemServerParameter.openBISUrl);
+ int openBISTimeout = configuration.getIntegerProperty(AtomicFileSystemServerParameter.openBISTimeout);
+ v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, openBISUrl, openBISTimeout);
+ storageRoot = configuration.getStringProperty(AtomicFileSystemServerParameter.storageRoot);
+ storageUuid = configuration.getStringProperty(AtomicFileSystemServerParameter.storageUuid);
}
//
@@ -36,28 +58,33 @@ public class ExecutorProxy extends AbstractProxy {
//
@Override
- public void begin(UUID transactionId) throws Exception {
+ public void begin(UUID transactionId) throws Exception
+ {
workerContext.setTransactionId(transactionId);
workerContext.getConnection().begin(transactionId);
}
@Override
- public Boolean prepare() throws Exception {
+ public Boolean prepare() throws Exception
+ {
return workerContext.getConnection().prepare();
}
@Override
- public void commit() throws Exception {
+ public void commit() throws Exception
+ {
workerContext.getConnection().commit();
}
@Override
- public void rollback() throws Exception {
+ public void rollback() throws Exception
+ {
workerContext.getConnection().rollback();
}
@Override
- public List<UUID> recover() throws Exception {
+ public List<UUID> recover() throws Exception
+ {
return workerContext.getConnection().recover();
}
@@ -65,45 +92,95 @@ public class ExecutorProxy extends AbstractProxy {
// File System Operations
//
- public String getPath(String owner, String source) {
- return String.join(""+IOUtils.PATH_SEPARATOR, "", owner.toString(), source);
+ public String getPath(String owner, String source)
+ {
+ if (storageUuid == null)
+ {
+ // AFS does not reuse DSS store folder
+ return String.join("" + IOUtils.PATH_SEPARATOR, "", owner.toString(), source);
+ } else
+ {
+ // AFS reuses DSS store folder
+ IPermIdHolder foundOwner = ProxyUtil.findOwner(v3, workerContext.getSessionToken(), owner);
+
+ if (foundOwner == null)
+ {
+ throw AFSExceptions.NotAPath.getInstance(owner);
+ }
+
+ String foundOwnerPath = null;
+
+ if (foundOwner instanceof DataSet)
+ {
+ DataSet foundDataSet = (DataSet) foundOwner;
+ foundOwnerPath = foundDataSet.getPhysicalData().getShareId() + "/" + foundDataSet.getPhysicalData().getLocation();
+ } else
+ {
+ String[] shares = IOUtils.getShares(storageRoot);
+ String[] shards = IOUtils.getShards(owner);
+
+ for (String share : shares)
+ {
+ String potentialOwnerPath = share + "/" + storageUuid + String.join("/", shards) + "/" + foundOwner.getPermId().toString();
+ if (Files.exists(Paths.get(potentialOwnerPath)))
+ {
+ foundOwnerPath = potentialOwnerPath;
+ break;
+ }
+ }
+ }
+
+ if (foundOwnerPath == null)
+ {
+ throw AFSExceptions.NotAPath.getInstance(owner);
+ }
+
+ return String.join("" + IOUtils.PATH_SEPARATOR, "", foundOwnerPath, source);
+ }
}
@Override
- public List<File> list(String owner, String source, Boolean recursively) throws Exception {
+ public List<File> list(String owner, String source, Boolean recursively) throws Exception
+ {
return workerContext.getConnection().list(getPath(owner, source), recursively)
.stream()
.map(file -> convertToFile(owner, file))
.collect(Collectors.toList());
}
- private File convertToFile(String owner, ch.ethz.sis.afs.api.dto.File file) {
+ private File convertToFile(String owner, ch.ethz.sis.afs.api.dto.File file)
+ {
return new File(owner, file.getPath().substring(owner.length() + 1), file.getName(), file.getDirectory(), file.getSize(),
file.getLastModifiedTime(), file.getCreationTime(), file.getLastAccessTime());
}
@Override
- public byte[] read(String owner, String source, Long offset, Integer limit) throws Exception {
+ public byte[] read(String owner, String source, Long offset, Integer limit) throws Exception
+ {
return workerContext.getConnection().read(getPath(owner, source), offset, limit);
}
@Override
- public Boolean write(String owner, String source, Long offset, byte[] data, byte[] md5Hash) throws Exception {
+ public Boolean write(String owner, String source, Long offset, byte[] data, byte[] md5Hash) throws Exception
+ {
return workerContext.getConnection().write(getPath(owner, source), offset, data, md5Hash);
}
@Override
- public Boolean delete(String owner, String source) throws Exception {
+ public Boolean delete(String owner, String source) throws Exception
+ {
return workerContext.getConnection().delete(getPath(owner, source));
}
@Override
- public Boolean copy(String sourceOwner, String source, String targetOwner, String target) throws Exception {
+ public Boolean copy(String sourceOwner, String source, String targetOwner, String target) throws Exception
+ {
return workerContext.getConnection().copy(getPath(sourceOwner, source), getPath(targetOwner, target));
}
@Override
- public Boolean move(String sourceOwner, String source, String targetOwner, String target) throws Exception {
+ public Boolean move(String sourceOwner, String source, String targetOwner, String target) throws Exception
+ {
return workerContext.getConnection().move(getPath(sourceOwner, source), getPath(targetOwner, target));
}
diff --git a/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ProxyUtil.java b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ProxyUtil.java
new file mode 100644
index 00000000000..07c7dbdbf86
--- /dev/null
+++ b/server-data-store/src/main/java/ch/ethz/sis/afsserver/worker/proxy/ProxyUtil.java
@@ -0,0 +1,109 @@
+package ch.ethz.sis.afsserver.worker.proxy;
+
+import java.util.List;
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPermIdHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+
+public class ProxyUtil
+{
+
+ public static IPermIdHolder findOwner(IApplicationServerApi v3, String sessionToken, String owner)
+ {
+ Experiment foundExperiment = findExperiment(v3, sessionToken, owner);
+
+ if (foundExperiment != null)
+ {
+ return foundExperiment;
+ }
+
+ Sample foundSample = ProxyUtil.findSample(v3, sessionToken, owner);
+
+ if (foundSample != null)
+ {
+ return foundSample;
+ }
+
+ return ProxyUtil.findDataSet(v3, sessionToken, owner);
+ }
+
+ public static Experiment findExperiment(IApplicationServerApi v3, String sessionToken, String experimentPermIdOrIdentifier)
+ {
+ IExperimentId experimentId;
+
+ if (experimentPermIdOrIdentifier.contains("/"))
+ { // Is Identifier
+ experimentId = new ExperimentIdentifier(experimentPermIdOrIdentifier);
+ } else
+ { // Is permId
+ experimentId = new ExperimentPermId(experimentPermIdOrIdentifier);
+ }
+
+ Map<IExperimentId, Experiment> experiments = v3.getExperiments(sessionToken, List.of(experimentId), new ExperimentFetchOptions());
+
+ if (!experiments.isEmpty())
+ {
+ return experiments.get(experimentId);
+ } else
+ {
+ return null;
+ }
+ }
+
+ public static Sample findSample(IApplicationServerApi v3, String sessionToken, String samplePermIdOrIdentifier)
+ {
+ ISampleId sampleId;
+
+ if (samplePermIdOrIdentifier.contains("/"))
+ { // Is Identifier
+ sampleId = new SampleIdentifier(samplePermIdOrIdentifier);
+ } else
+ { // Is permId
+ sampleId = new SamplePermId(samplePermIdOrIdentifier);
+ }
+
+ Map<ISampleId, Sample> samples = v3.getSamples(sessionToken, List.of(sampleId), new SampleFetchOptions());
+
+ if (!samples.isEmpty())
+ {
+ return samples.get(sampleId);
+ } else
+ {
+ return null;
+ }
+ }
+
+ public static DataSet findDataSet(IApplicationServerApi v3, String sessionToken, String dataSetPermId)
+ {
+ IDataSetId dataSetId = new DataSetPermId(dataSetPermId);
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withPhysicalData();
+
+ Map<IDataSetId, DataSet> dataSets = v3.getDataSets(sessionToken, List.of(dataSetId), fo);
+
+ if (!dataSets.isEmpty())
+ {
+ return dataSets.get(dataSetId);
+ } else
+ {
+ return null;
+ }
+ }
+
+}
--
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