diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
index 38c2d1a2822d39c34d9dca5810cf7ddc2dfc3109..5e8a2400139581dec0ae19820dbd0545888f5ad5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
@@ -22,7 +22,6 @@ import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -44,6 +43,10 @@ import javax.persistence.Version;
import javax.validation.constraints.NotNull;
import javax.validation.constraints.Pattern;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentityHolder;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
@@ -62,9 +65,6 @@ import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.collection.UnmodifiableSetDecorator;
import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentityHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AttachmentHolderKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -129,32 +129,29 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
private String permId;
- private Set<SampleRelationshipPE> parentRelationships = new LinkedHashSet<SampleRelationshipPE>();
+ private Set<SampleRelationshipPE> parentRelationships;
- private Set<SampleRelationshipPE> childRelationships = new LinkedHashSet<SampleRelationshipPE>();
+ private Set<SampleRelationshipPE> childRelationships;
private Set<MetaprojectAssignmentPE> metaprojectAssignments =
new HashSet<MetaprojectAssignmentPE>();
- @OptimisticLock(excluded = true)
- @OneToMany(fetch = FetchType.LAZY, mappedBy = "parentSample")
- @Fetch(FetchMode.SUBSELECT)
+ @Transient
private Set<SampleRelationshipPE> getSampleChildRelationships()
{
+ if (childRelationships == null) {
+ if (id == null) {
+ childRelationships = new HashSet<>();
+ } else {
+ childRelationships = new HashSet<>(CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().listSampleChildren(List.of(id)));
+ }
+ }
return childRelationships;
}
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private void setSampleChildRelationships(final Set<SampleRelationshipPE> childRelationships)
- {
- this.childRelationships = childRelationships;
- }
-
@Transient
public Set<SampleRelationshipPE> getChildRelationships()
{
-
return new UnmodifiableSetDecorator<SampleRelationshipPE>(getSampleChildRelationships());
}
@@ -171,23 +168,22 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
{
relationship.setParentSample(this);
getSampleChildRelationships().add(relationship);
+ CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().persist(List.of(relationship));
}
- @OptimisticLock(excluded = true)
- @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "childSample", orphanRemoval = true)
- @Fetch(FetchMode.SUBSELECT)
+ @Transient
private Set<SampleRelationshipPE> getSampleParentRelationships()
{
+ if (parentRelationships == null) {
+ if (id == null) {
+ parentRelationships = new HashSet<>();
+ } else {
+ parentRelationships = new HashSet<>(CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().listSampleParents(List.of(id)));
+ }
+ }
return parentRelationships;
}
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private void setSampleParentRelationships(final Set<SampleRelationshipPE> parentRelationships)
- {
- this.parentRelationships = parentRelationships;
- }
-
@Transient
public Set<SampleRelationshipPE> getParentRelationships()
{
@@ -205,6 +201,7 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
public void setParentRelationships(final Set<SampleRelationshipPE> parentRelationships)
{
+ CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().delete(getSampleParentRelationships());
getSampleParentRelationships().clear();
for (final SampleRelationshipPE sampleRelationship : parentRelationships)
{
@@ -221,6 +218,7 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
{
relationship.setChildSample(this);
getSampleParentRelationships().add(relationship);
+ CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().persist(List.of(relationship));
}
public void removeParentRelationship(final SampleRelationshipPE relationship)
@@ -229,6 +227,7 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
relationship.getParentSample().getSampleChildRelationships().remove(relationship);
relationship.setChildSample(null);
relationship.setParentSample(null);
+ CommonServiceProvider.getDAOFactory().getSampleRelationshipDAO().delete(List.of(relationship));
}
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
index 01082f5e085e9e0df9f6634d8fe5ce990b7c3ca4..77b1bddfd9924e819cd3bd6852f15a4dad9bd492 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
@@ -1,4 +1,5 @@
-define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria', 'as/dto/datastore/fetchoptions/DataStoreFetchOptions', 'as/dto/common/search/SearchResult' ], function(jquery,
+define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria', 'as/dto/datastore/fetchoptions/DataStoreFetchOptions',
+ 'as/dto/common/search/SearchResult'], function(jquery,
stjsUtil, DataStoreSearchCriteria, DataStoreFetchOptions, SearchResult) {
jquery.noConflict();
@@ -128,11 +129,11 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
}
- this._createUrlWithParameters = function(dataStore, servlet, parameters) {
+ function createUrlWithParameters(dataStore, servlet, parameters) {
return dataStore.downloadUrl + "/datastore_server/" + servlet + parameters;
}
- this._createUrl = function(dataStore) {
+ function createUrl(dataStore) {
return dataStore.downloadUrl + "/datastore_server/rmi-data-store-server-v3.json";
}
@@ -141,7 +142,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
return this._getDataStores().then(function(dataStores) {
var promises = dataStores.map(function(dataStore) {
return facade._private.ajaxRequest({
- url : thisFacade._createUrl(dataStore),
+ url : createUrl(dataStore),
data : {
"method" : "searchFiles",
"params" : [ facade._private.sessionToken, criteria, fetchOptions ]
@@ -192,7 +193,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
var dsCode = dataStore.getCode();
if (dsCode in creationsByStore) {
promises.push(facade._private.ajaxRequest({
- url : thisFacade._createUrl(dataStore),
+ url : createUrl(dataStore),
data : {
"method" : "createDataSets",
"params" : [ facade._private.sessionToken, creationsByStore[dsCode] ]
@@ -269,60 +270,185 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
this.createUploadedDataSet = function(creation) {
+ var dfd = jquery.Deferred();
+ this._getDataStores().done(function(dataStores) {
+ if (dataStores.length === 1) {
+ facade._private.ajaxRequest({
+ url: createUrl(dataStores[0]),
+ data: {
+ "method": "createUploadedDataSet",
+ "params": [facade._private.sessionToken, creation]
+ },
+ returnType: {
+ name: "DataSetPermId"
+ }
+ }).done(function (response) {
+ dfd.resolve(response);
+ }).fail(function (error) {
+ dfd.reject(error);
+ });
+ } else {
+ dfd.reject("Please specify exactly one data store");
+ }
+ });
+ return dfd.promise();
+ }
+
+ function getUUID() {
+ return ([1e7]+-1e3+-4e3+-8e3+-1e11).replace(/[018]/g, c =>
+ (c ^ crypto.getRandomValues(new Uint8Array(1))[0] & 15 >> c / 4).toString(16)
+ );
+ }
+
+ this.uploadFileWorkspaceDSS = function(files) {
var thisFacade = this;
- return this._getDataStores().then(function(dataStores) {
- if (dataStores.length > 1) {
- var dfd = jquery.Deferred();
+ var uploadId = getUUID();
+ var dfd = jquery.Deferred();
+ this._uploadFileWorkspaceDSSEmptyDir(uploadId).done(function() {
+ thisFacade._uploadFileWorkspaceDSS(files, 0, uploadId, new Set()).done(function() {
+ dfd.resolve(uploadId);
+ }).fail(function(error) {
+ dfd.reject(error);
+ });
+ }).fail(function(error) {
+ dfd.reject(error);
+ });
+ return dfd.promise();
+ }
+
+ this._uploadFileWorkspaceDSS = function(files, index, parentId, createdDirectories) {
+ var thisFacade = this;
+ var dfd = jquery.Deferred();
+ if (index < files.length) {
+ var relativePath = files[index].webkitRelativePath;
+ var directoryRelativePath = relativePath.substring(0, relativePath.lastIndexOf("/") + 1);
+ if (directoryRelativePath && !createdDirectories.has(directoryRelativePath)) {
+ this._uploadFileWorkspaceDSSEmptyDir(parentId + "/" + directoryRelativePath)
+ .done(function() {
+ createdDirectories.add(directoryRelativePath);
+ thisFacade._uploadFileWorkspaceDSSFile(files[index], parentId)
+ .done(function() {
+ thisFacade._uploadFileWorkspaceDSS(files, index + 1, parentId, createdDirectories)
+ .done(function() {
+ dfd.resolve();
+ })
+ .fail(function(error) {
+ dfd.reject(error);
+ });
+ })
+ .fail(function(error) {
+ dfd.reject(error);
+ });
+ })
+ .fail(function(error) {
+ dfd.reject(error);
+ });
+ } else {
+ this._uploadFileWorkspaceDSSFile(files[index], parentId)
+ .done(function() {
+ thisFacade._uploadFileWorkspaceDSS(files, index + 1, parentId, createdDirectories)
+ .done(function() {
+ dfd.resolve();
+ })
+ .fail(function(error) {
+ dfd.reject(error);
+ });
+ })
+ .fail(function(error) {
+ dfd.reject(error);
+ });
+ }
+ } else {
+ dfd.resolve();
+ }
+ return dfd.promise();
+ }
+
+ this._uploadFileWorkspaceDSSEmptyDir = function(pathToDir) {
+ var sessionID = facade._private.sessionToken;
+ var filename = encodeURIComponent(pathToDir);
+ var dfd = jquery.Deferred();
+ this._getDataStores().done(function (dataStores) {
+ if (dataStores.length === 1) {
+ fetch(createUrlWithParameters(dataStores[0], "session_workspace_file_upload",
+ "?sessionID=" + sessionID +
+ "&filename=" + filename +
+ "&id=1&startByte=0&endByte=0&size=0&emptyFolder=true"), {
+ method: "POST",
+ headers: {
+ "Content-Type": "multipart/form-data"
+ }
+ }).then(function (response) {
+ dfd.resolve(response);
+ }).catch(function (error) {
+ dfd.reject(error);
+ });
+ } else {
dfd.reject("Please specify exactly one data store");
- return dfd.promise();
}
+ }).fail(function(error) {
+ dfd.reject(error);
+ });
+ return dfd.promise();
+ }
- return facade._private.ajaxRequest({
- url : thisFacade._createUrl(dataStores[0]),
- data : {
- "method" : "createUploadedDataSet",
- "params" : [ facade._private.sessionToken, creation ]
+ this._uploadFileWorkspaceDSSFile = function(file, parentId) {
+ const dfd = jquery.Deferred();
+ this._getDataStores().done(function(dataStores) {
+ uploadBlob(dataStores[0], parentId, facade._private.sessionToken, file, 0, 1048576)
+ .done(function() {
+ dfd.resolve();
+ }).fail(function(error) {
+ dfd.reject(error);
+ });
+ }).fail(function(error) {
+ dfd.reject(error);
+ });
+ return dfd.promise();
+ }
+
+ function uploadBlob(dataStore, parentId, sessionID, file, startByte, chunkSize) {
+ var fileSize = file.size;
+ var promises = [];
+ for (var byte = startByte; byte < fileSize; byte += chunkSize) {
+ const dfd = jquery.Deferred();
+ fetch(createUrlWithParameters(dataStore, "session_workspace_file_upload",
+ "?sessionID=" + sessionID +
+ "&filename=" + encodeURIComponent(parentId + "/" +
+ (file.webkitRelativePath ? file.webkitRelativePath : file.name)) +
+ "&id=1&startByte=" + byte +
+ "&endByte=" + (byte + chunkSize) +
+ "&size=" + fileSize +
+ "&emptyFolder=false"), {
+ method: "POST",
+ headers: {
+ "Content-Type": "multipart/form-data"
},
- returnType : {
- name : "DataSetPermId"
- }
+ body: makeChunk(file, byte, Math.min(byte + chunkSize, fileSize))
+ }).then(function () {
+ dfd.resolve();
+ }).catch(function (error) {
+ console.error("Error:", error);
+ dfd.reject(error);
});
- });
+ promises.push(dfd);
+ }
+
+ return jquery.when.apply(jquery, promises);
}
- this.uploadFileWorkspaceDSS = function(file) {
- var thisFacade = this;
-
- var getUUID = function() {
- return ([1e7]+-1e3+-4e3+-8e3+-1e11).replace(/[018]/g, c =>
- (c ^ crypto.getRandomValues(new Uint8Array(1))[0] & 15 >> c / 4).toString(16)
- );
- };
-
- //File
- var sessionID = facade._private.sessionToken
- var id = 0;
- var filename = file.name;
- var startByte = 0;
- var endByte = file.size;
-
- return this._getDataStores().then(function(dataStores) {
- if (dataStores.length > 1) {
- var dfd = jquery.Deferred();
- dfd.reject("Please specify exactly one data store");
- return dfd.promise();
- }
-
- var parameters = "?sessionID=" + sessionID + "&filename=" + encodeURIComponent(filename) + "&id=" + id + "&startByte=" + startByte + "&endByte=" + endByte;
- return facade._private.ajaxRequest({
- url : thisFacade._createUrlWithParameters(dataStores[0], "session_workspace_file_upload", parameters),
- contentType: "multipart/form-data",
- data: file
- });
- });
- }
-
-}
+ function makeChunk(file, startByte, endByte) {
+ var blob = undefined;
+ if (file.slice) {
+ blob = file.slice(startByte, endByte);
+ } else if (file.webkitSlice) {
+ blob = file.webkitSlice(startByte, endByte);
+ } else if (file.mozSlice) {
+ blob = file.mozSlice(startByte, endByte);
+ }
+ return blob;
+ }
+ }
var facade = function(openbisUrl) {
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
index 44d8b658618314371655ba475d3a10aa82e99808..1ba56ddbeb0504e6d106c44b4ed4cdc76797b431 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
@@ -885,6 +885,9 @@ public final class SampleBOTest extends AbstractBOTest
one(sampleTypeDAO).tryFindSampleTypeByCode(DILUTION_PLATE);
will(returnValue(new SampleTypePE()));
+ one(permIdDAO).createPermId();
+ will(returnValue("2023010112341234-10"));
+
one(propertiesConverter).convertProperties(IEntityProperty.EMPTY_ARRAY, null,
EXAMPLE_PERSON);
@@ -921,6 +924,9 @@ public final class SampleBOTest extends AbstractBOTest
one(sampleTypeDAO).tryFindSampleTypeByCode(DILUTION_PLATE);
will(returnValue(new SampleTypePE()));
+ one(permIdDAO).createPermId();
+ will(returnValue("2023010112341234-10"));
+
one(propertiesConverter).convertProperties(IEntityProperty.EMPTY_ARRAY, null,
EXAMPLE_PERSON);
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/OpenBISAPI.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/OpenBISAPI.java
new file mode 100644
index 0000000000000000000000000000000000000000..ad3536e726558db21e35dd8def89c1b908ae0a5a
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/OpenBISAPI.java
@@ -0,0 +1,224 @@
+package ch.ethz.sis.openbis.generic;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Path;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.UUID;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeoutException;
+
+import org.apache.log4j.Logger;
+import org.eclipse.jetty.client.api.ContentResponse;
+import org.eclipse.jetty.client.api.Request;
+import org.eclipse.jetty.client.util.BytesContentProvider;
+import org.eclipse.jetty.http.HttpMethod;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.UploadedDataSetCreation;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+
+public class OpenBISAPI {
+
+ private static final Logger OPERATION_LOG = LogFactory.getLogger(LogCategory.OPERATION, OpenBISAPI.class);
+
+ private static final int DEFAULT_TIMEOUT_IN_MILLIS = 30000; //30 seconds
+
+ private static final int CHUNK_SIZE = 1048576; // 1 MiB
+
+ private static final Collection<Integer> ACCEPTABLE_STATUSES = List.of(200);
+
+ private final IApplicationServerApi asFacade;
+
+ private final IDataStoreServerApi dssFacade;
+
+ private String sessionToken;
+
+ private final int timeout;
+
+ private final String asURL;
+
+ private final String dssURL;
+
+ public OpenBISAPI(final String asURL, final String dssURL)
+ {
+ this(asURL, dssURL, DEFAULT_TIMEOUT_IN_MILLIS);
+ }
+
+ public OpenBISAPI(final String asURL, final String dssURL, final int timeout)
+ {
+ this.timeout = timeout;
+ this.asURL = asURL;
+ asFacade = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, this.asURL + IApplicationServerApi.SERVICE_URL, timeout);
+ this.dssURL = dssURL;
+ dssFacade = HttpInvokerUtils.createServiceStub(IDataStoreServerApi.class, this.dssURL + IDataStoreServerApi.SERVICE_URL, timeout);
+ }
+
+ public String getSessionToken()
+ {
+ return sessionToken;
+ }
+
+ public void setSessionToken(final String sessionToken)
+ {
+ this.sessionToken = sessionToken;
+ }
+
+ public String login(String userId, String password) {
+ String sessionToken = asFacade.login(userId, password);
+ setSessionToken(sessionToken);
+ return sessionToken;
+ }
+
+ public void logout() {
+ asFacade.logout(sessionToken);
+ }
+
+ public DataSetPermId createUploadedDataSet(final UploadedDataSetCreation newDataSet)
+ {
+ return dssFacade.createUploadedDataSet(sessionToken, newDataSet);
+ }
+
+ public String uploadFileWorkspaceDSS(final Path fileOrFolder)
+ {
+ String uploadId = uploadFileWorkspaceDSSEmptyDir(UUID.randomUUID().toString());
+ uploadFileWorkspaceDSS(fileOrFolder.toFile(), uploadId);
+ return uploadId;
+ }
+
+ //
+ // Helper Methods to upload files to DSS Session Workspace
+ //
+
+ /**
+ * Upload file or folder to the DSS SessionWorkspaceFileUploadServlet and return the ID to be used by createUploadedDataSet
+ * This method hides the complexities of uploading a folder with many files and does the uploads in chunks.
+ */
+ private String uploadFileWorkspaceDSS(final File fileOrFolder, final String parentsOrNull)
+ {
+ if (fileOrFolder.exists() == false)
+ {
+ throw new UserFailureException("Path doesn't exist: " + fileOrFolder);
+ }
+ String fileNameOrFolderName = "";
+ if (parentsOrNull != null)
+ {
+ fileNameOrFolderName = parentsOrNull + "/";
+ }
+ fileNameOrFolderName += fileOrFolder.getName();
+
+ if (fileOrFolder.isDirectory())
+ {
+ uploadFileWorkspaceDSSEmptyDir(fileNameOrFolderName);
+ for (File file : fileOrFolder.listFiles())
+ {
+ uploadFileWorkspaceDSS(file, fileNameOrFolderName);
+ }
+ } else {
+ uploadFileWorkspaceDSSFile(fileNameOrFolderName, fileOrFolder);
+ }
+ return fileNameOrFolderName;
+ }
+
+ private String uploadFileWorkspaceDSSEmptyDir(String pathToDir) {
+ final org.eclipse.jetty.client.HttpClient client = JettyHttpClientFactory.getHttpClient();
+ final Request httpRequest = client.newRequest(dssURL + "/session_workspace_file_upload")
+ .method(HttpMethod.POST);
+ httpRequest.param("sessionID", sessionToken);
+ httpRequest.param("id", "1");
+ httpRequest.param("filename", pathToDir);
+ httpRequest.param("startByte", Long.toString(0));
+ httpRequest.param("endByte", Long.toString(0));
+ httpRequest.param("size", Long.toString(0));
+ httpRequest.param("emptyFolder", Boolean.TRUE.toString());
+
+ try {
+ final ContentResponse response = httpRequest.send();
+ final int status = response.getStatus();
+ if (status != 200)
+ {
+ throw new IOException(response.getContentAsString());
+ }
+ } catch (final IOException | TimeoutException | InterruptedException | ExecutionException e)
+ {
+ throw new RuntimeException(e);
+ }
+ return pathToDir;
+ }
+
+ private String uploadFileWorkspaceDSSFile(String pathToFile, File file) {
+ try {
+ long start = 0;
+ for (byte[] chunk : streamFile(file, CHUNK_SIZE)) {
+ final long end = start + chunk.length;
+
+ final org.eclipse.jetty.client.HttpClient client = JettyHttpClientFactory.getHttpClient();
+ final Request httpRequest = client.newRequest(dssURL + "/session_workspace_file_upload")
+ .method(HttpMethod.POST);
+ httpRequest.param("sessionID", sessionToken);
+ httpRequest.param("id", "1");
+ httpRequest.param("filename", pathToFile);
+ httpRequest.param("startByte", Long.toString(start));
+ httpRequest.param("endByte", Long.toString(end));
+ httpRequest.param("size", Long.toString(file.length()));
+ httpRequest.content(new BytesContentProvider(chunk));
+ final ContentResponse response = httpRequest.send();
+ final int status = response.getStatus();
+ if (status != 200) {
+ throw new IOException(response.getContentAsString());
+ }
+ start += CHUNK_SIZE;
+ }
+ } catch (final IOException | TimeoutException | InterruptedException | ExecutionException e) {
+ throw new RuntimeException(e);
+ }
+ return pathToFile;
+ }
+
+ private Iterable<byte[]> streamFile(final File file, final int chunkSize) throws FileNotFoundException
+ {
+ final InputStream inputStream = new FileInputStream(file);
+
+ return new Iterable<byte[]>() {
+ @Override
+ public Iterator<byte[]> iterator() {
+ return new Iterator<byte[]>() {
+ public boolean hasMore = true;
+
+ public boolean hasNext() {
+ return hasMore;
+ }
+
+ public byte[] next() {
+ try {
+ byte[] bytes = inputStream.readNBytes(chunkSize);
+ if (bytes.length < chunkSize) {
+ hasMore = false;
+ inputStream.close();
+ }
+ return bytes;
+ } catch (final IOException e) {
+ try {
+ inputStream.close();
+ } catch (final IOException ex) {
+ throw new RuntimeException(ex);
+ }
+ throw new RuntimeException(e);
+ }
+ }
+ };
+ }
+ };
+ }
+}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 5c4fd14cc39983a3a196f9149f37ba6ffbc82570..9565d715b0f63b16145540dc4d72e7e83d6f5ef4 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
@@ -151,10 +151,12 @@ def validateDataSize(entitiesToExport, tr):
estimatedSizeInBytes += 12000; # AVG File Metadata size
estimatedSizeInMegabytes = estimatedSizeInBytes / 1000000;
operationLog.info(
- "Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes) + " > " + " estimatedSizeInBytes: " + str(estimatedSizeInBytes));
+ u"Size Limit check - limitDataSizeInBytes: " + str(limitDataSizeInBytes).encode('utf-8') +
+ u" > estimatedSizeInBytes: " + str(estimatedSizeInBytes).encode('utf-8'));
if estimatedSizeInBytes > limitDataSizeInBytes:
- raise UserFailureException("The selected data is " + str(estimatedSizeInMegabytes) + " MB that is bigger than the configured limit of " + str(
- limitDataSizeInMegabytes) + " MB");
+ raise UserFailureException(u"The selected data is " + estimatedSizeInMegabytes +
+ u" MB that is bigger than the configured limit of " +
+ limitDataSizeInMegabytes + u" MB");
def findEntitiesToExport(params):
@@ -172,17 +174,17 @@ def findEntitiesToExport(params):
if entity.get("expand"):
entitiesToExpand.append(entityAsPythonMap);
- operationLog.info("Found %d entities to expand." % len(entitiesToExpand))
+ operationLog.info(u"Found %d entities to expand." % len(entitiesToExpand))
while entitiesToExpand:
entityToExpand = entitiesToExpand.popleft();
type = entityToExpand["type"];
permId = entityToExpand["permId"];
- operationLog.info("Expanding type: " + str(type) + " permId: " + str(permId));
+ operationLog.info(u"Expanding type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
if type == "ROOT":
criteria = SpaceSearchCriteria();
results = v3.searchSpaces(sessionToken, criteria, SpaceFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " spaces");
+ operationLog.info(u"Found: %d spaces" % results.getTotalCount());
for space in results.getObjects():
entityFound = {"type": "SPACE", "permId": space.getCode(), "registrationDate": space.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -191,7 +193,7 @@ def findEntitiesToExport(params):
criteria = ProjectSearchCriteria();
criteria.withSpace().withCode().thatEquals(permId);
results = v3.searchProjects(sessionToken, criteria, ProjectFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " projects");
+ operationLog.info(u"Found: %d projects" % results.getTotalCount());
for project in results.getObjects():
entityFound = {"type": "PROJECT", "permId": project.getPermId().getPermId(), "registrationDate": project.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -200,7 +202,7 @@ def findEntitiesToExport(params):
criteria = ExperimentSearchCriteria();
criteria.withProject().withPermId().thatEquals(permId);
results = v3.searchExperiments(sessionToken, criteria, ExperimentFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " experiments");
+ operationLog.info(u"Found: %d experiments" % results.getTotalCount());
for experiment in results.getObjects():
entityFound = {"type": "EXPERIMENT", "permId": experiment.getPermId().getPermId(),
"registrationDate": experiment.getRegistrationDate()};
@@ -210,7 +212,7 @@ def findEntitiesToExport(params):
criteria = SampleSearchCriteria();
criteria.withExperiment().withPermId().thatEquals(permId);
results = v3.searchSamples(sessionToken, criteria, SampleFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
+ operationLog.info(u"Found: %d samples" % results.getTotalCount());
dCriteria = DataSetSearchCriteria();
dCriteria.withExperiment().withPermId().thatEquals(permId);
@@ -218,13 +220,13 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
dResults = v3.searchDataSets(sessionToken, dCriteria, fetchOptions);
- operationLog.info("Found: " + str(dResults.getTotalCount()) + " datasets");
+ operationLog.info(u"Found: %d datasets" % dResults.getTotalCount());
for dataset in dResults.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
entitiesToExpand.append(entityFound);
- operationLog.info("Found: " + str(results.getTotalCount()) + " samples");
+ operationLog.info(u"Found: %d samples" % results.getTotalCount());
for sample in results.getObjects():
entityFound = {"type": "SAMPLE", "permId": sample.getPermId().getPermId(), "registrationDate": sample.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -235,7 +237,7 @@ def findEntitiesToExport(params):
fetchOptions = DataSetFetchOptions()
fetchOptions.withDataStore()
results = v3.searchDataSets(sessionToken, criteria, fetchOptions);
- operationLog.info("Found: " + str(results.getTotalCount()) + " datasets");
+ operationLog.info(u"Found: %d datasets" % results.getTotalCount());
for dataset in results.getObjects():
entityFound = {"type": "DATASET", "permId": dataset.getPermId().getPermId(), "registrationDate": dataset.getRegistrationDate()};
addToExportWithoutRepeating(entitiesToExport, entityFound);
@@ -244,7 +246,7 @@ def findEntitiesToExport(params):
criteria = DataSetFileSearchCriteria();
criteria.withDataSet().withPermId().thatEquals(permId);
results = v3d.searchFiles(sessionToken, criteria, DataSetFileFetchOptions());
- operationLog.info("Found: " + str(results.getTotalCount()) + " files");
+ operationLog.info(u"Found: %d files" % results.getTotalCount());
for file in results.getObjects():
entityFound = {"type": "FILE", "permId": permId, "path": file.getPath(), "isDirectory": file.isDirectory(),
"length": file.getFileLength()};
@@ -282,7 +284,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
for entity in entities:
type = entity["type"];
permId = entity["permId"];
- operationLog.info("exporting type: " + str(type) + " permId: " + str(permId));
+ operationLog.info(u"exporting type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8"));
entityObj = None;
entityFilePath = None;
@@ -383,8 +385,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
if entityObj is not None:
objectCache[permId] = entityObj;
- operationLog.info("--> Entity type: " + type + " permId: " + permId + " obj: " + str(entityObj is not None) + " path: " + str(
- entityFilePath) + " before files.");
+ operationLog.info(u"--> Entity type: %s permId: %s obj: %s path: %s before files." % (type, permId, str(entityObj is not None), entityFilePath));
if entityObj is not None and entityFilePath is not None:
# JSON
entityJson = String(objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(entityObj));
@@ -403,19 +404,20 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, de
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
- operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
+ operationLog.info(u"--> Entity type: " + type.encode("utf-8") + u" permId: " + permId.encode("utf-8") +
+ u" post html.");
if emptyZip:
- raise IOError('Nothing added to ZIP file.')
+ raise IOError("Nothing added to ZIP file.")
return fileMetadata
def generateDownloadUrl(sessionToken, tempZipFileName, tempZipFilePath):
# Store on workspace to be able to generate a download link
- operationLog.info("Zip file can be found on the temporal directory: " + tempZipFilePath);
+ operationLog.info(u"Zip file can be found on the temporal directory: " + tempZipFilePath.encode("utf-8"));
dssService = ServiceProvider.getApplicationContext().getBean("dss-service-rpc-generic")
dssService.putFileToSessionWorkspace(sessionToken, tempZipFileName, FileInputStream(File(tempZipFilePath)))
tempZipFileWorkspaceURL = DataStoreServer.getConfigParameters().getDownloadURL() + "/datastore_server/session_workspace_file_download?sessionID=" + sessionToken + "&filePath=" + tempZipFileName;
- operationLog.info("Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL);
+ operationLog.info(u"Zip file can be downloaded from the workspace: " + tempZipFileWorkspaceURL.encode("utf-8"));
return tempZipFileWorkspaceURL