diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/OpenBIS.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/OpenBIS.java
index ede5ae601e1850100b5e77f56382d0dc22983b42..76ba0dae6246adf2359a34a1d51770650f9183c2 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/OpenBIS.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/OpenBIS.java
@@ -34,9 +34,13 @@ import java.util.UUID;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeoutException;
+import org.eclipse.jetty.client.HttpClient;
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.client.util.MultiPartContentProvider;
+import org.eclipse.jetty.client.util.PathContentProvider;
+import org.eclipse.jetty.client.util.StringContentProvider;
import org.eclipse.jetty.http.HttpMethod;
import ch.ethz.sis.afsapi.api.OperationsAPI;
@@ -116,7 +120,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.update.ExternalDmsUp
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -1241,7 +1245,7 @@ public class OpenBIS
return asFacadeWithTransactions.createCodes(sessionToken, prefix, entityKind, count);
}
- public void executeImport(IImportData importData, ImportOptions importOptions) {
+ public void executeImport(ImportData importData, ImportOptions importOptions) {
asFacadeWithTransactions.executeImport(sessionToken, importData, importOptions);
}
@@ -1249,6 +1253,45 @@ public class OpenBIS
return asFacadeWithTransactions.executeExport(sessionToken, exportData, exportOptions);
}
+ public String uploadToSessionWorkspace(final Path fileOrFolder)
+ {
+ if (transactionId != null)
+ {
+ throw new IllegalStateException("AS session workspace SHOULD NOT be used during transactions.");
+ }
+
+ String uploadId = UUID.randomUUID().toString() + "/" + fileOrFolder.getFileName().toString();
+
+ try
+ {
+ HttpClient httpClient = JettyHttpClientFactory.getHttpClient();
+
+ MultiPartContentProvider multiPart = new MultiPartContentProvider();
+ multiPart.addFieldPart("sessionKeysNumber", new StringContentProvider("1"), null);
+ multiPart.addFieldPart("sessionKey_0", new StringContentProvider("openbis-file-upload"), null);
+ multiPart.addFilePart("openbis-file-upload", uploadId, new PathContentProvider(fileOrFolder), null);
+ multiPart.addFieldPart("keepOriginalFileName", new StringContentProvider("True"), null);
+ multiPart.addFieldPart("sessionID", new StringContentProvider(this.sessionToken), null);
+ multiPart.close();
+
+ ContentResponse response = httpClient.newRequest(this.asURL + "/upload")
+ .method(HttpMethod.POST)
+ .content(multiPart)
+ .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 uploadId;
+ }
+
//
// DSS Facade methods
//
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
index bd1ec54d8cec68848cb6ffe19e7017edaf66d141..c58a8be081a0980d9a16540c824afa355a50e5fb 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
@@ -89,7 +89,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.update.ExternalDmsUp
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -2262,7 +2263,7 @@ public interface IApplicationServerApi extends IRpcService
*/
public List<String> createCodes(String sessionToken, String prefix, EntityKind entityKind, int count);
- public void executeImport(String sessionToken, IImportData importData, ImportOptions importOptions);
+ public ImportResult executeImport(String sessionToken, ImportData importData, ImportOptions importOptions);
public ExportResult executeExport(String sessionToken, ExportData exportData, ExportOptions exportOptions);
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperation.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperation.java
index 509ee42d9781903c7c0162e4a46e13957a9430aa..479452c9b9841166b7ab85d028b09e81db8bb35c 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperation.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperation.java
@@ -24,7 +24,7 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.ObjectToString;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.operation.IOperation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.systemsx.cisd.base.annotation.JsonObject;
@@ -35,7 +35,7 @@ public class ImportOperation implements Serializable, IOperation
private static final long serialVersionUID = 1L;
@JsonProperty
- private IImportData importData;
+ private ImportData importData;
@JsonProperty
private ImportOptions importOptions;
@@ -45,7 +45,7 @@ public class ImportOperation implements Serializable, IOperation
{
}
- public ImportOperation(final IImportData importData, final ImportOptions importOptions)
+ public ImportOperation(final ImportData importData, final ImportOptions importOptions)
{
this.importData = importData;
this.importOptions = importOptions;
@@ -58,13 +58,13 @@ public class ImportOperation implements Serializable, IOperation
}
@JsonIgnore
- public IImportData getImportData()
+ public ImportData getImportData()
{
return importData;
}
@JsonIgnore
- public void setImportData(final IImportData importData)
+ public void setImportData(final ImportData importData)
{
this.importData = importData;
}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperationResult.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperationResult.java
index a28b89ee5f3c05a1fcecc0435662dd63c556abe0..54e9619942e2aff248c18b6972b54ec644c21ad2 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperationResult.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportOperationResult.java
@@ -19,6 +19,9 @@ package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer;
import java.io.Serializable;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.operation.IOperationResult;
import ch.systemsx.cisd.base.annotation.JsonObject;
@@ -28,12 +31,35 @@ public class ImportOperationResult implements Serializable, IOperationResult
private static final long serialVersionUID = 1L;
+ @JsonProperty
+ private ImportResult importResult;
+
+ public ImportOperationResult()
+ {
+ }
+
+ public ImportOperationResult(final ImportResult importResult)
+ {
+ this.importResult = importResult;
+ }
+
@Override
public String getMessage()
{
return toString();
}
+ @JsonIgnore
+ public ImportResult getImportResult()
+ {
+ return importResult;
+ }
+
+ public void setImportResult(final ImportResult importResult)
+ {
+ this.importResult = importResult;
+ }
+
@Override
public String toString()
{
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportScript.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportResult.java
similarity index 59%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportScript.java
rename to api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportResult.java
index 4307d2ff86c753ce26a9c42d1ddb1ccf3d2929cf..29ca23329d807b456294d2050e6c3027bc6fe47e 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportScript.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/ImportResult.java
@@ -14,67 +14,53 @@
* limitations under the License.
*/
-package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data;
+package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer;
import java.io.Serializable;
+import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.ObjectToString;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
import ch.systemsx.cisd.base.annotation.JsonObject;
-@JsonObject("as.dto.importer.data.ImportScript")
-public class ImportScript implements Serializable
+@JsonObject("as.dto.importer.ImportResult")
+public class ImportResult implements Serializable
{
private static final long serialVersionUID = 1L;
@JsonProperty
- private String name;
-
- @JsonProperty
- private String source;
+ private List<IObjectId> objectIds;
@SuppressWarnings("unused")
- public ImportScript()
- {
- }
-
- public ImportScript(final String name, final String source)
+ public ImportResult()
{
- this.name = name;
- this.source = source;
}
- @JsonIgnore
- public String getName()
- {
- return name;
- }
-
- @JsonIgnore
- public void setName(final String name)
+ public ImportResult(final List<IObjectId> objectIds)
{
- this.name = name;
+ this.objectIds = objectIds;
}
@JsonIgnore
- public String getSource()
+ public List<IObjectId> getObjectIds()
{
- return source;
+ return objectIds;
}
@JsonIgnore
- public void setSource(final String source)
+ public void setObjectIds(final List<IObjectId> objectIds)
{
- this.source = source;
+ this.objectIds = objectIds;
}
@Override
public String toString()
{
- return new ObjectToString(this).append("name", name).append("source", source).toString();
+ return new ObjectToString(this).append("objectIds", objectIds).toString();
}
}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/IImportData.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/IImportData.java
deleted file mode 100644
index 4f47167bdca1a88a117f8a56475c629b63600d91..0000000000000000000000000000000000000000
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/IImportData.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-
-@JsonObject("as.dto.importer.data.IImportData")
-public interface IImportData extends Serializable
-{
-}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ZipImportData.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportData.java
similarity index 74%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ZipImportData.java
rename to api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportData.java
index d3a95e6bbd35b02a1091889c8fd17ce38cf460ac..02137385311c6446a995290c96f66ac6d0b53f7b 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ZipImportData.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportData.java
@@ -24,8 +24,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.ObjectToString;
import ch.systemsx.cisd.base.annotation.JsonObject;
-@JsonObject("as.dto.importer.data.ZipImportData")
-public class ZipImportData implements Serializable, IImportData
+@JsonObject("as.dto.importer.data.ImportData")
+public class ImportData implements Serializable
{
private static final long serialVersionUID = 1L;
@@ -33,17 +33,17 @@ public class ZipImportData implements Serializable, IImportData
private ImportFormat format;
@JsonProperty
- private byte[] file;
+ private String[] sessionWorkspaceFiles;
@SuppressWarnings("unused")
- public ZipImportData()
+ public ImportData()
{
}
- public ZipImportData(final ImportFormat format, final byte[] file)
+ public ImportData(final ImportFormat format, final String... sessionWorkspaceFiles)
{
this.format = format;
- this.file = file;
+ this.sessionWorkspaceFiles = sessionWorkspaceFiles;
}
@JsonIgnore
@@ -58,16 +58,14 @@ public class ZipImportData implements Serializable, IImportData
this.format = format;
}
- @JsonIgnore
- public byte[] getFile()
+ public String[] getSessionWorkspaceFiles()
{
- return file;
+ return sessionWorkspaceFiles;
}
- @JsonIgnore
- public void setFile(final byte[] file)
+ public void setSessionWorkspaceFiles(String[] sessionWorkspaceFiles)
{
- this.file = file;
+ this.sessionWorkspaceFiles = sessionWorkspaceFiles;
}
@Override
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportFormat.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportFormat.java
index 3bd858e12712669ecd3d96ed0ec4738bff954153..415b5c6295014dbd9efc5128f5bce07e1daf8242 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportFormat.java
+++ b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportFormat.java
@@ -22,6 +22,6 @@ import ch.systemsx.cisd.base.annotation.JsonObject;
public enum ImportFormat
{
- XLS
+ EXCEL
}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportValue.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportValue.java
deleted file mode 100644
index 005b3e1059aef790c9dcfebe2eb0b4b205cdae86..0000000000000000000000000000000000000000
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/ImportValue.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data;
-
-import java.io.Serializable;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.ObjectToString;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-
-@JsonObject("as.dto.importer.data.ImportValue")
-public class ImportValue implements Serializable
-{
-
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private String name;
-
- @JsonProperty
- private String value;
-
- @SuppressWarnings("unused")
- public ImportValue()
- {
- }
-
- public ImportValue(final String name, final String value)
- {
- this.name = name;
- this.value = value;
- }
-
- @JsonIgnore
- public String getName()
- {
- return name;
- }
-
- @JsonIgnore
- public void setName(final String name)
- {
- this.name = name;
- }
-
- @JsonIgnore
- public String getValue()
- {
- return value;
- }
-
- @JsonIgnore
- public void setValue(final String value)
- {
- this.value = value;
- }
-
- @Override
- public String toString()
- {
- final ObjectToString builder = new ObjectToString(this).append("name", name);
- if (value == null)
- {
- builder.append("value", null);
- } else if (value.length() <= 255)
- {
- builder.append("value", value);
- } else
- {
- builder.append("value", value.substring(0, 255) + "...");
- }
- return builder.toString();
- }
-
-}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/UncompressedImportData.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/UncompressedImportData.java
deleted file mode 100644
index 44113b16817213fa7c372fa3871779ce4e91b2a8..0000000000000000000000000000000000000000
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/UncompressedImportData.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data;
-
-import java.io.Serializable;
-import java.util.Collection;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.ObjectToString;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-
-@JsonObject("as.dto.importer.data.UncompressedImportData")
-public class UncompressedImportData implements Serializable, IImportData
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private ImportFormat format;
-
- @JsonProperty
- private byte[] file;
-
- @JsonProperty
- private Collection<ImportScript> scripts;
-
- @JsonProperty
- private Collection<ImportValue> importValues;
-
- @SuppressWarnings("unused")
- public UncompressedImportData()
- {
- }
-
- public UncompressedImportData(final ImportFormat format, final byte[] file, final Collection<ImportScript> scripts,
- final Collection<ImportValue> importValues)
- {
- this.format = format;
- this.file = file;
- this.scripts = scripts;
- this.importValues = importValues;
- }
-
- @JsonIgnore
- public ImportFormat getFormat()
- {
- return format;
- }
-
- @JsonIgnore
- public void setFormat(final ImportFormat format)
- {
- this.format = format;
- }
-
- @JsonIgnore
- public byte[] getFile()
- {
- return file;
- }
-
- @JsonIgnore
- public void setFile(final byte[] file)
- {
- this.file = file;
- }
-
- @JsonIgnore
- public Collection<ImportScript> getScripts()
- {
- return scripts;
- }
-
- @JsonIgnore
- public void setScripts(final Collection<ImportScript> scripts)
- {
- this.scripts = scripts;
- }
-
- @JsonIgnore
- public Collection<ImportValue> getImportValues()
- {
- return importValues;
- }
-
- @JsonIgnore
- public void setImportValues(final Collection<ImportValue> importValues)
- {
- this.importValues = importValues;
- }
-
- @Override
- public String toString()
- {
- return new ObjectToString(this).append("format", format).append("scripts", scripts).toString();
- }
-
-}
diff --git a/api-openbis-java/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt b/api-openbis-java/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
index af8a6580cf705a2d6aa1ca7516aa93231d96f283..21daba1c397710945af2d28792ee8cb41812b2c3 100644
--- a/api-openbis-java/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
+++ b/api-openbis-java/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
@@ -464,6 +464,7 @@ Event Sort Options
Event Tech Id
Event Type
Event Type Search Criteria
+EXCEL
exec
execute Aggregation Service
Execute Aggregation Service Operation
@@ -1282,7 +1283,6 @@ IExternalDmsId
IFileFormatTypeId
IGNORE_EXISTING
IIdentifierHolder
-IImportData
ILocatorTypeId
ImagingDataSetConfig
ImagingDataSetControl
@@ -1300,8 +1300,6 @@ ImportModes
ImportOperation
ImportOperationResult
ImportOptions
-ImportScript
-ImportValue
indent
indexOf
INSTANCE
@@ -2495,7 +2493,6 @@ UNARCHIVE_PENDING
UnarchiveDataSetsOperation
UnarchiveDataSetsOperationResult
UnauthorizedObjectAccessException
-UncompressedImportData
UNDEFINED
UNIQUE_SUBCODES
UNKNOWN
@@ -2903,7 +2900,6 @@ XlsTextFormat
XLSX
XML
YES
-ZipImportData
I Transaction Coordinator Api
I Transaction Participant Api
APPLICATION_SERVER_PARTICIPANT_ID
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/ImportOperation.js b/api-openbis-javascript/src/v3/as/dto/importer/ImportOperation.js
index 717aa8112bffde1141a8bb3bf359ee5e6ce61d21..aeb00d41c2da7c72016158de687936c5779d0dc6 100644
--- a/api-openbis-javascript/src/v3/as/dto/importer/ImportOperation.js
+++ b/api-openbis-javascript/src/v3/as/dto/importer/ImportOperation.js
@@ -46,7 +46,7 @@ define(["stjs", "as/dto/common/operation/IOperation"],
};
},
{
- importData: "IImportData",
+ importData: "ImportData",
importOptions: "ImportOptions"
}
);
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/ImportOperationResult.js b/api-openbis-javascript/src/v3/as/dto/importer/ImportOperationResult.js
index 8644008309f35a02da7fcdeee25354a5a1d0b28c..9bdfca0689c2e34d47404b78eee237965fee1918 100644
--- a/api-openbis-javascript/src/v3/as/dto/importer/ImportOperationResult.js
+++ b/api-openbis-javascript/src/v3/as/dto/importer/ImportOperationResult.js
@@ -17,7 +17,8 @@
define(["stjs", "as/dto/common/operation/IOperationResult"],
function (stjs, IOperationResult) {
- var ImportOperationResult = function() {
+ var ImportOperationResult = function(importResult) {
+ this.importResult = importResult;
}
stjs.extend(
@@ -28,12 +29,23 @@ define(["stjs", "as/dto/common/operation/IOperationResult"],
prototype["@type"] = "as.dto.importer.ImportOperationResult";
constructor.serialVersionUID = 1;
+ prototype.importResult = null;
prototype.getMessage = function() {
return "ImportOperationResult";
};
+
+ prototype.getImportResult = function() {
+ return this.importResult;
+ };
+
+ prototype.setImportResult = function(importResult) {
+ this.importResult = importResult;
+ };
},
- {}
+ {
+ importResult: "ImportResult"
+ }
);
return ImportOperationResult;
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportScript.js b/api-openbis-javascript/src/v3/as/dto/importer/ImportResult.js
similarity index 58%
rename from api-openbis-javascript/src/v3/as/dto/importer/data/ImportScript.js
rename to api-openbis-javascript/src/v3/as/dto/importer/ImportResult.js
index 64545851a6271a2595aec39c671ec1c5858d1456..29daa115a9837ac0624ea98a7f5600e087b4b51d 100644
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportScript.js
+++ b/api-openbis-javascript/src/v3/as/dto/importer/ImportResult.js
@@ -15,40 +15,36 @@
*
*/
-define(["stjs"],
- function (stjs) {
- var ImportScript = function() {
+define(["stjs"], function (stjs) {
+ var ImportResult = function(objectIds) {
+ this.objectIds = objectIds;
}
stjs.extend(
- ImportScript,
+ ImportResult,
null,
[],
function (constructor, prototype) {
- prototype["@type"] = "as.dto.importer.data.ImportScript";
+ prototype["@type"] = "as.dto.importer.ImportResult";
constructor.serialVersionUID = 1;
- prototype.name = null;
- prototype.source = null;
+ prototype.objectIds = null;
- prototype.getName = function() {
- return this.name;
+ prototype.getObjectIds = function() {
+ return this.objectIds;
};
- prototype.setName = function(name) {
- this.name = name;
- };
-
- prototype.getSource = function() {
- return this.source;
- };
-
- prototype.setSource = function(source) {
- this.source = source;
+ prototype.setObjectIds = function(objectIds) {
+ this.objectIds = objectIds;
};
},
- {}
+ {
+ objectIds: {
+ name: "List",
+ arguments: ["IObjectId"]
+ }
+ }
);
- return ImportScript;
+ return ImportResult;
});
\ No newline at end of file
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/IImportData.js b/api-openbis-javascript/src/v3/as/dto/importer/data/IImportData.js
deleted file mode 100644
index 1289c8e8e4d5fc079dc7015a826b2e4cb6f0d821..0000000000000000000000000000000000000000
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/IImportData.js
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-define(["stjs"], function (stjs) {
- var IImportData = function () {
- };
- stjs.extend(IImportData, null, [], null, {});
- return IImportData;
-});
\ No newline at end of file
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/ZipImportData.js b/api-openbis-javascript/src/v3/as/dto/importer/data/ImportData.js
similarity index 61%
rename from api-openbis-javascript/src/v3/as/dto/importer/data/ZipImportData.js
rename to api-openbis-javascript/src/v3/as/dto/importer/data/ImportData.js
index 918cc534cd6552fff8c56e05034e0815f33aa253..9786a7ef566b7f8ed41bb4bae185b15b2d644237 100644
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/ZipImportData.js
+++ b/api-openbis-javascript/src/v3/as/dto/importer/data/ImportData.js
@@ -15,21 +15,22 @@
*
*/
-define(["stjs", "as/dto/importer/data/IImportData"],
- function (stjs, IImportData) {
- var ZipImportData = function() {
+define(["stjs"], function (stjs) {
+ var ImportData = function(format, sessionWorkspaceFiles) {
+ this.format = format;
+ this.sessionWorkspaceFiles = sessionWorkspaceFiles;
}
stjs.extend(
- ZipImportData,
- IImportData,
- [IImportData],
+ ImportData,
+ null,
+ [],
function (constructor, prototype) {
- prototype["@type"] = "as.dto.importer.data.ZipImportData";
+ prototype["@type"] = "as.dto.importer.data.ImportData";
constructor.serialVersionUID = 1;
prototype.format = null;
- prototype.file = null;
+ prototype.sessionWorkspaceFiles = null;
prototype.getFormat = function() {
return this.format;
@@ -39,19 +40,19 @@ define(["stjs", "as/dto/importer/data/IImportData"],
this.format = format;
};
- prototype.getFile = function() {
- return this.file;
+ prototype.getSessionWorkspaceFiles = function() {
+ return this.sessionWorkspaceFiles;
};
- prototype.setFile = function(file) {
- this.file = file;
+ prototype.setSessionWorkspaceFiles = function(sessionWorkspaceFiles) {
+ this.sessionWorkspaceFiles = sessionWorkspaceFiles;
};
},
{
format: "ImportFormat",
- file: "byte[]"
+ sessionWorkspaceFiles: "String[]"
}
);
- return ZipImportData;
+ return ImportData;
});
\ No newline at end of file
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportFormat.js b/api-openbis-javascript/src/v3/as/dto/importer/data/ImportFormat.js
index 982b7ff16bf67abb8fba38779fe10f233d4997d0..4ffb6dd245409c3c821af477395dc5f15e11b058 100644
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportFormat.js
+++ b/api-openbis-javascript/src/v3/as/dto/importer/data/ImportFormat.js
@@ -17,7 +17,7 @@
define(["stjs", "as/dto/common/Enum"], function (stjs, Enum) {
var ImportFormat = function() {
- Enum.call(this, ["XLS"]);
+ Enum.call(this, ["EXCEL"]);
}
stjs.extend(
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportValue.js b/api-openbis-javascript/src/v3/as/dto/importer/data/ImportValue.js
deleted file mode 100644
index e8bddc19ddbc290d97453e38dded0705365fe526..0000000000000000000000000000000000000000
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/ImportValue.js
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright ETH 2024 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-define(["stjs"],
- function (stjs) {
- var ImportValue = function() {
- }
-
- stjs.extend(
- ImportValue,
- null,
- [],
- function (constructor, prototype) {
- prototype["@type"] = "as.dto.importer.data.ImportValue";
-
- constructor.serialVersionUID = 1;
- prototype.name = null;
- prototype.value = null;
-
- prototype.getName = function() {
- return this.name;
- };
-
- prototype.setName = function(name) {
- this.name = name;
- };
-
- prototype.getValue = function() {
- return this.value;
- };
-
- prototype.setValue = function(value) {
- this.value = value;
- };
- },
- {}
- );
-
- return ImportValue;
- });
\ No newline at end of file
diff --git a/api-openbis-javascript/src/v3/as/dto/importer/data/UncompressedImportData.js b/api-openbis-javascript/src/v3/as/dto/importer/data/UncompressedImportData.js
deleted file mode 100644
index 49084d1b71cc60392c1ff59c3a47f06f3657bcb8..0000000000000000000000000000000000000000
--- a/api-openbis-javascript/src/v3/as/dto/importer/data/UncompressedImportData.js
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-define(["stjs", "as/dto/importer/data/IImportData"],
- function (stjs, IImportData) {
- var UncompressedImportData = function() {
- }
-
- stjs.extend(
- UncompressedImportData,
- IImportData,
- [IImportData],
- function (constructor, prototype) {
- prototype["@type"] = "as.dto.importer.data.UncompressedImportData";
-
- constructor.serialVersionUID = 1;
- prototype.format = null;
- prototype.file = null;
- prototype.scripts = null;
- prototype.importValues = null;
-
- prototype.getFormat = function() {
- return this.format;
- };
-
- prototype.setFormat = function(format) {
- this.format = format;
- };
-
- prototype.getFile = function() {
- return this.file;
- };
-
- prototype.setFile = function(file) {
- this.file = file;
- };
-
- prototype.getScripts = function() {
- return this.scripts;
- };
-
- prototype.setScripts = function(scripts) {
- this.scripts = scripts;
- };
-
- prototype.getImportValues = function() {
- return this.importValues;
- };
-
- prototype.setImportValues = function(importValues) {
- this.importValues = importValues;
- };
- },
- {
- format: "ImportFormat",
- file: "byte[]",
- scripts: {
- name: "Collection",
- arguments: ["ImportScript"]
- },
- importValues: {
- name: "Collection",
- arguments: ["ImportValue"]
- }
- }
- );
-
- return UncompressedImportData;
- });
\ No newline at end of file
diff --git a/api-openbis-javascript/src/v3/openbis.js b/api-openbis-javascript/src/v3/openbis.js
index f7a8d669586eb261f939331da483b19ba15f9469..a5c1a6be3fdc922f885e489e1ce466a5655f0d51 100644
--- a/api-openbis-javascript/src/v3/openbis.js
+++ b/api-openbis-javascript/src/v3/openbis.js
@@ -2728,6 +2728,34 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
})
}
+ this.uploadToSessionWorkspace = function(file) {
+ //Building Form Data Object for Multipart File Upload
+ var formData = new FormData();
+ formData.append("sessionKeysNumber", "1");
+ formData.append("sessionKey_0", "openbis-file-upload");
+ formData.append("openbis-file-upload", file);
+ formData.append("keepOriginalFileName", "True");
+ formData.append("sessionID", this._private.sessionToken);
+
+ var dfd = jquery.Deferred();
+
+ jquery.ajax({
+ type: "POST",
+ url: "/openbis/openbis/upload",
+ contentType: false,
+ processData: false,
+ data: formData,
+ success: function() {
+ dfd.resolve();
+ },
+ error: function() {
+ dfd.reject();
+ }
+ });
+
+ return dfd.promise();
+ }
+
/**
* =======================
* OpenBIS webapp context
diff --git a/api-openbis-typescript/source/java/ch/ethz/sis/openbis/generic/typescript/dto/OpenBISJavaScriptFacade.java b/api-openbis-typescript/source/java/ch/ethz/sis/openbis/generic/typescript/dto/OpenBISJavaScriptFacade.java
index cb1cb28377795d66cf6b5f7992296c72e2738e45..c55846a1f9fde3aebeb570d293bea8779f16dd8e 100644
--- a/api-openbis-typescript/source/java/ch/ethz/sis/openbis/generic/typescript/dto/OpenBISJavaScriptFacade.java
+++ b/api-openbis-typescript/source/java/ch/ethz/sis/openbis/generic/typescript/dto/OpenBISJavaScriptFacade.java
@@ -75,7 +75,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.update.ExternalDmsUp
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -1322,9 +1323,9 @@ public class OpenBISJavaScriptFacade implements IApplicationServerApi
}
@TypeScriptMethod
- @Override public void executeImport(final String sessionToken, final IImportData importData, final ImportOptions importOptions)
+ @Override public ImportResult executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
-
+ return null;
}
@TypeScriptMethod
@@ -1333,6 +1334,11 @@ public class OpenBISJavaScriptFacade implements IApplicationServerApi
return null;
}
+ @TypeScriptMethod(sessionToken = false)
+ public void uploadToSessionWorkspace(final Object file)
+ {
+ }
+
@TypeScriptMethod(sessionToken = false)
@Override public int getMajorVersion()
{
diff --git a/core-plugin-openbis/.dynamic_property_evaluator_queue b/core-plugin-openbis/.dynamic_property_evaluator_queue
deleted file mode 100644
index 2e08dce276e43c677d121d627a250d1710fed824..0000000000000000000000000000000000000000
Binary files a/core-plugin-openbis/.dynamic_property_evaluator_queue and /dev/null differ
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java
index 69708ddf23d89fd553aaf7281023c434a8e05b94..42c27477f7a1f22381655cc8e63bb66905b6532e 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java
@@ -16,6 +16,9 @@
package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.UUID;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.testng.AbstractTransactionalTestNGSpringContextTests;
@@ -24,8 +27,10 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeSuite;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
import ch.systemsx.cisd.openbis.generic.server.util.TestInitializer;
import ch.systemsx.cisd.openbis.generic.shared.Constants;
+import ch.systemsx.cisd.openbis.generic.shared.ISessionWorkspaceProvider;
import ch.systemsx.cisd.openbis.generic.shared.coreplugin.CorePluginsUtils;
public class AbstractImportTest extends AbstractTransactionalTestNGSpringContextTests
@@ -41,6 +46,10 @@ public class AbstractImportTest extends AbstractTransactionalTestNGSpringContext
protected static final String PASSWORD = "password";
+ protected static final String VALIDATION_SCRIPT = "full/scripts/valid.py";
+
+ protected static final String DYNAMIC_SCRIPT = "full/scripts/dynamic/dynamic.py";
+
@Autowired
protected IApplicationServerInternalApi v3api;
@@ -54,6 +63,7 @@ public class AbstractImportTest extends AbstractTransactionalTestNGSpringContext
System.setProperty(XLS_VERSIONING_DIR, VERSIONING_JSON);
System.setProperty(CorePluginsUtils.CORE_PLUGINS_FOLDER_KEY, "dist/core-plugins");
System.setProperty(Constants.ENABLED_MODULES_KEY, "xls-import");
+ System.setProperty(Constants.PROJECT_SAMPLES_ENABLED_KEY, "false");
TestInitializer.initEmptyDbNoIndex();
}
@@ -71,4 +81,31 @@ public class AbstractImportTest extends AbstractTransactionalTestNGSpringContext
v3api.logout(sessionToken);
}
+ protected static String uploadToAsSessionWorkspace(final String sessionToken, final String filePath) throws IOException
+ {
+ final ISessionWorkspaceProvider sessionWorkspaceProvider = CommonServiceProvider.getSessionWorkspaceProvider();
+ final String destination = UUID.randomUUID() + "/" + new File(filePath).getName();
+
+ sessionWorkspaceProvider.write(sessionToken, destination, new FileInputStream("sourceTest/java/" + filePath));
+
+ return destination;
+ }
+
+ protected static String[] uploadToAsSessionWorkspace(final String sessionToken, final String... filePaths) throws IOException
+ {
+ final ISessionWorkspaceProvider sessionWorkspaceProvider = CommonServiceProvider.getSessionWorkspaceProvider();
+ final UUID uploadId = UUID.randomUUID();
+
+ final String[] destinations = new String[filePaths.length];
+ for (int i = 0; i < filePaths.length; i++)
+ {
+ destinations[i] = uploadId
+ + (filePaths[i].toLowerCase().endsWith(".xls") || filePaths[i].toLowerCase().endsWith(".xlsx") ? "/" : "/scripts/")
+ + new File(filePaths[i]).getName();
+ sessionWorkspaceProvider.write(sessionToken, destinations[i], new FileInputStream("sourceTest/java/" + filePaths[i]));
+ }
+
+ return destinations;
+ }
+
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java
index 1a13a1028e60b5f4765d916cbe7db1cf80f38315..bf607e4745614b3ce160f5beeade93dac21b4ba8 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java
@@ -70,13 +70,16 @@ public class ImportDatasetTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, DATASET_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
List<String> propertyNames = Arrays.asList("$NAME", "NOTES");
List<PropertyAssignment> propertyAssignments = TestUtils.extractAndSortPropertyAssignmentsPerGivenPropertyName(rawData, propertyNames);
PropertyAssignment nameProperty = propertyAssignments.get(0);
PropertyAssignment notesProperty = propertyAssignments.get(1);
+
// THEN
assertEquals(rawData.getCode(), "RAW_DATA");
assertEquals(rawData.getPropertyAssignments().size(), 2);
@@ -101,9 +104,12 @@ public class ImportDatasetTypesTest extends AbstractImportTest
public void testDatasetTypesWithoutPropertiesTypesAreCreated() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_WITHOUT_PROPERTIES)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, DATASET_WITHOUT_PROPERTIES));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
+
// THEN
assertEquals(rawData.getCode(), "RAW_DATA");
assertEquals(rawData.getPropertyAssignments().size(), 0);
@@ -114,10 +120,13 @@ public class ImportDatasetTypesTest extends AbstractImportTest
public void testDatasetTypesWithValidationScript() throws Exception
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
- Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_WITH_VALIDATION_SCRIPT)));
+ final String[] sessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, DATASET_WITH_VALIDATION_SCRIPT), FilenameUtils.concat(FILES_DIR, VALIDATION_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePaths[0]));
+
// WHEN
DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
+
// THEN
assertEquals(rawData.getValidationPlugin().getName().toUpperCase(), "RAW_DATA.VALID");
}
@@ -130,15 +139,19 @@ public class ImportDatasetTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, DATASET_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getDynamicPluginMap(), UpdateMode.UPDATE_IF_EXISTS,
- Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_TYPES_UPDATE)));
+ final String[] sessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, DATASET_TYPES_UPDATE), FilenameUtils.concat(FILES_DIR, DYNAMIC_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePaths[0]));
DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
List<String> propertyNames = Arrays.asList("$NAME", "NOTES");
List<PropertyAssignment> propertyAssignments = TestUtils.extractAndSortPropertyAssignmentsPerGivenPropertyName(rawData, propertyNames);
PropertyAssignment nameProperty = propertyAssignments.get(0);
PropertyAssignment notesProperty = propertyAssignments.get(1);
+
// THEN
// Property Assignment updates are not supported, no change here between updates.
assertTrue(nameProperty.isMandatory());
@@ -157,10 +170,11 @@ public class ImportDatasetTypesTest extends AbstractImportTest
assertEquals(notesProperty.getPlugin(), null);
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header should contain 'Code'.*")
public void shouldThrowExceptionIfNoSampleCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, DATASET_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java
index f8f56716ddd3b2675eab3e22e5fc357ab82c6738..843e6c02e72f27794f013002bc82bdaf7bb71bb5 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java
@@ -73,13 +73,16 @@ public class ImportExperimentTypesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
ExperimentType collection = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
List<String> propertyNames = Arrays.asList("$NAME", "DEFAULT_OBJECT_TYPE");
List<PropertyAssignment> propertyAssignments = TestUtils.extractAndSortPropertyAssignmentsPerGivenPropertyName(collection, propertyNames);
PropertyAssignment nameProperty = propertyAssignments.get(0);
PropertyAssignment defaultObjectTypeProperty = propertyAssignments.get(1);
+
// THEN
assertEquals(collection.getCode(), "COLLECTION");
assertEquals(collection.getPropertyAssignments().size(), 2);
@@ -108,15 +111,19 @@ public class ImportExperimentTypesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getDynamicPluginMap(), UpdateMode.UPDATE_IF_EXISTS,
- Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_UPDATE)));
+ final String[] updateSessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_UPDATE), FilenameUtils.concat(FILES_DIR, DYNAMIC_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(updateSessionWorkspaceFilePaths[0]));
ExperimentType collection = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
List<String> propertyNames = Arrays.asList("$NAME", "DEFAULT_OBJECT_TYPE");
List<PropertyAssignment> propertyAssignments = TestUtils.extractAndSortPropertyAssignmentsPerGivenPropertyName(collection, propertyNames);
PropertyAssignment nameProperty = propertyAssignments.get(0);
PropertyAssignment defaultObjectTypeProperty = propertyAssignments.get(1);
+
// THEN
// Property Assignment updates are not supported, no change here between updates.
assertTrue(nameProperty.isMandatory());
@@ -141,18 +148,22 @@ public class ImportExperimentTypesTest extends AbstractImportTest
public void testExperimentTypesWithValidationScript() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
- Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_WITH_VALIDATION_SCRIPT)));
+ final String[] sessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_WITH_VALIDATION_SCRIPT), FilenameUtils.concat(FILES_DIR, VALIDATION_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePaths[0]));
+
// WHEN
ExperimentType collection = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
+
// THEN
assertEquals(collection.getValidationPlugin().getName().toUpperCase(), "COLLECTION.VALID");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Mandatory field is missing or empty: Code.*")
public void shouldThrowExceptionIfNoSampleCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java
index 742ed9ffbe57a62a5dcde02244b8be6a1fdbc1c5..ec529f6dcff09d55c73999459e0d3e03b5583c27 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java
@@ -96,9 +96,12 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.FAIL_IF_EXISTS, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -114,9 +117,12 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT2", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT2");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -132,12 +138,23 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -153,12 +170,22 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -166,20 +193,36 @@ public class ImportExperimentsTest extends AbstractImportTest
assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Experiment type COLLECTION not found.*")
public void shouldThrowExceptionIfExperimentTypeDoesntExist() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Entity \\[/TEST_SPACE/TEST_PROJECT\\] could not be found\\..*")
public void shouldThrowExceptionIfProjectDoesntExist() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ // the Excel contains internally property types which can be only manipulated by the system user
+ sessionToken = v3api.loginAsSystem();
+
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
}
@Test
@@ -190,10 +233,17 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -209,12 +259,23 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectSessionWorkspaceFilePath));
+
+ final String experimentsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentsSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -225,7 +286,8 @@ public class ImportExperimentsTest extends AbstractImportTest
@Test(expectedExceptions = UserFailureException.class)
public void shouldThrowExceptionIfExperimentNoCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -236,9 +298,13 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_NON_MANDATORY_PROPERTY_MISSING)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_NON_MANDATORY_PROPERTY_MISSING));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -249,7 +315,9 @@ public class ImportExperimentsTest extends AbstractImportTest
@Test(expectedExceptions = RuntimeException.class)
public void shouldThrowExceptionIfExperimentNoProject() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_PROJECT_ATTRIBUTE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_PROJECT_ATTRIBUTE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -260,11 +328,19 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_SPACE_AND_PROJECT_ELSEWHERE)));
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectSessionWorkspaceFilePath));
+
+ final String elsewhereWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_SPACE_AND_PROJECT_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(elsewhereWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -280,10 +356,16 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_SPACE_ELSEWHERE)));
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String spaceElsewhereSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_SPACE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceElsewhereSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -299,11 +381,20 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_AND_SPACE_ELSEWHERE)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String elsewhereSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_AND_SPACE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(elsewhereSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -314,7 +405,9 @@ public class ImportExperimentsTest extends AbstractImportTest
@Test(expectedExceptions = UserFailureException.class)
public void shouldThrowExceptionIfMandatoryPropertyMissing() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_MISSING)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_MISSING));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -325,9 +418,13 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_PRESENT)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_PRESENT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -343,9 +440,13 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -361,11 +462,17 @@ public class ImportExperimentsTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS_TYPE_ON_SERVER)));
+ final String experimentTypeSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(experimentTypeSessionWorkspaceFilePath));
+
+ final String elsewhereSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS_TYPE_ON_SERVER));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(elsewhereSessionWorkspaceFilePath));
+
// WHEN
Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
// THEN
assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
@@ -373,19 +480,26 @@ public class ImportExperimentsTest extends AbstractImportTest
assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
}
-// @Test
-// @DirtiesContext
-// public void testExperimentsUpdate() throws Exception
-// {
-// // GIVEN
-// TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
-// // WHEN
-// TestUtils.createFrom(v3api, sessionToken, TestUtils.getDynamicPluginMap(), UpdateMode.UPDATE_IF_EXISTS,
-// Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_UPDATE)));
-// Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
-// // THEN
-// assertEquals(experiment.getProperties().get("$NAME"), "NameUpdate");
-// assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "DefaultObjectTypeUpdate");
-// }
+ @Test
+ @DirtiesContext
+ public void testExperimentsUpdate() throws Exception
+ {
+ // the Excel contains internally managed property types which can be only manipulated by the system user
+ String sessionToken = v3api.loginAsSystem();
+
+ // GIVEN
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
+ // WHEN
+ final String[] updateSessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, EXPERIMENT_UPDATE), FilenameUtils.concat(FILES_DIR, DYNAMIC_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(updateSessionWorkspaceFilePaths[0]));
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+
+ // THEN
+ assertEquals(experiment.getProperties().get("$NAME"), "NameUpdate");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "DefaultObjectTypeUpdate");
+ }
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportFromExcelTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportFromExcelTest.java
index 46549e079efda295eecd5a620564f51efba59ce7..758adcb28d77a380d399b824e5d849edcf571716 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportFromExcelTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportFromExcelTest.java
@@ -21,7 +21,6 @@ import static org.testng.Assert.assertNotNull;
import java.io.IOException;
import java.nio.file.Paths;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import org.apache.commons.io.FilenameUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
@@ -34,6 +33,7 @@ import org.testng.annotations.Test;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
@ContextConfiguration(locations = "classpath:applicationContext.xml")
@Transactional(transactionManager = "transaction-manager")
@@ -53,21 +53,23 @@ public class ImportFromExcelTest extends AbstractImportTest
FILES_DIR = f.substring(0, f.length() - ImportExperimentTypesTest.class.getSimpleName().length()) + "/test_files/";
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(?s).*Content found after a double blank row that should mark the end of a page\\..*")
@DirtiesContext
public void testFileWithManyBlankRowsWasParsed() throws Exception
{
// the Excel contains internally managed property types which can be only manipulated by the system user
sessionToken = v3api.loginAsSystem();
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, WITH_BLANKS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, WITH_BLANKS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
ExperimentType propertyType = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
assertNotNull(propertyType); // the last line on the first sheet was read
assertEquals(propertyType.getPropertyAssignments().size(), 2);
assertEquals(propertyType.getPropertyAssignments().get(1).getPropertyType().getCode(), "LAST_ROW_EXP_TYPE");
- Sample sample = TestUtils.getSample(v3api, sessionToken, "LAST_SAMPLE", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "LAST_SAMPLE");
assertNotNull(sample); // the last line on the second sheet was read
}
}
\ No newline at end of file
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java
index 0c827f35dd518bf89b739e9b8b597cfcc7af136c..01aa8bc54627e88ac3d4ba001632bcccb77aaac5 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java
@@ -69,9 +69,12 @@ public class ImportProjectsTest extends AbstractImportTest
public void testProjectsAreCreated() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_XLS));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.FAIL_IF_EXISTS, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+
// THEN
assertEquals(project.getCode(), "TEST_PROJECT");
assertEquals(project.getDescription(), "TEST");
@@ -83,10 +86,14 @@ public class ImportProjectsTest extends AbstractImportTest
public void testExistProjectIsUpdated() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_XLS));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
- TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_UPDATE)));
+ final String updateSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_UPDATE));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(updateSessionWorkspaceFilePath));
Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT", "TEST_SPACE2");
+
// THEN
assertEquals(project.getCode(), "TEST_PROJECT");
assertEquals(project.getDescription(), "UPDATE");
@@ -98,19 +105,23 @@ public class ImportProjectsTest extends AbstractImportTest
public void testProjectsAreCreatedSecondProject() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT2");
+
// THEN
assertEquals(project.getCode(), "TEST_PROJECT2");
assertEquals(project.getDescription(), "description of another project");
assertEquals(project.getSpace().getCode(), "TEST_SPACE2");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Code' is missing.*")
public void shouldThrowExceptionIfNoProjectCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -118,19 +129,23 @@ public class ImportProjectsTest extends AbstractImportTest
public void testProjectsAreCreatedNoDescription() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_DESCRIPTION)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_NO_DESCRIPTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+
// THEN
assertEquals(project.getCode(), "TEST_PROJECT");
assertEquals(project.getDescription(), null);
assertEquals(project.getSpace().getCode(), "TEST_SPACE");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Space' is missing.*")
public void shouldThrowExceptionIfNoProjectSpace() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_SPACE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROJECTS_NO_SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -138,10 +153,16 @@ public class ImportProjectsTest extends AbstractImportTest
public void testProjectsAreCreatedSpaceOnServer() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_WITH_SPACES_ON_SERVER)));
+ final String spaceSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACES));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(spaceSessionWorkspaceFilePath));
+
+ final String projectsSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROJECTS_WITH_SPACES_ON_SERVER));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(projectsSessionWorkspaceFilePath));
+
// WHEN
Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+
// THEN
assertEquals(project.getCode(), "TEST_PROJECT");
assertEquals(project.getDescription(), "TEST");
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java
index b7963f77f1f69bfd27dd3d963b44d5a45c7e284d..fc35b51fa4bd6757a89be8d1897184d67303dd54 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java
@@ -17,6 +17,7 @@ package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
@@ -25,7 +26,6 @@ import java.nio.file.Paths;
import java.util.Arrays;
import org.apache.commons.io.FilenameUtils;
-import org.python27.core.PyException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.annotation.Rollback;
@@ -50,6 +50,7 @@ public class ImportPropertyTypesTest extends AbstractImportTest
private IApplicationServerInternalApi v3api;
private static final String PROPERTY_TYPES_XLS = "property_types/normal_property_type.xls";
+
private static final String PROPERTY_TYPES_WITH_PATTERN_XLS = "property_types/normal_property_type_with_pattern.xls";
private static final String PROPERTY_NO_CODE = "property_types/no_code.xls";
@@ -74,7 +75,7 @@ public class ImportPropertyTypesTest extends AbstractImportTest
public void setupClass() throws IOException
{
String f = ImportPropertyTypesTest.class.getName().replace(".", "/");
- FILES_DIR = f.substring(0, f.length() - ImportPropertyTypesTest.class.getSimpleName().length()) + "/test_files/";
+ FILES_DIR = f.substring(0, f.length() - ImportPropertyTypesTest.class.getSimpleName().length()) + "test_files/";
}
@Test
@@ -85,9 +86,12 @@ public class ImportPropertyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "NOTES");
+
// THEN
assertEquals(notes.getCode(), "NOTES");
assertEquals(notes.getLabel(), "Notes");
@@ -105,9 +109,13 @@ public class ImportPropertyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_WITH_PATTERN_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_WITH_PATTERN_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "PATTERN_PATTERN");
+
// THEN
assertEquals(notes.getCode(), "PATTERN_PATTERN");
assertEquals(notes.getLabel(), "Pattern");
@@ -127,9 +135,12 @@ public class ImportPropertyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "$INTERNAL_PROP");
+
// THEN
assertEquals(notes.getCode(), "$INTERNAL_PROP");
assertEquals(notes.getLabel(), "Name");
@@ -144,9 +155,13 @@ public class ImportPropertyTypesTest extends AbstractImportTest
public void testDuplicatesPropertiesAreAllowedIfTheyAreTheSame() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_DUPLICATES_SAME)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_DUPLICATES_SAME));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "NOTES");
+
// THEN
assertEquals(notes.getCode(), "NOTES");
assertEquals(notes.getLabel(), "Notes");
@@ -157,76 +172,96 @@ public class ImportPropertyTypesTest extends AbstractImportTest
assertNull(notes.getVocabulary());
}
- @Test(expectedExceptions = RuntimeException.class)
+ @Test(expectedExceptions = RuntimeException.class, expectedExceptionsMessageRegExp = "(?s).*Mandatory field is missing or empty: Code.*")
public void testPropertyTypeNoCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Property label' is missing.*")
public void testPropertyTypeNoLabel() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_LABEL)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_NO_LABEL));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(?s).*Ambiguous property NOTES found, it has been declared before with different attributes.*")
public void testPropertyTypesDuplicatesAreDifferent() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_DUPLICATES_DIFFERENT)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROPERTY_DUPLICATES_DIFFERENT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = RuntimeException.class)
+ @Test(expectedExceptions = RuntimeException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Vocabulary code' is missing.*")
public void testPropertyTypeNoVocabularyCodeWhenVocabularyType() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_VOCAB_TYPE_NO_VOCABULARY_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROPERTY_VOCAB_TYPE_NO_VOCABULARY_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = RuntimeException.class)
+ @Test(expectedExceptions = RuntimeException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Data type' is missing.*")
public void testPropertyTypeNoDataType() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DATA_TYPE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DATA_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Description' is missing.*")
public void testPropertyTypeNoDescription() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DESCRIPTION)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DESCRIPTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Entity \\[DETECTION\\] could not be found..*")
public void testPropertyTypeVocabularyCodeToNonVocabularyType() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NON_VOCAB_TYPE_VOCABULARY_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, PROPERTY_NON_VOCAB_TYPE_VOCABULARY_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = Exception.class)
+ @Test/*(expectedExceptions = Exception.class)*/
@DirtiesContext
public void deleteProjectFromDBButNotFromJSON() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ // the Excel contains internally property types which can be only manipulated by the system user
+ sessionToken = v3api.loginAsSystem();
+
+ final String sessionWorkspaceFilePath1 = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.FAIL_IF_EXISTS, Paths.get(sessionWorkspaceFilePath1));
PropertyType type = TestUtils.getPropertyType(v3api, sessionToken, "$INTERNAL_PROP");
+ assertNotNull(type);
PropertyTypeDeletionOptions deletionOptions = new PropertyTypeDeletionOptions();
deletionOptions.setReason("test");
v3api.deletePropertyTypes(sessionToken, Arrays.asList(type.getPermId()), deletionOptions);
// After deleting one property, the exception is not thrown.
// Because it can be deleted by the user an DB is fine.
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ final String sessionWorkspaceFilePath2 = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath2));
// remove all data from DB
type = TestUtils.getPropertyType(v3api, sessionToken, "$INTERNAL_PROP");
+ assertNotNull(type);
deletionOptions = new PropertyTypeDeletionOptions();
deletionOptions.setReason("test");
v3api.deletePropertyTypes(sessionToken, Arrays.asList(type.getPermId()), deletionOptions);
type = TestUtils.getPropertyType(v3api, sessionToken, "NOTES");
+ assertNotNull(type);
deletionOptions = new PropertyTypeDeletionOptions();
deletionOptions.setReason("test");
v3api.deletePropertyTypes(sessionToken, Arrays.asList(type.getPermId()), deletionOptions);
// exception should be thrown because DB is empty.
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ final String sessionWorkspaceFilePath3 = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath3));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java
index 4f37c6bd3f32276f9816aed00373bca8400f0cbe..e2a4cf0ee6a3ac9bf5a6fc3df82480b12e4f17eb 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java
@@ -72,7 +72,7 @@ public class ImportSampleTypesTest extends AbstractImportTest
public void setupClass() throws IOException
{
String f = ImportSampleTypesTest.class.getName().replace(".", "/");
- FILES_DIR = f.substring(0, f.length() - ImportSampleTypesTest.class.getSimpleName().length()) + "/test_files/";
+ FILES_DIR = f.substring(0, f.length() - ImportSampleTypesTest.class.getSimpleName().length()) + "test_files/";
}
@Test
@@ -83,9 +83,12 @@ public class ImportSampleTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
assertFalse(antibody.isAutoGeneratedCode());
}
@@ -98,9 +101,12 @@ public class ImportSampleTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
boolean allMandatory = antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isMandatory() == true);
boolean allShownInEditView =
@@ -125,9 +131,13 @@ public class ImportSampleTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS_DIFFERENT_PROPERTY_ASSIGN)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS_DIFFERENT_PROPERTY_ASSIGN));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
boolean allNotMandatory = antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isMandatory() == false);
boolean allNotShownInEditView =
@@ -146,9 +156,12 @@ public class ImportSampleTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
boolean namePropertyExists =
antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getPropertyType().getCode().equals("$NAME"));
@@ -171,15 +184,18 @@ public class ImportSampleTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getDynamicPluginMap(),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_DYNAMIC_SCRIPT)));
+ final String[] sessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_DYNAMIC_SCRIPT), FilenameUtils.concat(FILES_DIR, DYNAMIC_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePaths[0]));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
- Plugin dynamicScript = antibody.getPropertyAssignments().get(0).getPlugin();
+ final Plugin dynamicScript = antibody.getPropertyAssignments().get(0).getPlugin();
assertNotNull(dynamicScript);
assertEquals(dynamicScript.getName().toUpperCase(), "$NAME.DYNAMIC");
- assertEquals(dynamicScript.getScript(), TestUtils.getDynamicScript());
+ assertEquals(dynamicScript.getScript(), "def calculate():\n return 1");
assertEquals(dynamicScript.getPluginType(), PluginType.DYNAMIC_PROPERTY);
}
@@ -188,15 +204,18 @@ public class ImportSampleTypesTest extends AbstractImportTest
public void testSampleTypesWithPropertyHavingValidationScript() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VALIDATION_SCRIPT)));
+ final String[] sessionWorkspaceFilePaths = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VALIDATION_SCRIPT), FilenameUtils.concat(FILES_DIR, VALIDATION_SCRIPT));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePaths[0]));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
Plugin validationScript = antibody.getValidationPlugin();
assertNotNull(validationScript);
assertEquals(validationScript.getName().toUpperCase(), "ANTIBODY.VALID");
- assertEquals(validationScript.getScript(), TestUtils.getValidationScript());
+ assertEquals(validationScript.getScript(), "def validate(entity, isNew):\n if isNew:\n return");
assertEquals(validationScript.getPluginType(), PluginType.ENTITY_VALIDATION);
}
@@ -205,9 +224,13 @@ public class ImportSampleTypesTest extends AbstractImportTest
public void testSampleTypesWithVocabularyInXls() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
PropertyAssignment propertyAssignment = antibody.getPropertyAssignments().get(0);
assertNotNull(propertyAssignment);
@@ -219,10 +242,17 @@ public class ImportSampleTypesTest extends AbstractImportTest
public void testSampleTypesWithVocabularyOnServer() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_DETECTION)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY_ON_SERVER)));
+ final String vocabularySessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_DETECTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(vocabularySessionWorkspaceFilePath));
+
+ final String sampleTypesSessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY_ON_SERVER));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sampleTypesSessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+
// THEN
PropertyAssignment propertyAssignment = antibody.getPropertyAssignments().get(0);
assertNotNull(propertyAssignment);
@@ -234,17 +264,22 @@ public class ImportSampleTypesTest extends AbstractImportTest
public void testSampleTypesWithAutoGeneratedCodeAttribute() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_AUTO_GENERATED_CODES)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_AUTO_GENERATED_CODES));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "SECONDBODY");
+
// THEN
assertTrue(antibody.isAutoGeneratedCode());
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(s?).*Mandatory field is missing or empty: Code.*")
public void shouldThrowExceptionIfNoSampleCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java
index f92702dfa16db252c708a8ab8f0af6254aaaf19d..55567f48535513c4456921074ecd09a38dd45563 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java
@@ -15,15 +15,15 @@
*/
package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+
import java.io.IOException;
import java.nio.file.Paths;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
-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 org.apache.commons.io.FilenameUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
@@ -33,15 +33,16 @@ import org.springframework.transaction.annotation.Transactional;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+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.space.Space;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import static org.testng.Assert.*;
-
@ContextConfiguration(locations = "classpath:applicationContext.xml")
@Transactional(transactionManager = "transaction-manager")
@Rollback
@@ -109,9 +110,12 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.FAIL_IF_EXISTS, Paths.get(sessionWorkspaceFile));
+
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "AAA", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "AAA");
+
// THEN
assertEquals(sample.getCode(), "AAA");
assertEquals(sample.getProject(), null);
@@ -127,9 +131,10 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertEquals(sample.getCode(), "VVV");
assertEquals(sample.getProject(), null);
@@ -145,9 +150,10 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SAMPLES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "S1", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "S1");
// THEN
assertEquals(sample.getCode(), "S1");
assertEquals(sample.getProject(), null);
@@ -163,10 +169,13 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)));
+ final String sessionWorkspaceFilePathForSpace = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSpace));
+ final String sessionWorkspaceFilePathForSamplesSpaceElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSamplesSpaceElsewhere));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
}
@@ -179,19 +188,28 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)));
+ final String sessionWorkspaceFilePathForSpace = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACE));
+ final String sessionWorkspaceFilePathForSamplesSpaceElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSpace),
+ Paths.get(sessionWorkspaceFilePathForSamplesSpaceElsewhere));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(s?).*Entity \\[TEST_SPACE\\] could not be found. "
+ + "Either you forgot to register it or mistyped the identifier.*")
public void shouldThrowExceptionIfSpaceDoesntExist() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)));
+ // the Excel contains internally property types which can be only manipulated by the system user
+ sessionToken = v3api.loginAsSystem();
+
+ final String sessionWorkspaceFilePathForSamplesSpaceElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSamplesSpaceElsewhere));
}
@Test
@@ -202,10 +220,17 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC)));
- List<IObjectId> ids = TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC)));
+ final String sessionWorkspaceFilePathForVocabularyType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE));
+ final String sessionWorkspaceFilePathForSampleType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForVocabularyType),
+ Paths.get(sessionWorkspaceFilePathForSampleType));
+
+ final String sessionWorkspaceFilePathForSampleTypeElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC));
+ List<IObjectId> ids = TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS,
+ Paths.get(sessionWorkspaceFilePathForSampleTypeElsewhere));
List<ISampleId> sampleIds = List.of((SampleIdentifier)ids.get(9), (SampleIdentifier)ids.get(10), (SampleIdentifier)ids.get(11));
// WHEN
List<Sample> samples = (List<Sample>) TestUtils.getSamplesById(v3api, sessionToken, sampleIds);
@@ -226,13 +251,22 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
+ final String sessionWorkspaceFilePathForVocabularyType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE));
+ final String sessionWorkspaceFilePathForSampleType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC_FIX_TYPE));
+
TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC_FIX_TYPE)));
- List<IObjectId> ids = TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC)));
+ Paths.get(sessionWorkspaceFilePathForVocabularyType),
+ Paths.get(sessionWorkspaceFilePathForSampleType));
+
+ final String sessionWorkspaceFilePathForSampleTypeElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC));
+ List<IObjectId> ids = TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS,
+ Paths.get(sessionWorkspaceFilePathForSampleTypeElsewhere));
List<ISampleId> sampleIds = List.of((SampleIdentifier)ids.get(9), (SampleIdentifier)ids.get(10), (SampleIdentifier)ids.get(11));
// WHEN
- List<Sample> samples = (List<Sample>) TestUtils.getSamplesById(v3api, sessionToken, sampleIds);
+ List<Sample> samples = TestUtils.getSamplesById(v3api, sessionToken, sampleIds);
Set<String> differentCyclicAssignments = new HashSet<>();
for (Sample sample:samples) {
differentCyclicAssignments.add((String)sample.getProperty("CYCLIC_SAMPLE_PROPERTY"));
@@ -242,7 +276,8 @@ public class ImportSamplesTest extends AbstractImportTest
assertEquals(differentCyclicAssignments.size(), 2);
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(?s).*Property CYCLIC_SAMPLE_PROPERTY is not a sample of type ANTIBODY but of type TEST_TYPE.*")
@DirtiesContext
public void testSamplesAreCreatedWhenSampleTypeCyclicOnServerFixTypeWrongType() throws IOException
{
@@ -250,10 +285,18 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
+ final String sessionWorkspaceFilePathForVocabularyType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE));
+ final String sessionWorkspaceFilePathForSampleType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC_FIX_TYPE));
+
TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_CYCLIC_FIX_TYPE)));
- List<IObjectId> ids = TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC_WRONG_TYPE)));
+ Paths.get(sessionWorkspaceFilePathForVocabularyType),
+ Paths.get(sessionWorkspaceFilePathForSampleType));
+
+ final String sessionWorkspaceFilePathForSampleTypeElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE_CYCLIC_WRONG_TYPE));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePathForSampleTypeElsewhere));
}
@Test
@@ -264,12 +307,19 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
+ final String sessionWorkspaceFilePathForVocabularyType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE));
+ final String sessionWorkspaceFilePathForSampleType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE));
TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE)));
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE)));
+ Paths.get(sessionWorkspaceFilePathForVocabularyType),
+ Paths.get(sessionWorkspaceFilePathForSampleType));
+
+ final String sessionWorkspaceFilePathForSampleTypeElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSampleTypeElsewhere));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
}
@@ -282,11 +332,14 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE)),
- Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE)));
+ final String sessionWorkspaceFilePathForSampleType = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE));
+ final String sessionWorkspaceFilePathForSampleTypeElsewhere = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePathForSampleType),
+ Paths.get(sessionWorkspaceFilePathForSampleTypeElsewhere));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
}
@@ -299,10 +352,10 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, CHILD_AS_IDENTIFIER)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, CHILD_AS_IDENTIFIER));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFile));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
assertEquals(sample.getChildren().size(), 1);
@@ -319,10 +372,10 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, PARENT_AS_IDENTIFIER)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PARENT_AS_IDENTIFIER));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFile));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
assertEquals(sample.getParents().size(), 1);
@@ -339,10 +392,10 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, CHILD_AS_DOLLARTAG)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, CHILD_AS_DOLLARTAG));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFile));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
assertEquals(sample.getChildren().size(), 1);
@@ -359,10 +412,10 @@ public class ImportSamplesTest extends AbstractImportTest
String sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, PARENT_AS_DOLLARTAG)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, PARENT_AS_DOLLARTAG));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFile));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "VVV");
// THEN
assertNotNull(sample);
assertEquals(sample.getParents().size(), 1);
@@ -379,10 +432,10 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken,
- Paths.get(FilenameUtils.concat(FILES_DIR, NON_MANDATORY_FIELD_MISSING)));
+ final String sessionWorkspaceFile = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, NON_MANDATORY_FIELD_MISSING));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFile));
// WHEN
- Sample sample = TestUtils.getSample(v3api, sessionToken, "AAA", "TEST_SPACE");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "TEST_SPACE", "AAA");
// THEN
assertNotNull(sample);
assertEquals(sample.getProperties().get("FOR_WHAT"), null);
@@ -396,9 +449,9 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
-
- List<IObjectId> result = TestUtils.createFrom(v3api, sessionToken, UpdateMode.IGNORE_EXISTING,
- Paths.get(FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_LEVEL)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_LEVEL));
+ List<IObjectId> result = TestUtils.createFrom(v3api, sessionToken, UpdateMode.IGNORE_EXISTING, Paths.get(sessionWorkspaceFilePath));
String permId = result.get(result.size() - 1).toString();
// WHEN
@@ -416,8 +469,9 @@ public class ImportSamplesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- List<IObjectId> result = TestUtils.createFrom(v3api, sessionToken, UpdateMode.IGNORE_EXISTING,
- Paths.get(FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_TYPE_LEVEL)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_TYPE_LEVEL));
+ List<IObjectId> result = TestUtils.createFrom(v3api, sessionToken, UpdateMode.IGNORE_EXISTING, Paths.get(sessionWorkspaceFilePath));
String permId = result.get(result.size() - 1).toString();
// WHEN
@@ -434,10 +488,11 @@ public class ImportSamplesTest extends AbstractImportTest
// the Excel contains internally managed property types which can be only manipulated by the system user
sessionToken = v3api.loginAsSystem();
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, GENERAL_ELN_SETTINGS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, GENERAL_ELN_SETTINGS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// test sample before update
- Sample sample = TestUtils.getSample(v3api, sessionToken, "GENERAL_ELN_SETTINGS", "ELN_SETTINGS");
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "ELN_SETTINGS", "GENERAL_ELN_SETTINGS");
assertNotNull(sample);
// properties are empty
assertEquals(sample.getProperties().size(), 0);
@@ -456,11 +511,12 @@ public class ImportSamplesTest extends AbstractImportTest
assertEquals(experiment.getProperties().containsKey("$NAME"), true);
assertEquals(experiment.getProperties().get("$NAME"), "Default Experiment");
- TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS,
- Paths.get(FilenameUtils.concat(FILES_DIR, GENERAL_ELN_SETTINGS_UPDATE)));
+ final String sessionWorkspaceFilePathForUpdate = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, GENERAL_ELN_SETTINGS_UPDATE));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePathForUpdate));
// test sample after update
- sample = TestUtils.getSample(v3api, sessionToken, "GENERAL_ELN_SETTINGS", "ELN_SETTINGS");
+ sample = TestUtils.getSample(v3api, sessionToken, "ELN_SETTINGS", "GENERAL_ELN_SETTINGS");
assertNotNull(sample);
// properties have been updated
assertEquals(sample.getProperties().size(), 1);
@@ -483,16 +539,28 @@ public class ImportSamplesTest extends AbstractImportTest
assertEquals(experiment.getProperties().get("$NAME"), "Default Experiment Updated");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(s?).*Entity \\[TEST_SPACE, /TEST_SPACE/TEST_PROJECT/TEST_EXPERIMENT\\] could not be found. "
+ + "Either you forgot to register it or mistyped the identifier.*")
public void shouldThrowExceptionIfSamplesSpaceProjectDoesntExist() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_PROJECT_EXPERIMENT_ELSEWHERE)));
+ // the Excel contains internally property types which can be only manipulated by the system user
+ sessionToken = v3api.loginAsSystem();
+
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_PROJECT_EXPERIMENT_ELSEWHERE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class,
+ expectedExceptionsMessageRegExp = "(s?).*Header 'name' is neither an attribute, property code or property label.*")
public void shouldThrowExceptionIfMandatoryPropertyIsMissing() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, MANDATORY_FIELD_MISSING)));
+ // the Excel contains internally property types which can be only manipulated by the system user
+ sessionToken = v3api.loginAsSystem();
+
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, MANDATORY_FIELD_MISSING));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java
index 75fb6f688e44cb5cfcae88979eae971ef0099761..8024fecf89ea4ea66f6fb3c4adb9f5d117c7f4c9 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java
@@ -53,7 +53,7 @@ public class ImportSpacesTest extends AbstractImportTest
public void setupClass() throws IOException
{
String f = ImportSpacesTest.class.getName().replace(".", "/");
- FILES_DIR = f.substring(0, f.length() - ImportSpacesTest.class.getSimpleName().length()) + "/test_files/";
+ FILES_DIR = f.substring(0, f.length() - ImportSpacesTest.class.getSimpleName().length()) + "test_files/";
}
@Test
@@ -61,7 +61,8 @@ public class ImportSpacesTest extends AbstractImportTest
public void testNormalSpacesAreCreated() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// WHEN
Space rawData = TestUtils.getSpace(v3api, sessionToken, "TEST_SPACE");
// THEN
@@ -74,7 +75,8 @@ public class ImportSpacesTest extends AbstractImportTest
public void testNormalSpacesAreCreatedSecondSpace() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// WHEN
Space space = TestUtils.getSpace(v3api, sessionToken, "TEST_SPACE2");
// THEN
@@ -82,17 +84,19 @@ public class ImportSpacesTest extends AbstractImportTest
assertEquals(space.getDescription(), "TEST desc");
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Code' is missing.*")
public void shouldThrowExceptionIfNoSpaceCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACES_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = UserFailureException.class)
+ @Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = "(?s).*Header 'Description' is missing.*")
@DirtiesContext
public void shouldCreateSpaceWhenNoDescription() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_NO_DESCRIPTION)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, SPACES_NO_DESCRIPTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java
index 3b10cf00fe995b4615240409319fd99900a47dd2..707d1ab1ef31ef2f4108f5594760b5a00770df8d 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java
@@ -40,7 +40,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create.VocabularyTerm
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
@ContextConfiguration(locations = "classpath:applicationContext.xml")
@Transactional(transactionManager = "transaction-manager")
@@ -75,7 +74,7 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
public void setupClass() throws IOException
{
String f = ImportVocabularyTypesTest.class.getName().replace(".", "/");
- FILES_DIR = f.substring(0, f.length() - ImportVocabularyTypesTest.class.getSimpleName().length()) + "/test_files/";
+ FILES_DIR = f.substring(0, f.length() - ImportVocabularyTypesTest.class.getSimpleName().length()) + "test_files/";
}
@Test
@@ -86,7 +85,8 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
// THEN
@@ -102,9 +102,12 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
VocabularyTerm term = detection.getTerms().get(0);
assertEquals(term.getCode(), "HRP");
@@ -120,9 +123,12 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
List<Vocabulary> vocabularies = TestUtils.getAllVocabularies(v3api, sessionToken);
+
// THEN
assertEquals(vocabularies.size(), 3); // 2 created + 1 default
}
@@ -135,9 +141,12 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
sessionToken = v3api.loginAsSystem();
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
VocabularyTerm term = detection.getTerms().get(1);
assertEquals(term.getCode(), "TEST_VOC");
@@ -150,24 +159,30 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
public void testVocabularyWithNoTermDescriptionShouldBeCreated() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_DESCRIPTION)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_DESCRIPTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
assertNotNull(detection);
assertNull(detection.getTerms().get(0).getDescription());
}
- @Test(expectedExceptions = RuntimeException.class)
+ @Test(expectedExceptions = RuntimeException.class, expectedExceptionsMessageRegExp = "(s?).*Mandatory field is missing or empty: Code.*")
public void shouldThrowExceptionIfNoVocabularyCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
- @Test(expectedExceptions = RuntimeException.class)
+ @Test(expectedExceptions = RuntimeException.class, expectedExceptionsMessageRegExp = "(s?).*Mandatory field is missing or empty: Code.*")
public void shouldThrowExceptionIfNoTermCode() throws IOException
{
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_CODE)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_CODE));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
}
@Test
@@ -175,9 +190,13 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
public void shouldNotThrowExceptionIfNoVocabularyDescription() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_DESCRIPTION)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_DESCRIPTION));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
assertNotNull(detection);
assertNull(detection.getDescription());
@@ -188,9 +207,12 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
public void shouldNotThrowExceptionIfNoTermLabel() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_LABEL)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_LABEL));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
assertNotNull(detection);
assertNull(detection.getTerms().get(0).getLabel());
@@ -201,9 +223,12 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
public void shouldNotThrowExceptionIfNoTerms() throws IOException
{
// GIVEN
- TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERMS)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERMS));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(sessionWorkspaceFilePath));
+
// WHEN
Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+
// THEN
assertNotNull(detection);
}
@@ -214,7 +239,8 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
{
TestUtils.createVocabulary(v3api, sessionToken, "TEST_VOCABULARY_TYPE", "Test desc");
// there should be no exceptions
- TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(FilenameUtils.concat(FILES_DIR, EXIST_VOCABULARIES)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(sessionToken, FilenameUtils.concat(FILES_DIR, EXIST_VOCABULARIES));
+ TestUtils.createFrom(v3api, sessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePath));
Vocabulary test = TestUtils.getVocabulary(v3api, sessionToken, "TEST_VOCABULARY_TYPE");
assertNotNull(test);
}
@@ -250,8 +276,9 @@ public class ImportVocabularyTypesTest extends AbstractImportTest
assertEquals(beforeTerm.getDescription(), "Original Description");
assertEquals(beforeTerm.getRegistrator().getUserId(), TEST_USER);
- TestUtils.createFrom(v3api, systemSessionToken, UpdateMode.UPDATE_IF_EXISTS,
- Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_WITH_TERM_TO_TAKE_OVER)));
+ final String sessionWorkspaceFilePath = uploadToAsSessionWorkspace(systemSessionToken,
+ FilenameUtils.concat(FILES_DIR, VOCABULARY_WITH_TERM_TO_TAKE_OVER));
+ TestUtils.createFrom(v3api, systemSessionToken, UpdateMode.UPDATE_IF_EXISTS, Paths.get(sessionWorkspaceFilePath));
Vocabulary afterVocabulary = v3api.getVocabularies(instanceAdminSessionToken, Arrays.asList(vocabularyId), fetchOptions).get(vocabularyId);
VocabularyTerm afterTerm = afterVocabulary.getTerms().get(0);
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java
index adbb3a91ba45a39e82ce887e9c3e615352a65525..8681e8e9cb335b9352f26fb00f78c25d6066e5f6 100644
--- a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java
+++ b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java
@@ -15,23 +15,15 @@
*/
package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
-import java.io.ByteArrayOutputStream;
import java.io.IOException;
-import java.io.InputStream;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create.VocabularyCreation;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IEntityType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
@@ -44,6 +36,11 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.Experime
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportFormat;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportMode;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search.ProjectSearchCriteria;
@@ -60,12 +57,11 @@ 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.openbis.generic.asapi.v3.dto.sample.search.SampleTypeSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.CustomASServiceExecutionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.CustomASServiceCode;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create.VocabularyCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularySearchCriteria;
@@ -73,19 +69,6 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi
public class TestUtils
{
- private static final String TEST_XLS = "TEST-XLS";
-
- private static final String XLS_NAME = "xls_name";
-
- private static final String UPDATE_MODE = "update_mode";
-
- private static final String XLS_PARAM = "xls";
-
- public static final String CSV_PARAM = "csv";
-
- private static final String SCRIPTS_PARAM = "scripts";
-
- private static final String XLS_IMPORT_API = "xls-import-api";
static Vocabulary getVocabulary(IApplicationServerInternalApi v3api, String sessionToken, String code)
{
@@ -276,7 +259,7 @@ public class TestUtils
}
}
- static Sample getSample(IApplicationServerInternalApi v3api, String sessionToken, String sampleCode, String spaceCode)
+ static Sample getSample(IApplicationServerInternalApi v3api, String sessionToken, String spaceCode, String sampleCode)
{
List<ISampleId> ids = new ArrayList<>();
ids.add(new SampleIdentifier(spaceCode, null, null, sampleCode));
@@ -351,83 +334,11 @@ public class TestUtils
static List<IObjectId> createFrom(IApplicationServerInternalApi v3api, String sessionToken, UpdateMode updateMode, Path... xls_paths)
throws IOException
{
- List<byte[]> excels = new ArrayList<>();
- for (Path xls_path : xls_paths)
- {
- byte[] xls = readData(xls_path);
- excels.add(xls);
- }
- CustomASServiceExecutionOptions options = new CustomASServiceExecutionOptions();
- options.withParameter(XLS_PARAM, excels);
- options.withParameter(UPDATE_MODE, updateMode.name());
- options.withParameter(XLS_NAME, TEST_XLS);
- return (List<IObjectId>) v3api.executeCustomASService(sessionToken, new CustomASServiceCode(XLS_IMPORT_API), options);
- }
-
- static String createFromCsv(IApplicationServerInternalApi v3api, String sessionToken, Path... csv_paths) throws IOException
- {
- List<byte[]> csvs = new ArrayList<>();
- for (Path csv_path : csv_paths)
- {
- byte[] csv = readData(csv_path);
- csvs.add(csv);
- }
- CustomASServiceExecutionOptions options = new CustomASServiceExecutionOptions();
- options.withParameter(CSV_PARAM, csvs);
- options.withParameter(UPDATE_MODE, UpdateMode.IGNORE_EXISTING.name());
- options.withParameter(XLS_NAME, TEST_XLS);
- return v3api.executeCustomASService(sessionToken, new CustomASServiceCode(XLS_IMPORT_API), options).toString();
- }
-
- static String createFrom(IApplicationServerInternalApi v3api, String sessionToken, Map<String, String> scripts, Path... xls_paths)
- throws IOException
- {
- return TestUtils.createFrom(v3api, sessionToken, scripts, UpdateMode.IGNORE_EXISTING, xls_paths);
- }
-
- static String createFrom(IApplicationServerInternalApi v3api, String sessionToken, Map<String, String> scripts, UpdateMode updateMode,
- Path... xls_paths) throws IOException
- {
- List<byte[]> excels = new ArrayList<>();
- for (Path xls_path : xls_paths)
- {
- byte[] xls = readData(xls_path);
- excels.add(xls);
- }
- CustomASServiceExecutionOptions options = new CustomASServiceExecutionOptions();
- options.withParameter(XLS_PARAM, excels);
- options.withParameter(SCRIPTS_PARAM, scripts);
- options.withParameter(UPDATE_MODE, updateMode.name());
- options.withParameter(XLS_NAME, TEST_XLS);
- return v3api.executeCustomASService(sessionToken, new CustomASServiceCode(XLS_IMPORT_API), options).toString();
- }
-
- static String getValidationScript()
- {
- return "def validate(entity, isNew):\n if isNew:\n return";
- }
+ final String[] sessionWorkspaceFiles = Arrays.stream(xls_paths).map(Path::toString).toArray(String[]::new);
+ final ImportResult importResult = v3api.executeImport(sessionToken, new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles),
+ new ImportOptions(ImportMode.valueOf(updateMode.name())));
- static String getDynamicScript()
- {
- return "def calculate():\n return 1";
- }
-
- static Map<String, String> getValidationPluginMap()
- {
- String dynamicScriptString = getValidationScript();
- Map<String, String> scriptsMap = new HashMap<>();
- scriptsMap.put("valid.py", dynamicScriptString);
-
- return scriptsMap;
- }
-
- static Map<String, String> getDynamicPluginMap()
- {
- String dynamicScriptString = getDynamicScript();
- Map<String, String> scriptsMap = new HashMap<>();
- scriptsMap.put("dynamic/dynamic.py", dynamicScriptString);
-
- return scriptsMap;
+ return importResult.getObjectIds();
}
static VocabularyPermId createVocabulary(IApplicationServerInternalApi v3api, String sessionToken, String code, String description)
@@ -447,17 +358,6 @@ public class TestUtils
}
}
- static String extractSamplePermIdFromResults(String result)
- {
- // Note this will work only if we created single sample!!
- int indexOfSamples = result.indexOf("CreateSamplesOperationResult");
- int permIdStart = indexOfSamples + "CreateSamplesOperationResult".length();
- int permIdEnd = result.indexOf("]", indexOfSamples);
- String permId = result.substring(permIdStart, permIdEnd);
- permId = StringUtils.strip(permId, "[]");
- return permId;
- }
-
static List<PropertyAssignment> extractAndSortPropertyAssignmentsPerGivenPropertyName(IEntityType rawData, List<String> propertyNames)
throws Exception
{
@@ -477,15 +377,4 @@ public class TestUtils
return sortedPropertyAssignments;
}
- private static byte[] readData(Path xls_path) throws IOException
- {
- String path = xls_path.toString();
- try (InputStream resourceAsStream = TestUtils.class.getClassLoader().getResourceAsStream(path))
- {
- ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
- IOUtils.copy(resourceAsStream, byteArrayOutputStream);
- return byteArrayOutputStream.toByteArray();
- }
- }
-
}
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/experiments/update.xls b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/experiments/update.xls
index 60bfe80c3e8fea6978f0145f164c9cb71130df34..ab24558768f2a6600fff42053a2ea52a5125cbe4 100644
Binary files a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/experiments/update.xls and b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/experiments/update.xls differ
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/property_types/normal_property_type.xls b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/property_types/normal_property_type.xls
index 633a047ccafd7d2b61987293ac60eaa7c4699d17..21a24d210d4513255e21f55db657a2fcd929d162 100644
Binary files a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/property_types/normal_property_type.xls and b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/property_types/normal_property_type.xls differ
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/sample_types/with_dynamic_script.xls b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/sample_types/with_dynamic_script.xls
index 1f4512890f85a50466176aa79763c5cb03309cb4..59ad19a0a9394856024903b37ec0b635d4f5ff77 100644
Binary files a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/sample_types/with_dynamic_script.xls and b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/sample_types/with_dynamic_script.xls differ
diff --git a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/samples/space_project_experiment_elsewhere.xls b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/samples/space_project_experiment_elsewhere.xls
index 2ba767a0c663d8d29d81131d1507ace8ec071198..40d3452f0b4f42da9c6cec7ebb25a5f8c673a41c 100644
Binary files a/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/samples/space_project_experiment_elsewhere.xls and b/core-plugin-openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/samples/space_project_experiment_elsewhere.xls differ
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
index df54c5679c00ae347859bbca0e5318e136d8713e..1d4263cd87b16fbe2ed4e4d27b644f02266d05f7 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
@@ -173,7 +173,9 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriter
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.SearchGloballyOperation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.SearchGloballyOperationResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperationResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -1818,9 +1820,10 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
}
@Override
- public void executeImport(final String sessionToken, final IImportData importData, final ImportOptions importOptions)
+ public ImportResult executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
- executeOperation(sessionToken, new ImportOperation(importData, importOptions));
+ final ImportOperationResult operationResult = executeOperation(sessionToken, new ImportOperation(importData, importOptions));
+ return operationResult.getImportResult();
}
@Override
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
index b730776794ffb04fb7ffb8c6d4456c2e4bd97bc8..fbf88fbd32aaaf79c93a576e1366553af53b76e5 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
@@ -18,7 +18,6 @@ package ch.ethz.sis.openbis.generic.server.asapi.v3;
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.authorizationgroup.AuthorizationGroup;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.authorizationgroup.create.AuthorizationGroupCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.authorizationgroup.delete.AuthorizationGroupDeletionOptions;
@@ -90,7 +89,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.update.ExternalDmsUp
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -1374,9 +1374,10 @@ public class ApplicationServerApiLogger extends AbstractServerLogger implements
}
@Override
- public void executeImport(final String sessionToken, final IImportData importData, final ImportOptions importOptions)
+ public ImportResult executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
- logAccess(sessionToken, "execute-import", "IImportData(%s) ImportOptions(%s)", importData, importOptions);
+ logAccess(sessionToken, "execute-import", "ImportData(%s) ImportOptions(%s)", importData, importOptions);
+ return null;
}
@Override
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiPersonalAccessTokenInvocationHandler.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiPersonalAccessTokenInvocationHandler.java
index 1eba23cd4650c3f3bbda3dff28015498fc1281e3..fbce5f0a9ac2f6b51fddd924f836207fea1e942c 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiPersonalAccessTokenInvocationHandler.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiPersonalAccessTokenInvocationHandler.java
@@ -91,7 +91,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.update.ExternalDmsUp
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
@@ -1258,9 +1259,9 @@ public class ApplicationServerApiPersonalAccessTokenInvocationHandler implements
}
@Override
- public void executeImport(final String sessionToken, final IImportData importData, final ImportOptions importOptions)
+ public ImportResult executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
- invocation.proceedWithNewFirstArgument(converter.convert(sessionToken));
+ return invocation.proceedWithNewFirstArgument(converter.convert(sessionToken));
}
@Override
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/IImportExecutor.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/IImportExecutor.java
index ae242abdc90c11999c57c0353907d98078b7b674..e90d0fca54cf7ecc12189af5f33befd28f67ab98 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/IImportExecutor.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/IImportExecutor.java
@@ -18,11 +18,12 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.importer;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
public interface IImportExecutor
{
- void doImport(final IOperationContext context, final ImportOperation operation);
+ ImportResult doImport(final IOperationContext context, final ImportOperation operation);
}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportExecutor.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportExecutor.java
index 51363987d1fd87e1efc9ee8d1b47da8bbeacfee3..2957d712024196b15cd1166a85a797230332fe2b 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportExecutor.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportExecutor.java
@@ -17,23 +17,13 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.importer;
-import java.io.ByteArrayInputStream;
import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.Collectors;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-import ch.ethz.sis.openbis.generic.server.xls.importer.utils.FileServerUtils;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportScript;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportValue;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.UncompressedImportData;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ZipImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
@@ -46,110 +36,11 @@ import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
public class ImportExecutor implements IImportExecutor
{
- private static final String ZIP_PATH_SEPARATOR = "/";
-
- private static final String SCRIPTS_FOLDER_NAME = "scripts" + ZIP_PATH_SEPARATOR;
-
- private static final String DATA_FOLDER_NAME = "data" + ZIP_PATH_SEPARATOR;
-
- private static final String MISCELLANEOUS_FOLDER_NAME = "miscellaneous" + ZIP_PATH_SEPARATOR;
-
- private static final String FILE_SERVICES_FOLDER_NAME = MISCELLANEOUS_FOLDER_NAME + "file-service" + ZIP_PATH_SEPARATOR;
-
- private static final String XLS_EXTENSION = "." + "xls";
-
- private static final String XLSX_EXTENSION = "." + "xlsx";
-
@Override
- public void doImport(final IOperationContext context, final ImportOperation operation)
+ public ImportResult doImport(final IOperationContext context, final ImportOperation operation)
{
- final IImportData importData = operation.getImportData();
-
- try
- {
- if (importData instanceof UncompressedImportData)
- {
- // XLS file
-
- final UncompressedImportData uncompressedImportData = (UncompressedImportData) importData;
-
- final Map<String, String> scripts = uncompressedImportData.getScripts() != null
- ? uncompressedImportData.getScripts().stream().collect(Collectors.toMap(ImportScript::getName, ImportScript::getSource))
- : null;
- final Map<String, String> importValues = uncompressedImportData.getImportValues() != null
- ? uncompressedImportData.getImportValues().stream().collect(Collectors.toMap(ImportValue::getName, ImportValue::getValue))
- : null;
- importXls(context, operation, scripts, importValues, uncompressedImportData.getFile(), null);
- } else if (importData instanceof ZipImportData)
- {
- // ZIP file
- final Map<String, String> scripts = new HashMap<>();
- final Map<String, String> importValues = new HashMap<>();
- byte[] xlsFileContent = null;
+ final ImportData importData = operation.getImportData();
- final ZipImportData zipImportData = (ZipImportData) importData;
- try (final ZipInputStream zip = new ZipInputStream(new ByteArrayInputStream(zipImportData.getFile())))
- {
- ZipEntry entry;
- while ((entry = zip.getNextEntry()) != null)
- {
- final String entryName = entry.getName();
- if (entry.isDirectory())
- {
- if (!SCRIPTS_FOLDER_NAME.equals(entryName) && !DATA_FOLDER_NAME.equals(entryName) && !MISCELLANEOUS_FOLDER_NAME.equals(entryName))
- {
- throw UserFailureException.fromTemplate("Illegal directory '%s' is found inside the imported file.", entryName);
- }
- } else
- {
- if (!entryName.contains(ZIP_PATH_SEPARATOR) && (entryName.endsWith(XLS_EXTENSION) || entryName.endsWith(XLSX_EXTENSION)))
- {
- if (xlsFileContent == null)
- {
- xlsFileContent = zip.readAllBytes();
- } else
- {
- throw UserFailureException.fromTemplate("More than one XLS file found in the root of the imported ZIP file.");
- }
- } else if (entryName.startsWith(SCRIPTS_FOLDER_NAME))
- {
- scripts.put(entryName.substring(SCRIPTS_FOLDER_NAME.length()), new String(zip.readAllBytes()));
- } else if (entryName.startsWith(DATA_FOLDER_NAME))
- {
- importValues.put(entryName.substring(DATA_FOLDER_NAME.length()), new String(zip.readAllBytes()));
- } else
- {
- throw UserFailureException.fromTemplate(
- "Entry '%s' is not allowed. Only one root XLS file is allowed and files inside the '%s' or '%s' folder",
- entryName, SCRIPTS_FOLDER_NAME, DATA_FOLDER_NAME);
- }
- }
- }
- }
-
- if (xlsFileContent != null)
- {
- importXls(context, operation, scripts, importValues, xlsFileContent, zipImportData.getFile());
- } else
- {
- throw UserFailureException.fromTemplate("XLS file not found in the root of the imported ZIP file.");
- }
-
- } else
- {
- throw UserFailureException.fromTemplate("Unknown instance of import data '%s'.",
- importData != null ? importData.getClass().getName() : null);
- }
- } catch (final IOException e)
- {
- throw UserFailureException.fromTemplate(e, "IO exception importing.");
- }
- }
-
- private static void importXls(final IOperationContext context, final ImportOperation operation, final Map<String, String> scripts,
- final Map<String, String> importValues, final byte[] xlsContent, byte[] zipImportDataOrNull)
- throws IOException
- {
final IApplicationServerInternalApi applicationServerApi = CommonServiceProvider.getApplicationServerApi();
final ImportOptions importOptions = operation.getImportOptions();
@@ -160,31 +51,18 @@ public class ImportExecutor implements IImportExecutor
.get("project-samples-enabled"));
importerImportOptions.setAllowProjectSamples(projectSamplesEnabled);
- final XLSImport xlsImport = new XLSImport(context.getSession().getSessionToken(), applicationServerApi, scripts,
- importValues, ImportModes.valueOf(importOptions.getMode().name()), importerImportOptions, "DEFAULT");
-
- xlsImport.importXLS(xlsContent);
- if (zipImportDataOrNull != null)
+ try
{
- importZipData(zipImportDataOrNull);
- }
- }
-
- public static void importZipData(byte[] zipImportDataOrNull) throws IOException
- {
- try (final ZipInputStream zip = new ZipInputStream(new ByteArrayInputStream(zipImportDataOrNull)))
+ final XLSImport xlsImport = new XLSImport(context.getSession().getSessionToken(), applicationServerApi,
+ ImportModes.valueOf(importOptions.getMode().name()), importerImportOptions, importData.getSessionWorkspaceFiles(), false);
+ return new ImportResult(xlsImport.start());
+ } catch (final IOException e)
{
- ZipEntry entry;
- while ((entry = zip.getNextEntry()) != null)
- {
- final String filePath = entry.getName();
- if (!entry.isDirectory() && filePath.startsWith(FILE_SERVICES_FOLDER_NAME))
- {
- String fileServicePath = ZIP_PATH_SEPARATOR + filePath.substring(FILE_SERVICES_FOLDER_NAME.length());
- byte[] fileBytes = zip.readAllBytes();
- FileServerUtils.write(fileServicePath, fileBytes);
- }
- }
+ throw UserFailureException.fromTemplate(e, "IO exception importing.");
+ } catch (final Exception e)
+ {
+ throw UserFailureException.fromTemplate(e,"Exception importing data: %s", e.getMessage());
}
}
+
}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportOperationExecutor.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportOperationExecutor.java
index ef4032eeaa8069acad357189f88a7ad6bd389419..7702c16e50ea06f63a6466f3b7b2d19a972f337b 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportOperationExecutor.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/importer/ImportOperationExecutor.java
@@ -22,6 +22,7 @@ import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportOperationResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.ImportResult;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor;
@@ -41,8 +42,8 @@ public class ImportOperationExecutor extends OperationExecutor<ImportOperation,
@Override
protected ImportOperationResult doExecute(final IOperationContext context, final ImportOperation operation)
{
- executor.doImport(context, operation);
- return new ImportOperationResult();
+ final ImportResult importResult = executor.doImport(context, operation);
+ return new ImportOperationResult(importResult);
}
}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/export/helper/AbstractXLSExportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/export/helper/AbstractXLSExportHelper.java
index 2e15b9a1a959b074293d744d8ba23030bf31ad4b..5d7c32c7277e67b10cbe7976b0c13c07e907f6ec 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/export/helper/AbstractXLSExportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/export/helper/AbstractXLSExportHelper.java
@@ -220,8 +220,7 @@ public abstract class AbstractXLSExportHelper<ENTITY_TYPE extends IEntityType> i
final String filePath = matcher.group(3);
try
{
- final byte[] fileContent = FileServerUtils.read(filePath);
- imageFiles.put(filePath, fileContent);
+ imageFiles.put(filePath, FileServerUtils.readAllBytes(filePath));
} catch (final IOException e)
{
warnings.add(String.format("Could not read the file at path '%s'.", filePath));
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/MainImportXlsTest.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/MainImportXlsTest.java
deleted file mode 100644
index 715cfae1dd0bdae8ff65e74cfb2d6ff7ced32c3b..0000000000000000000000000000000000000000
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/MainImportXlsTest.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * Copyright ETH 2022 - 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package ch.ethz.sis.openbis.generic.server.xls.importer;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
-import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportModes;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegistrationHelper;
-
-public class MainImportXlsTest
-{
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, MainImportXlsTest.class);
-
- private static final int TIMEOUT = 10000;
-
- private static final String URL =
- "http://localhost:8888/openbis/openbis" + IApplicationServerApi.SERVICE_URL;
-
- private static final File ELN_MASTER_DATA_PATH =
- new File("../core-plugin-openbis/dist/core-plugins/eln-lims/1/as");
-
- private static final File LIFE_SCIENCES_MASTER_DATA_PATH =
- new File("../core-plugin-openbis/dist/core-plugins/eln-lims-life-sciences/1/as");
-
- // used only for development!
- public static void main(String[] args)
- {
- IApplicationServerApi v3 =
- HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, URL, TIMEOUT);
- String sessionToken = v3.login("system", "a");
-
- Map<String, String> scripts = getListScripts(ELN_MASTER_DATA_PATH.getPath());
- ImportOptions options = new ImportOptions();
-
- XLSImport importXls =
- new XLSImport(sessionToken, v3, scripts, Map.of(), ImportModes.UPDATE_IF_EXISTS, options,
- "ELN-LIMS");
- Collection<IObjectId> importedIds = new ArrayList<>();
-
- File commonDataModel = new File(ELN_MASTER_DATA_PATH, "/master-data/common-data-model.xls");
- importedIds.addAll(importXls.importXLS(FileUtilities.loadToByteArray(commonDataModel)));
- File singleGroupDataModel =
- new File(ELN_MASTER_DATA_PATH, "/master-data/single-group-data-model.xls");
- importedIds.addAll(
- importXls.importXLS(FileUtilities.loadToByteArray(singleGroupDataModel)));
-
- Map<String, String> lifeSciencesImporterScripts =
- getListScripts(LIFE_SCIENCES_MASTER_DATA_PATH.getPath());
- XLSImport lifeSciencesImporter =
- new XLSImport(sessionToken, v3, lifeSciencesImporterScripts,
- Map.of(), ImportModes.UPDATE_IF_EXISTS, options, "ELN-LIMS-LIFE-SCIENCES");
- File lifeSciencesDataModel =
- new File(LIFE_SCIENCES_MASTER_DATA_PATH, "/master-data/data-model.xls");
- importedIds.addAll(lifeSciencesImporter.importXLS(
- FileUtilities.loadToByteArray(lifeSciencesDataModel)));
- }
-
- private static Map<String, String> getListScripts(String path)
- {
- MasterDataRegistrationHelper helper = new MasterDataRegistrationHelper(Arrays.asList(path));
- return helper.getAllScripts();
- }
-}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/XLSImport.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/XLSImport.java
index 6340b3a5b13bee7351dd9fec47c67bc94a6589a9..64c3dc87bf60033ec122f3ba47d0377c80c09fae 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/XLSImport.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/XLSImport.java
@@ -15,12 +15,29 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.apache.log4j.Logger;
+
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
import ch.ethz.sis.openbis.generic.server.xls.importer.delay.DelayedExecutionDecorator;
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportModes;
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportTypes;
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ScriptTypes;
+import ch.ethz.sis.openbis.generic.server.xls.importer.handler.ExcelParser;
import ch.ethz.sis.openbis.generic.server.xls.importer.handler.VersionInfoHandler;
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.DatasetTypeImportHelper;
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.ExperimentImportHelper;
@@ -35,20 +52,34 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.helper.SemanticAnnotation
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.SpaceImportHelper;
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.VocabularyImportHelper;
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.VocabularyTermImportHelper;
-import ch.ethz.sis.openbis.generic.server.xls.importer.handler.ExcelParser;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.DatabaseConsistencyChecker;
+import ch.ethz.sis.openbis.generic.server.xls.importer.utils.FileServerUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import org.apache.log4j.Logger;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ISessionWorkspaceProvider;
public class XLSImport
{
+ private static final String PATH_SEPARATOR = "/";
+
+ private static final String SCRIPTS_FOLDER_NAME = "scripts" + PATH_SEPARATOR;
+
+ private static final String DATA_FOLDER_NAME = "data" + PATH_SEPARATOR;
+
+ private static final String MISCELLANEOUS_FOLDER_NAME = "miscellaneous" + PATH_SEPARATOR;
+
+ private static final String FILE_SERVICES_FOLDER_NAME = MISCELLANEOUS_FOLDER_NAME + "file-service" + PATH_SEPARATOR;
+
+ private static final String XLS_EXTENSION = "." + "xls";
+
+ private static final String XLSX_EXTENSION = "." + "xlsx";
+
+ private static final int XLSX_DOCUMENT_LIMIT = 536870912; // 512 MB
+
+ private static final int EMBEDDED_DOCUMENT_LIMIT = 16777216; // 16 MB
+
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, XLSImport.class);
private final String sessionToken;
@@ -85,8 +116,6 @@ public class XLSImport
private final PropertyAssignmentImportHelper propertyAssignmentHelper;
- private final ScriptImportHelper scriptHelper;
-
private final SemanticAnnotationImportHelper semanticAnnotationImportHelper;
private final DatabaseConsistencyChecker dbChecker;
@@ -95,8 +124,20 @@ public class XLSImport
private final Map<String, String> importValues;
- public XLSImport(String sessionToken, IApplicationServerApi api, Map<String, String> scripts, Map<String, String> importValues,
- ImportModes mode, ImportOptions options, String xlsName)
+ private final ScriptImportHelper scriptHelper;
+
+ private final String[] sessionWorkspaceFiles;
+
+ private final byte[][] xls;
+
+ private static final String ZIP_EXTENSION = "." + "zip";
+
+ public XLSImport(String sessionToken,
+ IApplicationServerApi api,
+ ImportModes mode,
+ ImportOptions options,
+ String[] sessionWorkspaceFiles,
+ boolean shouldCheckVersionsOnDatabase) throws IOException
{
this.sessionToken = sessionToken;
this.api = api;
@@ -105,8 +146,6 @@ public class XLSImport
this.afterVersions = VersionInfoHandler.loadAllVersions(options);
this.dbChecker = new DatabaseConsistencyChecker(this.sessionToken, this.api, this.afterVersions);
this.delayedExecutor = new DelayedExecutionDecorator(this.sessionToken, this.api);
- this.importValues = importValues;
-
this.vocabularyHelper = new VocabularyImportHelper(this.delayedExecutor, mode, options, afterVersions);
this.vocabularyTermHelper = new VocabularyTermImportHelper(this.delayedExecutor, mode, options, afterVersions);
this.sampleTypeHelper = new SampleTypeImportHelper(this.delayedExecutor, mode, options, afterVersions);
@@ -118,122 +157,238 @@ public class XLSImport
this.sampleHelper = new SampleImportHelper(this.delayedExecutor, mode, options);
this.propertyHelper = new PropertyTypeImportHelper(this.delayedExecutor, mode, options, afterVersions);
this.propertyAssignmentHelper = new PropertyAssignmentImportHelper(this.delayedExecutor, mode, options, beforeVersions);
- this.scriptHelper = new ScriptImportHelper(this.delayedExecutor, mode, options, scripts);
this.semanticAnnotationImportHelper = new SemanticAnnotationImportHelper(this.delayedExecutor, mode, options);
- this.shouldCheckVersionsOnDatabase = xlsName == null || xlsName.equals("DEFAULT") == false;
- }
+ this.shouldCheckVersionsOnDatabase = shouldCheckVersionsOnDatabase;
- public List<IObjectId> importXLS(byte xls[])
- {
- if (shouldCheckVersionsOnDatabase)
- {
- this.dbChecker.checkVersionsOnDataBase();
- }
+ // File Parsing
+ this.sessionWorkspaceFiles = sessionWorkspaceFiles;
+ final ISessionWorkspaceProvider sessionWorkspaceProvider = CommonServiceProvider.getSessionWorkspaceProvider();
- List<List<List<String>>> lines = ExcelParser.parseExcel(xls, importValues);
- int pageNumber = 0;
- int lineNumber;
+ final Map<String, String> scripts = new HashMap<>();
+ byte[][] xls = new byte[sessionWorkspaceFiles.length][];
+ this.importValues = new HashMap<>();
- while (pageNumber < lines.size())
+ for (int i = 0; i < sessionWorkspaceFiles.length; i++)
{
- lineNumber = 0;
- List<List<String>> page = lines.get(pageNumber);
- int pageEnd = getPageEnd(page);
- while (lineNumber < pageEnd)
+ InputStream read = sessionWorkspaceProvider.read(sessionToken, sessionWorkspaceFiles[i]);
+ if (sessionWorkspaceFiles[i].toLowerCase().endsWith(ZIP_EXTENSION))
{
- int blockEnd = getBlockEnd(page, lineNumber);
- ImportTypes blockType;
- try
+ try (final ZipInputStream zip = new ZipInputStream(read))
{
- blockType = ImportTypes.valueOf(page.get(lineNumber).get(0));
- } catch (Exception e)
- {
- throw new UserFailureException(
- "Exception at page " + (pageNumber + 1) + " and line " + (lineNumber + 1) + " with message: " + e.getMessage());
- }
- lineNumber++;
-
- switch (blockType)
- {
- case VOCABULARY_TYPE:
- vocabularyHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
- if (lineNumber + 2 != blockEnd)
+ ZipEntry entry;
+ while ((entry = zip.getNextEntry()) != null)
+ {
+ final String entryName = entry.getName();
+ if (entry.isDirectory())
{
- vocabularyTermHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- }
- break;
- case SAMPLE_TYPE:
- // parse and create scripts
- scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
- // parse and create sample type
- sampleTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
- semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2, ImportTypes.SAMPLE_TYPE);
- // parse and assignment properties
- if (lineNumber + 2 != blockEnd)
+ if (!SCRIPTS_FOLDER_NAME.equals(entryName) && !DATA_FOLDER_NAME.equals(entryName) &&
+ !entryName.startsWith(MISCELLANEOUS_FOLDER_NAME))
+ {
+ throw UserFailureException.fromTemplate("Illegal directory '%s' is found inside the imported file.", entryName);
+ }
+ } else
{
- scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
- propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
- propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.SAMPLE_TYPE);
- semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd, ImportTypes.SAMPLE_TYPE);
+ if (!entryName.contains(PATH_SEPARATOR) && (entryName.endsWith(XLS_EXTENSION) || entryName.endsWith(XLSX_EXTENSION)))
+ {
+ validateEntrySize(entry.getSize(), XLSX_DOCUMENT_LIMIT);
+ if (xls[i] == null)
+ {
+ xls[i] = zip.readAllBytes();
+ } else
+ {
+ throw UserFailureException.fromTemplate("More than one XLS file found in the root of the imported ZIP file.");
+ }
+ } else if (entryName.startsWith(SCRIPTS_FOLDER_NAME))
+ {
+ validateEntrySize(entry.getSize(), EMBEDDED_DOCUMENT_LIMIT);
+ scripts.put(entryName.substring(SCRIPTS_FOLDER_NAME.length()), new String(zip.readAllBytes()));
+ } else if (entryName.startsWith(DATA_FOLDER_NAME))
+ {
+ validateEntrySize(entry.getSize(), EMBEDDED_DOCUMENT_LIMIT);
+ this.importValues.put(entryName.substring(DATA_FOLDER_NAME.length()), new String(zip.readAllBytes()));
+ } else if (!entryName.startsWith(MISCELLANEOUS_FOLDER_NAME))
+ {
+ throw UserFailureException.fromTemplate(
+ "Entry '%s' is not allowed. Only one root XLS file is allowed and files inside the '%s' or '%s' folder",
+ entryName, SCRIPTS_FOLDER_NAME, DATA_FOLDER_NAME);
+ }
}
- break;
- case EXPERIMENT_TYPE:
- // parse and create scripts
- scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
- // parse and create experiment type
- experimentTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
- semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2, ImportTypes.EXPERIMENT_TYPE);
- // parse and assignment properties
- if (lineNumber + 2 != blockEnd)
+ }
+ }
+ } else
+ {
+ final File canonicalFile = sessionWorkspaceProvider.getCanonicalFile(sessionToken, sessionWorkspaceFiles[i]);
+ validateEntrySize(canonicalFile.length(), XLSX_DOCUMENT_LIMIT);
+ xls[i] = sessionWorkspaceProvider.readAllBytes(sessionToken, sessionWorkspaceFiles[i]);
+
+ // Script folder support
+ final String scriptsFolderName = canonicalFile.getParent()
+ + PATH_SEPARATOR + SCRIPTS_FOLDER_NAME;
+
+ final File scriptsFolder = new File(scriptsFolderName);
+ if (scriptsFolder.exists() && scriptsFolder.isDirectory())
+ {
+ final File[] files = scriptsFolder.listFiles();
+ if (files != null)
+ {
+ for (final File file : files)
{
- scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
- propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
- propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.EXPERIMENT_TYPE);
- semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd, ImportTypes.EXPERIMENT_TYPE);
+ scripts.put(file.getName(), Files.readString(file.toPath(), StandardCharsets.UTF_8));
}
- break;
- case DATASET_TYPE:
- // parse and create scripts
- scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
- // parse and create dataset type
- datasetTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
- semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2, ImportTypes.DATASET_TYPE);
- // parse and assignment properties
- if (lineNumber + 2 != blockEnd)
+ }
+ }
+
+ // Data folder support
+ final String dataFolderName = canonicalFile.getParent()
+ + PATH_SEPARATOR + DATA_FOLDER_NAME;
+
+ final File dataFolder = new File(dataFolderName);
+ if (dataFolder.exists() && dataFolder.isDirectory())
+ {
+ final File[] files = dataFolder.listFiles();
+ if (files != null)
+ {
+ for (final File file : files)
{
- scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
- propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
- propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.DATASET_TYPE);
- semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd, ImportTypes.DATASET_TYPE);
+ this.importValues.put(file.getName(), Files.readString(file.toPath(), StandardCharsets.UTF_8));
}
- break;
- case SPACE:
- spaceHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- break;
- case PROJECT:
- projectHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- break;
- case EXPERIMENT:
- experimentHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- break;
- case SAMPLE:
- sampleHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- break;
- case PROPERTY_TYPE:
- propertyHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
- semanticAnnotationImportHelper.importBlockForPropertyType(page, pageNumber, lineNumber, blockEnd);
- break;
- default:
- throw new UserFailureException("Unknown type: " + blockType);
+ }
}
- lineNumber = blockEnd + 1;
}
- pageNumber++;
}
- this.delayedExecutor.hasFinished();
+ this.xls = xls;
+ this.scriptHelper = new ScriptImportHelper(this.delayedExecutor, mode, options, scripts);
+ }
+
+ private static void validateEntrySize(final long size, final int limit)
+ {
+ if (size > limit)
+ {
+ throw UserFailureException.fromTemplate("Document limit exceeded: %d.", size);
+ }
+ }
+ public List<IObjectId> start() throws IOException
+ {
+ if (shouldCheckVersionsOnDatabase)
+ {
+ this.dbChecker.checkVersionsOnDataBase();
+ }
+
+ for (int i = 0; i < this.xls.length; i++)
+ {
+ List<List<List<String>>> lines = ExcelParser.parseExcel(this.xls[i], importValues);
+ int pageNumber = 0;
+ int lineNumber;
+
+ while (pageNumber < lines.size())
+ {
+ lineNumber = 0;
+ List<List<String>> page = lines.get(pageNumber);
+ int pageEnd = getPageEnd(page);
+ while (lineNumber < pageEnd)
+ {
+ int blockEnd = getBlockEnd(page, lineNumber);
+ ImportTypes blockType;
+ try
+ {
+ blockType = ImportTypes.valueOf(page.get(lineNumber).get(0));
+ } catch (Exception e)
+ {
+ throw new UserFailureException(
+ "Exception at page " + (pageNumber + 1) + " and line " + (lineNumber + 1) + " with message: " + e.getMessage());
+ }
+ lineNumber++;
+
+ switch (blockType)
+ {
+ case VOCABULARY_TYPE:
+ vocabularyHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
+ if (lineNumber + 2 != blockEnd)
+ {
+ vocabularyTermHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ }
+ break;
+ case SAMPLE_TYPE:
+ // parse and create scripts
+ scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
+ // parse and create sample type
+ sampleTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
+ semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2,
+ ImportTypes.SAMPLE_TYPE);
+ // parse and assignment properties
+ if (lineNumber + 2 != blockEnd)
+ {
+ scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
+ propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
+ propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.SAMPLE_TYPE);
+ semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd,
+ ImportTypes.SAMPLE_TYPE);
+ }
+ break;
+ case EXPERIMENT_TYPE:
+ // parse and create scripts
+ scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
+ // parse and create experiment type
+ experimentTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
+ semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2,
+ ImportTypes.EXPERIMENT_TYPE);
+ // parse and assignment properties
+ if (lineNumber + 2 != blockEnd)
+ {
+ scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
+ propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
+ propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.EXPERIMENT_TYPE);
+ semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd,
+ ImportTypes.EXPERIMENT_TYPE);
+ }
+ break;
+ case DATASET_TYPE:
+ // parse and create scripts
+ scriptHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2, ScriptTypes.VALIDATION_SCRIPT);
+ // parse and create dataset type
+ datasetTypeHelper.importBlock(page, pageNumber, lineNumber, lineNumber + 2);
+ semanticAnnotationImportHelper.importBlockForEntityType(page, pageNumber, lineNumber, lineNumber + 2,
+ ImportTypes.DATASET_TYPE);
+ // parse and assignment properties
+ if (lineNumber + 2 != blockEnd)
+ {
+ scriptHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd, ScriptTypes.DYNAMIC_SCRIPT);
+ propertyHelper.importBlock(page, pageNumber, lineNumber + 2, blockEnd);
+ propertyAssignmentHelper.importBlock(page, pageNumber, lineNumber, blockEnd, ImportTypes.DATASET_TYPE);
+ semanticAnnotationImportHelper.importBlockForEntityTypeProperty(page, pageNumber, lineNumber, blockEnd,
+ ImportTypes.DATASET_TYPE);
+ }
+ break;
+ case SPACE:
+ spaceHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ break;
+ case PROJECT:
+ projectHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ break;
+ case EXPERIMENT:
+ experimentHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ break;
+ case SAMPLE:
+ sampleHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ break;
+ case PROPERTY_TYPE:
+ propertyHelper.importBlock(page, pageNumber, lineNumber, blockEnd);
+ semanticAnnotationImportHelper.importBlockForPropertyType(page, pageNumber, lineNumber, blockEnd);
+ break;
+ default:
+ throw new UserFailureException("Unknown type: " + blockType);
+ }
+ lineNumber = blockEnd + 1;
+ }
+ pageNumber++;
+ }
+ }
+
+ this.delayedExecutor.hasFinished();
VersionInfoHandler.writeAllVersions(options, afterVersions);
+ importZipData();
return new ArrayList<>(this.delayedExecutor.getIds());
}
@@ -290,4 +445,34 @@ public class XLSImport
}
return true;
}
+
+
+ private void importZipData() throws IOException
+ {
+ for (int i = 0; i < this.sessionWorkspaceFiles.length; i++)
+ {
+ if (this.sessionWorkspaceFiles[i].toLowerCase().endsWith(ZIP_EXTENSION))
+ {
+ final ISessionWorkspaceProvider sessionWorkspaceProvider = CommonServiceProvider.getSessionWorkspaceProvider();
+ InputStream read = sessionWorkspaceProvider.read(this.sessionToken, this.sessionWorkspaceFiles[i]);
+
+ try (final ZipInputStream zip = new ZipInputStream(read))
+ {
+ ZipEntry entry;
+ while ((entry = zip.getNextEntry()) != null)
+ {
+ final String filePath = entry.getName();
+ if (!entry.isDirectory() && filePath.startsWith(FILE_SERVICES_FOLDER_NAME))
+ {
+ String fileServicePath = PATH_SEPARATOR + filePath.substring(FILE_SERVICES_FOLDER_NAME.length());
+ try (final OutputStream outputStream = FileServerUtils.newOutputStream(fileServicePath))
+ {
+ zip.transferTo(outputStream);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
\ No newline at end of file
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/delay/DelayedExecutionDecorator.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/delay/DelayedExecutionDecorator.java
index b67fb2fb56570b5e595f56bebbf0c27ba54f85b4..6d596c17d8086f3a5e93c18681a0110ebfd4f4c6 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/delay/DelayedExecutionDecorator.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/delay/DelayedExecutionDecorator.java
@@ -15,6 +15,18 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.delay;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Stream;
+
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IEntityType;
@@ -26,7 +38,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.update.DataSetTypeUpdate;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.IEntityTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
@@ -94,10 +105,6 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportTypes;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import java.io.Serializable;
-import java.util.*;
-import java.util.stream.Stream;
-
public class DelayedExecutionDecorator
{
private String sessionToken;
@@ -123,7 +130,7 @@ public class DelayedExecutionDecorator
this.v3 = v3;
this.ids = new LinkedHashSet<>();
this.resolvedVariables = new HashMap<>();
- this.delayedExecutions = new HashMap<>();
+ this.delayedExecutions = new LinkedHashMap<>(); // The only reason this is a linked Hash Map is so the list of error messages is on the same order as the delayed executions are added.
this.propertyTypeCache = new HashMap<>();
}
@@ -173,7 +180,7 @@ public class DelayedExecutionDecorator
if (!delayedExecutions.isEmpty())
{
List<String> errors = new ArrayList<>();
- Set<DelayedExecution> delayedExecutionsAsList = new HashSet<>();
+ Set<DelayedExecution> delayedExecutionsAsList = new LinkedHashSet<>(); // The only reason this is a linked Hash Set is so the list of error messages is on the same order as the delayed executions are added.
for (List<DelayedExecution> valueList : delayedExecutions.values())
{
delayedExecutionsAsList.addAll(valueList);
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/BasicImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/BasicImportHelper.java
index 68e38eb2b438447d8c8fbdcb979911340a8a8b24..27692bc4fdd2e32d2b98ae7b9ea071b1178774eb 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/BasicImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/BasicImportHelper.java
@@ -87,7 +87,10 @@ public abstract class BasicImportHelper extends AbstractImportHelper
switch (mode)
{
case FAIL_IF_EXISTS:
- throw new UserFailureException("Mode FAIL_IF_EXISTS - Found existing " + getTypeName());
+ if (!(this instanceof SemanticAnnotationImportHelper))
+ {
+ throw new UserFailureException("Mode FAIL_IF_EXISTS - Found existing " + getTypeName());
+ }
case UPDATE_IF_EXISTS:
updateObject(header, page.get(lineIndex), pageIndex, lineIndex);
updateVersion(header, page.get(lineIndex));
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/DatasetTypeImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/DatasetTypeImportHelper.java
index 1b0e34aba048eee4b08115d57e8631bab3c87f30..e7087238d59e7aaddfd685449c6345b28cdda3c1 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/DatasetTypeImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/DatasetTypeImportHelper.java
@@ -15,6 +15,9 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.update.DataSetTypeUpdate;
@@ -28,9 +31,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class DatasetTypeImportHelper extends BasicImportHelper
{
@@ -81,9 +82,15 @@ public class DatasetTypeImportHelper extends BasicImportHelper
@Override protected boolean isNewVersion(Map<String, Integer> header, List<String> values)
{
- String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
+ String version = getValueByColumnName(header, values, Attribute.Version);
+
if (version == null || version.isEmpty()) {
return true;
} else {
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentImportHelper.java
index 1c90876232a28322f5bed4f01a1c225a1e75b8cb..fea3039b97e4375afb28885fc5092ef7c40e81aa 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentImportHelper.java
@@ -92,7 +92,7 @@ public class ExperimentImportHelper extends BasicImportHelper
experimentType = new EntityTypePermId(getValueByColumnName(header, page.get(lineIndex), EXPERIMENT_TYPE_FIELD));
if(experimentType.getPermId() == null || experimentType.getPermId().isEmpty()) {
- throw new UserFailureException("Mandatory field missing or empty: " + EXPERIMENT_TYPE_FIELD);
+ throw new UserFailureException("Mandatory field is missing or empty: " + EXPERIMENT_TYPE_FIELD);
}
// first check that experiment type exist.
@@ -171,7 +171,6 @@ public class ExperimentImportHelper extends BasicImportHelper
@Override protected void updateObject(Map<String, Integer> header, List<String> values, int page, int line)
{
String identifier = getValueByColumnName(header, values, Attribute.Identifier);
- String project = getValueByColumnName(header, values, Attribute.Project);
if (identifier == null || identifier.isEmpty())
{
@@ -182,6 +181,8 @@ public class ExperimentImportHelper extends BasicImportHelper
IExperimentId experimentId = new ExperimentIdentifier(identifier);
update.setExperimentId(experimentId);
+ String project = getValueByColumnName(header, values, Attribute.Project);
+
// Project is used to "MOVE", only set if present since can't be null
if (project != null && !project.isEmpty())
{
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentTypeImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentTypeImportHelper.java
index 274c1a36a4b2970e52e859b3228533b195bb5e07..7b816377c5b8d3c8bd41202afeb49d9dce30a11c 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentTypeImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ExperimentTypeImportHelper.java
@@ -15,6 +15,9 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
@@ -28,9 +31,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class ExperimentTypeImportHelper extends BasicImportHelper
{
@@ -81,9 +82,15 @@ public class ExperimentTypeImportHelper extends BasicImportHelper
@Override protected boolean isNewVersion(Map<String, Integer> header, List<String> values)
{
- String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
+ String version = getValueByColumnName(header, values, Attribute.Version);
+
if (version == null || version.isEmpty()) {
return true;
} else {
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyAssignmentImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyAssignmentImportHelper.java
index a8b9c170e663cb8e19b9128746cccc5d28c7ee47..5eba0433083b649799dd2da7a50820d3d121c5f6 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyAssignmentImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyAssignmentImportHelper.java
@@ -15,6 +15,13 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IEntityType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.ListUpdateValue;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
@@ -43,13 +50,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Collectors;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class PropertyAssignmentImportHelper extends BasicImportHelper
{
@@ -123,9 +124,15 @@ public class PropertyAssignmentImportHelper extends BasicImportHelper
@Override protected boolean isNewVersion(Map<String, Integer> header, List<String> values)
{
- String version = getValueByColumnName(header, values, PropertyAssignmentImportHelper.Attribute.Version);
String code = getValueByColumnName(header, values, PropertyAssignmentImportHelper.Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
+ String version = getValueByColumnName(header, values, PropertyAssignmentImportHelper.Attribute.Version);
+
if (version == null || version.isEmpty()) {
return true;
} else {
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyTypeImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyTypeImportHelper.java
index 74b87f10c9abcc7a1a671f81dd722cd020fdce1f..7f7ebd0b6d554061fd49b0eef1eba56a2bc544f7 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyTypeImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/PropertyTypeImportHelper.java
@@ -15,6 +15,15 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import static ch.ethz.sis.openbis.generic.server.xls.importer.utils.PropertyTypeSearcher.SAMPLE_DATA_TYPE_MANDATORY_TYPE;
+import static ch.ethz.sis.openbis.generic.server.xls.importer.utils.PropertyTypeSearcher.SAMPLE_DATA_TYPE_PREFIX;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
@@ -29,21 +38,13 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.delay.DelayedExecutionDec
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportModes;
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportTypes;
import ch.ethz.sis.openbis.generic.server.xls.importer.handler.JSONHandler;
-import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
+import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import org.apache.log4j.Logger;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import static ch.ethz.sis.openbis.generic.server.xls.importer.utils.PropertyTypeSearcher.SAMPLE_DATA_TYPE_MANDATORY_TYPE;
-import static ch.ethz.sis.openbis.generic.server.xls.importer.utils.PropertyTypeSearcher.SAMPLE_DATA_TYPE_PREFIX;
public class PropertyTypeImportHelper extends BasicImportHelper
{
@@ -132,8 +133,7 @@ public class PropertyTypeImportHelper extends BasicImportHelper
}
if (!propertyData.equals(this.propertyCache.get(code)))
{
- throw new UserFailureException(
- "Unambiguous property " + code + " found, has been declared before with different attributes.");
+ throw new UserFailureException("Ambiguous property " + code + " found, it has been declared before with different attributes.");
}
}
@@ -149,6 +149,11 @@ public class PropertyTypeImportHelper extends BasicImportHelper
String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
boolean isInternalNamespace = ImportUtils.isInternalNamespace(code);
boolean isSystem = delayedExecutor.isSystem();
boolean canUpdate = (isInternalNamespace == false) || isSystem;
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleImportHelper.java
index 0847c18c62584723972d69a6d5b7c13c3a61cd46..1d59d9745cb3a94c2c83d5b5b7c347fb032a44bd 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleImportHelper.java
@@ -107,7 +107,7 @@ public class SampleImportHelper extends BasicImportHelper
sampleType = new EntityTypePermId(getValueByColumnName(header, page.get(lineIndex), SAMPLE_TYPE_FIELD));
if(sampleType.getPermId() == null || sampleType.getPermId().isEmpty()) {
- throw new UserFailureException("Mandatory field missing or empty: " + SAMPLE_TYPE_FIELD);
+ throw new UserFailureException("Mandatory field is missing or empty: " + SAMPLE_TYPE_FIELD);
}
// first check that sample type exist.
@@ -268,7 +268,7 @@ public class SampleImportHelper extends BasicImportHelper
}
if (identifier == null || identifier.isEmpty()) {
- throw new UserFailureException("'Identifier' is missing, is mandatory since is needed to select a sample to update.");
+ throw new UserFailureException("'Identifier' is missing, it is mandatory since it is needed to select a sample to update.");
}
ISampleId sampleId = ImportUtils.buildSampleIdentifier(identifier);
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleTypeImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleTypeImportHelper.java
index 7597d8ba6a2ddc6ccab2c244356a44d3b3d602e6..91f624ebce1a80442b2343af412a7d43128ed96f 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleTypeImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/SampleTypeImportHelper.java
@@ -15,6 +15,9 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.id.PluginPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create.SampleTypeCreation;
@@ -28,9 +31,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class SampleTypeImportHelper extends BasicImportHelper
{
@@ -83,9 +84,15 @@ public class SampleTypeImportHelper extends BasicImportHelper
@Override protected boolean isNewVersion(Map<String, Integer> header, List<String> values)
{
- String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
+ String version = getValueByColumnName(header, values, Attribute.Version);
+
if (version == null || version.isEmpty()) {
return true;
} else {
@@ -110,6 +117,12 @@ public class SampleTypeImportHelper extends BasicImportHelper
@Override protected boolean isObjectExist(Map<String, Integer> header, List<String> values)
{
String code = getValueByColumnName(header, values, Attribute.Code);
+
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
EntityTypePermId id = new EntityTypePermId(code);
return delayedExecutor.getSampleType(id, new SampleTypeFetchOptions()) != null;
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ScriptImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ScriptImportHelper.java
index 1c116252adf7e16587d9af314271bed5b19684a1..bec20f48cd5d0425d7f225554bc4695264c5d477 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ScriptImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/ScriptImportHelper.java
@@ -15,6 +15,10 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.PluginType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.create.PluginCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.fetchoptions.PluginFetchOptions;
@@ -27,9 +31,6 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ImportTypes;
import ch.ethz.sis.openbis.generic.server.xls.importer.enums.ScriptTypes;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
-import java.util.List;
-import java.util.Map;
-
public class ScriptImportHelper extends BasicImportHelper
{
private static final String OWNER_CODE = "Code";
@@ -80,36 +81,42 @@ public class ScriptImportHelper extends BasicImportHelper
{
String scriptPath = getValueByColumnName(header, values, scriptType.getColumnName());
- if (scriptPath == null || scriptPath.isEmpty())
+ if (scriptPath != null && !scriptPath.isEmpty())
{
- return;
- }
-
- PluginCreation creation = new PluginCreation();
- creation.setName(getScriptName(header, values));
- creation.setScript(this.scripts.get(scriptPath));
- switch (scriptType) {
- case VALIDATION_SCRIPT:
- creation.setPluginType(PluginType.ENTITY_VALIDATION);
- break;
- case DYNAMIC_SCRIPT:
- creation.setPluginType(PluginType.DYNAMIC_PROPERTY);
- break;
+ String script = this.scripts.get(new File(scriptPath).getName());
+ if (script != null)
+ {
+ PluginCreation creation = new PluginCreation();
+ creation.setName(getScriptName(header, values));
+ creation.setScript(script);
+ switch (scriptType)
+ {
+ case VALIDATION_SCRIPT:
+ creation.setPluginType(PluginType.ENTITY_VALIDATION);
+ break;
+ case DYNAMIC_SCRIPT:
+ creation.setPluginType(PluginType.DYNAMIC_PROPERTY);
+ break;
+ }
+ delayedExecutor.createPlugin(creation);
+ }
}
- delayedExecutor.createPlugin(creation);
}
@Override protected void updateObject(Map<String, Integer> header, List<String> values, int page, int line)
{
String scriptPath = getValueByColumnName(header, values, scriptType.getColumnName());
- String script = this.scripts.get(scriptPath);
- if (script != null)
+ if (scriptPath != null && !scriptPath.isEmpty())
{
- PluginUpdate update = new PluginUpdate();
- PluginPermId permId = new PluginPermId(getScriptName(header, values));
- update.setPluginId(permId);
- update.setScript(this.scripts.get(scriptPath));
- delayedExecutor.updatePlugin(update);
+ String script = this.scripts.get(new File(scriptPath).getName());
+ if (script != null)
+ {
+ PluginUpdate update = new PluginUpdate();
+ PluginPermId permId = new PluginPermId(getScriptName(header, values));
+ update.setPluginId(permId);
+ update.setScript(script);
+ delayedExecutor.updatePlugin(update);
+ }
}
}
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyImportHelper.java
index 7554dec7cac9ae9c2da369664f75921719682e81..758795589b87f09ac32e7403a9c48903db57414e 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyImportHelper.java
@@ -15,6 +15,9 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create.VocabularyCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
@@ -27,9 +30,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class VocabularyImportHelper extends BasicImportHelper
{
@@ -79,6 +80,11 @@ public class VocabularyImportHelper extends BasicImportHelper
String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
boolean isInternalNamespace = ImportUtils.isInternalNamespace(code);
boolean isSystem = delayedExecutor.isSystem();
boolean canUpdate = (isInternalNamespace == false) || isSystem;
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyTermImportHelper.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyTermImportHelper.java
index cb22b739a744704837de575ce31805d1fd00e251..32d35170e47e690fea96d69042827a7a4428178e 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyTermImportHelper.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/helper/VocabularyTermImportHelper.java
@@ -15,6 +15,9 @@
*/
package ch.ethz.sis.openbis.generic.server.xls.importer.helper;
+import java.util.List;
+import java.util.Map;
+
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create.VocabularyTermCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyTermFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
@@ -28,9 +31,7 @@ import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.IAttribute;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.ImportUtils;
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.VersionUtils;
-
-import java.util.List;
-import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class VocabularyTermImportHelper extends BasicImportHelper
{
@@ -92,6 +93,11 @@ public class VocabularyTermImportHelper extends BasicImportHelper
String version = getValueByColumnName(header, values, Attribute.Version);
String code = getValueByColumnName(header, values, Attribute.Code);
+ if (code == null)
+ {
+ throw new UserFailureException("Mandatory field is missing or empty: " + Attribute.Code);
+ }
+
boolean isInternalNamespace = ImportUtils.isInternalNamespace(code) || ImportUtils.isInternalNamespace(vocabularyCode);
boolean isSystem = delayedExecutor.isSystem();
boolean canUpdate = (isInternalNamespace == false) || isSystem;
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/FileServerUtils.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/FileServerUtils.java
index e8f8b280404a50993ba94c981ba9ad3ea380e1df..7f461860a818bb2b42b3c7db6aeba328a9762448 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/FileServerUtils.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/FileServerUtils.java
@@ -5,6 +5,8 @@ import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
import java.io.File;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Set;
@@ -47,15 +49,27 @@ public class FileServerUtils
}
}
- public static byte[] read(String filePath) throws IOException
+ public static InputStream read(String src) throws IOException
{
- return Files.readAllBytes(getFilePath(filePath));
+ return Files.newInputStream(getFilePath(src));
}
- public static Path write(String filePath, byte[] bytes) throws IOException
+ public static byte[] readAllBytes(final String src) throws IOException
{
- Path filePathAsPath = getFilePath(filePath);
- Files.createDirectories(filePathAsPath);
- return Files.write(filePathAsPath, bytes);
+ final Path filePathAsPath = getFilePath(src);
+ return Files.readAllBytes(filePathAsPath);
}
+
+ public static long write(final InputStream src, final String dst) throws IOException
+ {
+ final Path filePathAsPath = getFilePath(dst);
+ return Files.copy(src, filePathAsPath);
+ }
+
+ public static OutputStream newOutputStream(String dst) throws IOException
+ {
+ final Path filePathAsPath = getFilePath(dst);
+ return Files.newOutputStream(filePathAsPath);
+ }
+
}
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
index d845b16a11d2e9c72ebb8136315c929faf376277..2c1a170dd54b4da4937ac96064247449a1782568 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
@@ -127,7 +127,7 @@ public final class UploadServiceServlet extends AbstractController
//
@Override
- @RequestMapping({ "/upload", "/openbis/upload" })
+ @RequestMapping({ "/upload", "/openbis/upload", "/openbis/openbis/upload" })
protected ModelAndView handleRequestInternal(final HttpServletRequest request,
final HttpServletResponse response) throws Exception
{
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionWorkspaceProvider.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionWorkspaceProvider.java
index 7ed1f3ff06893945900508ebd6ec81b50b0a753b..736746dde6b61b3183915f8dff25738e605de97c 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionWorkspaceProvider.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionWorkspaceProvider.java
@@ -31,6 +31,8 @@ public interface ISessionWorkspaceProvider
File getSessionWorkspace(String sessionToken);
+ File getCanonicalFile(String sessionToken, String relativePathToFile) throws IOException;
+
void deleteSessionWorkspace(String sessionToken);
void write(String sessionToken, String relativePathToFile, InputStream inputStream) throws IOException;
@@ -39,6 +41,8 @@ public interface ISessionWorkspaceProvider
InputStream read(String sessionToken, String relativePathToFile) throws IOException;
+ byte[] readAllBytes(String sessionToken, String relativePathToFile) throws IOException;
+
void delete(String sessionToken, String relativePathToFile) throws IOException;
}
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/SessionWorkspaceProvider.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/SessionWorkspaceProvider.java
index b33d92b9ccf2879974d2b713edab98b214854d7c..a66afc20af4fd2faa89a7943f10caaf19f6ae188 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/SessionWorkspaceProvider.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/shared/SessionWorkspaceProvider.java
@@ -133,6 +133,14 @@ public class SessionWorkspaceProvider implements ISessionWorkspaceProvider
return sessionWorkspace;
}
+ @Override
+ public File getCanonicalFile(String sessionToken, String relativePathToFile) throws IOException
+ {
+ File sessionWorkspace = getSessionWorkspace(sessionToken);
+ File targetFile = new File(sessionWorkspace, relativePathToFile);
+ return targetFile.getCanonicalFile();
+ }
+
@Override
public void deleteSessionWorkspace(String sessionTokenOrPAT)
{
@@ -156,6 +164,7 @@ public class SessionWorkspaceProvider implements ISessionWorkspaceProvider
public void write(String sessionToken, String relativePathToFile, InputStream inputStream) throws IOException {
File sessionWorkspace = getSessionWorkspace(sessionToken);
File targetFile = new File(sessionWorkspace, relativePathToFile);
+ targetFile.getParentFile().mkdirs();
Files.copy(inputStream, targetFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
}
@@ -172,6 +181,13 @@ public class SessionWorkspaceProvider implements ISessionWorkspaceProvider
return Files.newInputStream(targetFile.toPath());
}
+ @Override
+ public byte[] readAllBytes(String sessionToken, String relativePathToFile) throws IOException {
+ File sessionWorkspace = getSessionWorkspace(sessionToken);
+ File targetFile = new File(sessionWorkspace, relativePathToFile);
+ return Files.readAllBytes(targetFile.toPath());
+ }
+
@Override
public void delete(String sessionToken, String relativePathToFile) throws IOException {
File sessionWorkspace = getSessionWorkspace(sessionToken);
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractImportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractImportTest.java
index f67f997478f3a2de43f15ce8f0dec63faafb78c1..21abc7ef30e554fe6530a67bae9ae1f999f89a51 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractImportTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractImportTest.java
@@ -18,13 +18,18 @@
package ch.ethz.sis.openbis.systemtest.asapi.v3;
import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
-import java.io.InputStream;
+import java.util.Arrays;
+import java.util.UUID;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeSuite;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ISessionWorkspaceProvider;
+
public class AbstractImportTest extends AbstractTest
{
@@ -59,20 +64,26 @@ public class AbstractImportTest extends AbstractTest
v3api.logout(sessionToken);
}
- protected static byte[] getFileContent(final String fileName)
+ protected static String[] uploadToAsSessionWorkspace(final String sessionToken, final String... relativeFilePaths) throws IOException
{
- try (final InputStream is = AbstractImportTest.class.getResourceAsStream("test_files/import/" + fileName))
- {
- if (is == null)
- {
- throw new RuntimeException();
- }
+ final String[] canonicalFilePaths = getFilePaths(relativeFilePaths);
+ final ISessionWorkspaceProvider sessionWorkspaceProvider = CommonServiceProvider.getSessionWorkspaceProvider();
+ final String uploadId = UUID.randomUUID().toString();
+ final String[] destinations = new String[canonicalFilePaths.length];
- return is.readAllBytes();
- } catch (final IOException e)
+ for (int i = 0; i < canonicalFilePaths.length; i++)
{
- throw new RuntimeException(e);
+ destinations[i] = uploadId + "/" + relativeFilePaths[i];
+ sessionWorkspaceProvider.write(sessionToken, destinations[i], new FileInputStream(canonicalFilePaths[i]));
}
+
+ return destinations;
+ }
+
+ private static String[] getFilePaths(final String... fileNames)
+ {
+ return Arrays.stream(fileNames).map(fileName -> AbstractImportTest.class.getResource("test_files/import/" + fileName).getPath())
+ .toArray(String[]::new);
}
}
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
index 972d9eced25f0e2c51965d2301e8ff0eb246e290..b229afb708d0239dbe127639d95dfaf0dd7b3116 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
@@ -20,6 +20,9 @@ import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.fail;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
import java.lang.reflect.Method;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
@@ -161,6 +164,8 @@ import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.test.AssertionUtil;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ISessionWorkspaceProvider;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UncompressedImportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UncompressedImportTest.java
index 534803e5b09b244a585a1db87c59fdd44f4bcbbf..94ebd7a52ee8d6d6973dd45965229a55d0dad5ff 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UncompressedImportTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UncompressedImportTest.java
@@ -16,8 +16,8 @@
package ch.ethz.sis.openbis.systemtest.asapi.v3;
+import static org.junit.Assert.assertNotNull;
import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.util.Arrays;
@@ -25,21 +25,17 @@ import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
-import ch.systemsx.cisd.common.action.IDelegatedAction;
-import org.testng.annotations.Test;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportFormat;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportScript;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportValue;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.UncompressedImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportMode;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.Plugin;
@@ -55,15 +51,18 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.VocabularyTerm;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularySearchCriteria;
+import ch.systemsx.cisd.common.action.IDelegatedAction;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class UncompressedImportTest extends AbstractImportTest
{
@Test
- public void testDataImport()
+ public void testDataImport() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("import.xlsx"), null, null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -85,10 +84,11 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testLargeDataImport()
+ public void testLargeDataImport() throws Exception
{
- final UncompressedImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("import_large_cell.xlsx"), null,
- List.of(new ImportValue("value-M20.txt", new String(getFileContent("data/value-M20.txt")))));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import_large_cell.xlsx", "data/value-M20.txt");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles[0]);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -110,9 +110,11 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testImportOptionsUpdateIfExists()
+ public void testImportOptionsUpdateIfExists() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.xlsx"), null, null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -137,9 +139,11 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testImportOptionsIgnoreExisting()
+ public void testImportOptionsIgnoreExisting() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.xlsx"), null, null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.IGNORE_EXISTING);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -164,21 +168,23 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = ".*FAIL_IF_EXISTS.*")
- public void testImportOptionsFailIfExists()
+ public void testImportOptionsFailIfExists() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.xlsx"), null, null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.FAIL_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
}
@Test
- public void testWithValidationScript()
+ public void testWithValidationScript() throws Exception
{
final String name = "valid.py";
final String source = "print 'Test validation script'";
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("validation_script.xls"),
- List.of(new ImportScript(name, source)), null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "validation_script.xls", "scripts/" + name);
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles[0]);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -203,12 +209,12 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testWithDynamicScript()
+ public void testWithDynamicScript() throws Exception
{
final String name = "dynamic.py";
final String source = "1+1";
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("dynamic_script.xls"),
- List.of(new ImportScript(name, source)), null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "dynamic_script.xls", "scripts/" + name);
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles[0]);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -238,9 +244,11 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testInternalTypes_failForNormalUser()
+ public void testInternalTypes_failForNormalUser() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("import_internal_type.xlsx"), null, null);
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import_internal_type.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
assertUserFailureException(new IDelegatedAction()
@@ -255,13 +263,15 @@ public class UncompressedImportTest extends AbstractImportTest
}
@Test
- public void testInternalTypes()
+ public void testInternalTypes() throws Exception
{
- final IImportData importData = new UncompressedImportData(ImportFormat.XLS, getFileContent("import_internal_type.xlsx"), null, null);
- final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
-
final String systemSessionToken = v3api.loginAsSystem();
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(systemSessionToken, "import_internal_type.xlsx");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
+ final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
+
v3api.executeImport(systemSessionToken, importData, importOptions);
final DataSetTypeSearchCriteria dataSetTypeSearchCriteria = new DataSetTypeSearchCriteria();
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ZipImportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ZipImportTest.java
index 43807a6b2b4e0fa69d8351ec9e8cec314725eb12..d2196dd938d69289bccd70265a96d1c1248067a9 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ZipImportTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ZipImportTest.java
@@ -25,19 +25,17 @@ import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
-import ch.systemsx.cisd.common.action.IDelegatedAction;
-import org.testng.annotations.Test;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.IImportData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ImportFormat;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data.ZipImportData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportMode;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.options.ImportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.Plugin;
@@ -53,15 +51,18 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.VocabularyTerm;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularySearchCriteria;
+import ch.systemsx.cisd.common.action.IDelegatedAction;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class ZipImportTest extends AbstractImportTest
{
@Test
- public void testDataImport()
+ public void testDataImport() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("import.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -82,9 +83,11 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testDataImportInternalTypes_failForNormalUser()
+ public void testDataImportInternalTypes_failForNormalUser() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("import_internal_type.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import_internal_type.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
assertUserFailureException(new IDelegatedAction()
@@ -99,13 +102,15 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testDataImportInternalTypes_systemUser()
+ public void testDataImportInternalTypes_systemUser() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("import_internal_type.zip"));
- final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
-
final String systemSessionToken = v3api.loginAsSystem();
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(systemSessionToken, "import_internal_type.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
+ final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
+
v3api.executeImport(systemSessionToken, importData, importOptions);
final DataSetTypeSearchCriteria dataSetTypeSearchCriteria = new DataSetTypeSearchCriteria();
@@ -130,7 +135,6 @@ public class ZipImportTest extends AbstractImportTest
assertEquals(sampleTypeSearchResult.getTotalCount(), 1);
assertEquals(sampleTypeSearchResult.getObjects().get(0).getDescription(), "Internal Sample Type");
-
final ExperimentTypeSearchCriteria experimentTypeSearchCriteria = new ExperimentTypeSearchCriteria();
experimentTypeSearchCriteria.withCode().thatEquals("$INTERNAL_EXPERIMENT_TYPE");
@@ -144,9 +148,11 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testLargeDataImport()
+ public void testLargeDataImport() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("import_large_cell.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "import_large_cell.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -168,9 +174,11 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testImportOptionsUpdateIfExists()
+ public void testImportOptionsUpdateIfExists() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -195,9 +203,11 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testImportOptionsIgnoreExisting()
+ public void testImportOptionsIgnoreExisting() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.IGNORE_EXISTING);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -222,20 +232,24 @@ public class ZipImportTest extends AbstractImportTest
}
@Test(expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = ".*FAIL_IF_EXISTS.*")
- public void testImportOptionsFailIfExists()
+ public void testImportOptionsFailIfExists() throws Exception
{
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("existing_vocabulary.zip"));
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "existing_vocabulary.zip");
+
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.FAIL_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
}
@Test
- public void testWithValidationScript()
+ public void testWithValidationScript() throws Exception
{
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "validation_script.zip");
+
final String name = "valid.py";
final String source = "print 'Test validation script'";
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("validation_script.zip"));
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
@@ -260,11 +274,13 @@ public class ZipImportTest extends AbstractImportTest
}
@Test
- public void testWithDynamicScript()
+ public void testWithDynamicScript() throws Exception
{
+ final String[] sessionWorkspaceFiles = uploadToAsSessionWorkspace(sessionToken, "dynamic_script.zip");
+
final String name = "dynamic.py";
final String source = "1+1";
- final IImportData importData = new ZipImportData(ImportFormat.XLS, getFileContent("dynamic_script.zip"));
+ final ImportData importData = new ImportData(ImportFormat.EXCEL, sessionWorkspaceFiles);
final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
v3api.executeImport(sessionToken, importData, importOptions);
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/dynamic.py b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/dynamic.py
index c040fa67d3452162197945543e1ca9974e202924..07d91dc6abdd2cc89ac1acf5afcdb9bc93838ee9 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/dynamic.py
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/dynamic.py
@@ -1 +1 @@
-1+1
+1+1
\ No newline at end of file
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/valid.py b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/valid.py
new file mode 100644
index 0000000000000000000000000000000000000000..d23f9285861417fe45f0016056e72c385dfc6843
--- /dev/null
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/import/scripts/valid.py
@@ -0,0 +1 @@
+print 'Test validation script'
\ No newline at end of file
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
index aa489331b1f5f1bd2ce33b7cab50f89efc4f1404..26d12018fc51c6536baa5e5f9cde3d2be6ee11de 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
@@ -1288,6 +1288,26 @@ define([ 'jquery', 'underscore'], function($, _) {
this.assert.ok(false, msg);
};
+ this.base64ToBlob = (b64Data, contentType='', sliceSize=512) => {
+ var byteCharacters = atob(b64Data);
+ var byteArrays = [];
+
+ for (var offset = 0; offset < byteCharacters.length; offset += sliceSize) {
+ var slice = byteCharacters.slice(offset, offset + sliceSize);
+
+ var byteNumbers = new Array(slice.length);
+ for (var i = 0; i < slice.length; i++) {
+ byteNumbers[i] = slice.charCodeAt(i);
+ }
+
+ var byteArray = new Uint8Array(byteNumbers);
+ byteArrays.push(byteArray);
+ }
+
+ var blob = new Blob(byteArrays, {type: contentType});
+ return blob;
+ }
+
};
return Common;
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
index 8d498fe2aedd1fa482ee3462643c8a582fe7676c..64d5520347628ad2e6d49483dd02170bfbf1c82c 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
@@ -58,12 +58,9 @@ var fullTypes = [
"as/dto/importer/options/ImportMode",
"as/dto/importer/ImportOperation",
"as/dto/importer/ImportOperationResult",
+"as/dto/importer/ImportResult",
+"as/dto/importer/data/ImportData",
"as/dto/importer/data/ImportFormat",
-"as/dto/importer/data/ZipImportData",
-"as/dto/importer/data/UncompressedImportData",
-"as/dto/importer/data/ImportValue",
-"as/dto/importer/data/ImportScript",
-"as/dto/importer/data/IImportData",
"as/dto/entitytype/update/IEntityTypeUpdate",
"as/dto/entitytype/update/PropertyAssignmentListUpdateValue",
"as/dto/entitytype/EntityKind",
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
index 8f57a107fb9f6b3bc58d7f136d2c10eecced9969..e17ce32cf2ad37119c20a223c966747f6e37dede 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
@@ -709,7 +709,7 @@ define([], function() {
this.executeImport = function (importData, importOptions) {
return this._executeOperation(new dtos.ImportOperation(importData, importOptions)).then(function (results) {
- return results.getResults()[0]
+ return results.getResults()[0].getImportResult()
})
}
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-import-export.ts b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-import-export.ts
index df54153e4ff10d1bec2714c024ff8ce4f57f6598..b6b7f5065f7ef3050ee11cc02e1f7dac048247ee 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-import-export.ts
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-import-export.ts
@@ -15,10 +15,10 @@
*
*/
-import jquery from "./types/jquery"
-import underscore from "./types/underscore"
-import common from "./types/common"
-import openbis from "./types/openbis.esm"
+import jquery from './types/jquery'
+import underscore from './types/underscore'
+import common from './types/common'
+import openbis from './types/openbis.esm'
exports.default = new Promise((resolve) => {
require(["jquery", "underscore", "openbis", "test/common", "test/openbis-execute-operations", "test/dtos"], function (
@@ -29,62 +29,7 @@ exports.default = new Promise((resolve) => {
openbisExecuteOperations,
dtos
) {
- var fileContent =
- "UEsDBBQACAgIAEh8FVcAAAAAAAAAAAAAAAALAAAAX3JlbHMvLnJlbHOtksFOwzAMhu97iir3Nd1ACKGmu0xIuyE0HsAkbhu1iaPEg/L2RBMSDI2" +
- "yw45xfn/+YqXeTG4s3jAmS16JVVmJAr0mY32nxMv+cXkvNs2ifsYROEdSb0Mqco9PSvTM4UHKpHt0kEoK6PNNS9EB52PsZAA9QIdyXVV3Mv5kiOaEWeyMEnFnVqLYfwS8hE1ta" +
- "zVuSR8cej4z4lcikyF2yEpMo3ynOLwSDWWGCnneZX25y9/vlA4ZDDBITRGXIebuyBbTt44h/ZTL6ZiYE7q55nJwYvQGzbwShDBndHtNI31ITO6fFR0zX0qLWp78y+YTUEsHCIW" +
- "aNJruAAAAzgIAAFBLAwQUAAgICABIfBVXAAAAAAAAAAAAAAAAGgAAAHhsL19yZWxzL3dvcmtib29rLnhtbC5yZWxzrZFNa8MwDIbv/RVG98VJB2OMOL2MQa/9+AHGUeLQxDaS1" +
- "rX/fi4bWwpl7NCT0Nfzvkj16jSN6ojEQwwGqqIEhcHFdgi9gf3u7eEZVs2i3uBoJY+wHxKrvBPYgBdJL1qz8zhZLmLCkDtdpMlKTqnXybqD7VEvy/JJ05wBzRVTrVsDtG4rULt" +
- "zwv+wY9cNDl+je58wyA0JzXIekTPRUo9i4CsvMgf0bfnlPeU/Ih3YI8qvg59SNncJ1V9mHu96C28J261Qfuz8JPPyt5lFra/e3XwCUEsHCE/w+XrSAAAAJQIAAFBLAwQUAAgIC" +
- "ABIfBVXAAAAAAAAAAAAAAAADwAAAHhsL3dvcmtib29rLnhtbI1T23LaMBB971d49A6+cCkwmAw1eJKZ3iakybNsr7GKLHmkJUA6/feuZZym0z70AaS96OzZ3ePlzbmW3jMYK7S" +
- "KWTgMmAcq14VQ+5h9e0gHM+ZZ5KrgUiuI2QUsu1m9W560OWRaHzx6r2zMKsRm4fs2r6DmdqgbUBQptak5kmn2vm0M8MJWAFhLPwqCqV9zoViHsDD/g6HLUuSw0fmxBoUdiAHJk" +
- "djbSjSWrZalkPDYNeTxpvnMa6KdcJkzf/VK+6vxMp4fjk1K2TErubRAjVb69CX7DjlSR1xK5hUcIZwH4z7lDwiNlEllyNk6HgWc7O94azrEW23Ei1bI5S43WsqYoTleqxFRFPm" +
- "/Irt2UA88s73z/CRUoU8xoxVd3txP7vokCqxogdPRbNz7bkHsK4zZLJxHzEOe3beDitkkoGelMBZdEYfCqZNnoHqtRQ35bzpyO+tPT7mBupdhS5XOu4IqO50ghZ6FFZkkxmYhK" +
- "GDuisgh9jDUbk7zFwiG8hN9VEQhbDkZKD/pgiDWhHaNvy7nam9AIieSwyAIwhYXzvjRojuvUpKa7n/JSYrMQCcgpyXmHY2I2Y/302iazKbRIFqHo0EYbieDD6PxZJBu05Qml2y" +
- "SefqTdOVQF/RLOv4WDX0k91DuLrTbc8y25xzk2nHyKa37d9T8XhOrX1BLBwg0mo9c+wEAAHADAABQSwMEFAAICAgASHwVVwAAAAAAAAAAAAAAAA0AAAB4bC9zdHlsZXMueG1s7" +
- "Vldb5swFH3fr7D8vkISmrYTUHWdmPYyVWsqTZr24IABq8ZGttOG/vrZmBBI231k6kYq+mJ8fM+5h4sNjuufrwsK7rCQhLMATo5cCDCLeUJYFsCbRfT2FAKpEEsQ5QwHsMISnod" +
- "vfKkqiq9zjBXQCkwGMFeqfOc4Ms5xgeQRLzHTIykXBVK6KzJHlgKjRBpSQZ2p686dAhEGQ5+tiqhQEsR8xZS20ULANp8SDc49CKzcJU+0lY+YYYEodELfaQRCP+VsqzOHFgh9+" +
- "QDuENUiUxMec8oFENkygFHk1n8GZqjANuwSUbIUxIApKgitLGzJORJS37bVq7PbHDuZdiQvBLFeu4LuwOhLO6DECpuxVm320lV7LrH3conrxswYQmk7Y6bQAqFfIqWwYJHugOZ" +
- "6UZV62jG9DqxMHfeL6EygajI97hDqRuddcpHodded8xYCCUEZZ4jelAFMEZUYttAHfs82YOhTnCotLEiWm1bx0jEiSvFCX2w4JrVVbi90+hhTem0W8dd0e/euFl2njxcdqzv63" +
- "WC8N5dWqemgsqRVxI1I/Qwt8L4O6UEXlGSswDuBV4IrHKv6HVTDoY82gSDngjxoafMAs2bNm1eWIrGB7P1CoPBafeEKWRXt6V6gcqHBtoiEJXViPSZzQdjtgkekHdZlKlsbgPL" +
- "4FicbkzlJNLUT6azTnUq52zpN9q1T43O3UF24W6nNNDgcM9PRzDNm9l5bo5nRzGhmNDOa2ceMNxvSl9KbDMqNNyg30yG5OfvPZpzu9t1u5jv7+Pm+2/h1+th5189fWj+0Pf0/K" +
- "tvr+iHUK5r3Z0X7/VXyims2rIlmzhiGXrHjIc2ysWCHvCyd5lPaOSDrfVZbFJjjxwB+NgfStFO25YpQRZjtOY8Jl7wo0CZ+ctwjzJ4lgG/u95Y075HmT5JWQmAWVy3npMfxfsb" +
- "p5Trt8U6e4l1hEetn0FLOehR79Lktpu5s/3cQ/gBQSwcIAAc48d4CAACAGAAAUEsDBBQACAgIAEh8FVcAAAAAAAAAAAAAAAAYAAAAeGwvd29ya3NoZWV0cy9zaGVldDEueG1sv" +
- "Vffc9o4EH6/v8Lj9+JfGIcM0GnD5Xozaelc0nbm3oQtY01kyScJCPnrbyXZxsEuydxwfUiQdle737crw+fZ+6eSOjssJOFs7gYj33UwS3lG2Gbufnu4fXflOlIhliHKGZ67Byz" +
- "d94vfZnsuHmWBsXIgAZNzt1CquvY8mRa4RHLEK8zAk3NRIgVbsfFkJTDKzKGSeqHvT7wSEebaDNfiLTl4npMUL3m6LTFTNonAFCmALwtSySbbU/amfJlAe6Da4OlAXFpPmy8Y9" +
- "/KVJBVc8lyNUl7W0Posp970Bc8nEf63TEEMVHdETypskpXpW1iWSDxuq3eQu4JOrQkl6mAIu4uZyf9VODmhCovPPIMh54hKDL4KbfA9Vt8q41cP/CsYGre3mHn14cUsIzAPjcw" +
- "ROJ+7H4LrZaIjTMB3gveys3Zkwfe3gG9LkWzSGeMfgmR3hGGwKrGtjX/x/Q2nn6AXcE27jr8xNK0xCLIpAOEdzlWbUqH1PaY4VTjrnlttFYUi94dyzWmbIMM52lKlIUA5Lhr7D" +
- "hDPXabbSSElr3SJG0yppuk6qY79E/JPxq7zzHl5nyIKTQp8v7P/Yo6fWnU779CBb01baq9+stacP2qTzuvrIRkWur0V0k9hjcJ1EFh32KL5eNXd26OO/McMBHztvHTi7roZza2" +
- "5MTDquhPQhR8kU4XGNYqm4zgKwrjtE0zlE9Y9B3c8SsDxDONoTPUAuO30Hd5hCgcMoq4NSliC3gsEixl0VZr/ur8UVVJPsE6abqXiZQ3NzqggWYbZYFlTs0RPABM+CTOfUh3Mj" +
- "KDbNk0Y6P5ctl5Y1wsH6kXJ5etFdb1oqJ5/+Xrjut54oF5g75sdo/0+RQotZoLvHWECbVU78baQuU2TUdxDYKPP3C4Dq8cNKOty+jmVZhBwWIJ1t/Bn3k4DhD/A1AILfzGwsAc" +
- "saIGZiI/9iPBlxE0/IhomF50jZ5/hy7KLDLLIIGOD7GxE0ME+HsY+Pof96n/APjbIxmcmYyPiM5PpR8QvI5b9iJ/MLv7Vs4tfnV3cm93khH8/IhlmNznL7tLUJq9Sm/SAX51Q6" +
- "0dMh6kl56glo+ji7JJX2SU97IF/Qm8g5CTLMqmvrtcQ9jrf85UgTK0qI8udAqQbSOmj1NscZd6pBeRm+yPEBXnmTCF6A1ofi85PFrywKJL2HZ7VrJ+R2BAoTI0Y9EdJLQ/rNag" +
- "ns4LWr7mCXje7wmhMvYuD4CoI/DCahKE/hjM552rY5bU6eVuBPKuwuCfP8GM4hf50pKDRz42eqretgHIdnWIlTPWM79lDgdkKWMLgBQGS5gVn7lZcKIEICL81RenjB5b9KIhqJ" +
- "bkDrzMd+ZuCDLzhpX5TklrBshdNXVZE6wL/2M2jJeUVweYCADvblVvTACcjeQ4dZ+qWCHks1ZpXWfb77niZFzOeZVa6wwXprGFpM1pzu+4Wg237mrn4F1BLBwh76zOXRQQAAKo" +
- "OAABQSwMEFAAICAgASHwVVwAAAAAAAAAAAAAAABQAAAB4bC9zaGFyZWRTdHJpbmdzLnhtbI2STU/DMAyG7/yKyHeWMgmEpjRTKeM0BJo6pJ2mkJo1UvNBnE7w7wkFiRvK0fbj9" +
- "7Uti/WHHdkZIxnvarhaVMDQad8bd6ph3z1c3gKjpFyvRu+whk8kWMsLQZRYbnVUw5BSWHFOekCraOEDulx589GqlMN44hQiqp4GxGRHvqyqG26VccC0n1zKttfAJmfeJ2x/E0u" +
- "QgowUs8mKgtLZO6sQxjOCfHlqm7v9ttkdjt3heSN4koJ/8//1/CxZxLa+xyLwHklHE1Kp8Dx4EblVrzgWkd1m93hsitAyahYsm7KMmgXbssv/UTz/mPwCUEsHCEgvXEPsAAAAo" +
- "QIAAFBLAwQUAAgICABIfBVXAAAAAAAAAAAAAAAAEQAAAGRvY1Byb3BzL2NvcmUueG1sfVJNT8MwDL3zK6rcu6QtGlO0dhIguDCBxCYQt5C6I9AmUeJ9/XvSbi1fEzf7vZdnO/Z" +
- "0tmvqaAPOK6NzkowYiUBLUyq9yslycRNPSORR6FLURkNO9uDJrDibSsulcfDgjAWHCnwUjLTn0ubkDdFySr18g0b4UVDoQFbGNQJD6lbUCvkhVkBTxsa0ARSlQEFbw9gOjuRoW" +
- "crB0q5d3RmUkkINDWj0NBkl9EuL4Bp/8kHHfFM2CvcWTkp7clDvvBqE2+12tM06aeg/oc/zu8du1Fjp9qskkGJ6bIRLBwKhjIIBP5Trmafs6npxQ4qUpSxm45iliyTjGeNp9jK" +
- "lv963hofYuGKupDPeVBjdV5WSEC09uPbJoGjVJXjplMWw2KIjfwAhr4VercMWCtDx7WUnGaB2v7XwOA+XUCkoL/fB4wTWt9kcsf/nzGI2idNkkVzw7Jwn429z9gZdZQcb1R5kk" +
- "XVFh7Tt2q9f30HiYaQhCTEqrOEA9+GfIy0+AVBLBwgoNK7AewEAAPACAABQSwMEFAAICAgASHwVVwAAAAAAAAAAAAAAABMAAABkb2NQcm9wcy9jdXN0b20ueG1snc6xCsIwFIX" +
- "h3acI2dtUB5HStIs4O1T3kN62AXNvyE2LfXsjgu6Ohx8+TtM9/UOsENkRarkvKykALQ0OJy1v/aU4ScHJ4GAehKDlBiy7dtdcIwWIyQGLLCBrOacUaqXYzuANlzljLiNFb1Kec" +
- "VI0js7CmeziAZM6VNVR2YUT+SJ8Ofnx6jX9Sw5k3+/43m8he22jfmfbF1BLBwjh1gCAlwAAAPEAAABQSwMEFAAICAgASHwVVwAAAAAAAAAAAAAAABAAAABkb2NQcm9wcy9hcHA" +
- "ueG1snZBNa8MwDIbv+xXB9Jo4CUtWiuOyMXYqbIes7BY8W2k9/IXtlPTfz21Z2/Oki754JL1kPWuVHcAHaU2HqqJEGRhuhTS7Dn32b/kSZSEyI5iyBjp0hIDW9IF8eOvARwkhS" +
- "wQTOrSP0a0wDnwPmoUitU3qjNZrFlPqd9iOo+TwavmkwURcl2WLYY5gBIjcXYHoQlwd4n+hwvLTfWHbH13iUdKDdopFoATfwt5GpnqpgVapfE3Is3NKchaTInQjvz28n1fgp6J" +
- "JXi820kzz8LVsh/YxuxsY0gs/wCNuysXLJJXIa4LvYSfy9iI1rZqiTHYe+KsRfFOV/gJQSwcIRY4uEvgAAACaAQAAUEsDBBQACAgIAEh8FVcAAAAAAAAAAAAAAAATAAAAW0Nvb" +
- "nRlbnRfVHlwZXNdLnhtbL2UTU/DMAyG7/yKKlfUZuOAEGq3Ax9HmMQ4o5C4bVjzoSQb27/H6QZMo2xMqzhFjf2+j+22zsdL1SQLcF4aXZBhNiAJaG6E1FVBnqf36RUZj87y6cq" +
- "CTzBX+4LUIdhrSj2vQTGfGQsaI6VxigV8dBW1jM9YBfRiMLik3OgAOqQhepBRfgslmzchuVvi9ZqLcpLcrPMiqiDM2kZyFjBMY5R26hw0fo9wocVOdemmsgyVbY6vpfXnvxOsr" +
- "nYAUsXO4n234s1Ct6QNoOYRx+2kgGTCXHhgChPoS+yEZj3300VaNhvYu3GzV2NmGSb/E3gbeRzNlKXkIAyfK5Rk3jpgwtcAAYtvz0wxqQ/wfVg14Pumt6Z/6LwVeNoew56L+PI" +
- "/NIGaORBPweH/3fsgtr331YH6iTPW42ZwcHwRn19eVKcWjcAFuf8NfBPnPhh1cuNrm2PhyDiZDHHRCBA/2Wc5bbf06ANQSwcItuOWgmMBAADUBQAAUEsBAhQAFAAICAgASHwVV" +
- "4WaNJruAAAAzgIAAAsAAAAAAAAAAAAAAAAAAAAAAF9yZWxzLy5yZWxzUEsBAhQAFAAICAgASHwVV0/w+XrSAAAAJQIAABoAAAAAAAAAAAAAAAAAJwEAAHhsL19yZWxzL3dvcmt" +
- "ib29rLnhtbC5yZWxzUEsBAhQAFAAICAgASHwVVzSaj1z7AQAAcAMAAA8AAAAAAAAAAAAAAAAAQQIAAHhsL3dvcmtib29rLnhtbFBLAQIUABQACAgIAEh8FVcABzjx3gIAAIAYA" +
- "AANAAAAAAAAAAAAAAAAAHkEAAB4bC9zdHlsZXMueG1sUEsBAhQAFAAICAgASHwVV3vrM5dFBAAAqg4AABgAAAAAAAAAAAAAAAAAkgcAAHhsL3dvcmtzaGVldHMvc2hlZXQxLnh" +
- "tbFBLAQIUABQACAgIAEh8FVdIL1xD7AAAAKECAAAUAAAAAAAAAAAAAAAAAB0MAAB4bC9zaGFyZWRTdHJpbmdzLnhtbFBLAQIUABQACAgIAEh8FVcoNK7AewEAAPACAAARAAAAA" +
- "AAAAAAAAAAAAEsNAABkb2NQcm9wcy9jb3JlLnhtbFBLAQIUABQACAgIAEh8FVfh1gCAlwAAAPEAAAATAAAAAAAAAAAAAAAAAAUPAABkb2NQcm9wcy9jdXN0b20ueG1sUEsBAhQ" +
- "AFAAICAgASHwVV0WOLhL4AAAAmgEAABAAAAAAAAAAAAAAAAAA3Q8AAGRvY1Byb3BzL2FwcC54bWxQSwECFAAUAAgICABIfBVXtuOWgmMBAADUBQAAEwAAAAAAAAAAAAAAAAATE" +
- "QAAW0NvbnRlbnRfVHlwZXNdLnhtbFBLBQYAAAAACgAKAIACAAC3EgAAAAA="
+ var fileContent = "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"
var executeModule = function (moduleName: string, facade: openbis.openbis, dtos: openbis.bundle) {
QUnit.module(moduleName)
@@ -117,14 +62,23 @@ exports.default = new Promise((resolve) => {
var c = new common(assert, dtos)
var fAction = function (facade: openbis.openbis) {
- var importData = new dtos.UncompressedImportData()
- importData.setFormat("XLS")
- importData.setFile(fileContent)
-
- var importOptions = new dtos.ImportOptions()
- importOptions.setMode("UPDATE_IF_EXISTS")
-
- return facade.executeImport(importData, importOptions)
+ var fileName = "model.xlsx"
+ var data = new window.File([c.base64ToBlob(fileContent)], fileName)
+ return facade.uploadToSessionWorkspace(data)
+ .then(function() {
+ c.ok("uploadToSessionWorkspace")
+ var importData = new dtos.ImportData()
+ importData.setFormat("EXCEL")
+ importData.setSessionWorkspaceFiles([fileName])
+
+ var importOptions = new dtos.ImportOptions()
+ importOptions.setMode("UPDATE_IF_EXISTS")
+
+ return facade.executeImport(importData, importOptions)
+ .then(function() {
+ c.ok("executeImport")
+ })
+ })
}
var fCheck = function (facade: openbis.openbis) {
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/common.d.ts b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/common.d.ts
index e05938aadc3c9957d0f211457fc50b2b54543e10..eea599e1d417a1a8d985ef56e9e33e6ef9b3da7d 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/common.d.ts
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/common.d.ts
@@ -152,5 +152,6 @@ export namespace common {
ok(msg?): void
section(msg): void
fail(msg?): void
+ base64ToBlob(b64Data: string, contentType: string='', sliceSize: number=512): Blob
}
}
diff --git a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/openbis.esm.d.ts b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/openbis.esm.d.ts
index 6add41dd7ece762e7136c8d3a9ab1faf1be4a175..7f6dc21ff7eba597609748c9a4e96190f61edc3d 100644
--- a/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/openbis.esm.d.ts
+++ b/test-api-openbis-javascript/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/types/openbis.esm.d.ts
@@ -11139,9 +11139,6 @@ export namespace openbis {
getIdentifier(): ObjectIdentifier;
}
- interface IImportData extends Serializable {
- }
-
interface ILabelHolder {
getLabel(): string;
@@ -11619,12 +11616,32 @@ export namespace openbis {
new <T extends IObjectId>(): IdsSearchCriteria<T>;
}
+ interface ImportData extends Serializable {
+
+ getFormat(): ImportFormat;
+
+ getSessionWorkspaceFiles(): string[];
+
+ setFormat(arg0: ImportFormat): void;
+
+ setSessionWorkspaceFiles(arg0: string[]): void;
+ }
+
+ /**
+ */
+ interface ImportDataConstructor {
+
+ new (): ImportData;
+
+ new (arg0: ImportFormat, arg1: string[]): ImportData;
+ }
+
/**
*/
interface ImportFormatObject {
/**
*/
- XLS: ImportFormat<> = "XLS";
+ EXCEL: ImportFormat<> = "EXCEL";
}
/**
@@ -11643,13 +11660,13 @@ export namespace openbis {
interface ImportOperation extends Serializable, IOperation {
- getImportData(): IImportData;
+ getImportData(): ImportData;
getImportOptions(): ImportOptions;
getMessage(): string;
- setImportData(arg0: IImportData): void;
+ setImportData(arg0: ImportData): void;
setImportOptions(arg0: ImportOptions): void;
}
@@ -11660,12 +11677,16 @@ export namespace openbis {
new (): ImportOperation;
- new (arg0: IImportData, arg1: ImportOptions): ImportOperation;
+ new (arg0: ImportData, arg1: ImportOptions): ImportOperation;
}
interface ImportOperationResult extends Serializable, as_dto_common_operation_IOperationResult {
+ getImportResult(): ImportResult;
+
getMessage(): string;
+
+ setImportResult(arg0: ImportResult): void;
}
/**
@@ -11673,6 +11694,8 @@ export namespace openbis {
interface ImportOperationResultConstructor {
new (): ImportOperationResult;
+
+ new (arg0: ImportResult): ImportOperationResult;
}
interface ImportOptions extends Serializable {
@@ -11691,44 +11714,20 @@ export namespace openbis {
new (arg0: ImportMode): ImportOptions;
}
- interface ImportScript extends Serializable {
-
- getName(): string;
-
- getSource(): string;
-
- setName(arg0: string): void;
-
- setSource(arg0: string): void;
- }
-
- /**
- */
- interface ImportScriptConstructor {
-
- new (): ImportScript;
-
- new (arg0: string, arg1: string): ImportScript;
- }
+ interface ImportResult extends Serializable {
- interface ImportValue extends Serializable {
-
- getName(): string;
-
- getValue(): string;
-
- setName(arg0: string): void;
+ getObjectIds(): IObjectId[];
- setValue(arg0: string): void;
+ setObjectIds(arg0: IObjectId[]): void;
}
/**
*/
- interface ImportValueConstructor {
+ interface ImportResultConstructor {
- new (): ImportValue;
+ new (): ImportResult;
- new (arg0: string, arg1: string): ImportValue;
+ new (arg0: IObjectId[]): ImportResult;
}
interface LabelSearchCriteria extends StringFieldSearchCriteria {
@@ -13851,7 +13850,7 @@ export namespace openbis {
executeExport(arg1: ExportData, arg2: ExportOptions): Promise<ExportResult>;
- executeImport(arg1: IImportData, arg2: ImportOptions): Promise<void>;
+ executeImport(arg1: ImportData, arg2: ImportOptions): Promise<ImportResult>;
executeOperations(arg1: IOperation[], arg2: IOperationExecutionOptions): Promise<IOperationExecutionResults>;
@@ -14068,6 +14067,8 @@ export namespace openbis {
updateVocabularies(arg1: VocabularyUpdate[]): Promise<void>;
updateVocabularyTerms(arg1: VocabularyTermUpdate[]): Promise<void>;
+
+ uploadToSessionWorkspace(arg0: any): Promise<void>;
}
/**
@@ -23027,34 +23028,6 @@ export namespace openbis {
new (): UnarchiveDataSetsOperationResult;
}
- interface UncompressedImportData extends Serializable, IImportData {
-
- getFile(): string;
-
- getFormat(): ImportFormat;
-
- getImportValues(): ImportValue[];
-
- getScripts(): ImportScript[];
-
- setFile(arg0: string): void;
-
- setFormat(arg0: ImportFormat): void;
-
- setImportValues(arg0: ImportValue[]): void;
-
- setScripts(arg0: ImportScript[]): void;
- }
-
- /**
- */
- interface UncompressedImportDataConstructor {
-
- new (): UncompressedImportData;
-
- new (arg0: ImportFormat, arg1: string, arg2: ImportScript[], arg3: ImportValue[]): UncompressedImportData;
- }
-
interface UnknownRelatedObjectId extends IObjectId {
getRelatedObjectId(): string;
@@ -24590,26 +24563,6 @@ export namespace openbis {
RICH: XlsTextFormat<> = "RICH";
}
- interface ZipImportData extends Serializable, IImportData {
-
- getFile(): string;
-
- getFormat(): ImportFormat;
-
- setFile(arg0: string): void;
-
- setFormat(arg0: ImportFormat): void;
- }
-
- /**
- */
- interface ZipImportDataConstructor {
-
- new (): ZipImportData;
-
- new (arg0: ImportFormat, arg1: string): ZipImportData;
- }
-
interface as_dto_common_operation_IOperationResult extends Serializable {
getMessage(): string;
@@ -25182,13 +25135,13 @@ export namespace openbis {
IdSearchCriteria: IdSearchCriteriaConstructor;
IdentifierSearchCriteria: IdentifierSearchCriteriaConstructor;
IdsSearchCriteria: IdsSearchCriteriaConstructor;
+ ImportData: ImportDataConstructor;
ImportFormat: ImportFormatObject;
ImportMode: ImportModeObject;
ImportOperation: ImportOperationConstructor;
ImportOperationResult: ImportOperationResultConstructor;
ImportOptions: ImportOptionsConstructor;
- ImportScript: ImportScriptConstructor;
- ImportValue: ImportValueConstructor;
+ ImportResult: ImportResultConstructor;
LabelSearchCriteria: LabelSearchCriteriaConstructor;
LastNameSearchCriteria: LastNameSearchCriteriaConstructor;
LinkedData: LinkedDataConstructor;
@@ -25571,7 +25524,6 @@ export namespace openbis {
TimeZone: TimeZoneConstructor;
UnarchiveDataSetsOperation: UnarchiveDataSetsOperationConstructor;
UnarchiveDataSetsOperationResult: UnarchiveDataSetsOperationResultConstructor;
- UncompressedImportData: UncompressedImportDataConstructor;
UnknownRelatedObjectId: UnknownRelatedObjectIdConstructor;
UnlockDataSetsOperation: UnlockDataSetsOperationConstructor;
UnlockDataSetsOperationResult: UnlockDataSetsOperationResultConstructor;
@@ -25649,7 +25601,6 @@ export namespace openbis {
WebAppSettingsSortOptions: WebAppSettingsSortOptionsConstructor;
WebAppSettingsUpdateValue: WebAppSettingsUpdateValueConstructor;
XlsTextFormat: XlsTextFormatObject;
- ZipImportData: ZipImportDataConstructor;
as_dto_attachment_Attachment: AttachmentConstructor;
as_dto_attachment_create_AttachmentCreation: AttachmentCreationConstructor;
as_dto_attachment_fetchoptions_AttachmentFetchOptions: AttachmentFetchOptionsConstructor;
@@ -26024,11 +25975,9 @@ export namespace openbis {
as_dto_history_id_UnknownRelatedObjectId: UnknownRelatedObjectIdConstructor;
as_dto_importer_ImportOperation: ImportOperationConstructor;
as_dto_importer_ImportOperationResult: ImportOperationResultConstructor;
+ as_dto_importer_ImportResult: ImportResultConstructor;
+ as_dto_importer_data_ImportData: ImportDataConstructor;
as_dto_importer_data_ImportFormat: ImportFormatObject;
- as_dto_importer_data_ImportScript: ImportScriptConstructor;
- as_dto_importer_data_ImportValue: ImportValueConstructor;
- as_dto_importer_data_UncompressedImportData: UncompressedImportDataConstructor;
- as_dto_importer_data_ZipImportData: ZipImportDataConstructor;
as_dto_importer_options_ImportMode: ImportModeObject;
as_dto_importer_options_ImportOptions: ImportOptionsConstructor;
as_dto_material_Material: MaterialConstructor;
@@ -26695,7 +26644,7 @@ MATERIAL : "MATERIAL",
SAMPLE : "SAMPLE"} as const
const ImportFormat = {
-XLS : "XLS"} as const
+EXCEL : "EXCEL"} as const
const ImportMode = {
FAIL_IF_EXISTS : "FAIL_IF_EXISTS",
@@ -26979,7 +26928,7 @@ MATERIAL : "MATERIAL",
SAMPLE : "SAMPLE"} as const
const as_dto_importer_data_ImportFormat = {
-XLS : "XLS"} as const
+EXCEL : "EXCEL"} as const
const as_dto_importer_options_ImportMode = {
FAIL_IF_EXISTS : "FAIL_IF_EXISTS",
@@ -27882,15 +27831,15 @@ SAMPLE : "SAMPLE"} as const
export const IdsSearchCriteria:IdsSearchCriteriaConstructor
+ export const ImportData:ImportDataConstructor
+
export const ImportOperation:ImportOperationConstructor
export const ImportOperationResult:ImportOperationResultConstructor
export const ImportOptions:ImportOptionsConstructor
- export const ImportScript:ImportScriptConstructor
-
- export const ImportValue:ImportValueConstructor
+ export const ImportResult:ImportResultConstructor
export const LabelSearchCriteria:LabelSearchCriteriaConstructor
@@ -28624,8 +28573,6 @@ SAMPLE : "SAMPLE"} as const
export const UnarchiveDataSetsOperationResult:UnarchiveDataSetsOperationResultConstructor
- export const UncompressedImportData:UncompressedImportDataConstructor
-
export const UnknownRelatedObjectId:UnknownRelatedObjectIdConstructor
export const UnlockDataSetsOperation:UnlockDataSetsOperationConstructor
@@ -28778,8 +28725,6 @@ SAMPLE : "SAMPLE"} as const
export const WebAppSettingsUpdateValue:WebAppSettingsUpdateValueConstructor
- export const ZipImportData:ZipImportDataConstructor
-
export const as_dto_attachment_Attachment:AttachmentConstructor
export const as_dto_attachment_create_AttachmentCreation:AttachmentCreationConstructor
@@ -29490,13 +29435,9 @@ SAMPLE : "SAMPLE"} as const
export const as_dto_importer_ImportOperationResult:ImportOperationResultConstructor
- export const as_dto_importer_data_ImportScript:ImportScriptConstructor
-
- export const as_dto_importer_data_ImportValue:ImportValueConstructor
-
- export const as_dto_importer_data_UncompressedImportData:UncompressedImportDataConstructor
+ export const as_dto_importer_ImportResult:ImportResultConstructor
- export const as_dto_importer_data_ZipImportData:ZipImportDataConstructor
+ export const as_dto_importer_data_ImportData:ImportDataConstructor
export const as_dto_importer_options_ImportOptions:ImportOptionsConstructor
@@ -31466,17 +31407,11 @@ SAMPLE : "SAMPLE"} as const
type as_dto_importer_ImportOperationResult = ImportOperationResult
- type as_dto_importer_data_IImportData = IImportData
+ type as_dto_importer_ImportResult = ImportResult
- type as_dto_importer_data_ImportFormat = typeof as_dto_importer_data_ImportFormat[keyof typeof as_dto_importer_data_ImportFormat]
-
- type as_dto_importer_data_ImportScript = ImportScript
-
- type as_dto_importer_data_ImportValue = ImportValue
+ type as_dto_importer_data_ImportData = ImportData
- type as_dto_importer_data_UncompressedImportData = UncompressedImportData
-
- type as_dto_importer_data_ZipImportData = ZipImportData
+ type as_dto_importer_data_ImportFormat = typeof as_dto_importer_data_ImportFormat[keyof typeof as_dto_importer_data_ImportFormat]
type as_dto_importer_options_ImportMode = typeof as_dto_importer_options_ImportMode[keyof typeof as_dto_importer_options_ImportMode]
diff --git a/test-integration/sourceTest/java/ch/ethz/sis/openbis/systemtests/IntegrationSessionWorkspaceTest.java b/test-integration/sourceTest/java/ch/ethz/sis/openbis/systemtests/IntegrationSessionWorkspaceTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..49768482efe4933db4c61dd9f2eaab44133a7552
--- /dev/null
+++ b/test-integration/sourceTest/java/ch/ethz/sis/openbis/systemtests/IntegrationSessionWorkspaceTest.java
@@ -0,0 +1,90 @@
+package ch.ethz.sis.openbis.systemtests;
+
+import static ch.ethz.sis.transaction.TransactionTestUtil.TestTransaction;
+import static ch.ethz.sis.transaction.TransactionTestUtil.assertTransactions;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import java.io.File;
+import java.lang.reflect.Method;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.sql.Connection;
+import java.sql.ResultSet;
+import java.sql.Statement;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.UUID;
+
+import javax.sql.DataSource;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.OpenBIS;
+import ch.ethz.sis.openbis.generic.asapi.v3.ITransactionCoordinatorApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create.ProjectCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create.SpaceCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.SpacePermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.TransactionConfiguration;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.TransactionCoordinatorApi;
+import ch.ethz.sis.openbis.systemtests.common.AbstractIntegrationTest;
+import ch.ethz.sis.transaction.TransactionStatus;
+
+public class IntegrationSessionWorkspaceTest extends AbstractIntegrationTest
+{
+
+ @Test
+ public void testUploadToSessionWorkspace() throws Exception
+ {
+ final OpenBIS openBIS = createOpenBIS();
+ final String sessionToken = openBIS.login(USER, PASSWORD);
+
+ final Path originalFilePath = Path.of("sourceTest/java/tests.xml");
+
+ // Testing upload
+
+ final String uploadId = openBIS.uploadToSessionWorkspace(originalFilePath);
+
+ // Verifying upload ID
+
+ assertTrue(uploadId.endsWith("tests.xml"));
+
+ // Verifying file info
+
+ final Path uploadedFilePath = Path.of(String.format("targets/sessionWorkspace/%s/tests.xml", sessionToken));
+ final File originalFile = originalFilePath.toFile();
+ final File uploadedFile = uploadedFilePath.toFile();
+
+ assertTrue(uploadedFile.exists());
+ assertEquals(uploadedFile.length(), originalFile.length());
+
+ // Verifying file content
+
+ final byte[] originalFileContent = Files.readAllBytes(originalFilePath);
+ final byte[] uploadedFileContent = Files.readAllBytes(uploadedFilePath);
+
+ assertEquals(uploadedFileContent, originalFileContent);
+
+ openBIS.logout();
+ }
+
+}
diff --git a/ui-admin/src/core-plugins/admin/1/as/services/xls-import/xls-import.py b/ui-admin/src/core-plugins/admin/1/as/services/xls-import/xls-import.py
index dce1366af7d630109fcc750585e6ee770fa84411..441ff4576e099e134ff8ce110b401fec7368bbbb 100644
--- a/ui-admin/src/core-plugins/admin/1/as/services/xls-import/xls-import.py
+++ b/ui-admin/src/core-plugins/admin/1/as/services/xls-import/xls-import.py
@@ -1,19 +1,11 @@
-import base64
-from ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl import MasterDataRegistrationHelper
from ch.ethz.sis.openbis.generic.server.xls.importer import ImportOptions
from ch.ethz.sis.openbis.generic.server.xls.importer import XLSImport
from ch.ethz.sis.openbis.generic.server.xls.importer.enums import ImportModes
from ch.systemsx.cisd.common.exceptions import UserFailureException
from java.util import ArrayList
-from org.apache.commons.io import FileUtils
-from java.io import File
-from java.lang import Long
-from java.lang import System
-from java.nio.file import Path
-from ch.ethz.sis.openbis.generic.server.asapi.v3.executor.importer import ImportExecutor
-def get_update_mode(parameters):
- update_mode = parameters.get('update_mode', 'FAIL_IF_EXISTS')
+def getMode(parameters):
+ update_mode = parameters.get('mode', 'FAIL_IF_EXISTS')
if update_mode == "IGNORE_EXISTING":
return ImportModes.IGNORE_EXISTING
elif update_mode == "FAIL_IF_EXISTS":
@@ -25,20 +17,16 @@ def get_update_mode(parameters):
str(update_mode) if update_mode else 'None'))
-def get_import_options(parameters):
+def getImportOptions(parameters):
options = ImportOptions()
- experiments_by_type = parameters.get('experiments_by_type', None)
- options.setExperimentsByType(experiments_by_type)
- spaces_by_type = parameters.get('spaces_by_type', None)
- options.setSpacesByType(spaces_by_type)
- definitions_only = parameters.get('definitions_only', False)
- options.setDefinitionsOnly(definitions_only)
- disallow_creations = parameters.get("disallow_creations", False)
- options.setDisallowEntityCreations(disallow_creations)
- ignore_versioning = parameters.get('ignore_versioning', False)
- options.setIgnoreVersioning(ignore_versioning)
- render_result = parameters.get('render_result', True)
- options.setRenderResult(render_result)
+ allowedSampleTypes = parameters.get("allowedSampleTypes")
+
+ options.setExperimentsByType(parameters.get('experimentsByType', None))
+ options.setSpacesByType(parameters.get('spacesByType', None))
+ options.setDefinitionsOnly(False)
+ options.setDisallowEntityCreations(False)
+ options.setIgnoreVersioning(False)
+ options.setRenderResult(True)
return options
@@ -47,82 +35,20 @@ def process(context, parameters):
result = None
if method == "import":
- zip = parameters.get('zip', False)
- temp = None
- zip_bytes = None
- if zip: # Zip mode uses xls_base64 for all multiple XLS + script files
- zip_bytes = base64.b64decode(parameters.get('xls_base64'))
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()))
- temp.delete()
- temp.mkdir()
- tempPath = temp.getAbsolutePath()
- MasterDataRegistrationHelper.extractToDestination(zip_bytes, tempPath)
- if (len(temp.listFiles()) == 1):
- singleFile = temp.listFiles()[0]
- if (singleFile.isDirectory()):
- temp = singleFile
- tempPath = singleFile.getAbsolutePath()
- byteArrays = MasterDataRegistrationHelper.getByteArrays(Path.of(tempPath), ".xls")
- if len(byteArrays) == 0:
- raise UserFailureException('No .xls or .xlsx files found on the root folder of the zip file. This error could be caused by the way the zip file was generated.')
- parameters.put('xls', byteArrays)
- allScripts = MasterDataRegistrationHelper.getAllScripts(Path.of(tempPath))
- parameters.put('scripts', allScripts)
- largeValues = MasterDataRegistrationHelper.getAllLargeValues(Path.of(tempPath))
- parameters.put('values', largeValues)
- else:
- # Check if xls_base64 is used for a single XLS
- xls_base64_string = parameters.get('xls_base64', None)
- if xls_base64_string is not None:
- parameters.put('xls', [ base64.b64decode(xls_base64_string) ])
- result = _import(context, parameters, zip_bytes)
- if temp is not None:
- FileUtils.deleteDirectory(temp)
+ result = _import(context, parameters)
return result
-def _import(context, parameters, zip_bytes):
- """
- Excel import AS service.
- For extensive documentation of usage and Excel layout,
- please visit https://wiki-bsse.ethz.ch/display/openBISDoc/Excel+import+service
+def _import(context, parameters):
+ fileName = parameters.get("fileName")
- :param context: Standard Openbis AS Service context object
- :param parameters: Contains two elements
- {
- 'xls' : excel byte blob, - optional
- 'xls_base64' : base64-encoded excel byte blob - optional
- 'xls_name': identifier of excel file - mandatory
- 'zip' : True / False - optional (default: False)
- 'scripts': { - optional
- file path: loaded file
- },
- 'experiments_by_type', - optional
- 'spaces_by_type', - optional
- 'definitions_only', - optional (default: False)
- 'disallow_creations', - optional (default: False)
- 'ignore_versioning', - optional (default: False)
- 'render_result', - optional (default: True)
- 'update_mode': [IGNORE_EXISTING|FAIL_IF_EXISTS|UPDATE_IF_EXISTS] - optional, default FAIL_IF_EXISTS
- This only takes duplicates that are ON THE SERVER
- }
- :return: Openbis's execute operations result string. It should contain report on what was created.
- """
session_token = context.sessionToken
api = context.applicationService
- scripts = parameters.get('scripts', {})
- values = parameters.get('values', {})
- mode = get_update_mode(parameters)
- options = get_import_options(parameters)
- xls_name = parameters.get('xls_name', None)
+ mode = getMode(parameters)
+ options = getImportOptions(parameters)
- importXls = XLSImport(session_token, api, scripts, values, mode, options, xls_name)
+ importXLS = XLSImport(session_token, api, mode, options, [fileName], False)
ids = ArrayList()
- xls_byte_arrays = parameters.get('xls', None)
- for xls_byte_array in xls_byte_arrays:
- ids.addAll(importXls.importXLS(xls_byte_array))
- if zip_bytes is not None:
- ImportExecutor.importZipData(zip_bytes)
-
+ ids.addAll(importXLS.start())
return ids
diff --git a/ui-admin/src/js/components/tools/form/import/all/ImportAllFormFacade.js b/ui-admin/src/js/components/tools/form/import/all/ImportAllFormFacade.js
index c1bf057f5f3d30ef74756bb93a93b0321d6cecb0..5bf59d1a984274045fe2dc47828aecd0c0891717 100644
--- a/ui-admin/src/js/components/tools/form/import/all/ImportAllFormFacade.js
+++ b/ui-admin/src/js/components/tools/form/import/all/ImportAllFormFacade.js
@@ -3,25 +3,19 @@ import openbis from '@src/js/services/openbis.js'
export default class ImportAllFormFacade {
async import(file, updateMode) {
return new Promise((resolve, reject) => {
- const reader = new FileReader()
- reader.onload = () => {
- const resultBase64 = reader.result.split(',')[1]
- const serviceId = new openbis.CustomASServiceCode('xls-import')
- const serviceOptions = new openbis.CustomASServiceExecutionOptions()
- serviceOptions.withParameter('method', 'import')
- serviceOptions.withParameter(
- 'zip',
- file.name.toLowerCase().endsWith('.zip')
- )
- serviceOptions.withParameter('xls_name', 'DEFAULT')
- serviceOptions.withParameter('xls_base64', resultBase64)
- serviceOptions.withParameter('update_mode', updateMode)
- openbis.executeService(serviceId, serviceOptions).then(result => {
- resolve(result)
- }, reject)
- }
- reader.onerror = reject
- reader.readAsDataURL(file)
- })
+ openbis.uploadToSessionWorkspace(file)
+ .then(() => {
+ const serviceId = new openbis.CustomASServiceCode('xls-import')
+ const serviceOptions = new openbis.CustomASServiceExecutionOptions()
+
+ serviceOptions.withParameter('method', 'import')
+ serviceOptions.withParameter('mode', updateMode)
+ serviceOptions.withParameter('fileName', file.name)
+
+ return openbis.executeService(serviceId, serviceOptions)
+ .then(result => resolve(result))
+ .catch(error => reject(error))
+ }, (error) => reject(error));
+ });
}
}
diff --git a/ui-admin/src/js/services/openbis/api.js b/ui-admin/src/js/services/openbis/api.js
index d79fc89e1d378fb298b26038aee61949f4ffe308..40bd2e7e6ccd4ead4ec0b886a1a6115020c8105a 100644
--- a/ui-admin/src/js/services/openbis/api.js
+++ b/ui-admin/src/js/services/openbis/api.js
@@ -252,6 +252,10 @@ class Facade {
return this.promise(this.v3.evaluatePlugin(options))
}
+ uploadToSessionWorkspace(file) {
+ return this.promise(this.v3.uploadToSessionWorkspace(file))
+ }
+
executeCustomDSSService(serviceId, options) {
return this.promise(this.v3.getDataStoreFacade().executeCustomDSSService(serviceId, options));
}
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/services/as-eln-lims-api/script.py b/ui-eln-lims/src/core-plugins/eln-lims/1/as/services/as-eln-lims-api/script.py
index 2ab162548baabc0e8cdc6ee51eff4f92fc208e7e..60ea54881c25a362a82f678bf342aef2ec9942ad 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/services/as-eln-lims-api/script.py
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/services/as-eln-lims-api/script.py
@@ -2,15 +2,12 @@ import ch.systemsx.cisd.openbis.generic.server.ComponentNames as ComponentNames
import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider as CommonServiceProvider
import ch.ethz.sis.openbis.generic.server.xls.export.XLSExportExtendedService as XLSExportExtendedService
import ch.systemsx.cisd.common.exceptions.UserFailureException as UserFailureException
-import base64
import json
import re
import ch.ethz.sis.openbis.generic.server.xls.importer.utils.AttributeValidator as AttributeValidator
import ch.ethz.sis.openbis.generic.server.xls.importer.helper.SampleImportHelper as SampleImportHelper
import ch.systemsx.cisd.common.logging.LogCategory as LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory as LogFactory;
-from java.nio.file import Files
-from java.io import File
isOpenBIS2020 = True;
enableNewSearchEngine = isOpenBIS2020;
@@ -79,8 +76,6 @@ def process(context, parameters):
result = getUserManagementMaintenanceTaskReport(context, parameters)
elif method == "removeUserManagementMaintenanceTaskReport":
result = removeUserManagementMaintenanceTaskReport(context, parameters)
- elif method == "importSamples":
- result = importSamples(context, parameters)
elif method == "getSamplesImportTemplate":
result = getSamplesImportTemplate(context, parameters)
elif method == "createSpace":
@@ -343,21 +338,6 @@ def _create_cell(row, cell_index, style, value):
cell.setCellValue(value)
return cell_index + 1
-def importSamples(context, parameters):
- sessionKey = parameters.get("sessionKey")
- allowedSampleTypes = parameters.get("allowedSampleTypes")
- experimentsByType = parameters.get("experimentsByType", {})
- spacesByType = parameters.get("spacesByType", {})
- mode = parameters.get("mode")
- barcodeValidationInfo = json.loads(parameters.get("barcodeValidationInfo"))
- sessionManager = CommonServiceProvider.getApplicationContext().getBean("session-manager")
- sessionWorkspaceProvider = CommonServiceProvider.getApplicationContext().getBean("session-workspace-provider")
- workspaceFolder = sessionWorkspaceProvider.getSessionWorkspace(context.getSessionToken())
- uploadedFile = File(workspaceFolder, sessionKey)
- bytes = Files.readAllBytes(uploadedFile.toPath())
- results = importData(context, bytes, sessionKey, experimentsByType, spacesByType, mode, False)
- return results
-
def validateExperimentOrSpaceDefined(row_number, properties, mode, experiment, space):
if experiment is None and space is None and not mode.startswith("UPDATE"):
exp = properties.get("experiment")
@@ -380,29 +360,6 @@ def validateBarcode(row_number, properties, barcodeValidationInfo):
raise UserFailureException("Error in row %s: custom barcode %s does not match "
"the regular expression '%s'." % (row_number, barcode, pattern.pattern))
-def importData(context, bytes, file_name, experimentsByType, spacesByType, mode, definitionsOnly):
- from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
- from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
- from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentIdentifier
-
- sessionToken = context.getSessionToken()
- api = context.getApplicationService()
- props = CustomASServiceExecutionOptions().withParameter('xls', [bytes])
- props.withParameter('method', 'import')
- props.withParameter('zip', False)
- props.withParameter('xls_name', 'DEFAULT')
- props.withParameter('update_mode', mode)
- props.withParameter('disallow_creations', mode == 'UPDATE_IF_EXISTS')
- props.withParameter('render_result', False)
- props.withParameter('ignore_versioning', True)
- if definitionsOnly:
- props.withParameter('definitions_only', True)
- if experimentsByType is not None:
- props.withParameter('experiments_by_type', experimentsByType)
- if spacesByType is not None:
- props.withParameter('spaces_by_type', spacesByType)
- return api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
-
def getUserManagementMaintenanceTaskConfig(context, parameters):
from ch.systemsx.cisd.common.filesystem import FileUtilities
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
index 026ab63b8ea644509f599c92da9ff30fcaa5c585..188deda519f031916000c14027c4a62693ab329c 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
@@ -120,19 +120,16 @@ function ServerFacade(openbisServer) {
});
}
- this.registerSamples = function(allowedSampleTypes, experimentsByType, spacesByType, barcodeValidationInfo, sessionKey, callback) {
- this.customELNASAPI({
- "method" : "importSamples",
- "allowedSampleTypes" : allowedSampleTypes,
- "experimentsByType" : experimentsByType,
- "spacesByType" : spacesByType,
- "barcodeValidationInfo" : barcodeValidationInfo,
- "mode" : "FAIL_IF_EXISTS",
- "sessionKey" : sessionKey
- }, function(result) {
- callback(result)
- }, true);
- }
+ this.importSamples = function(mode, sessionKey, allowedSampleTypes, experimentsByType, spacesByType, callback) {
+ this.customASService({
+ "method" : "import",
+ "mode" : mode,
+ "fileName" : sessionKey,
+ "allowedSampleTypes" : allowedSampleTypes,
+ "experimentsByType" : experimentsByType,
+ "spacesByType" : spacesByType,
+ }, callback, "xls-import", null, true);
+ }
this.deleteSpace = function(code, reason, callback) {
this.customELNASAPI({
@@ -144,18 +141,6 @@ function ServerFacade(openbisServer) {
});
}
- this.updateSamples = function(allowedSampleTypes, barcodeValidationInfo, sessionKey, callback) {
- this.customELNASAPI({
- "method" : "importSamples",
- "allowedSampleTypes" : allowedSampleTypes,
- "barcodeValidationInfo" : barcodeValidationInfo,
- "mode" : "UPDATE_IF_EXISTS",
- "sessionKey" : sessionKey
- }, function(result) {
- callback(result)
- }, true);
- }
-
this.getSamplesImportTemplate = function(allowedSampleTypes, templateType, importMode, callback) {
this.customELNASAPI({
"method" : "getSamplesImportTemplate",
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
index baed546316871ea84500080ab4d3ba51291db8e8..c9cc4f1e290e5b9e1f08cc2634018cdcdc75259d 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleTable/SampleTableController.js
@@ -173,13 +173,13 @@ function SampleTableController(parentController, title, experimentIdentifier, pr
var allowSampleTypeSelection = experimentIdentifier == null;
var batchController = new BatchController(title, "REGISTRATION", allowedSampleTypes, allowSampleTypeSelection, function(file, selectedSampleTypes) {
Util.blockUI();
- mainController.serverFacade.fileUpload(file, function() {
- mainController.serverFacade.registerSamples(selectedSampleTypes, experimentsByType, spacesByType,
- _this.getBarcodeValidationInfo(), file.name,
- function(result) {
+ mainController.openbisV3.uploadToSessionWorkspace(file)
+ .done(function() {
+ mainController.serverFacade.importSamples("FAIL_IF_EXISTS", file.name, selectedSampleTypes, experimentsByType, spacesByType,
+ function(result) {
_this._handleResult(result, "created", experimentIdentifier);
- });
- });
+ });
+ });
});
batchController.init();
}
@@ -196,11 +196,11 @@ function SampleTableController(parentController, title, experimentIdentifier, pr
var allowSampleTypeSelection = experimentIdentifier == null;
var batchController = new BatchController(title, "UPDATE", allowedSampleTypes, allowSampleTypeSelection, function(file, selectedSampleTypes) {
Util.blockUI();
- mainController.serverFacade.fileUpload(file, function() {
- mainController.serverFacade.updateSamples(selectedSampleTypes,
- _this.getBarcodeValidationInfo(), file.name,
- function(result) {
- _this._handleResult(result, "updated", experimentIdentifier);
+ mainController.openbisV3.uploadToSessionWorkspace(file)
+ .done(function() {
+ mainController.serverFacade.importSamples("UPDATE_IF_EXISTS", file.name, selectedSampleTypes, experimentsByType, spacesByType,
+ function(result) {
+ _this._handleResult(result, "updated", experimentIdentifier);
});
});
});