From 6d49b93ca2ffe5ec3014c24238901f7a10bc2a58 Mon Sep 17 00:00:00 2001
From: vkovtun <vkovtun@ethz.ch>
Date: Thu, 17 Aug 2023 16:29:24 +0200
Subject: [PATCH] SSDM-13926: Writing tests for import/export API.
---
.../asapi/v3/IApplicationServerApi.java | 5 +-
.../importer/data/UncompressedImportData.java | 8 +-
.../asapi/v3/ApplicationServerApiLogger.java | 5 +-
...iPersonalAccessTokenInvocationHandler.java | 3 +-
.../v3/executor/importer/ImportExecutor.java | 7 +-
.../importer/ImportOperationExecutor.java | 2 +
.../operation/OperationsExecutor.java | 5 +
.../systemtest/asapi/v3/ImportTest.java | 97 ++++++++++++++++++
.../asapi/v3/test_files/xls/import.xlsx | Bin 0 -> 9238 bytes
9 files changed, 119 insertions(+), 13 deletions(-)
create mode 100644 server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ImportTest.java
create mode 100644 server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/xls/import.xlsx
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 0a24c8350ad..976bf70c80f 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
@@ -75,9 +75,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentSear
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.update.ExperimentTypeUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.update.ExperimentUpdate;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.exporter.ExportResult;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.exporter.data.ExportData;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.exporter.options.ExportOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.create.ExternalDmsCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.delete.ExternalDmsDeletionOptions;
@@ -2264,6 +2261,6 @@ public interface IApplicationServerApi extends IRpcService
public void executeImport(String sessionToken, ImportData importData, ImportOptions importOptions);
- public ExportResult executeExport(String sessionToken, ExportData exportData, ExportOptions exportOptions);
+// 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/data/UncompressedImportData.java b/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/importer/data/UncompressedImportData.java
index 71184cd8a6c..0305a2d2690 100644
--- 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
@@ -17,7 +17,7 @@
package ch.ethz.sis.openbis.generic.asapi.v3.dto.importer.data;
import java.io.Serializable;
-import java.util.List;
+import java.util.Collection;
import ch.systemsx.cisd.base.annotation.JsonObject;
@@ -30,9 +30,9 @@ public class UncompressedImportData implements Serializable, ImportData
private final byte[] file;
- private final List<ImportScript> scripts;
+ private final Collection<ImportScript> scripts;
- public UncompressedImportData(final ImportFormat format, final byte[] file, final List<ImportScript> scripts)
+ public UncompressedImportData(final ImportFormat format, final byte[] file, final Collection<ImportScript> scripts)
{
this.format = format;
this.file = file;
@@ -49,7 +49,7 @@ public class UncompressedImportData implements Serializable, ImportData
return file;
}
- public List<ImportScript> getScripts()
+ public Collection<ImportScript> getScripts()
{
return scripts;
}
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 f7effd8acfe..f22e5f58378 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
@@ -87,6 +87,7 @@ 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.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;
@@ -1365,9 +1366,9 @@ public class ApplicationServerApiLogger extends AbstractServerLogger implements
}
@Override
- public void doImport(final String sessionToken, final byte[] file, final ImportOptions importOptions)
+ public void executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
- logAccess(sessionToken, "do-import", "Path(%s) ImportOptions(%s)", file, importOptions);
+ logAccess(sessionToken, "execute-import", "ImportData(%s) ImportOptions(%s)", importData, importOptions);
}
}
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 309d0c278e6..7b13dffafa7 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
@@ -88,6 +88,7 @@ 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.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;
@@ -1254,7 +1255,7 @@ public class ApplicationServerApiPersonalAccessTokenInvocationHandler implements
}
@Override
- public void doImport(final String sessionToken, final byte[] file, final ImportOptions importOptions)
+ public void executeImport(final String sessionToken, final ImportData importData, final ImportOptions importOptions)
{
invocation.proceedWithNewFirstArgument(converter.convert(sessionToken));
}
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 658d7533798..eb2490c96e9 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
@@ -63,12 +63,15 @@ public class ImportExecutor implements IImportExecutor
{
// XLS file
- importXls(context, operation, Map.of(), ((UncompressedImportData) importData).getFile());
+ final UncompressedImportData uncompressedImportData = (UncompressedImportData) importData;
+
+ importXls(context, operation, Map.of(), uncompressedImportData.getFile());
} else if (importData instanceof ZipImportData)
{
// ZIP file
- try (final ZipInputStream zip = new ZipInputStream(new ByteArrayInputStream(((ZipImportData) importData).getFile())))
+ final ZipImportData zipImportData = (ZipImportData) importData;
+ try (final ZipInputStream zip = new ZipInputStream(new ByteArrayInputStream(zipImportData.getFile())))
{
final Map<String, String> scripts = new HashMap<>();
byte[] xlsFileContent = null;
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 72d971a4a9c..ef4032eeaa8 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
@@ -18,12 +18,14 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.importer;
import org.springframework.beans.factory.annotation.Autowired;
+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.server.asapi.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.OperationExecutor;
+@Component
public class ImportOperationExecutor extends OperationExecutor<ImportOperation, ImportOperationResult>
{
diff --git a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
index 87b6cd191b6..999b6798774 100644
--- a/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
+++ b/server-application-server/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
@@ -76,6 +76,7 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.externaldms.IGetExte
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.externaldms.ISearchExternalDmsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.externaldms.IUpdateExternalDmsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.globalsearch.ISearchGloballyOperationExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.importer.ImportOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.material.ICreateMaterialTypesOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.material.ICreateMaterialsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.material.IDeleteMaterialTypesOperationExecutor;
@@ -651,6 +652,9 @@ public class OperationsExecutor implements IOperationsExecutor
@Autowired
private IGetSessionInformationOperationExecutor getSessionInformationExecutor;
+ @Autowired
+ private ImportOperationExecutor importOperationExecutor;
+
@Override
public List<IOperationResult> execute(IOperationContext context, List<? extends IOperation> operations, IOperationExecutionOptions options)
{
@@ -681,6 +685,7 @@ public class OperationsExecutor implements IOperationsExecutor
executeCreations(operations, resultMap, context);
executeUpdates(operations, resultMap, context);
resultMap.putAll(internalOperationExecutor.execute(context, operations));
+ resultMap.putAll(importOperationExecutor.execute(context, operations));
flushCurrentSession();
clearCurrentSession();
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ImportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ImportTest.java
new file mode 100644
index 00000000000..c42172366a9
--- /dev/null
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ImportTest.java
@@ -0,0 +1,97 @@
+/*
+ * 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.systemtest.asapi.v3;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.testng.annotations.BeforeClass;
+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.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.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.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;
+
+public class ImportTest extends AbstractTest
+{
+
+ private final Map<String, String> IMPORT_SCRIPT_MAP = Map.of("Script 1", "Value 1", "Script 2", "Value 2");
+
+ private final Collection<ImportScript> IMPORT_SCRIPTS = IMPORT_SCRIPT_MAP.entrySet().stream()
+ .map(entry -> new ImportScript(entry.getKey(), entry.getValue())).collect(Collectors.toList());
+
+ private static byte[] fileContent;
+
+ @BeforeClass
+ public void setupClass()
+ {
+ try (final InputStream is = ImportTest.class.getResourceAsStream("test_files/xls/import.xlsx"))
+ {
+ if (is == null)
+ {
+ throw new RuntimeException();
+ }
+
+ fileContent = is.readAllBytes();
+ } catch (final IOException e)
+ {
+ throw new RuntimeException(e);
+ }
+ }
+
+ @Test
+ public void testUncompressedDataImport()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final ImportData importData = new UncompressedImportData(ImportFormat.XLS, fileContent, IMPORT_SCRIPTS);
+ final ImportOptions importOptions = new ImportOptions(ImportMode.UPDATE_IF_EXISTS);
+
+ v3api.executeImport(sessionToken, importData, importOptions);
+
+ final VocabularySearchCriteria vocabularySearchCriteria = new VocabularySearchCriteria();
+ vocabularySearchCriteria.withCode().thatEquals("DETECTION");
+
+ final VocabularyFetchOptions vocabularyFetchOptions = new VocabularyFetchOptions();
+ vocabularyFetchOptions.withTerms();
+
+ final SearchResult<Vocabulary> vocabularySearchResult =
+ v3api.searchVocabularies(sessionToken, vocabularySearchCriteria, vocabularyFetchOptions);
+
+ assertEquals(1, vocabularySearchResult.getTotalCount());
+
+ final List<VocabularyTerm> vocabularyTerms = vocabularySearchResult.getObjects().get(0).getTerms();
+ assertEquals(2, vocabularyTerms.size());
+ assertEquals(Set.of("HRP", "AAA"), vocabularyTerms.stream().map(VocabularyTerm::getCode).collect(Collectors.toSet()));
+ }
+
+}
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/xls/import.xlsx b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/test_files/xls/import.xlsx
new file mode 100644
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GitLab