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 4321114f5b109a7ef16ac900a0399f5ddd1be07a..32160bd9de0a396a03be4b4d471dfbcb514a3d24 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
@@ -12,16 +12,28 @@ public class FileServerUtils
{
private static Path getFilePath(String filePath) throws IOException
{
- String repositoryPathAsString = CommonServiceProvider.tryToGetProperty(
- FileServiceServlet.REPO_PATH_KEY);
- String repositoryFilePathAsString = repositoryPathAsString + filePath;
- Path repositoryPath = Path.of(new File(repositoryPathAsString).getCanonicalPath());
- Path repositoryFilePath = Path.of(new File(repositoryFilePathAsString).getCanonicalPath());
- //Security Test that repositoryFilePath is indeed inside repositoryPath
- if(!repositoryFilePath.startsWith(repositoryPath)) {
- throw new IllegalArgumentException("File Path is not inside the Repository Path");
+ if (CommonServiceProvider.getApplicationContext() != null)
+ {
+ // Runtime mode.
+ String repositoryPathAsString = CommonServiceProvider.tryToGetProperty(
+ FileServiceServlet.REPO_PATH_KEY);
+ String repositoryFilePathAsString = repositoryPathAsString + filePath;
+ Path repositoryPath = Path.of(new File(repositoryPathAsString).getCanonicalPath());
+ Path repositoryFilePath = Path.of(new File(repositoryFilePathAsString).getCanonicalPath());
+ //Security Test that repositoryFilePath is indeed inside repositoryPath
+ if (!repositoryFilePath.startsWith(repositoryPath))
+ {
+ throw new IllegalArgumentException("File Path is not inside the Repository Path");
+ }
+
+ return repositoryFilePath;
+ } else
+ {
+ // Testing mode.
+
+ // Return some default testing path.
+ return Path.of(new File("./sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/" + filePath).getCanonicalPath());
}
- return repositoryFilePath;
}
public static byte[] read(String filePath) throws IOException
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/SampleCellWithImageReferencesExpectations.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/SampleCellWithImageReferencesExpectations.java
new file mode 100644
index 0000000000000000000000000000000000000000..3641c49cac816330be63efcfdf76e11ee7eda1c9
--- /dev/null
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/SampleCellWithImageReferencesExpectations.java
@@ -0,0 +1,235 @@
+/*
+ * Copyright ETH 2022 - 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.
+ *
+ */
+package ch.ethz.sis.openbis.generic.server.xls.export;
+
+import java.util.Arrays;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import org.jmock.Expectations;
+import org.jmock.api.Invocation;
+import org.jmock.lib.action.CustomAction;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+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.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyAssignmentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+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.space.Space;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.SpacePermId;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.CollectionMatcher;
+
+class SampleCellWithImageReferencesExpectations extends Expectations
+{
+
+ public SampleCellWithImageReferencesExpectations(final IApplicationServerApi api, final boolean exportReferred)
+ {
+ if (exportReferred)
+ {
+ allowing(api).getSamples(with(XLSExportTest.SESSION_TOKEN),
+ with(new CollectionMatcher<>(List.of(new SamplePermId("200001010000000-0001")))),
+ with(any(SampleFetchOptions.class)));
+ }
+ allowing(api).getSamples(with(XLSExportTest.SESSION_TOKEN), with(new CollectionMatcher<>(
+ List.of(new SamplePermId("200001010000000-0001")))), with(any(SampleFetchOptions.class))
+ );
+
+ will(new CustomAction("getting samples")
+ {
+
+ @Override
+ public Object invoke(final Invocation invocation) throws Throwable
+ {
+ final SampleFetchOptions fetchOptions = (SampleFetchOptions) invocation.getParameter(2);
+ final PropertyAssignment namePropertyAssignment = getNamePropertyAssignment();
+ final PropertyAssignment experimentalDescriptionPropertyAssignment = getExperimentalDescriptionPropertyAssignment();
+ final PropertyAssignment experimentalGoalsPropertyAssignment = getExperimentalGoalsPropertyAssignment();
+
+ final SampleType sampleType = new SampleType();
+ sampleType.setCode("STORAGE");
+ sampleType.setPermId(new EntityTypePermId("STORAGE", EntityKind.SAMPLE));
+ sampleType.setFetchOptions(fetchOptions.withType());
+ sampleType.setPropertyAssignments(List.of(namePropertyAssignment, experimentalDescriptionPropertyAssignment,
+ experimentalGoalsPropertyAssignment));
+
+ final Space space = new Space();
+ space.setCode("ELN_SETTINGS");
+ space.setPermId(new SpacePermId("ELN_SETTINGS"));
+
+ final Project project = new Project();
+ project.setCode("STORAGES");
+ project.setIdentifier(new ProjectIdentifier("/ELN_SETTINGS/STORAGES"));
+
+ final Experiment experiment = new Experiment();
+ experiment.setCode("STORAGES_COLLECTION");
+ experiment.setIdentifier(new ExperimentIdentifier("/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION"));
+
+ final Experiment defaultExperiment = new Experiment();
+ defaultExperiment.setCode("DEFAULT");
+ defaultExperiment.setIdentifier(new ExperimentIdentifier("/DEFAULT/DEFAULT/DEFAULT"));
+
+ final Calendar calendar = Calendar.getInstance();
+ calendar.set(2023, Calendar.MARCH, 10, 17, 23, 44);
+ final Date registrationDate = calendar.getTime();
+
+ calendar.set(2023, Calendar.MARCH, 11, 17, 23, 44);
+ final Date modificationDate = calendar.getTime();
+
+ final Person registrator = new Person();
+ registrator.setUserId("system");
+
+ final Person modifier = new Person();
+ modifier.setUserId("test");
+
+ final Sample[] samples = new Sample[1];
+
+ samples[0] = new Sample();
+ samples[0].setType(sampleType);
+ samples[0].setFetchOptions(fetchOptions);
+ samples[0].setPermId(new SamplePermId("200001010000000-0001"));
+ samples[0].setCode("BENCH");
+ samples[0].setIdentifier(new SampleIdentifier(space.getCode(), project.getCode(), null, "BENCH"));
+ samples[0].setSpace(space);
+ samples[0].setProject(project);
+ samples[0].setExperiment(experiment);
+ samples[0].setProperty("$NAME", "<p>This is some text.</p>"
+ + "<figure class=\"image\">"
+ + "<img src=\"/openbis/openbis/file-service/eln-lims/7b/77/90/7b77903f-e685-4700-974a-5a5d7e109638/"
+ + "7b77903f-e685-4700-974a-5a5d7e109638.jpg\">"
+ + "</figure>"
+ + "<p>Then we have more text between images.</p>"
+ + "<figure class=\"image\">"
+ + "<img src=\"/openbis/openbis/file-service/eln-lims/08/b2/96/08b2968c-1685-4fa8-bef2-f5a80a8210ba/"
+ + "08b2968c-1685-4fa8-bef2-f5a80a8210ba.jpg\">"
+ + "</figure>"
+ + "<p>And some text at the end.</p>");
+ samples[0].setProperty("EXPERIMENTAL_STEP.EXPERIMENTAL_DESCRIPTION", "<p>This is some text.</p>"
+ + "<figure class=\"image\">"
+ + "<img src=\"/openbis/openbis/file-service/eln-lims/c1/b2/91/"
+ + "c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.jpg\">"
+ + "</figure>"
+ + "<p>Then we have more text between images.</p>"
+ + "<figure class=\"image\"><img src=\"/openbis/openbis/file-service/eln-lims/46/63/05/"
+ + "466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.jpg\">"
+ + "</figure>"
+ + "<p>And some text at the end.</p>");
+ samples[0].setProperty("EXPERIMENTAL_STEP.EXPERIMENTAL_GOALS", "<p>This is some text.</p><figure class=\"image\">"
+ + "<img src=\"/openbis/openbis/file-service/eln-lims/c0/1b/2e/c01b2e1f-8212-4562-ae8a-9072bf92e687/"
+ + "c01b2e1f-8212-4562-ae8a-9072bf92e687.jpg\">"
+ + "</figure>"
+ + "<p>Then we have more text between images.</p>"
+ + "<figure class=\"image\">"
+ + "<img src=\"/openbis/openbis/file-service/eln-lims/f3/e4/0c/f3e40c2e-109c-4191-bed0-2cf931de185a/"
+ + "f3e40c2e-109c-4191-bed0-2cf931de185a.jpg\">"
+ + "</figure>"
+ + "<p>And some text at the end.</p>");
+ samples[0].setRegistrator(registrator);
+ samples[0].setModifier(modifier);
+ samples[0].setRegistrationDate(registrationDate);
+ samples[0].setModificationDate(modificationDate);
+
+ return Arrays.stream(samples).collect(Collectors.toMap(Sample::getPermId, Function.identity(),
+ (sample1, sample2) -> sample2, LinkedHashMap::new));
+ }
+
+ private PropertyAssignment getExperimentalDescriptionPropertyAssignment()
+ {
+ final PropertyType propertyType = new PropertyType();
+ propertyType.setCode("EXPERIMENTAL_STEP.EXPERIMENTAL_DESCRIPTION");
+ propertyType.setLabel("Experimental description");
+ propertyType.setDescription("Experimental description");
+ propertyType.setDataType(DataType.MULTILINE_VARCHAR);
+ propertyType.setManagedInternally(false);
+ propertyType.setMetaData(Map.of("custom_widget", "Word Processor"));
+
+ final PropertyAssignment propertyAssignment = new PropertyAssignment();
+ propertyAssignment.setFetchOptions(getPropertyAssignmentFetchOptions());
+ propertyAssignment.setPropertyType(propertyType);
+ propertyAssignment.setMandatory(false);
+ propertyAssignment.setShowInEditView(true);
+ propertyAssignment.setSection("General info");
+
+ return propertyAssignment;
+ }
+
+ private PropertyAssignment getExperimentalGoalsPropertyAssignment()
+ {
+ final PropertyType propertyType = new PropertyType();
+ propertyType.setCode("EXPERIMENTAL_STEP.EXPERIMENTAL_GOALS");
+ propertyType.setLabel("Experimental goals");
+ propertyType.setDescription("Experimental goals");
+ propertyType.setDataType(DataType.MULTILINE_VARCHAR);
+ propertyType.setManagedInternally(false);
+ propertyType.setMetaData(Map.of("custom_widget", "")); // No "Word Processor" for this one.
+
+ final PropertyAssignment propertyAssignment = new PropertyAssignment();
+ propertyAssignment.setFetchOptions(getPropertyAssignmentFetchOptions());
+ propertyAssignment.setPropertyType(propertyType);
+ propertyAssignment.setMandatory(false);
+ propertyAssignment.setShowInEditView(true);
+ propertyAssignment.setSection("General info");
+
+ return propertyAssignment;
+ }
+
+ private PropertyAssignment getNamePropertyAssignment()
+ {
+ final PropertyType propertyType = new PropertyType();
+ propertyType.setCode("$NAME");
+ propertyType.setLabel("Name");
+ propertyType.setDescription("Name");
+ propertyType.setDataType(DataType.VARCHAR);
+ propertyType.setManagedInternally(true);
+
+ final PropertyAssignment propertyAssignment = new PropertyAssignment();
+ propertyAssignment.setFetchOptions(getPropertyAssignmentFetchOptions());
+ propertyAssignment.setPropertyType(propertyType);
+ propertyAssignment.setMandatory(false);
+ propertyAssignment.setShowInEditView(true);
+ propertyAssignment.setSection("General info");
+
+ return propertyAssignment;
+ }
+
+ private PropertyAssignmentFetchOptions getPropertyAssignmentFetchOptions()
+ {
+ final PropertyAssignmentFetchOptions fetchOptions = new PropertyAssignmentFetchOptions();
+ fetchOptions.withPropertyType();
+ return fetchOptions;
+ }
+
+ });
+ }
+
+}
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/XLSExportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/XLSExportTest.java
index e7e215a9ab755c01e38949c70b8d0f92665b6272..1902171de4d52df00ea6a23bd892672f84b9f923 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/XLSExportTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/XLSExportTest.java
@@ -27,6 +27,7 @@ import static ch.ethz.sis.openbis.generic.server.xls.export.ExportableKind.SPACE
import static ch.ethz.sis.openbis.generic.server.xls.export.ExportableKind.VOCABULARY_TYPE;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
@@ -315,6 +316,45 @@ public class XLSExportTest
assertTrue(entry.getValue().length() > Short.MAX_VALUE);
}
+ /**
+ * Tests export of cells that contain references to images.
+ */
+ @Test
+ public void testImageReferencesExport() throws IOException
+ {
+ final Expectations expectations = new SampleCellWithImageReferencesExpectations(api, false);
+ mockery.checking(expectations);
+
+ final XLSExport.PrepareWorkbookResult actualResult = XLSExport.prepareWorkbook(
+ api, SESSION_TOKEN, List.of(new ExportablePermId(SAMPLE, new SpacePermId("200001010000000-0001"))),
+ false, null, XLSExport.TextFormatting.RICH, false);
+ assertTrue(actualResult.getScripts().isEmpty());
+ assertTrue(actualResult.getWarnings().isEmpty());
+
+ final InputStream stream = getClass().getClassLoader().getResourceAsStream(
+ "ch/ethz/sis/openbis/generic/server/xls/export/resources/export-sample-cell-with-images.xlsx");
+ if (stream == null)
+ {
+ throw new IllegalArgumentException("File not found.");
+ }
+ final Workbook expectedResult = new XSSFWorkbook(stream);
+
+ assertWorkbooksEqual(actualResult.getWorkbook(), expectedResult);
+
+ final Map<String, byte[]> miscellaneousFiles = actualResult.getMiscellaneousFiles();
+ assertEquals(miscellaneousFiles.size(), 2);
+
+ final byte[] bytes1 = miscellaneousFiles.get(
+ "/eln-lims/c1/b2/91/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.jpg");
+ assertNotNull(bytes1);
+ assertTrue(bytes1.length > 0);
+
+ final byte[] bytes2 = miscellaneousFiles.get(
+ "/eln-lims/46/63/05/466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.jpg");
+ assertNotNull(bytes2);
+ assertTrue(bytes2.length > 0);
+ }
+
public static void assertWorkbooksEqual(final Workbook actual, final Workbook expected)
{
final int sheetsCount = expected.getNumberOfSheets();
diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/resources/export-sample-cell-with-images.xlsx b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/export/resources/export-sample-cell-with-images.xlsx
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/46/63/05/466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.jpg b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/46/63/05/466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.jpg
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/7b/77/90/7b77903f-e685-4700-974a-5a5d7e109638/7b77903f-e685-4700-974a-5a5d7e109638.jpg b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/7b/77/90/7b77903f-e685-4700-974a-5a5d7e109638/7b77903f-e685-4700-974a-5a5d7e109638.jpg
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/c0/1b/2e/c01b2e1f-8212-4562-ae8a-9072bf92e687/c01b2e1f-8212-4562-ae8a-9072bf92e687.jpg b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/c0/1b/2e/c01b2e1f-8212-4562-ae8a-9072bf92e687/c01b2e1f-8212-4562-ae8a-9072bf92e687.jpg
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/c1/b2/91/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.jpg b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/c1/b2/91/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.jpg
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/f3/e4/0c/f3e40c2e-109c-4191-bed0-2cf931de185a/f3e40c2e-109c-4191-bed0-2cf931de185a.jpg b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/generic/server/xls/importer/utils/eln-lims/f3/e4/0c/f3e40c2e-109c-4191-bed0-2cf931de185a/f3e40c2e-109c-4191-bed0-2cf931de185a.jpg
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diff --git a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ExportTest.java b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ExportTest.java
index 49597cd9290cdfc878efb4c99b9267841c6e2bf7..a12126bfed96481d4e29044b8da124f76a6ac302 100644
--- a/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ExportTest.java
+++ b/server-application-server/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ExportTest.java
@@ -287,11 +287,11 @@ public class ExportTest extends AbstractTest
bigCellSampleCreation.setProperty(RICH_TEXT_PROPERTY_NAME, "<p>This is some text.</p>"
+ "<figure class=\"image\">"
+ "<img src=\"/openbis/openbis/file-service/eln-lims/c1/b2/91/"
- + "c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.png\">"
+ + "c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c/c1b2912a-2ed6-40d6-8d9f-8c3ec2b29c5c.jpg\">"
+ "</figure>"
+ "<p>Then we have more text between images.</p>"
+ "<figure class=\"image\"><img src=\"/openbis/openbis/file-service/eln-lims/46/63/05/"
- + "466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.png\">"
+ + "466305f0-4842-441f-b21c-777ea82079b4/466305f0-4842-441f-b21c-777ea82079b4.jpg\">"
+ "</figure>"
+ "<p>And some text at the end.</p>");
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