diff --git a/integration-tests/test_openbis_sync.py b/integration-tests/test_openbis_sync.py
index c3426a623a3a82882348fa1a5e0fd0e9139ef6a1..d97415da3e67d2169903d86e786550370a1b52dd 100755
--- a/integration-tests/test_openbis_sync.py
+++ b/integration-tests/test_openbis_sync.py
@@ -295,7 +295,9 @@ class TestCase(systemtest.testcase.TestCase):
base64string = base64.encodestring('%s:%s' % (user, password)).replace('\n', '')
request.add_header("Authorization", "Basic %s" % base64string)
data = urllib.urlencode({'mode' : 'test'})
- response = urllib2.urlopen(request, data, context=ssl._create_unverified_context())
+# response = urllib2.urlopen(request, data, context=ssl._create_unverified_context())
+# TODO if python version > 2.10: replace next line by the line above
+ response = urllib2.urlopen(request, data)
return response
def getHarvesterConfigFolder(self):
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
index 1a7b95d7e7228077f72eafcbf6cb04a7eefdc3e6..03dd43ea4abc1f5c627dece2b600d268d1ea83c4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
@@ -357,7 +357,7 @@ public class SampleUploadSectionsParser
return results;
}
- private static void generateIdentifiers(boolean projectSamplesEnabled,
+ static void generateIdentifiers(boolean projectSamplesEnabled,
String defaultGroupIdentifier,
SampleCodeGenerator sampleCodeGenerator, boolean isAutoGenerateCodes,
List<NewSamplesWithTypes> newSamplesWithTypes)
@@ -370,27 +370,28 @@ public class SampleUploadSectionsParser
List<String> codes = sampleCodeGenerator.generateCodes(newSamples.size());
for (int i = 0; i < newSamples.size(); i++)
{
+ NewSample sample = newSamples.get(i);
String spaceCodeOrNull = null;
- if (newSamples.get(i).getDefaultSpaceIdentifier() == null || newSamples.get(i).getDefaultSpaceIdentifier().isEmpty())
+ if (StringUtils.isBlank(sample.getDefaultSpaceIdentifier()))
{
spaceCodeOrNull = defaultGroupIdentifier;
} else
{
- spaceCodeOrNull = newSamples.get(i).getDefaultSpaceIdentifier();
+ spaceCodeOrNull = sample.getDefaultSpaceIdentifier();
}
spaceCodeOrNull = spaceCodeOrNull.substring(1);
String projectCodeOrNull = null;
- if (projectSamplesEnabled && newSamples.get(i).getExperimentIdentifier() != null
- && !newSamples.get(i).getExperimentIdentifier().isEmpty())
+ if (projectSamplesEnabled && StringUtils.isNotBlank(sample.getExperimentIdentifier()))
{
- String[] experimentIdentifierParts = newSamples.get(i).getExperimentIdentifier().split("/");
- if(experimentIdentifierParts.length != 4) {
- throw new UserFailureException("Incorrect format for the experiment identifier: " + newSamples.get(i).getExperimentIdentifier());
+ String[] experimentIdentifierParts = sample.getExperimentIdentifier().split("/");
+ if (experimentIdentifierParts.length != 4)
+ {
+ throw new UserFailureException("Incorrect format for the experiment identifier: " + sample.getExperimentIdentifier());
}
spaceCodeOrNull = experimentIdentifierParts[experimentIdentifierParts.length - 3];
projectCodeOrNull = experimentIdentifierParts[experimentIdentifierParts.length - 2];
}
- newSamples.get(i).setIdentifier(createIdentifier(spaceCodeOrNull, projectCodeOrNull, codes.get(i)));
+ sample.setIdentifier(createIdentifier(spaceCodeOrNull, projectCodeOrNull, codes.get(i)));
}
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParserTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..2814364ef0b89c7cd718b1a2c2c0afd4c2e40a9e
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParserTest.java
@@ -0,0 +1,153 @@
+/*
+ * Copyright 2018 ETH Zuerich, SIS
+ *
+ * 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.systemsx.cisd.openbis.generic.shared.parser;
+
+import static org.testng.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class SampleUploadSectionsParserTest
+{
+ private static final class Generator implements SampleUploadSectionsParser.SampleCodeGenerator
+ {
+ private int counter;
+
+ @Override
+ public List<String> generateCodes(int size)
+ {
+
+ List<String> codes = new ArrayList<>(size);
+ for (int i = 0; i < size; i++)
+ {
+ codes.add("S-" + counter++);
+ }
+ return codes;
+ }
+
+ }
+
+ @Test
+ public void testGenerateIdentifiersWithDefaultSpaceAndNoProjectSamples()
+ {
+ // Given
+ NewSamplesWithTypes swt1 = new NewSamplesWithTypes();
+ swt1.setNewEntities(Arrays.asList(s().defaultSpace("/MY_SPACE"),
+ s().experiment("/A/B/C")));
+ NewSamplesWithTypes swt2 = new NewSamplesWithTypes();
+ swt2.setNewEntities(Arrays.asList(s().defaultSpace("/ABC").experiment("/D/E/F")));
+
+ // When
+ SampleUploadSectionsParser.generateIdentifiers(false, "/DEFAULT", new Generator(), true, Arrays.asList(swt1, swt2));
+
+ // Then
+ assertEquals(extractIdentifiers(swt1).toString(), "[/MY_SPACE/S-0, /DEFAULT/S-1]");
+ assertEquals(extractIdentifiers(swt2).toString(), "[/ABC/S-2]");
+ }
+
+ @Test
+ public void testGenerateIdentifiersWithNoDefaultSpaceAndNoProjectSamples()
+ {
+ // Given
+ NewSamplesWithTypes swt1 = new NewSamplesWithTypes();
+ swt1.setNewEntities(Arrays.asList(s().defaultSpace("/MY_SPACE"),
+ s().defaultSpace("/A1").experiment("/A/B/C")));
+ NewSamplesWithTypes swt2 = new NewSamplesWithTypes();
+ swt2.setNewEntities(Arrays.asList(s().defaultSpace("/ABC").experiment("/D/E/F")));
+
+ // When
+ SampleUploadSectionsParser.generateIdentifiers(false, null, new Generator(), true, Arrays.asList(swt1, swt2));
+
+ // Then
+ assertEquals(extractIdentifiers(swt1).toString(), "[/MY_SPACE/S-0, /A1/S-1]");
+ assertEquals(extractIdentifiers(swt2).toString(), "[/ABC/S-2]");
+ }
+
+ @Test
+ public void testGenerateIdentifiersWithDefaultSpaceAndProjectSamples()
+ {
+ // Given
+ NewSamplesWithTypes swt1 = new NewSamplesWithTypes();
+ swt1.setNewEntities(Arrays.asList(s().defaultSpace("/MY_SPACE"),
+ s().experiment("/A/B/C")));
+ NewSamplesWithTypes swt2 = new NewSamplesWithTypes();
+ swt2.setNewEntities(Arrays.asList(s().defaultSpace("/ABC").experiment("/D/E/F")));
+
+ // When
+ SampleUploadSectionsParser.generateIdentifiers(true, "/DEFAULT", new Generator(), true, Arrays.asList(swt1, swt2));
+
+ // Then
+ assertEquals(extractIdentifiers(swt1).toString(), "[/MY_SPACE/S-0, /A/B/S-1]");
+ assertEquals(extractIdentifiers(swt2).toString(), "[/D/E/S-2]");
+ }
+
+ @Test
+ public void testGenerateIdentifiersWithNoDefaultSpaceAndProjectSamples()
+ {
+ // Given
+ NewSamplesWithTypes swt1 = new NewSamplesWithTypes();
+ swt1.setNewEntities(Arrays.asList(s().defaultSpace("/MY_SPACE"), s().defaultSpace("/A1").experiment("/A/B/C")));
+ NewSamplesWithTypes swt2 = new NewSamplesWithTypes();
+ swt2.setNewEntities(Arrays.asList(s().defaultSpace("/ABC").experiment("/D/E/F"),
+ s().defaultSpace("/S1").experiment("/C/D/E")));
+
+ // When
+ SampleUploadSectionsParser.generateIdentifiers(true, null, new Generator(), true, Arrays.asList(swt1, swt2));
+
+ // Then
+ assertEquals(extractIdentifiers(swt1).toString(), "[/MY_SPACE/S-0, /A/B/S-1]");
+ assertEquals(extractIdentifiers(swt2).toString(), "[/D/E/S-2, /C/D/S-3]");
+ }
+
+ private List<String> extractIdentifiers(NewSamplesWithTypes samplesWithTypes)
+ {
+ return samplesWithTypes.getNewEntities().stream().map(NewSample::getIdentifier).collect(Collectors.toList());
+ }
+
+ private NewSampleBuilder s()
+ {
+ return new NewSampleBuilder();
+ }
+
+ private static final class NewSampleBuilder extends NewSample
+ {
+ private static final long serialVersionUID = 1L;
+
+ public NewSampleBuilder defaultSpace(String defaultSpaceIdentifier)
+ {
+ setDefaultSpaceIdentifier(defaultSpaceIdentifier);
+ return this;
+ }
+
+ public NewSampleBuilder experiment(String experimentIdentifier)
+ {
+ setExperimentIdentifier(experimentIdentifier);
+ return this;
+ }
+ }
+
+}