From 7c09059e9933daefc6c02612cd8413e3103b93d5 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Tue, 6 Oct 2009 12:28:33 +0000
Subject: [PATCH] [LMS-1191] extended data set upload form and cifex extractor
SVN: 12854
---
.../cifex/CifexDataSetInfoExtractor.java | 33 ++++-
.../ui/data/DataSetUploadForm.java | 117 ++++++++++++++++--
.../application/ui/widget/FieldUtil.java | 6 +-
.../shared/basic/DataSetUploadInfo.java | 102 +++++++++++++--
.../dataset/DataSetParentsArea.java | 2 +-
.../GenericSampleBatchRegistrationForm.java | 8 +-
.../generic/shared/DataSetInfoHelperTest.java | 86 ++++++++++---
7 files changed, 304 insertions(+), 50 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
index 11d07ab2bb4..623f80e3960 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.etlserver.cifex;
import static ch.systemsx.cisd.etlserver.AbstractDataSetInfoExtractor.extractDataSetProperties;
import java.io.File;
+import java.util.Arrays;
import java.util.Properties;
import ch.rinn.restrictions.Private;
@@ -28,13 +29,16 @@ import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.DataSetUploadInfo;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
- * {@link IDataSetInfoExtractor} extracting group and sample from CIFEX comment.
+ * {@link IDataSetInfoExtractor} extracting data from CIFEX comment.
*
* @author Izabela Adamczyk
+ * @author Piotr Buczek
*/
public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
{
@@ -59,12 +63,26 @@ public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
DataSetUploadInfo info = CifexExtratorHelper.getDataSetUploadInfo(incomingDataSetPath);
final DataSetInformation dataSetInformation = new DataSetInformation();
- SampleIdentifier identifier = SampleIdentifierFactory.parse(info.getSample());
- dataSetInformation.setSampleCode(identifier.getSampleCode());
- if (identifier.isGroupLevel())
+
+ // either sample is specified or experiment (with optional data set parents)
+
+ SampleIdentifier sampleIdentifierOrNull = tryGetSampleIdentifier(info);
+ if (sampleIdentifierOrNull != null)
{
- dataSetInformation.setGroupCode(identifier.getGroupLevel().getGroupCode());
+ dataSetInformation.setSampleCode(sampleIdentifierOrNull.getSampleCode());
+ if (sampleIdentifierOrNull.isGroupLevel())
+ {
+ dataSetInformation.setGroupCode(sampleIdentifierOrNull.getGroupLevel()
+ .getGroupCode());
+ }
+ } else
+ {
+ ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifierFactory(info.getExperiment()).createIdentifier();
+ dataSetInformation.setGroupCode(experimentIdentifier.getGroupCode());
+ dataSetInformation.setParentDataSetCodes(Arrays.asList(info.getParents()));
}
+
dataSetInformation.setUploadingUserEmail(CifexExtratorHelper
.getUploadingUserEmail(incomingDataSetPath));
dataSetInformation.setDataSetProperties(extractDataSetProperties(incomingDataSetPath,
@@ -72,4 +90,9 @@ public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
return dataSetInformation;
}
+ private SampleIdentifier tryGetSampleIdentifier(DataSetUploadInfo info)
+ {
+ return (info.getSample() == null) ? null : SampleIdentifierFactory.parse(info.getSample());
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetUploadForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetUploadForm.java
index 72facb08740..e2603aab96d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetUploadForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetUploadForm.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data;
+import com.extjs.gxt.ui.client.Events;
+import com.extjs.gxt.ui.client.event.FieldEvent;
+import com.extjs.gxt.ui.client.event.Listener;
import com.google.gwt.http.client.URL;
import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
@@ -26,15 +29,20 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CheckBoxField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.SampleChooserField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.SampleChooserField.SampleChooserFieldAdaptor;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.StringUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.DataSetUploadInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
import ch.systemsx.cisd.openbis.generic.shared.basic.DataSetUploadInfo.DataSetUploadInfoHelper;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.dataset.DataSetParentsArea;
/**
* Panel that allows to specify information necessary to upload data sets and redirects user to
@@ -49,15 +57,26 @@ public class DataSetUploadForm extends AbstractRegistrationForm
public static final String ID = GenericConstants.ID_PREFIX + ID_SUFFIX;
- private String cifexURL;
+ private final String cifexURL;
- private String cifexRecipient;
+ private final String cifexRecipient;
- private DataSetTypeSelectionWidget dataSetTypeSelectionWidget;
+ private final DataSetTypeSelectionWidget dataSetTypeSelectionWidget;
- private SampleChooserFieldAdaptor sampleChooser;
+ private final FileFormatTypeSelectionWidget fileTypeSelectionWidget;
- private FileFormatTypeSelectionWidget fileTypeSelectionWidget;
+ private final CheckBoxField connectedWithSampleCheckbox;
+
+ // two options:
+ // 1. connected with sample
+ private final SampleChooserFieldAdaptor sampleChooser;
+
+ // 2. not connected with sample
+ private final ExperimentChooserFieldAdaptor experimentChooser;
+
+ private final DataSetParentsArea parentsArea;
+
+ //
public DataSetUploadForm(IViewContext<ICommonClientServiceAsync> viewContext)
{
@@ -65,10 +84,31 @@ public class DataSetUploadForm extends AbstractRegistrationForm
cifexURL = viewContext.getModel().getApplicationInfo().getCIFEXURL();
cifexRecipient = viewContext.getModel().getApplicationInfo().getCifexRecipient();
saveButton.setText(viewContext.getMessage(Dict.BUTTON_UPLOAD_DATA_VIA_CIFEX));
+
+ connectedWithSampleCheckbox = new CheckBoxField("Connected with Sample", false);
+ connectedWithSampleCheckbox.setValue(true);
+ formPanel.add(connectedWithSampleCheckbox);
+
+ // both sample and experiment choosers are mandatory but only one will be shown
sampleChooser =
SampleChooserField.create(viewContext.getMessage(Dict.SAMPLE), true, null, false,
true, viewContext);
formPanel.add(sampleChooser.getField());
+ experimentChooser =
+ ExperimentChooserField.create(viewContext.getMessage(Dict.EXPERIMENT), true, null,
+ viewContext);
+ formPanel.add(experimentChooser.getField());
+ formPanel.add(parentsArea = new DataSetParentsArea(viewContext, ID_SUFFIX));
+
+ connectedWithSampleCheckbox.addListener(Events.Change, new Listener<FieldEvent>()
+ {
+ public void handleEvent(FieldEvent be)
+ {
+ updateFieldsVisibility();
+ }
+ });
+ updateFieldsVisibility();
+
formPanel.add(dataSetTypeSelectionWidget =
new DataSetTypeSelectionWidget(viewContext, ID_SUFFIX));
FieldUtil.markAsMandatory(dataSetTypeSelectionWidget);
@@ -82,6 +122,14 @@ public class DataSetUploadForm extends AbstractRegistrationForm
}
}
+ private void updateFieldsVisibility()
+ {
+ boolean connectedWithSample = connectedWithSampleCheckbox.getValue();
+ FieldUtil.setVisibility(connectedWithSample, sampleChooser.getField());
+ FieldUtil.setVisibility(connectedWithSample == false, experimentChooser.getField(),
+ parentsArea);
+ }
+
public static DatabaseModificationAwareComponent create(
IViewContext<ICommonClientServiceAsync> viewContext)
{
@@ -102,17 +150,64 @@ public class DataSetUploadForm extends AbstractRegistrationForm
@Override
protected void submitValidForm()
{
- String comment =
- encodeDataSetInfo(sampleChooser.getValue(), dataSetTypeSelectionWidget
- .tryGetSelected().getCode(), fileTypeSelectionWidget.tryGetSelected()
- .getCode());
+ final String sample = extractSampleIdentifier();
+ final String experiment = extractExperimentIdentifier();
+ final String dataSetType = extractDataSetTypeCode();
+ final String fileType = extractFileTypeCode();
+ final String[] parents = extractParentDatasetCodes();
+ String comment;
+ if (isConnectedWithSample())
+ {
+ comment = encodeDataSetInfo(sample, dataSetType, fileType);
+ } else
+ {
+ comment = encodeDataSetInfo(experiment, parents, dataSetType, fileType);
+ }
WindowUtils.openWindow(encodeCifexRequest(cifexURL, cifexRecipient, comment));
}
+ private Boolean isConnectedWithSample()
+ {
+ return connectedWithSampleCheckbox.getValue();
+ }
+
+ private String extractSampleIdentifier()
+ {
+ return sampleChooser.getValue();
+ }
+
+ private String extractExperimentIdentifier()
+ {
+ ExperimentIdentifier identifierOrNull = experimentChooser.tryToGetValue();
+ return identifierOrNull == null ? null : identifierOrNull.getIdentifier();
+ }
+
+ private String extractDataSetTypeCode()
+ {
+ return dataSetTypeSelectionWidget.tryGetSelected().getCode();
+ }
+
+ private String extractFileTypeCode()
+ {
+ return fileTypeSelectionWidget.tryGetSelected().getCode();
+ }
+
+ protected String[] extractParentDatasetCodes()
+ {
+ return parentsArea.tryGetModifiedParentCodes();
+ }
+
private String encodeDataSetInfo(String sample, String dataSetType, String fileType)
{
- return DataSetUploadInfoHelper.encodeAsCifexComment(new DataSetUploadInfo(sample,
- dataSetType, fileType));
+ return DataSetUploadInfoHelper.encodeAsCifexComment(new DataSetUploadInfo(sample, null,
+ null, dataSetType, fileType));
+ }
+
+ private String encodeDataSetInfo(String experiment, String[] parents, String dataSetType,
+ String fileType)
+ {
+ return DataSetUploadInfoHelper.encodeAsCifexComment(new DataSetUploadInfo(null, experiment,
+ parents, dataSetType, fileType));
}
private static String encodeCifexRequest(String cifexUrl, String recipient, String comment)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/FieldUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/FieldUtil.java
index 68f59e06f42..922a763e7c3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/FieldUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/FieldUtil.java
@@ -72,10 +72,14 @@ public class FieldUtil
{
field.setEnabled(visible);
field.setVisible(visible);
- // invalidation mark is not removed automatically when we make field invisible
if (visible == false)
{
+ // invalidation mark is not removed automatically when we make field invisible
field.clearInvalid();
+ } else if (field.isDirty())
+ {
+ // validate only if something have been modified and field is shown
+ field.validate();
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
index 2e9ed4e4068..4bffbd944c7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
@@ -22,7 +22,15 @@ package ch.systemsx.cisd.openbis.generic.shared.basic;
public class DataSetUploadInfo
{
- String sample;
+ private static final String PARENT_SEPARATOR = "|";
+
+ private static final String SEPARATOR = ",";
+
+ String sample; // may be null
+
+ String experiment; // may be null
+
+ String[] parents; // may be null
String dataSetType;
@@ -32,9 +40,12 @@ public class DataSetUploadInfo
{
}
- public DataSetUploadInfo(String sample, String dataSetType, String fileType)
+ public DataSetUploadInfo(String sample, String experiment, String[] parents,
+ String dataSetType, String fileType)
{
setSample(sample);
+ setExperiment(experiment);
+ setParents(parents);
setDataSetType(dataSetType);
setFileType(fileType);
}
@@ -69,42 +80,107 @@ public class DataSetUploadInfo
this.fileType = fileType;
}
+ public String getExperiment()
+ {
+ return experiment;
+ }
+
+ public void setExperiment(String experiment)
+ {
+ this.experiment = experiment;
+ }
+
+ public String[] getParents()
+ {
+ return parents;
+ }
+
+ public void setParents(String[] parents)
+ {
+ this.parents = parents;
+ }
+
public static class DataSetUploadInfoHelper
{
- private static final String SEPARATOR = ",";
enum CommentElements
{
- SAMPLE, DATA_SET_TYPE, FILE_TYPE;
+ SAMPLE, EXPERIMENT, PARENTS, DATA_SET_TYPE, FILE_TYPE;
}
public static String encodeAsCifexComment(DataSetUploadInfo info)
{
String[] commentElements = new String[CommentElements.values().length];
commentElements[CommentElements.SAMPLE.ordinal()] = info.getSample();
+ commentElements[CommentElements.EXPERIMENT.ordinal()] = info.getExperiment();
+ commentElements[CommentElements.PARENTS.ordinal()] = tryEncodeParentsAsString(info);
commentElements[CommentElements.DATA_SET_TYPE.ordinal()] = info.getDataSetType();
commentElements[CommentElements.FILE_TYPE.ordinal()] = info.getFileType();
- String comment = "";
+ StringBuilder commentBuilder = new StringBuilder();
for (String el : commentElements)
{
- if (comment.length() != 0)
- {
- comment += SEPARATOR;
- }
- comment += el;
+ commentBuilder.append(el);
+ commentBuilder.append(SEPARATOR);
}
- return comment;
+ return cutOffLastSeparator(commentBuilder, SEPARATOR);
}
public static DataSetUploadInfo extractFromCifexComment(String comment)
{
- String[] commentElements = comment.split(SEPARATOR);
+ String[] commentElements = comment.split(asEscapedRegexp(SEPARATOR));
DataSetUploadInfo result = new DataSetUploadInfo();
- result.setSample(commentElements[CommentElements.SAMPLE.ordinal()]);
+ result.setSample(nullify(commentElements[CommentElements.SAMPLE.ordinal()]));
+ result.setExperiment(nullify(commentElements[CommentElements.EXPERIMENT.ordinal()]));
+ result
+ .setParents(tryExtractParentsFromString(nullify(commentElements[CommentElements.PARENTS
+ .ordinal()])));
result.setDataSetType(commentElements[CommentElements.DATA_SET_TYPE.ordinal()]);
result.setFileType(commentElements[CommentElements.FILE_TYPE.ordinal()]);
return result;
}
+
+ private static String nullify(String string)
+ {
+ return string.equals("null") ? null : string;
+ }
+
+ private static String[] tryExtractParentsFromString(String parents)
+ {
+ return parents == null ? null : parents.split(asEscapedRegexp(PARENT_SEPARATOR));
+ }
+
+ private static String tryEncodeParentsAsString(DataSetUploadInfo info)
+ {
+ if (info.getParents() == null)
+ {
+ return null;
+ }
+ StringBuilder sb = new StringBuilder();
+ for (String parent : info.getParents())
+ {
+ sb.append(parent);
+ sb.append(PARENT_SEPARATOR);
+ }
+ return cutOffLastSeparator(sb, PARENT_SEPARATOR);
+ }
+
+ private static String asEscapedRegexp(String str)
+ {
+ return "\\Q" + str + "\\E";
+ }
+
+ private static String cutOffLastSeparator(StringBuilder builder, String sep)
+ {
+ // either builder is empty or it should end with separator
+ if (builder.length() == 0)
+ {
+ return "";
+ } else
+ {
+ assert builder.lastIndexOf(sep) == builder.length() - sep.length();
+ return builder.substring(0, builder.length() - sep.length());
+ }
+ }
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetParentsArea.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetParentsArea.java
index fb9c7ddaa5a..8d062ee3649 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetParentsArea.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetParentsArea.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
*
* @author Piotr Buczek
*/
-final class DataSetParentsArea extends TextArea
+public final class DataSetParentsArea extends TextArea
{
public static final String ID_SUFFIX_PARENTS = "_parents";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
index f9fd36e8a9f..8ceebccab43 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
@@ -76,9 +76,9 @@ public final class GenericSampleBatchRegistrationForm extends AbstractRegistrati
private final SampleType sampleType;
- private CheckBoxField generateCodesCheckbox;
+ private final CheckBoxField generateCodesCheckbox;
- private GroupSelectionWidget groupSelector;
+ private final GroupSelectionWidget groupSelector;
public GenericSampleBatchRegistrationForm(
final IViewContext<IGenericClientServiceAsync> viewContext, final SampleType sampleType)
@@ -100,9 +100,7 @@ public final class GenericSampleBatchRegistrationForm extends AbstractRegistrati
public void handleEvent(FieldEvent be)
{
boolean selected = (Boolean) be.value;
- groupSelector.setVisible(selected);
- groupSelector.setEnabled(selected);
- groupSelector.validate();
+ FieldUtil.setVisibility(selected, groupSelector);
}
});
addUploadFeatures(SESSION_KEY);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
index 7d712552087..4866c47dc09 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.shared;
+import org.apache.commons.lang.StringUtils;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
@@ -27,36 +28,93 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.DataSetUploadInfo.DataSetUp
*/
public class DataSetInfoHelperTest extends AssertJUnit
{
-
@Test
- public void testDataSetUploadInfoContructor()
+ public void testDataSetUploadInfoContructorWithSample()
{
+ // sample but no experiment and parents
String sample = "sampleA";
- String dataSetType = "dataSetTypeB";
- String fileType = "fileTypeC";
- DataSetUploadInfo info = new DataSetUploadInfo(sample, dataSetType, fileType);
+ String experiment = null;
+ String dataSetType = "dataSetTypeC";
+ String fileType = "fileTypeD";
+ String[] parents = null;
+ DataSetUploadInfo info =
+ new DataSetUploadInfo(sample, experiment, parents, dataSetType, fileType);
+ checkInfo(info, sample, experiment, parents, dataSetType, fileType);
+ }
+
+ @Test
+ public void testDataSetUploadInfoConstructorNoSample()
+ {
+ // no sample but experiment and parents
+ String sample = null;
+ String experiment = "experimentB";
+ String dataSetType = "dataSetTypeC";
+ String fileType = "fileTypeD";
+ String[] parents =
+ { "p1", "p2", "p3" };
+ DataSetUploadInfo info =
+ new DataSetUploadInfo(sample, experiment, parents, dataSetType, fileType);
+ checkInfo(info, sample, experiment, parents, dataSetType, fileType);
+ }
+
+ private void checkInfo(DataSetUploadInfo info, String sample, String experiment,
+ String[] parents, String dataSetType, String fileType)
+ {
assertEquals(info.getSample(), sample);
+ assertEquals(info.getExperiment(), experiment);
+ assertEquals(StringUtils.join(info.getParents(), ";"), StringUtils.join(parents, ";"));
assertEquals(info.getFileType(), fileType);
assertEquals(info.getDataSetType(), dataSetType);
}
@Test
- public void testExtractFromComment() throws Exception
+ public void testExtractFromCommentWithSample() throws Exception
{
- DataSetUploadInfo info = DataSetUploadInfoHelper.extractFromCifexComment("sA,dsB,ftC");
+ DataSetUploadInfo info =
+ DataSetUploadInfoHelper.extractFromCifexComment("sA,null,null,dsC,ftD");
assertEquals("sA", info.getSample());
- assertEquals("ftC", info.getFileType());
- assertEquals("dsB", info.getDataSetType());
+ assertNull(info.getExperiment());
+ assertNull(info.getParents());
+ assertEquals("dsC", info.getDataSetType());
+ assertEquals("ftD", info.getFileType());
}
@Test
- public void testEncodeAsComment()
+ public void testExtractFromCommentNoSample() throws Exception
+ {
+ DataSetUploadInfo info =
+ DataSetUploadInfoHelper.extractFromCifexComment("null,eB,p1|p2|p3,dsC,ftD");
+ assertNull(info.getSample());
+ assertEquals("eB", info.getExperiment());
+ assertEquals("p1;p2;p3", StringUtils.join(info.getParents(), ";"));
+ assertEquals("dsC", info.getDataSetType());
+ assertEquals("ftD", info.getFileType());
+ }
+
+ @Test
+ public void testEncodeAsCommentWithSample()
{
String sample = "sA";
- String dataSetType = "dsB";
- String fileType = "ftC";
- DataSetUploadInfo info = new DataSetUploadInfo(sample, dataSetType, fileType);
- assertEquals("sA,dsB,ftC", DataSetUploadInfoHelper.encodeAsCifexComment(info));
+ String experiment = null;
+ String[] parents = null;
+ String dataSetType = "dsC";
+ String fileType = "ftD";
+ DataSetUploadInfo info =
+ new DataSetUploadInfo(sample, experiment, parents, dataSetType, fileType);
+ assertEquals("sA,null,null,dsC,ftD", DataSetUploadInfoHelper.encodeAsCifexComment(info));
+ }
+ @Test
+ public void testEncodeAsCommentNoSample()
+ {
+ String sample = null;
+ String experiment = "eB";
+ String[] parents =
+ { "p1", "p2", "p3" };
+ String dataSetType = "dsC";
+ String fileType = "ftD";
+ DataSetUploadInfo info =
+ new DataSetUploadInfo(sample, experiment, parents, dataSetType, fileType);
+ assertEquals("null,eB,p1|p2|p3,dsC,ftD", DataSetUploadInfoHelper.encodeAsCifexComment(info));
}
}
--
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