diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
index cf2b6d65b8d998d35fbe748281a3e9938069f1d1..0f57e28f02a15200dd001bb10754ff923971960c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
@@ -17,28 +17,26 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.io.File;
-import java.text.SimpleDateFormat;
import java.util.ArrayList;
-import java.util.Date;
import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
-import ch.systemsx.cisd.common.utilities.SystemTimeProvider;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
/**
* Data set info extractor for MS injection data sets. Information is extracted from a properties
@@ -53,35 +51,30 @@ public class DataSetInfoExtractorForMSInjection implements IDataSetInfoExtractor
static final String DEFAULT_MS_INJECTION_PROPERTIES_FILE = "ms-injection.properties";
static final String PROJECT_CODE_KEY = "PROJECT_CODE";
- static final String MZXML_FILENAME_KEY = "MZXML_FILENAME";
+ static final String EXPERIMENT_CODE_KEY = "EXPERIMENT_CODE";
+ static final String SAMPLE_CODE_KEY = "SAMPLE_CODE";
static final String GROUP_CODE = "MS_DATA";
+ static final String EXPERIMENT_TYPE_CODE = "MS_INJECT";
static final String SAMPLE_TYPE_CODE = "MS_INJECTION";
- private static final SimpleDateFormat EXPERIMENT_CODE_TEMPLATE =
- new SimpleDateFormat("yyyy-MM");
-
private final String msInjectionPropertiesFileName;
private final IEncapsulatedOpenBISService service;
- private final ITimeProvider timeProvider;
-
public DataSetInfoExtractorForMSInjection(Properties properties)
{
this(properties.getProperty(MS_INJECTION_PROPERTIES_FILE_KEY,
- DEFAULT_MS_INJECTION_PROPERTIES_FILE), ServiceProvider.getOpenBISService(),
- SystemTimeProvider.SYSTEM_TIME_PROVIDER);
+ DEFAULT_MS_INJECTION_PROPERTIES_FILE), ServiceProvider.getOpenBISService());
}
DataSetInfoExtractorForMSInjection(String msInjectionPropertiesFileName,
- IEncapsulatedOpenBISService service, ITimeProvider timeProvider)
+ IEncapsulatedOpenBISService service)
{
this.msInjectionPropertiesFileName = msInjectionPropertiesFileName;
this.service = service;
- this.timeProvider = timeProvider;
}
@@ -93,12 +86,12 @@ public class DataSetInfoExtractorForMSInjection implements IDataSetInfoExtractor
loadMSInjectionProperties(incomingDataSetPath);
DataSetInformation info = new DataSetInformation();
info.setGroupCode(GROUP_CODE);
- info.setSampleCode(PropertyUtils.getMandatoryProperty(properties, MZXML_FILENAME_KEY));
+ info.setSampleCode(PropertyUtils.getMandatoryProperty(properties, SAMPLE_CODE_KEY));
NewSample sample = new NewSample();
SampleType sampleType = new SampleType();
sampleType.setCode(SAMPLE_TYPE_CODE);
sample.setSampleType(sampleType);
- sample.setExperimentIdentifier(createExperimentIdentifer(properties));
+ sample.setExperimentIdentifier(getOrCreateExperiment(properties));
sample.setIdentifier(info.getSampleIdentifier().toString());
List<EntityProperty> sampleProperties = createSampleProperties(properties);
sample.setProperties(sampleProperties.toArray(new EntityProperty[sampleProperties.size()]));
@@ -106,15 +99,19 @@ public class DataSetInfoExtractorForMSInjection implements IDataSetInfoExtractor
return info;
}
- private String createExperimentIdentifer(Properties msInjectionProperties)
+ private String getOrCreateExperiment(Properties msInjectionProperties)
{
String projectCode =
PropertyUtils.getMandatoryProperty(msInjectionProperties, PROJECT_CODE_KEY);
String experimentCode =
- EXPERIMENT_CODE_TEMPLATE.format(new Date(timeProvider.getTimeInMilliseconds()));
- return DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + GROUP_CODE
- + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + projectCode
- + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + experimentCode;
+ PropertyUtils.getMandatoryProperty(msInjectionProperties, EXPERIMENT_CODE_KEY);
+ ExperimentIdentifier identifier = new ExperimentIdentifier(null, GROUP_CODE, projectCode, experimentCode);
+ Experiment experiment = service.tryToGetExperiment(identifier);
+ if (experiment == null)
+ {
+ service.registerExperiment(new NewExperiment(identifier.toString(), EXPERIMENT_TYPE_CODE));
+ }
+ return identifier.toString();
}
private List<EntityProperty> createSampleProperties(Properties msInjectionProperties)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/index.html b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/index.html
index 609dc0c139f825777a1748b448568a276862799a..b6a4477b841a06f0fffa82ace463a1a17b750b50 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/index.html
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/index.html
@@ -6,7 +6,19 @@
<!--
// This script loads your compiled module. If you add any GWT meta tags, they must be added before this line.
-->
-<script language="javascript" src="ch.systemsx.cisd.openbis.plugin.phosphonetx.OpenBIS.nocache.js"></script>
+<script language="javascript"
+ src="ch.systemsx.cisd.openbis.plugin.phosphonetx.OpenBIS.nocache.js"></script>
+<script language="JavaScript">
+ // confirmation on exit depends on whether user is logged in
+ var allowConfirmOnExit = false;
+ window.onbeforeunload = confirmExit;
+ function confirmExit()
+ {
+ if (allowConfirmOnExit) {
+ return "WARNING: By doing this you will in fact leave openBIS!";
+ }
+ }
+</script>
<link rel="shortcut icon" href="images/favicon.ico" />
<link rel="icon" type="image/png" href="images/favicon.png" />
@@ -16,5 +28,36 @@
// The body can have arbitrary html, or you can leave the body empty if you want to create a completely dynamic ui.
-->
<body>
+<!-- Required by IE (GWT 1.7) -->
+<iframe id="__gwt_historyFrame" style="width: 0; height: 0; border: 0"></iframe>
+<div id="openbis_login_div" style="visibility: hidden">
+<form id="openbis_login_form" method="post" action="javascript:;">
+<table>
+ <tbody>
+ <tr>
+ <td><span>User:</span></td>
+ <td><input type="text" id="openbis_login_username"
+ name="openbis-username" style="width: 150px;"></td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td><span>Password:</span></td>
+ <td><input type="password" id="openbis_login_password"
+ name="openbis-password" style="width: 150px;"></td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td rowspan="3"> </td>
+ </tr>
+ <tr>
+ <td> </td>
+ <td> </td>
+ <td align="right"><input type="submit" id="openbis_login_submit"
+ value="Login"></td>
+ </tr>
+ </tbody>
+</table>
+</form>
+</div>
</body>
</html>
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
index 5eebb1441b5e596df922d323d9286d5c084d8950..0283bc0c54c474fd61f1aa06c7ab09d813027719 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
@@ -17,9 +17,11 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DEFAULT_MS_INJECTION_PROPERTIES_FILE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.EXPERIMENT_CODE_KEY;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.EXPERIMENT_TYPE_CODE;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.GROUP_CODE;
-import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.MZXML_FILENAME_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.PROJECT_CODE_KEY;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE;
import java.io.File;
@@ -43,16 +45,18 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.utilities.ITimeProvider;
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.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
/**
*
@@ -62,18 +66,18 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceId
public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTestCase
{
private static final String PROJECT_CODE = "MS2";
- private static final String MZXML_FILENAME = "U09-1242";
+ private static final String EXPERIMENT_CODE = "2010-02";
+ private static final String SAMPLE_CODE = "U09-1242";
private static final String SAMPLE_IDENTIFIER =
DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + GROUP_CODE
- + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + MZXML_FILENAME;
+ + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + SAMPLE_CODE;
private static final String EXPERIMENT_IDENTIFIER =
DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + GROUP_CODE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + PROJECT_CODE
- + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + "1973-04";
+ + DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + EXPERIMENT_CODE;
private Mockery context;
private IEncapsulatedOpenBISService service;
- private ITimeProvider timeProvider;
private IDataSetInfoExtractor extractor;
private File dataSet;
@@ -82,10 +86,9 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
{
context = new Mockery();
service = context.mock(IEncapsulatedOpenBISService.class);
- timeProvider = context.mock(ITimeProvider.class);
extractor =
new DataSetInfoExtractorForMSInjection(DEFAULT_MS_INJECTION_PROPERTIES_FILE,
- service, timeProvider);
+ service);
dataSet = new File(workingDirectory, "data-set");
dataSet.mkdirs();
}
@@ -132,7 +135,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
}
@Test
- public void testMissingMZXML()
+ public void testMissingSampleCode()
{
Properties properties = new Properties();
save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
@@ -143,7 +146,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException ex)
{
- assertEquals("Given key '" + MZXML_FILENAME_KEY + "' not found in properties '[]'", ex
+ assertEquals("Given key '" + SAMPLE_CODE_KEY + "' not found in properties '[]'", ex
.getMessage());
}
@@ -154,8 +157,8 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
public void testMissingProjectCode()
{
Properties properties = new Properties();
-
- properties.setProperty(MZXML_FILENAME_KEY, MZXML_FILENAME);
+
+ properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
try
@@ -165,9 +168,30 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
} catch (ConfigurationFailureException ex)
{
assertEquals("Given key '" + PROJECT_CODE_KEY + "' not found in properties '["
- + MZXML_FILENAME_KEY + "]'", ex.getMessage());
+ + SAMPLE_CODE_KEY + "]'", ex.getMessage());
}
-
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testMissingExperimentCode()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
+ save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("ConfigurationFailureException expected");
+ } catch (ConfigurationFailureException ex)
+ {
+ assertEquals("Given key '" + EXPERIMENT_CODE_KEY + "' not found in properties '["
+ + PROJECT_CODE_KEY + ", " + SAMPLE_CODE_KEY + "]'", ex.getMessage());
+ }
+
context.assertIsSatisfied();
}
@@ -176,12 +200,13 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
{
Properties properties = new Properties();
properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- properties.setProperty(MZXML_FILENAME_KEY, MZXML_FILENAME);
+ properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ properties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
properties.setProperty("TEMPERATURE", "47.11");
save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(MZXML_FILENAME_KEY, true);
+ SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
SampleTypePropertyType pt2 = createPropertyType("VOLUME", false);
- prepareTimeProviderAndGetSampleType(pt1, pt2);
+ prepareGetExperimentAndGetSampleType(false, pt1, pt2);
context.checking(new Expectations()
{
{
@@ -203,7 +228,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
map.put(property.getPropertyType().getCode(), property);
}
- assertEquals(MZXML_FILENAME, map.get(MZXML_FILENAME_KEY).getValue());
+ assertEquals(SAMPLE_CODE, map.get(SAMPLE_CODE_KEY).getValue());
assertEquals(1, map.size());
return true;
}
@@ -221,7 +246,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
assertEquals(GROUP_CODE, info.getGroupCode());
- assertEquals(MZXML_FILENAME, info.getSampleCode());
+ assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(null, info.getExperimentIdentifier());
context.assertIsSatisfied();
@@ -232,12 +257,13 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
{
Properties properties = new Properties();
properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- properties.setProperty(MZXML_FILENAME_KEY, MZXML_FILENAME);
+ properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ properties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(MZXML_FILENAME_KEY, true);
+ SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
SampleTypePropertyType pt2 = createPropertyType("VOLUME", true);
SampleTypePropertyType pt3 = createPropertyType("TEMPERATURE", true);
- prepareTimeProviderAndGetSampleType(pt1, pt2, pt3);
+ prepareGetExperimentAndGetSampleType(true, pt1, pt2, pt3);
try
{
@@ -252,14 +278,24 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
context.assertIsSatisfied();
}
- private void prepareTimeProviderAndGetSampleType(
- final SampleTypePropertyType... sampleTypePropertyTypes)
+ private void prepareGetExperimentAndGetSampleType(
+ final boolean experimentExists, final SampleTypePropertyType... sampleTypePropertyTypes)
{
context.checking(new Expectations()
{
{
- one(timeProvider).getTimeInMilliseconds();
- will(returnValue(4711L * 4711 * 4711));
+ ExperimentIdentifier identifier = new ExperimentIdentifier(null, GROUP_CODE, PROJECT_CODE,
+ EXPERIMENT_CODE);
+ one(service).tryToGetExperiment(identifier
+ );
+ will(returnValue(experimentExists ? new Experiment() : null));
+
+ if (experimentExists == false)
+ {
+ one(service).registerExperiment(
+ new NewExperiment(identifier.toString(), EXPERIMENT_TYPE_CODE));
+ }
+
one(service).getSampleType(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
SampleType sampleType = new SampleType();
sampleType.setSampleTypePropertyTypes(Arrays.asList(sampleTypePropertyTypes));