diff --git a/rtd_yeastx/resource/examples/allFields.quantML b/rtd_yeastx/resource/examples/allFields.quantML
index f66be98c85e303c2c46e6c2bb8fc9099840925c4..58b62984f0fb119ecf86f4ca5ce647feaa8b70b0 100644
--- a/rtd_yeastx/resource/examples/allFields.quantML
+++ b/rtd_yeastx/resource/examples/allFields.quantML
@@ -4,7 +4,7 @@
<source>msSoft</source>
<valid>true</valid>
<comment>no comment</comment>
- <registrationDate>2009-04-07 12:00:21</registrationDate>
+ <registrationDate>04-Apr-1980 12:00:21</registrationDate>
<registrator>John Doe</registrator>
<concentration>
<datasetParent>20090822211007858-23605</datasetParent>
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
index b69f0441fecd9720aa6d7825359886c2b11fe9a4..9845c86781cf99cc360aaf6a08028ed6cf659648 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
@@ -33,6 +33,8 @@ public class DBUtils
/** Current version of the database. */
public static final String DATABASE_VERSION = "003";
+ public static final String DATE_PATTERN = "dd-MMM-yyyy HH:mm:ss";
+
static
{
QueryTool.getTypeMap().put(float[].class, new FloatArrayMapper());
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
index fd876cb13173f9878e15ebf2bea2e9609db1f924..0861c7078fa2b4484388c9a4b6ebff3d461c2f1a 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
@@ -33,6 +33,7 @@ import org.xml.sax.helpers.DefaultHandler;
import ch.systemsx.cisd.base.convert.NativeData;
import ch.systemsx.cisd.base.convert.NativeData.ByteOrder;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* A file for parsing <code>eicML</code> files.
@@ -56,18 +57,18 @@ public class EICMLParser extends DefaultHandler
}
private static final ThreadLocal<DateFormat> dateFormatHolder = new ThreadLocal<DateFormat>();
-
+
public static DateFormat getDateFormat()
{
DateFormat dateFormat = dateFormatHolder.get();
if (dateFormat == null)
{
- dateFormat = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
+ dateFormat = new SimpleDateFormat(DBUtils.DATE_PATTERN);
dateFormatHolder.set(dateFormat);
}
return dateFormat;
}
-
+
private StringBuilder buffer = new StringBuilder();
private EICMSRunDTO msRun;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
index 39687b086c5329dfa264abd2709f37c6fde13be6..b8e9ef338a519453d96141c8cf1986df42b5f50e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
@@ -33,6 +33,7 @@ import org.xml.sax.helpers.DefaultHandler;
import ch.systemsx.cisd.base.convert.NativeData;
import ch.systemsx.cisd.base.convert.NativeData.ByteOrder;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* A file for parsing <code>eicML</code> files.
@@ -42,7 +43,7 @@ import ch.systemsx.cisd.base.convert.NativeData.ByteOrder;
public class FIAMLParser extends DefaultHandler
{
private final static String FIA_RUN = "fiaRun";
-
+
/** A role that observes {@link FIAMSRunDTO}s. */
public interface IMSRunObserver
{
@@ -56,7 +57,7 @@ public class FIAMLParser extends DefaultHandler
DateFormat dateFormat = dateFormatHolder.get();
if (dateFormat == null)
{
- dateFormat = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
+ dateFormat = new SimpleDateFormat(DBUtils.DATE_PATTERN);
dateFormatHolder.set(dateFormat);
}
return dateFormat;
@@ -65,7 +66,7 @@ public class FIAMLParser extends DefaultHandler
private StringBuilder buffer = new StringBuilder();
private FIAMSRunDTO msRun;
-
+
private FIAMSRunDataDTO fiaRunData;
private boolean parsingMsRun;
@@ -138,13 +139,17 @@ public class FIAMLParser extends DefaultHandler
throw new SAXException("Illegal polarity: must be of length 1");
}
msRun.setPolarity(value.charAt(0));
- } else if ("lowMz".equals(name)){
+ } else if ("lowMz".equals(name))
+ {
msRun.setLowMz(Float.parseFloat(value));
- } else if ("highMz".equals(name)){
+ } else if ("highMz".equals(name))
+ {
msRun.setHighMz(Float.parseFloat(value));
- } else if ("is".equals(name)){
+ } else if ("is".equals(name))
+ {
msRun.setInternalStandard(Float.parseFloat(value));
- } else if ("od".equals(name)){
+ } else if ("od".equals(name))
+ {
msRun.setOd(Float.parseFloat(value));
} else if ("operator".equals(name))
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
index d91ed30160d597af8b1df2b2a017653e2832d189..3fed98618f82c83fee3a9389ea88f5dd6704c57c 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
@@ -82,7 +82,6 @@ class QuantMLParser
private MSQuantificationsDTO doParseMSQuantifications(File dataSet)
{
-
try
{
Object object = unmarshaller.unmarshal(dataSet);
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
index 0a8efd546c24364f0a73b0fd8bfc247f9c96446a..6d3334ca433eb5915aee54aecc254e469b63e1b5 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
@@ -21,12 +21,14 @@ import java.util.Date;
import javax.xml.bind.annotation.adapters.XmlAdapter;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+
/**
* @author Tomasz Pylak
*/
public class XmlDateAdapter extends XmlAdapter<String, Date>
{
- static String PATTERN = "yyyy-MM-dd HH:mm:ss";
+ private static final String PATTERN = DBUtils.DATE_PATTERN;
@Override
public String marshal(Date date) throws Exception
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
index 5362ec35c8b06aadaa5818eb6dc2717efaaf2184..695bc4ecda87ed22e9d35b86412b321288f7597e 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
@@ -35,18 +35,23 @@ public abstract class AbstractDBTest
static
{
LogInitializer.init();
+ DBUtils.init(getDatabaseContext());
}
-
+
protected DataSource datasource;
-
+
@BeforeClass(alwaysRun = true)
public void setUpClass() throws SQLException
+ {
+ datasource = getDatabaseContext().getDataSource();
+ }
+
+ private static DatabaseConfigurationContext getDatabaseContext()
{
final DatabaseConfigurationContext context = DBUtils.createDefaultDBContext();
context.setDatabaseKind("dbtest");
context.setCreateFromScratch(true);
- DBUtils.init(context);
- datasource = context.getDataSource();
+ return context;
}
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
index a66cedc8ef04ff63908de3864a8f1612a8628fd0..f8d194dd8a8bd96e3d62056eb2159fbebb355711 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
@@ -53,9 +53,9 @@ public class EICMLTest extends AbstractDBTest
public void testUploadEicML() throws SQLException
{
EICML2Database db = new EICML2Database(datasource);
- db.uploadEicMLFile(new File("resource/examples/example.eicML"),
- new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
- "experiment perm id", "experiment name"));
+ db.uploadEicMLFile(new File("resource/examples/example.eicML"), new DMDataSetDTO(
+ "data set perm id eicml", "sample perm id eicml", "sample name eicml",
+ "experiment perm id eicml", "experiment name eicml"));
}
private void checkChromatograms(int count, ChromatogramDTO chrom)
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
index cfb4ed22690da413011a2d06e4f6be27786373f7..6d26f86aaf6fc7ab248eca39aed6728a29dd0433 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
@@ -60,7 +60,7 @@ public class FIAMLTest extends AbstractDBTest
{
FIAML2Database fiaML2Database = new FIAML2Database(datasource);
fiaML2Database.uploadFiaMLFile(new File("resource/examples/example.fiaML"),
- new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
+ new DMDataSetDTO("data set perm id fiaml", "sample perm id", "sample name",
"experiment perm id", "experiment name"));
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
index 45ef8ad8ba3dd560cd339e164f7be606702e146b..c6b4420711206f808ea05f659e6a618cb61adabc 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
@@ -72,7 +72,7 @@ public class QuantMLParserTest extends AssertJUnit
assertTrue(quantification.isValid());
assertEquals("no comment", quantification.getComment());
assertEquals("John Doe", quantification.getRegistrator());
- Date expectedDate = new XmlDateAdapter().unmarshal("2009-04-07 12:00:21");
+ Date expectedDate = new XmlDateAdapter().unmarshal("04-Apr-1980 12:00:21");
assertEquals(expectedDate, quantification.getRegistrationDate());
assertEquals(1, quantification.getConcentrations().size());
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
index 2885f5fde54c5ef4d7db1304e1845ed3de3a1ab9..14c3782430a1e5f513b3940ff6f6040daee38d99 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
@@ -55,7 +55,7 @@ public class QuantMSDAOTest extends AbstractDBTest
{
QuantML2Database uploader = new QuantML2Database(datasource);
DMDataSetDTO dataSetDTO =
- new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
+ new DMDataSetDTO("data set perm id quant", "sample perm id quant", "sample name",
"experiment perm id", "experiment name");
uploader.uploadQuantMLFile(new File("resource/examples/allFields.quantML"), dataSetDTO);
}