From 403c918fcddb41f9a50ab14f8b9c494e863e0e43 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 29 Sep 2009 20:11:05 +0000
Subject: [PATCH] LMS-1180 YeastX: use the same date format for
eicML/fiaML/quantML files. Fix unit tests.
SVN: 12774
---
.../resource/examples/allFields.quantML | 2 +-
.../ch/systemsx/cisd/yeastx/db/DBUtils.java | 2 ++
.../cisd/yeastx/eicml/EICMLParser.java | 7 ++++---
.../cisd/yeastx/fiaml/FIAMLParser.java | 19 ++++++++++++-------
.../cisd/yeastx/quant/QuantMLParser.java | 1 -
.../cisd/yeastx/quant/XmlDateAdapter.java | 4 +++-
.../cisd/yeastx/db/AbstractDBTest.java | 13 +++++++++----
.../systemsx/cisd/yeastx/eicml/EICMLTest.java | 6 +++---
.../systemsx/cisd/yeastx/fiaml/FIAMLTest.java | 2 +-
.../cisd/yeastx/quant/QuantMLParserTest.java | 2 +-
.../cisd/yeastx/quant/QuantMSDAOTest.java | 2 +-
11 files changed, 37 insertions(+), 23 deletions(-)
diff --git a/rtd_yeastx/resource/examples/allFields.quantML b/rtd_yeastx/resource/examples/allFields.quantML
index f66be98c85e..58b62984f0f 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 b69f0441fec..9845c86781c 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 fd876cb1317..0861c7078fa 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 39687b086c5..b8e9ef338a5 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 d91ed30160d..3fed98618f8 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 0a8efd546c2..6d3334ca433 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 5362ec35c8b..695bc4ecda8 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 a66cedc8ef0..f8d194dd8a8 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 cfb4ed22690..6d26f86aaf6 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 45ef8ad8ba3..c6b44207112 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 2885f5fde54..14c3782430a 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);
}
--
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