From 75e01f8b77bf818ac1a7725621f95d6f55f49525 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Mon, 25 Jul 2011 11:28:50 +0000
Subject: [PATCH] [LMS-2401] parse analysis procedures from GE XML file
SVN: 22256
---
.../dropbox-all-in-one-with-library.py | 5 +-
.../dss/test/SanofiDropboxJythonTest.java | 10 ++++
.../GEExplorerImageAnalysisResultParser.java | 54 +++++++++++++++++--
3 files changed, 63 insertions(+), 6 deletions(-)
diff --git a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
index 44c9ffed466..fac13fc4504 100644
--- a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
+++ b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
@@ -373,7 +373,8 @@ if incoming.isDirectory():
analysisFile = util.findFileByExt(incoming, "xml")
if analysisFile is not None:
analysisCSVFile = File(analysisFile.getPath() + ".csv")
- GEExplorerImageAnalysisResultParser(analysisFile.getPath()).writeCSV(analysisCSVFile)
+ geXmlParser = GEExplorerImageAnalysisResultParser(analysisFile.getPath())
+ geXmlParser.writeCSV(analysisCSVFile)
featureProps = Properties()
featureProps.setProperty("separator", ",")
@@ -381,7 +382,7 @@ if incoming.isDirectory():
featureProps.setProperty("well-name-col", "Well")
analysisDataSetDetails = factory.createFeatureVectorRegistrationDetails(analysisCSVFile.getPath(), featureProps)
- analysisProcedureCode = util.extractFileBasename(analysisFile.getName())
+ analysisProcedureCode = geXmlParser.getAnalysisProcedureName()
analysisDataSetDetails.getDataSetInformation().setAnalysisProcedure(analysisProcedureCode)
analysisDataSet = transaction.createNewDataSet(analysisDataSetDetails)
analysisDataSet.setSample(imageDataSet.getSample())
diff --git a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
index 359fc3062d3..3819f3ba6bb 100644
--- a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
+++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
@@ -404,6 +404,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
NewExternalData analysisDataSet = dataSetsRegistered.get(2);
assertEquals(ANALYSIS_DATA_SET_CODE, analysisDataSet.getCode());
assertEquals(ANALYSIS_DATA_SET_TYPE, analysisDataSet.getDataSetType());
+ assertEquals("NRF2ProdAnalysis_1.1_MatlabGeneral_1.1",
+ extractAnalysisProcedureCode(analysisDataSet));
AssertionUtil
@@ -414,6 +416,14 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
context.assertIsSatisfied();
}
+ private String extractAnalysisProcedureCode(NewExternalData analysisDataSet)
+ {
+ NewProperty property =
+ EntityHelper.tryFindProperty(analysisDataSet.getDataSetProperties(),
+ ScreeningConstants.ANALYSIS_PROCEDURE);
+ return (property != null) ? property.getValue() : null;
+ }
+
@Test
public void testFatalErrorSentToAdmin() throws IOException
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/custom/geexplorer/GEExplorerImageAnalysisResultParser.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/custom/geexplorer/GEExplorerImageAnalysisResultParser.java
index 9ca6e88fff7..f5f715e640c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/custom/geexplorer/GEExplorerImageAnalysisResultParser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/custom/geexplorer/GEExplorerImageAnalysisResultParser.java
@@ -31,6 +31,7 @@ import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
+import org.apache.commons.lang.StringUtils;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
@@ -49,17 +50,23 @@ public class GEExplorerImageAnalysisResultParser extends DefaultHandler
private static final String WELL_TAG = "Well";
- private static final String TABLE_TAG = "Table";
-
private static final String DATA_TAG = "Data";
+ private static final String ANALYSIS_TAG = "AutoLeadAnalysisProtocol";
+
+ private static final String ASSAY_TAG = "AutoLeadAssay";
+
private enum State
{
- INIT, DATA, TABLE, WELL, FINISHED
+ INIT, ANALYSIS, DATA, TABLE, WELL, FINISHED
}
private State state = State.INIT;
+ private String analysisProtocolWithVersion = StringUtils.EMPTY;
+
+ private String assayWithVersion = StringUtils.EMPTY;
+
private String currentWellId;
private HashSet<String> wells = new HashSet<String>();
@@ -99,8 +106,16 @@ public class GEExplorerImageAnalysisResultParser extends DefaultHandler
}
break;
case DATA:
- if (TABLE_TAG.equals(qName) && "Wells Summary".equals(attributes.getValue("title")))
+ if (ANALYSIS_TAG.equals(qName))
+ {
+ analysisProtocolWithVersion = parseNameAndVersion(attributes);
+ state = State.ANALYSIS;
+ }
+ break;
+ case ANALYSIS:
+ if (ASSAY_TAG.equals(qName))
{
+ assayWithVersion = parseNameAndVersion(attributes);
state = State.TABLE;
}
break;
@@ -224,4 +239,35 @@ public class GEExplorerImageAnalysisResultParser extends DefaultHandler
out.close();
}
+ public String getAnalysisProcedureName()
+ {
+ if (StringUtils.isEmpty(assayWithVersion))
+ {
+ return analysisProtocolWithVersion;
+ } else
+ {
+ return analysisProtocolWithVersion + "_" + assayWithVersion;
+ }
+ }
+
+ private String parseNameAndVersion(Attributes attributes)
+ {
+ String name = parseAttribute("name", attributes);
+ String version = parseAttribute("version", attributes);
+ if (StringUtils.isEmpty(version))
+ {
+ return name;
+ } else
+ {
+ return name + "_" + version;
+ }
+ }
+
+ private String parseAttribute(String attrName, Attributes attributes)
+ {
+ String attrValue = attributes.getValue(attrName);
+ return StringUtils.trimToEmpty(attrValue);
+ }
+
+
}
--
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