From d0b91be8a8c5411d7773cda2d0d99f613585b00e Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 16 Sep 2011 13:43:06 +0000
Subject: [PATCH] [LMS-2531] 1) revert previous changes. 2) Imports should
treat Gene SYMBOLS as a whitespace-separated list of values (not a single
code)
SVN: 22972
---
...QiagenScreeningLibraryColumnExtractor.java | 2 +-
.../server/LibraryRegistrationTask.java | 52 +++++++----------
.../server/LibraryRegistrationTaskTest.java | 58 ++-----------------
3 files changed, 28 insertions(+), 84 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/QiagenScreeningLibraryColumnExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/QiagenScreeningLibraryColumnExtractor.java
index 59d3fa5791c..64776f778c0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/QiagenScreeningLibraryColumnExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/QiagenScreeningLibraryColumnExtractor.java
@@ -109,7 +109,7 @@ public class QiagenScreeningLibraryColumnExtractor extends AbstractColumnExtract
public String getGeneSymbol(String[] row)
{
- return getCodeValue(row, GENE_SYMBOL);
+ return getValue(row, GENE_SYMBOL);
}
public String getGeneDescription(String[] row)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
index 9a6215b1b51..1160a83af40 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
@@ -193,44 +193,36 @@ class LibraryRegistrationTask implements IASyncAction
return;
}
- String normalizedValue = normalizeGeneValue(newGeneProp.getValue());
- String mergedGeneType = mergeGeneTypes(existingGene, normalizedValue);
- newGeneProp.setValue(mergedGeneType);
+ String mergedGeneSymbols = mergeGeneSymbols(existingGene, newGeneProp.getValue());
+ newGeneProp.setValue(mergedGeneSymbols);
}
- private String mergeGeneTypes(String existingType, String newType)
+ private String mergeGeneSymbols(String existingSymbols, String newSymbolString)
{
- if (StringUtils.isBlank(newType) || newType.equals(existingType))
+ if (StringUtils.isBlank(newSymbolString) || newSymbolString.equals(existingSymbols))
{
- return existingType;
+ return existingSymbols;
}
-
- boolean ignoreNewType =
- existingType.startsWith(newType + DELIM) || existingType.endsWith(DELIM + newType)
- || (existingType.indexOf(DELIM + newType + DELIM) > 0);
-
- if (ignoreNewType)
+
+ String[] newSymbols = newSymbolString.split("\\s+");
+ StringBuilder result = new StringBuilder(existingSymbols);
+ for (String newSymbol : newSymbols)
{
- return existingType;
- } else
- {
- return existingType + DELIM + newType;
- }
- }
+ if (StringUtils.isBlank(newSymbol))
+ {
+ continue;
+ }
+ boolean alreadyExisting =
+ existingSymbols.startsWith(newSymbol + DELIM) || existingSymbols.endsWith(DELIM + newSymbol)
+ || (existingSymbols.indexOf(DELIM + newSymbol + DELIM) > 0);
- /**
- * Remove leading and trailing underscores.
- */
- private String normalizeGeneValue(String value)
- {
- final String UNDERSCORE = "_";
- if (value.startsWith(UNDERSCORE) || value.endsWith(UNDERSCORE))
- {
- String normalized = value.replaceAll("_*$", "");
- normalized = normalized.replaceAll("^_*", "");
- return normalized;
+ if (false == alreadyExisting)
+ {
+ result.append(DELIM);
+ result.append(newSymbol);
+ }
}
- return value;
+ return result.toString();
}
public boolean doAction(Writer messageWriter)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
index ffe0cbb1e69..e73e7602343 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
@@ -89,15 +89,15 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
{
NewMaterial g1 = createNewGene("G1", "AB");
NewMaterial g2 = createNewGene("G2", "AB");
- NewMaterial g3 = createNewGene("G3", "AB");
- NewMaterial g4 = createNewGene("G4", "AB");
- NewMaterial g5 = createNewGene("G5", "AB");
+ NewMaterial g3 = createNewGene("G3", "BC AB");
+ NewMaterial g4 = createNewGene("G4", "AB AB");
+ NewMaterial g5 = createNewGene("G5", "AB DDD");
final List<NewMaterial> newGenes = Arrays.asList(g1, g2, g3, g4, g5);
final List<Material> existingGenes =
Arrays.asList(createExistingGene("G1", "ABC A"), createExistingGene("G2", "AB"),
createExistingGene("G3", "AB BC"), createExistingGene("G4", "XY AB"),
- createExistingGene("G5", "XY AB YZ"));
+ createExistingGene("G5", "XY AB YZ DDD"));
final RecordingMatcher<List<NewMaterialsWithTypes>> materialsWithTypesMatcher =
new RecordingMatcher<List<NewMaterialsWithTypes>>();
@@ -130,7 +130,7 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
assertEquals("AB", extractGeneSymbol(g2));
assertEquals("AB BC", extractGeneSymbol(g3));
assertEquals("XY AB", extractGeneSymbol(g4));
- assertEquals("XY AB YZ", extractGeneSymbol(g5));
+ assertEquals("XY AB YZ DDD", extractGeneSymbol(g5));
List<NewMaterialsWithTypes> materialsWithTypes =
LibraryRegistrationTask.createMaterialsWithTypes(
@@ -147,54 +147,6 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
}
}
- @Test
- public void testUpdateWithUnderscores()
- {
- NewMaterial g1 = createNewGene("G1", "_AB_");
- NewMaterial g2 = createNewGene("G2", "_AB_");
- NewMaterial g3 = createNewGene("G3", "_AB_");
- NewMaterial g4 = createNewGene("G4", "_AB_");
- NewMaterial g5 = createNewGene("G5", "_AB_");
-
- final List<NewMaterial> newGenes = Arrays.asList(g1, g2, g3, g4, g5);
- final List<Material> existingGenes =
- Arrays.asList(createExistingGene("G1", "ABC A"), createExistingGene("G2", "AB"),
- createExistingGene("G3", "AB BC"), createExistingGene("G4", "XY AB"),
- createExistingGene("G5", "XY AB YZ"));
- final RecordingMatcher<List<NewMaterialsWithTypes>> materialsWithTypesMatcher =
- new RecordingMatcher<List<NewMaterialsWithTypes>>();
-
- task =
- new LibraryRegistrationTask(SESSION_TOKEN, newGenes, null, null, commonServer,
- genericServer, daoFactory);
-
- context.checking(new Expectations()
- {
- {
- one(daoFactory).getEntityTypeDAO(EntityKind.MATERIAL);
- will(returnValue(entityTypeDAO));
-
- one(entityTypeDAO).tryToFindEntityTypeByCode(
- ScreeningConstants.GENE_PLUGIN_TYPE_CODE);
- will(returnValue(new MaterialTypePE()));
-
- one(commonServer).listMaterials(with(SESSION_TOKEN),
- with(any(ListMaterialCriteria.class)), with(true));
- will(returnValue(existingGenes));
-
- one(genericServer).registerOrUpdateMaterials(with(SESSION_TOKEN),
- with(materialsWithTypesMatcher));
- }
- });
-
- task.doAction(new StringWriter());
-
- assertEquals("ABC A AB", extractGeneSymbol(g1));
- assertEquals("AB", extractGeneSymbol(g2));
- assertEquals("AB BC", extractGeneSymbol(g3));
- assertEquals("XY AB", extractGeneSymbol(g4));
- assertEquals("XY AB YZ", extractGeneSymbol(g5));
- }
private NewMaterial createNewGene(String code, String geneSymbol)
{
IEntityProperty geneSymbolProperty = createGeneSymbolProperty(geneSymbol);
--
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