[LMS-1373] group -> space (yeastx; group still accepted)

SVN: 14919

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java

@@ -58,7 +58,7 @@ public class BatchDataSetInfoExtractor implements IDataSetInfoExtractor
             info.setComplete(true);
             info.setDataSetProperties(plainInfo.getProperties());
             setSampleOrExperiment(openbisService, log, plainInfo, info);
-            info.setGroupCode(plainInfo.getGroupCode());
+            info.setGroupCode(plainInfo.getSpaceOrGroupCode());
             MLConversionType conversion = getConversion(plainInfo.getConversion());
             info.setConversion(conversion);
             String parentDataSetCodes = plainInfo.getParentDataSetCodes();

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java

@@ -49,6 +49,8 @@ public class DataSetMappingInformation
 
     private List<NewProperty> properties;
 
+    private String spaceCode;
+
     public String getFileName()
     {
         return fileName;
@@ -107,15 +109,32 @@ public class DataSetMappingInformation
         this.projectCode = StringUtils.trimToNull(projectCode);
     }
 
+    // TODO 2010-02-23, IA: migrate to getSpaceCode after transition period (group->space)
+    public String getSpaceOrGroupCode()
+    {
+        return spaceCode == null ? groupCode : spaceCode;
+    }
+
     public String getGroupCode()
     {
         return groupCode;
     }
 
-    @BeanProperty(label = "group")
+    @BeanProperty(label = "group", optional = true)
     public void setGroupCode(String groupCode)
     {
-        this.groupCode = groupCode;
+        this.groupCode = StringUtils.trimToNull(groupCode);
+    }
+
+    public String getSpaceCode()
+    {
+        return spaceCode;
+    }
+
+    @BeanProperty(label = "space", optional = true)
+    public void setSpaceCode(String spaceCode)
+    {
+        this.spaceCode = StringUtils.trimToNull(spaceCode);
     }
 
     public String getConversion()

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java

@@ -180,7 +180,7 @@ class DatasetMappingResolver
                 tryGetExperimentIdentifier(mapping, experimentPropertyCodeOrNull);
         ListSamplesByPropertyCriteria criteria =
                 new ListSamplesByPropertyCriteria(samplePropertyCodeOrNull, sampleCodeOrLabel,
-                        mapping.getGroupCode(), experimentIdentifier);
+                        mapping.getSpaceOrGroupCode(), experimentIdentifier);
         return criteria;
     }
 
@@ -207,6 +207,23 @@ class DatasetMappingResolver
 
     public boolean isMappingCorrect(DataSetMappingInformation mapping, LogUtils log)
     {
+        if (mapping.getSpaceOrGroupCode() == null)
+        {
+            log
+                    .datasetMappingError(
+                            mapping,
+                            "mandatory property 'space' (previously called 'group') not specified. "
+                                    + "Note: the name 'group' may still be used but will be forbidden in the future.");
+            return false;
+        } else if (mapping.getSpaceCode() != null && mapping.getGroupCode() != null)
+        {
+            log
+                    .datasetMappingError(
+                            mapping,
+                            "either 'space' or 'group' should be specified - but not both. "
+                                    + "Note: the name 'group' may still be used but will be forbidden in the future.");
+            return false;
+        }
         if (isExperimentColumnCorrect(mapping, log) == false)
         {
             return false;
@@ -277,7 +294,8 @@ class DatasetMappingResolver
         String experimentCode = mapping.getExperimentName();
         if (project != null && experimentCode != null)
         {
-            return new ExperimentIdentifier(null, mapping.getGroupCode(), project, experimentCode);
+            return new ExperimentIdentifier(null, mapping.getSpaceOrGroupCode(), project,
+                    experimentCode);
         } else
         {
             return null;
@@ -350,8 +368,8 @@ class DatasetMappingResolver
     private SampleIdentifier createSampleIdentifier(String sampleCode,
             DataSetMappingInformation mapping)
     {
-        return new SampleIdentifier(new GroupIdentifier((String) null, mapping.getGroupCode()),
-                sampleCode);
+        return new SampleIdentifier(new GroupIdentifier((String) null, mapping
+                .getSpaceOrGroupCode()), sampleCode);
     }
 
     private boolean isExperimentColumnCorrect(DataSetMappingInformation mapping, LogUtils log)

rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java

@@ -53,7 +53,7 @@ public class DataSetInformationParserTest extends AbstractFileSystemTestCase
         List<DataSetMappingInformation> list = tryParse(indexFile);
         AssertJUnit.assertEquals(1, list.size());
         DataSetMappingInformation elem = list.get(0);
-        AssertJUnit.assertEquals("group1", elem.getGroupCode());
+        AssertJUnit.assertEquals("group1", elem.getSpaceOrGroupCode());
         AssertJUnit.assertEquals("parentCode", elem.getParentDataSetCodes());
         AssertJUnit.assertEquals("sample1", elem.getSampleCodeOrLabel());
         AssertJUnit.assertEquals("data.txt", elem.getFileName());
@@ -72,7 +72,7 @@ public class DataSetInformationParserTest extends AbstractFileSystemTestCase
         List<DataSetMappingInformation> list = tryParse(indexFile);
         AssertJUnit.assertEquals(1, list.size());
         DataSetMappingInformation elem = list.get(0);
-        AssertJUnit.assertEquals("group2", elem.getGroupCode());
+        AssertJUnit.assertEquals("group2", elem.getSpaceOrGroupCode());
         AssertJUnit.assertEquals("sample2", elem.getSampleCodeOrLabel());
         AssertJUnit.assertEquals("data2.txt", elem.getFileName());
     }
@@ -99,8 +99,8 @@ public class DataSetInformationParserTest extends AbstractFileSystemTestCase
         AssertJUnit.assertNull("error during parsing expected", result);
         List<String> logLines = readLogFile();
         AssertJUnit.assertEquals(2, logLines.size());
-        AssertionUtil.assertContains("Mandatory column(s) 'group', 'file_name' are missing",
-                logLines.get(1));
+        AssertionUtil
+                .assertContains("Mandatory column(s) 'file_name' are missing", logLines.get(1));
     }
 
     private List<DataSetMappingInformation> tryParse(File indexFile)