Changeset 20738

Timestamp:

26/02/10 16:10:04 (2 years ago)

Author:

julie

Message:

remove local version of StringUtils?.getEmpty(). we should use the apache commons one isntead

Location:

trunk

Files:

• bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java (modified) (3 diffs)
• bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/FlyBaseProcessor.java (modified) (3 diffs)
• bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeFeatureProcessor.java (modified) (20 diffs)
• bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeMetaDataProcessor.java (modified) (117 diffs)
• bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/WormBaseProcessor.java (modified) (4 diffs)
• bio/sources/flymine/flyatlas/main/src/org/intermine/bio/dataconversion/FlyAtlasConverter.java (modified) (2 diffs)
• intermine/integrate/main/src/org/intermine/xml/full/Item.java (modified) (3 diffs)
• intermine/objectstore/main/src/org/intermine/util/StringUtil.java (modified) (1 diff)
• intermine/pathquery/main/src/org/intermine/pathquery/PathQuery.java (modified) (3 diffs)
• intermine/web/main/src/org/intermine/web/logic/session/SessionMethods.java (modified) (1 diff)
• intermine/web/main/src/org/intermine/web/struts/HtmlHeadController.java (modified) (5 diffs)

trunk/bio/postprocess/main/src/org/intermine/bio/postprocess/CreateFlankingRegions.java

@@ -16 +16 @@
 import java.util.Map;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.intermine.bio.util.BioQueries;
@@ -30 +31 @@
 import org.intermine.objectstore.query.ResultsRow;
 import org.intermine.util.DynamicUtil;
-import org.intermine.util.StringUtil;
 
 /**
@@ -134 +134 @@
         // submissions.  This should work by DataSet but WormBase chado isn't setting a DataSet
         // correctly
-        if (StringUtil.isEmpty(gene.getSymbol())) {
+        if (StringUtils.isEmpty(gene.getSymbol())) {
             return;
         }

trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/FlyBaseProcessor.java

@@ -39 +39 @@
 import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.util.IntPresentSet;
-import org.intermine.util.StringUtil;
 import org.intermine.util.XmlUtil;
 import org.intermine.xml.full.Item;
@@ -1742 +1741 @@
                 // make a synonym for the protein we're about to discard
                 if (protein != null) {
-                    if (!StringUtil.isEmpty(uniqueName)
+                    if (StringUtils.isNotEmpty(uniqueName)
                                     && !protein.getExistingSynonyms().contains(uniqueName)) {
                         Item synonym = createSynonym(protein, "identifier", uniqueName, true,
@@ -1748 +1747 @@
                         store(synonym);
                     }
-                    if (!StringUtil.isEmpty(name)
+                    if (StringUtils.isNotEmpty(name)
                                     && !protein.getExistingSynonyms().contains(name)) {
                         Item synonym = createSynonym(protein, "name", name, false, null);

trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeFeatureProcessor.java

@@ -26 +26 @@
 import org.apache.commons.collections.keyvalue.MultiKey;
 import org.apache.commons.collections.map.MultiKeyMap;
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.intermine.bio.chado.config.ConfigAction;
@@ -31 +32 @@
 import org.intermine.bio.util.OrganismData;
 import org.intermine.objectstore.ObjectStoreException;
-import org.intermine.util.StringUtil;
 import org.intermine.util.TypeUtil;
 import org.intermine.xml.full.Attribute;
@@ -50 +50 @@
     private final List<Integer> dataList;
     private final String title;
-    
+
     private Set<String> commonFeatureInterMineTypes = new HashSet<String>();
 
     private static final String SUBFEATUREID_TEMP_TABLE_NAME = "modmine_subfeatureid_temp";
-
 
     // feature type to query from the feature table
@@ -91 +90 @@
      *                             i.e. the labItemIdentifier
      * @param dataList             the list of data ids to be used in the subquery
-     * @param title                the title           
+     * @param title                the title
      */
 
@@ -102 +101 @@
         this.dataList = dataList;
         this.title = title;
-        
+
         for (String chromosomeType : getChromosomeFeatureTypes()) {
             commonFeatureInterMineTypes.add(
@@ -184 +183 @@
         // (and merge the methods)
         // also: add match to query and do everything here
-        
+
         // process indirect locations via match features and featureloc feature<->match<->feature
         ResultSet matchLocRes = getMatchLocResultSet(connection);
@@ -199 +198 @@
             processLocationTable(connection, matchTypeLocRes);
         }
-                
+
         // adding scores
         processFeatureScores(connection);
@@ -207 +206 @@
     /**
      * Method to set the source for gene
-     * for modencode datasources it will add the title 
+     * for modencode datasources it will add the title
      * @param imObjectId the im object id
      * @param dataSourceName the data source
@@ -214 +213 @@
      */
     @Override
-    protected void setGeneSource(Integer imObjectId, String dataSourceName) 
+    protected void setGeneSource(Integer imObjectId, String dataSourceName)
     throws ObjectStoreException {
         String source = dataSourceName + "-" + title;
@@ -236 +235 @@
     }
 
-    private List<String> getMatchTypes(Connection connection) throws SQLException,
-    ObjectStoreException {
+    private List<String> getMatchTypes(Connection connection) throws SQLException {
         List<String> types = new ArrayList<String>();
         ResultSet res = getMatchTypesResultSet(connection);
@@ -250 +248 @@
 
     /**
-     * Return the match types, used to determine which additional query to run 
+     * Return the match types, used to determine which additional query to run
      * This is a protected method so that it can be overriden for testing
      * @param connection the db connection
@@ -264 +262 @@
         ResultSet res = stmt.executeQuery(query);
         LOG.debug("QUERY TIME feature match types: " + (System.currentTimeMillis() - bT));
-        return res;  
-    }
-    
-    
-    /**
-     * Return the interesting feature (EST, UST, RST, other?) matches 
+        return res;
+    }
+
+
+    /**
+     * Return the interesting feature (EST, UST, RST, other?) matches
      * from the featureloc and feature tables.
-     * 
+     *
      * feature<->featureloc<->match_feature<->featureloc<->feature
      * This is a protected method so that it can be overriden for testing
@@ -306 +304 @@
         return res;
     }
-    
+
 
     /**
@@ -369 +367 @@
                 Thread.currentThread().setContextClassLoader(currentClassLoader);
             }
-        } else {
-            DataSetStoreHook.setDataSets(getModel(), item, dataSetIdentifier, dataSourceIdentifier);
-        }
-    }
-
-    
+        }
+        DataSetStoreHook.setDataSets(getModel(), item, dataSetIdentifier, dataSourceIdentifier);
+    }
+
+
     /**
      * {@inheritDoc}
@@ -481 +478 @@
                 if (uniqueName.startsWith("chr")) {
                     // this is to fix some data problem with sub 146 in modmine
-                    // where there are duplicated chromosome_arm features, with 
+                    // where there are duplicated chromosome_arm features, with
                     // and without a 'chr' prefix (e.g. 3R and chr3R)
                     // The chr ones are not the location for any other feature.
@@ -489 +486 @@
         }
         Item feature = getChadoDBConverter().createItem(realInterMineType);
-  
+
         return feature;
     }
@@ -589 +586 @@
         String name = fdat.getChadoFeatureName();
         String type = fdat.getInterMineType();
-        
+
         if (identifier.equalsIgnoreCase(uniqueName)) {
             if (type.equalsIgnoreCase(CHROMOSOME)) {
@@ -600 +597 @@
                 }
             }
-            
-            // Piano submissions have Gene: and Transcript: 
+
+            // Piano submissions have Gene: and Transcript:
             // in front of gene and transcript identifiers
             if (type.equalsIgnoreCase("Gene")) {
@@ -610 +607 @@
         }
 
-        if (StringUtil.isEmpty(identifier)) {
-            if (StringUtil.isEmpty(name)) {
+        if (StringUtils.isEmpty(identifier)) {
+            if (StringUtils.isEmpty(name)) {
                 String fixedName = uniqueName.substring(uniqueName.lastIndexOf('.') + 1);
                 return fixedName;
@@ -618 +615 @@
             }
         }
-        return identifier;    
-    }
-    
+        return identifier;
+    }
+
     private void processFeatureScores(Connection connection) throws SQLException,
     ObjectStoreException {

trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeMetaDataProcessor.java

@@ -78 +78 @@
         new HashMap<Integer, AppliedData>();
 
-
     // project/lab/experiment/submission maps
     // --------------------------------------
@@ -104 +103 @@
     private Map<Integer, String> protocolItemIds = new HashMap<Integer, String>();
     private Map<String, Integer> protocolItemToObjectId = new HashMap<String, Integer>();
-    
+
     private Map<Integer, Integer> publicationIdMap = new HashMap<Integer, Integer>();
     private Map<Integer, String> publicationIdRefMap = new HashMap<Integer, String>();
-    
-    
-    
+
+
+
     private Map<Integer, String> protocolTypesMap = new HashMap<Integer, String>();
     private Map<Integer, Integer> appliedProtocolIdMap = new HashMap<Integer, Integer>();
@@ -139 +138 @@
     private IdResolverFactory wormResolverFactory = null;
     private Map<String, String> geneToItemIdentifier = new HashMap<String, String>();
-    
+
     private Map<DatabaseRecordKey, String> dbRecords = new HashMap<DatabaseRecordKey, String>();
 
-    
+
     private static class SubmissionDetails
     {
@@ -198 +197 @@
     }
 
-    
-    
+
+
     /**
      * Create a new ChadoProcessor object
@@ -233 +232 @@
         setSubmissionExperimetRefs(connection);
         setDAGRefs(connection);
-        
+
         // create DatabaseRecords where necessary for each submission
         createDatabaseRecords(connection);
@@ -250 +249 @@
     }
 
-    
+
     /**
      *
@@ -307 +306 @@
             String queryList = StringUtil.join(thisSubmissionDataIds, ",");
             processDataFeatureTable(connection, subFeatureMap, chadoExperimentId, queryList);
-            
+
             // read any genes that have been created so we can re-use the same item identifiers
             // when creating antibody/strain target genes later
@@ -315 +314 @@
     }
 
-    private void extractGenesFromSubFeatureMap(ModEncodeFeatureProcessor processor, 
+    private void extractGenesFromSubFeatureMap(ModEncodeFeatureProcessor processor,
             Map<Integer, FeatureData> subFeatureMap) {
         for (FeatureData fData : subFeatureMap.values()) {
@@ -324 +323 @@
         }
     }
-    
+
     /**
      * @param connection
@@ -343 +342 @@
             Integer dataId = new Integer(res.getInt("data_id"));
             Integer featureId = new Integer(res.getInt("feature_id"));
-            
+
             FeatureData featureData = featureMap.get(featureId);
             if (featureData == null) {
@@ -355 +354 @@
             // TODO: it needs correction: here stores only the last submission reference.
             Integer featureObjectId = featureData.getIntermineObjectId();
-            
+
             collection = new ReferenceList();
             collection.setName("submissions");
@@ -1059 +1058 @@
                     value = value.substring(value.indexOf(':') + 1);
                 }
-                
+
                 Item pub = getChadoDBConverter().createItem("Publication");
                 pub.setAttribute(fieldName, value);
                 Integer intermineObjectId = getChadoDBConverter().store(pub);
-                
+
                 publicationIdMap.put(submissionId, intermineObjectId);
                 publicationIdRefMap.put(submissionId, pub.getIdentifier());
                 continue;
             }
-            
+
             setAttribute(submissionMap.get(submissionId).interMineObjectId, fieldName, value);
             count++;
@@ -1100 +1099 @@
      * ==========================
      *
-     *    
+     *
      * @param connection
      * @throws SQLException
@@ -1115 +1114 @@
         ExperimentalFactor ef = null;
         String name = null;
-        
+
         while (res.next()) {
             Integer submissionId = new Integer(res.getInt("experiment_id"));
             Integer rank = new Integer(res.getInt("rank"));
             String  value    = res.getString("value");
-            
+
             // the data is alternating between EF types and names, in order.
             if (submissionId != prevSub) {
@@ -1150 +1149 @@
         }
         res.close();
-        LOG.info("created " + count + " experimental factors");        
+        LOG.info("created " + count + " experimental factors");
         LOG.info("PROCESS TIME experimental factors: " + (System.currentTimeMillis() - bT));
 }
@@ -1208 +1207 @@
     }
 
-    
+
     private String createProtocol(Integer chadoId, String name, String description, String wikiLink,
             Integer version) throws ObjectStoreException {
@@ -1219 +1218 @@
             protocol.setAttribute("version", "" + version);
             Integer intermineObjectId = getChadoDBConverter().store(protocol);
-            
-            
+
+
             protocolItemId = protocol.getIdentifier();
             protocolItemToObjectId.put(protocolItemId, intermineObjectId);
@@ -1232 +1231 @@
         return protocolItemToObjectId.get(protocolItemIds.get(chadoId));
     }
-    
-    
+
+
     /**
      * Return the rows needed from the protocol table.
@@ -1550 +1549 @@
     // first value in the list of synonyms is the 'preferred' value
     private static String[][] synonyms = new String[][]{
-            new String[] {"developmental stage", "stage", 
+            new String[] {"developmental stage", "stage",
                     "developmental_stage", "dev stage", "devstage"},
                     new String[] {"strain", "strain_or_line"},
@@ -1583 +1582 @@
         return unified;
     }
-    
-    
+
+
     private class SubmissionReference
     {
@@ -1594 +1593 @@
         private String dataValue;
     }
-    
+
     // process new query
     // get DCC id
@@ -1622 +1621 @@
         Integer lastDataId = new Integer(-1);
         Map<String, SubmissionProperty> props = new HashMap <String, SubmissionProperty>();
-        
-        Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes = 
+
+        Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes =
             new HashMap<Integer, Map<String, List<SubmissionProperty>>>();
 
         submissionRefs = new HashMap<Integer, SubmissionReference>();
-        
+
         while (res.next()) {
             Integer dataId = new Integer(res.getInt("data_id"));
@@ -1638 +1637 @@
             String attValue = res.getString("att_value");
             String attDbxref = res.getString("att_dbxref");
-            
+
             Integer submissionId = dataSubmissionMap.get(dataId);
             LOG.debug("DCC fetch: " + submissionId + ", " + dccIdMap.get(submissionId));
             String dccId = dccIdMap.get(submissionId);
 
-            writer.write(dccId + comma + dataHeading + comma + dataName + comma 
-                    + wikiPageUrl + comma + cvTerm + comma + attHeading + comma + attName 
+            writer.write(dccId + comma + dataHeading + comma + dataName + comma
+                    + wikiPageUrl + comma + cvTerm + comma + attHeading + comma + attName
                     + comma + attValue + comma + attDbxref + System.getProperty("line.separator"));
 
@@ -1655 +1654 @@
                 Integer referencedSubId = getSubmissionIdFromDccId(attValue);
                 if (referencedSubId != null) {
-                    SubmissionReference subRef = 
+                    SubmissionReference subRef =
                         new SubmissionReference(referencedSubId, wikiPageUrl);
                     submissionRefs.put(submissionId, subRef);
@@ -1667 +1666 @@
                     buildSubProperty = null;
                 } else {
-                    buildSubProperty = 
+                    buildSubProperty =
                         new SubmissionProperty(getPreferredSynonym(dataName), wikiPageUrl);
                     props.put(wikiPageUrl, buildSubProperty);
@@ -1687 +1686 @@
         // properties here
         addSubmissionPropsFromCharacteristics(subToTypes, connection);
- 
+
         // some submissions use reagents created in reference submissions, find the properties
         // of the reagents and add to referencing submission
         addSubmissionPropsFromReferencedSubmissions(subToTypes, props, submissionRefs);
-            
+
         // create and store properties of submission
         for (Integer submissionId : subToTypes.keySet()) {
             Integer storedSubmissionId = submissionMap.get(submissionId).interMineObjectId;
-            
+
             Map<String, List<SubmissionProperty>> typeToProp = subToTypes.get(submissionId);
 
             String dccId = dccIdMap.get(submissionId);
-            
+
             ExperimentalFactor ef = submissionEFMap.get(submissionId);
             if (ef == null) {
@@ -1705 +1704 @@
                 continue;
             }
-            Set<String> exFactorNames = unifyFactorNames(ef.efNames);            
+            Set<String> exFactorNames = unifyFactorNames(ef.efNames);
             LOG.info("PROPERTIES " + dccId + " typeToProp keys: " + typeToProp.keySet());
-            
+
             List<Item> allPropertyItems = new ArrayList<Item>();
-            
+
             // DEVELOPMENTAL STAGE
             List<Item> devStageItems = new ArrayList<Item>();
-            devStageItems.addAll(createFromWikiPage(dccId, "DevelopmentalStage", typeToProp, 
+            devStageItems.addAll(createFromWikiPage(dccId, "DevelopmentalStage", typeToProp,
                     makeLookupList("developmental stage")));
             if (devStageItems.isEmpty()) {
@@ -1724 +1723 @@
                         }));
                 if (!devStageItems.isEmpty()) {
-                 }                
+                 }
             }
             storeSubmissionCollection(storedSubmissionId, "developmentalStages", devStageItems);
@@ -1731 +1730 @@
                 exFactorNames.remove("developmental stage");
             }
-            allPropertyItems.addAll(devStageItems);            
-            
+            allPropertyItems.addAll(devStageItems);
+
             // STRAIN
             List<Item> strainItems = new ArrayList<Item>();
             strainItems.addAll(createFromWikiPage(
                     dccId, "Strain", typeToProp, makeLookupList("strain")));
-            
+
             storeSubmissionCollection(storedSubmissionId, "strains", strainItems);
             if (!strainItems.isEmpty() && exFactorNames.contains("strain")) {
@@ -1743 +1742 @@
                 exFactorNames.remove("strain");
             }
-            allPropertyItems.addAll(strainItems);            
-            
-            
+            allPropertyItems.addAll(strainItems);
+
+
             // ARRAY
             List<Item> arrayItems = new ArrayList<Item>();
@@ -1757 +1756 @@
                         }));
                 if (!arrayItems.isEmpty()) {
-                    LOG.debug("Attribute found in other wiki pages: " 
-                            + dccId + " ARRAY ");                    
+                    LOG.debug("Attribute found in other wiki pages: "
+                            + dccId + " ARRAY ");
                 }
             }
@@ -1766 +1765 @@
                 exFactorNames.remove("array");
             }
-            allPropertyItems.addAll(arrayItems);            
-            
+            allPropertyItems.addAll(arrayItems);
+
             // CELL LINE
             List<Item> lineItems = new ArrayList<Item>();
-            lineItems.addAll(createFromWikiPage(dccId, "CellLine", typeToProp, 
+            lineItems.addAll(createFromWikiPage(dccId, "CellLine", typeToProp,
                     makeLookupList("cell line")));
             storeSubmissionCollection(storedSubmissionId, "cellLines", lineItems);
@@ -1777 +1776 @@
                 exFactorNames.remove("cell line");
             }
-            allPropertyItems.addAll(lineItems);            
-            
+            allPropertyItems.addAll(lineItems);
+
             // RNAi REAGENT
             List<Item> reagentItems = new ArrayList<Item>();
-            reagentItems.addAll(createFromWikiPage(dccId, "SubmissionProperty", typeToProp, 
+            reagentItems.addAll(createFromWikiPage(dccId, "SubmissionProperty", typeToProp,
                     makeLookupList("dsRNA")));
             if (!reagentItems.isEmpty() && exFactorNames.contains("RNAi reagent")) {
@@ -1787 +1786 @@
                 exFactorNames.remove("RNAi reagent");
             }
-            allPropertyItems.addAll(reagentItems);      
-            
+            allPropertyItems.addAll(reagentItems);
+
             // ANTIBODY
             List<Item> antibodyItems = new ArrayList<Item>();
-            antibodyItems.addAll(createFromWikiPage(dccId, "Antibody", typeToProp, 
+            antibodyItems.addAll(createFromWikiPage(dccId, "Antibody", typeToProp,
                     makeLookupList("antibody")));
             if (antibodyItems.isEmpty()) {
@@ -1800 +1799 @@
                         }));
                 if (!antibodyItems.isEmpty()) {
-                    LOG.debug("Attribute found in other wiki pages: " 
-                            + dccId + " ANTIBODY ");                    
+                    LOG.debug("Attribute found in other wiki pages: "
+                            + dccId + " ANTIBODY ");
                 }
             }
@@ -1809 +1808 @@
                 exFactorNames.remove("antibody");
             }
-            allPropertyItems.addAll(antibodyItems);            
-
-            
+            allPropertyItems.addAll(antibodyItems);
+
+
             // TISSUE
             List<Item> tissueItems = new ArrayList<Item>();
@@ -1824 +1823 @@
                         }));
                 if (!tissueItems.isEmpty()) {
-                    LOG.info("Attribute found in other wiki pages: " 
-                            + dccId + " TISSUE");                    
-                } 
+                    LOG.info("Attribute found in other wiki pages: "
+                            + dccId + " TISSUE");
+                }
             }
             storeSubmissionCollection(storedSubmissionId, "tissues", tissueItems);
@@ -1833 +1832 @@
                 exFactorNames.remove("tissue");
             }
-            allPropertyItems.addAll(tissueItems);            
-
-            
-            
+            allPropertyItems.addAll(tissueItems);
+
+
+
             // There may be some other experimental factors that require SubmissionProperty objects
             // but don't fall into the categories above.  Create them here and set experimental
@@ -1843 +1842 @@
             for (String exFactor : extraPropNames) {
                 List<Item> extraPropItems = new ArrayList<Item>();
-                extraPropItems.addAll(lookForAttributesInOtherWikiPages("SubmissionProperty", 
+                extraPropItems.addAll(lookForAttributesInOtherWikiPages("SubmissionProperty",
                         typeToProp, new String[] {exFactor}));
-                allPropertyItems.addAll(extraPropItems); 
+                allPropertyItems.addAll(extraPropItems);
                 createExperimentalFactors(submissionId, exFactor, extraPropItems);
                 exFactorNames.remove(exFactor);
             }
 
-            
+
             // Store Submission.properties/ SubmissionProperty.submissions
             storeSubmissionCollection(storedSubmissionId, "properties", allPropertyItems);
-            
+
             // deal with remaining factor names (e.g. the ones for which we did
             // not find a corresponding attribute
@@ -1859 +1858 @@
                 String type = ef.efTypes.get(exFactor);
                 createEFItem(submissionId, type, exFactor, null);
-            }        
+            }
         }
         LOG.info("PROCESS TIME submission properties: " + (System.currentTimeMillis() - bT));
@@ -1865 +1864 @@
 
     // Traverse DAG following previous applied protocol links to build a list of all AppliedData
-    private void findAppliedProtocolsAndDataFromEarlierInDag(Integer startDataId, 
+    private void findAppliedProtocolsAndDataFromEarlierInDag(Integer startDataId,
             List<AppliedData> foundAppliedData, List<AppliedProtocol> foundAppliedProtocols) {
         AppliedData aData = appliedDataMap.get(startDataId);
@@ -1871 +1870 @@
             foundAppliedData.add(aData);
         }
-        
+
         for (Integer previousAppliedProtocolId : aData.previousAppliedProtocols) {
             AppliedProtocol ap = appliedProtocolMap.get(previousAppliedProtocolId);
@@ -1881 +1880 @@
                         foundAppliedProtocols);
             }
-        }            
-    }
-    
-    
-    private void createExperimentalFactors(Integer submissionId, String type, 
+        }
+    }
+
+
+    private void createExperimentalFactors(Integer submissionId, String type,
             Collection<Item> items) throws ObjectStoreException {
         for (Item item : items) {
-            createEFItem(submissionId, type, item.getAttribute("name").getValue(), 
+            createEFItem(submissionId, type, item.getAttribute("name").getValue(),
                     item.getIdentifier());
         }
     }
-    
-    
+
+
     private void createEFItem(Integer current, String type,
             String efName, String propertyIdentifier) throws ObjectStoreException {
@@ -1916 +1915 @@
 
 
-    private void addToSubToTypes(Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes, 
+    private void addToSubToTypes(Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes,
             Integer submissionId, SubmissionProperty prop) {
      // submissionId -> [type -> SubmissionProperty]
@@ -1928 +1927 @@
             subProps = new ArrayList<SubmissionProperty>();
             typeToSubProp.put(prop.type, subProps);
-        } 
+        }
         subProps.add(prop);
     }
-    
-    
+
+
     private void addSubmissionPropsFromCharacteristics(
-            Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes, 
-            Connection connection) 
+            Map<Integer, Map<String, List<SubmissionProperty>>> subToTypes,
+            Connection connection)
     throws SQLException {
-        
+
         ResultSet res = getAppliedDataCharacteristics(connection);
 
@@ -1946 +1945 @@
         Integer currentSubId = null;   // we need those to attach the property to the correct sub
         Integer previousSubId = null;
-        
+
         while (res.next()) {
             Integer dataId = new Integer(res.getInt("data_id"));
@@ -1953 +1952 @@
             String attValue = res.getString("att_value");
             Integer attDbxref = new Integer(res.getInt("att_dbxref"));
-            
+
             currentSubId = dataSubmissionMap.get(dataId);
 
-            LOG.debug("XXX " + currentSubId + ":" + dataId + "|" + attValue + "|" +attDbxref);            
+            LOG.debug("XXX " + currentSubId + ":" + dataId + "|" + attValue
+                    + "|" +attDbxref);
             if (attDbxref.intValue() != lastAttDbXref.intValue() ||
-                    currentSubId != previousSubId) {                
+                    currentSubId != previousSubId) {
                 // store the last build property if created, type is set only if we found an
                 // attHeading of Characteristics
                 // note: dbxref can remain the same in different subs -> or
                 if (buildSubProperty != null && buildSubProperty.type != null) {
-                    createdProps.put(lastAttDbXref, buildSubProperty);    
+                    createdProps.put(lastAttDbXref, buildSubProperty);
                     addToSubToTypes(subToTypes, previousSubId, buildSubProperty);
                 }
-                // set up for next attDbxref 
+                // set up for next attDbxref
                 if (createdProps.containsKey(attDbxref) && isValidCharacteristic) {
                     // seen this property before so just add for this submission, don't build again
@@ -1977 +1977 @@
                 }
             }
-            
+
             if (attHeading.startsWith("Characteristic")) {
-                isValidCharacteristic = true;                
-            }
-            
+                isValidCharacteristic = true;
+            }
+
             if (buildSubProperty != null) {
                 if (attHeading.startsWith("Characteristic")) {
@@ -1998 +1998 @@
 
         if (buildSubProperty != null && buildSubProperty.type != null) {
-            createdProps.put(lastAttDbXref, buildSubProperty);    
+            createdProps.put(lastAttDbXref, buildSubProperty);
             addToSubToTypes(subToTypes, currentSubId, buildSubProperty);
         }
     }
-    
+
     // Some submission mention e.g. an RNA Sample but the details of how that sample was created,
     // stage, strain, etc are in a previous submission.  There are references to previous submission
@@ -2013 +2013 @@
             Map<String, SubmissionProperty> props,
             Map<Integer, SubmissionReference> submissionRefs) {
-        
+
         for (Map.Entry<Integer, SubmissionReference> entry : submissionRefs.entrySet()) {
             Integer submissionId = entry.getKey();
             SubmissionReference subRef = entry.getValue();
-            
-            
+
+
             List<AppliedData> refAppliedData = findAppliedDataFromReferencedSubmission(subRef);
             for (AppliedData aData : refAppliedData) {
@@ -2029 +2029 @@
         }
     }
-    
+
     private List<AppliedData> findAppliedDataFromReferencedSubmission(SubmissionReference subRef) {
         List<AppliedData> foundAppliedData = new ArrayList<AppliedData>();
@@ -2035 +2035 @@
         return foundAppliedData;
     }
-    
+
     private List<AppliedProtocol> findAppliedProtocolsFromReferencedSubmission(
             SubmissionReference subRef) {
@@ -2042 +2042 @@
         return foundAppliedProtocols;
     }
-    
+
     private void findAppliedProtocolsAndDataFromReferencedSubmission(
             SubmissionReference subRef,
@@ -2055 +2055 @@
 
             if (refDataValue.equals(currentDataValue) && refSubId.equals(currentDataSubId)) {
-                LOG.info("REFSUBS found a matching data value: " + currentDataValue + " in sub " 
-                        + dccIdMap.get(currentDataSubId) + " ref sub = " 
+                LOG.info("REFSUBS found a matching data value: " + currentDataValue + " in sub "
+                        + dccIdMap.get(currentDataSubId) + " ref sub = "
                         + dccIdMap.get(refSubId));
-                
+
                 Integer foundDataId = aData.dataId;
 
@@ -2066 +2066 @@
         }
     }
-    
-    
-    private List<Item> createFromWikiPage(String dccId, String clsName, 
-            Map<String, List<SubmissionProperty>> typeToProp, List<String> types) 
+
+
+    private List<Item> createFromWikiPage(String dccId, String clsName,
+            Map<String, List<SubmissionProperty>> typeToProp, List<String> types)
             throws ObjectStoreException {
         List<Item> items = new ArrayList<Item>();
@@ -2084 +2084 @@
 
     private void storeSubmissionCollection(Integer storedSubmissionId, String name,
-            List<Item> items) 
+            List<Item> items)
     throws ObjectStoreException {
         if (!items.isEmpty()) {
@@ -2091 +2091 @@
         }
     }
-    
+
     private List<String> getIdentifiersFromItems(Collection<Item> items) {
         List<String> ids = new ArrayList<String>();
@@ -2099 +2099 @@
         return ids;
     }
-    
-    private List<Item> createItemsForSubmissionProperties(String dccId, String clsName, 
+
+    private List<Item> createItemsForSubmissionProperties(String dccId, String clsName,
             List<SubmissionProperty> subProps)
     throws ObjectStoreException {
@@ -2112 +2112 @@
         return items;
     }
-        
-    
+
+
 
     private Item getItemForSubmissionProperty(String clsName, SubmissionProperty prop, String dccId)
@@ -2128 +2128 @@
                 }
                 if (checkOfficialName == null) {
-                    LOG.info("Official name - missing for property: " 
+                    LOG.info("Official name - missing for property: "
                             + prop.type + ", " + prop.wikiPageUrl);
                     return null;
                 } else if (checkOfficialName.size() != 1) {
-                    LOG.info("Official name - multiple times for property: " 
-                            + prop.type + ", " + prop.wikiPageUrl + ", " 
+                    LOG.info("Official name - multiple times for property: "
+                            + prop.type + ", " + prop.wikiPageUrl + ", "
                             + checkOfficialName);
                 }
@@ -2141 +2141 @@
                 propItem.setAttribute("type", getPreferredSynonym(prop.type));
                 propItem.setAttribute("wikiLink", WIKI_URL + prop.wikiPageUrl);
-                if (clsName.equals("DevelopmentalStage")) {                    
+                if (clsName.equals("DevelopmentalStage")) {
                     setAttributeOnProp(prop, propItem, "sex", "sex");
-                    
+
                     List<String> devStageValues = prop.details.get("developmental stage");
                     if (devStageValues != null) {
                         for (String devStageValue : devStageValues) {
-                            propItem.addToCollection("ontologyTerms", 
+                            propItem.addToCollection("ontologyTerms",
                                     getDevStageTerm(devStageValue));
                         }
                     } else {
-                        LOG.error("METADATA FAIL: no 'developmental stage' values for wiki page: " 
+                        LOG.error("METADATA FAIL: no 'developmental stage' values for wiki page: "
                                 + prop.wikiPageUrl);
                     }
@@ -2165 +2165 @@
                 } else if (clsName.equals("CellLine")) {
                     setAttributeOnProp(prop, propItem, "sex", "sex");
-                    setAttributeOnProp(prop, propItem, "short description", 
+                    setAttributeOnProp(prop, propItem, "short description",
                             "description");
                     setAttributeOnProp(prop, propItem, "species", "species");
@@ -2178 +2178 @@
                     setAttributeOnProp(prop, propItem, "Description", "description");
                     setAttributeOnProp(prop, propItem, "details", "description");
-                    
+
                     setAttributeOnProp(prop, propItem, "aliases", "name");
                     setAttributeOnProp(prop, propItem, "reference", "reference");
@@ -2198 +2198 @@
             throws ObjectStoreException {
         String targetText = null;
-        String[] possibleTypes = new String[] {"target id"}; 
+        String[] possibleTypes = new String[] {"target id"};
 
         for (String targetType : possibleTypes) {
             if (prop.details.containsKey(targetType)) {
                 if (prop.details.get(targetType).size() != 1) {
-                    
-                    // we used to complain if multiple values, now only 
+
+                    // we used to complain if multiple values, now only
                     // if they don't have the same value
                     checkIfSameValue(prop, source, targetType);
@@ -2232 +2232 @@
     private void checkIfSameValue(SubmissionProperty prop, String source,
             String targetType) throws RuntimeException {
-        String value = prop.details.get(targetType).get(0);                    
+        String value = prop.details.get(targetType).get(0);
         for (int i = 1; i < prop.details.get(targetType).size(); i++) {
             String newValue = prop.details.get(targetType).get(i);
             if (!newValue.equals(value)) {
-              throw new RuntimeException(source + " should only have one value for '" + targetType 
-              + "' field: " + prop.details.get(targetType));                            
-            }
-        }
-    }
-
-
-    private void setAttributeOnProp(SubmissionProperty subProp, Item item, String metadataName, 
+              throw new RuntimeException(source + " should only have one value for '" + targetType
+              + "' field: " + prop.details.get(targetType));
+            }
+        }
+    }
+
+
+    private void setAttributeOnProp(SubmissionProperty subProp, Item item, String metadataName,
             String attributeName) {
 
@@ -2258 +2258 @@
                     }
                 }
-            } else if (metadataName.equalsIgnoreCase("description") 
+            } else if (metadataName.equalsIgnoreCase("description")
                     || metadataName.equalsIgnoreCase("details")) {
                 // description is often split in more than 1 line
@@ -2267 +2267 @@
                 }
                 item.setAttribute(attributeName, all);
-                
+
             } else {
                 String value = subProp.details.get(metadataName).get(0);
@@ -2273 +2273 @@
             }
         }
-    }       
-
-    
+    }
+
+
     private String getTargetGeneItemIdentfier(String geneTargetIdText, String dccId)
     throws ObjectStoreException {
         String taxonId = "";
         String originalId = null;
-        
+
         String flyPrefix = "fly_genes:";
         String wormPrefix = "worm_genes:";
-        
+
         if (geneTargetIdText.startsWith(flyPrefix)) {
             originalId = geneTargetIdText.substring(flyPrefix.length());
@@ -2297 +2297 @@
             taxonId = "" + or.getOrganismDataByFullName(organism).getTaxonId();
             originalId = geneTargetIdText;
-            LOG.info("RESOLVER: found organism '" + organism + "', taxon " + taxonId 
+            LOG.info("RESOLVER: found organism '" + organism + "', taxon " + taxonId
                     + " for submission " + dccId);
         }
@@ -2307 +2307 @@
             resolver = wormResolverFactory.getIdResolver();
         } else {
-            LOG.info("RESOLVER: unable to work out organism for target id text: " 
+            LOG.info("RESOLVER: unable to work out organism for target id text: "
                     + geneTargetIdText);
         }
@@ -2337 +2337 @@
                     + " found ids: " + resolver.resolveId(taxonId, originalId) + ".");
         } else {
-            primaryIdentifier = 
+            primaryIdentifier =
                 resolver.resolveId(taxonId, originalId).iterator().next();
-            LOG.info("RESOLVER found gene " + primaryIdentifier 
+            LOG.info("RESOLVER found gene " + primaryIdentifier
                     + " for original id: " + originalId);
         }
         return primaryIdentifier;
     }
-    
+
 
     private List<Item> lookForAttributesInOtherWikiPages(String clsName,
-            Map<String, List<SubmissionProperty>> typeToProp, String[] lookFor) 
+            Map<String, List<SubmissionProperty>> typeToProp, String[] lookFor)
             throws ObjectStoreException {
 
@@ -2359 +2359 @@
 
                 if (typeToProp.containsKey(type)) {
-                    for (SubmissionProperty subProp : typeToProp.get(type)) { 
+                    for (SubmissionProperty subProp : typeToProp.get(type)) {
                         if (subProp.details.containsKey(propName)) {
                             for (String value : subProp.details.get(propName)) {
-                                items.add(createNonWikiSubmissionPropertyItem(clsName, 
-                                        getPreferredSynonym(propName), 
+                                items.add(createNonWikiSubmissionPropertyItem(clsName,
+                                        getPreferredSynonym(propName),
                                         correctAttrValue(value)));
                             }
@@ -2376 +2376 @@
                 // which probably won't be a wiki page
                 if (typeToProp.containsKey(typeProp)) {
-                    for (SubmissionProperty subProp : typeToProp.get(typeProp)) { 
+                    for (SubmissionProperty subProp : typeToProp.get(typeProp)) {
 
                         String value = subProp.wikiPageUrl;
-                        
+
                         // This is an ugly special case to deal with 'exposure time/24 hours'
                         if (subProp.details.containsKey("Unit")) {
@@ -2385 +2385 @@
                             value = value + " " + unit + (unit.endsWith("s") ? "" : "s");
                         }
-                        
-                        items.add(createNonWikiSubmissionPropertyItem(clsName, subProp.type, 
+
+                        items.add(createNonWikiSubmissionPropertyItem(clsName, subProp.type,
                                 correctAttrValue(value)));
                     }
@@ -2394 +2394 @@
         return items;
     }
-  
+
     private String correctAttrValue(String value) {
         if (value == null) {
@@ -2400 +2400 @@
         }
         value = value.replace("–", "-");
-        return value;  
-    }
-
-    
-    private Item createNonWikiSubmissionPropertyItem(String clsName, String type, String name) 
+        return value;
+    }
+
+
+    private Item createNonWikiSubmissionPropertyItem(String clsName, String type, String name)
     throws ObjectStoreException {
         if (clsName.equals("DevelopmentalStage")) {
             name = correctDevStageTerm(name);
         }
-        
+
         Item item = nonWikiSubmissionProperties.get(name);
-        if (item == null) {    
+        if (item == null) {
             item = createSubmissionProperty(clsName, name);
             item.setAttribute("type", getPreferredSynonym(type));
-            
+
             if (clsName.equals("DevelopmentalStage")) {
                 String ontologyTermId = getDevStageTerm(name);
@@ -2425 +2425 @@
         return item;
     }
-    
+
     private Item createSubmissionProperty(String clsName, String name) {
-        Item subProp = getChadoDBConverter().createItem(clsName);        
-        if (name != null) {           
+        Item subProp = getChadoDBConverter().createItem(clsName);
+        if (name != null) {
             subProp.setAttribute("name", name);
         }
-        
+
         return subProp;
     }
-    
-    
+
+
     private String getCorrectedOfficialName(SubmissionProperty prop) {
         String preferredType = getPreferredSynonym(prop.type);
@@ -2448 +2448 @@
             for (String lookup : makeLookupList(prop.type)) {
                 if (prop.details.containsKey(lookup)) {
-                    name = prop.details.get(lookup).get(0);            
+                    name = prop.details.get(lookup).get(0);
                 }
             }
@@ -2454 +2454 @@
         return correctOfficialName(name, preferredType);
     }
-    
+
     /**
      * Unify variations on similar official names.
@@ -2465 +2465 @@
             return null;
         }
-        
+
         if (type.equals("developmental stage")) {
             name = name.replace("_", " ");
@@ -2490 +2490 @@
             if (name.matches(".*L\\d")) {
                 name = name + " stage larvae";
-            }            
+            }
             if (name.matches("WPP.*")) {
                 name = name.replaceFirst("WPP", "White prepupae (WPP)");
             }
         }
-        return name;  
-    }
-    
+        return name;
+    }
+
 
 
     private String getDevStageTerm(String value) throws ObjectStoreException {
         value = correctDevStageTerm(value);
-        
+
         String identifier = devStageTerms.get(value);
         if (identifier == null) {
             Item term = getChadoDBConverter().createItem("OntologyTerm");
             term.setAttribute("name", value);
-            getChadoDBConverter().store(term);            
+            getChadoDBConverter().store(term);
             devStageTerms.put(value, term.getIdentifier());
             identifier = term.getIdentifier();
@@ -2523 +2523 @@
     }
 
-    
+
     private Integer getSubmissionIdFromDccId(String dccId) {
         for (Map.Entry<Integer, String> entry : dccIdMap.entrySet()) {
@@ -2544 +2544 @@
 
         String sraAcc = "SRA acc";
-        
+
         String query = "SELECT d.data_id, d.heading as data_heading,"
             + " d.name as data_name, d.value as data_value,"
@@ -2584 +2584 @@
     }
 
-    private class SubmissionProperty 
+    private class SubmissionProperty
     {
         protected String type;
@@ -2604 +2604 @@
             if (values == null) {
                 values = new ArrayList<String>();
-                details.put(type, values);               
+                details.put(type, values);
             }
             values.add(value);
@@ -2614 +2614 @@
     }
 
-    
-    private class DatabaseRecordConfig 
+
+    private class DatabaseRecordConfig
     {
         private Set<Pattern> patterns = new HashSet<Pattern>();
@@ -2622 +2622 @@
         private String dbURL;
     }
-    
+
     private Set<DatabaseRecordConfig> initDatabaseRecordConfigs() {
         Set<DatabaseRecordConfig> configs = new HashSet<DatabaseRecordConfig>();
@@ -2645 +2645 @@
         sra.dbName = "SRA";
         sra.dbDescrition = "Sequence Read Archive (NCBI)";
-        sra.dbURL = 
+        sra.dbURL =
             "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=";
         p = Pattern.compile("SRA.*", Pattern.CASE_INSENSITIVE);
@@ -2654 +2654 @@
     }
 
-    
+
     /**
      * Query to get data attributes
@@ -2709 +2709 @@
 
         Set<DatabaseRecordConfig> configs = initDatabaseRecordConfigs();
-        
+
         for (Integer submissionId : submissionDataMap.keySet()) {
             List<String> submissionDbRecords = new ArrayList<String>();
@@ -2726 +2726 @@
                 if (!submissionDbRecords.isEmpty()) {
                     ReferenceList col = new ReferenceList("databaseRecords", submissionDbRecords);
-                    getChadoDBConverter().store(col, 
+                    getChadoDBConverter().store(col,
                             submissionMap.get(submissionId).interMineObjectId);
                 }
@@ -2734 +2734 @@
     }
 
-    
-    private List<String> createDatabaseRecords(String accession, DatabaseRecordConfig config) 
+
+    private List<String> createDatabaseRecords(String accession, DatabaseRecordConfig config)
     throws ObjectStoreException {
         List<String> dbRecordIds = new ArrayList<String>();
 
         Set<String> cleanAccessions = new HashSet<String>();
-        
+
         // NOTE - this is a special case to deal with a very strange SRA accession format in some
         // Celniker submissions.  The 'accession' is provided as e.g.
         //   SRR013492.225322.1;SRR013492.462158.1;...
-        // We just want the unique SRR ids        
+        // We just want the unique SRR ids
         if (config.dbName.equals("SRA") && (accession.indexOf(';') != -1
                 || accession.indexOf('.') != -1)) {
@@ -2757 +2757 @@
             cleanAccessions.add(accession);
         }
-        
+
         for (String cleanAccession : cleanAccessions) {
             dbRecordIds.add(createDatabaseRecord(cleanAccession, config));
@@ -2763 +2763 @@
         return dbRecordIds;
     }
-    
-    
-    private String createDatabaseRecord(String accession, DatabaseRecordConfig config) 
+
+
+    private String createDatabaseRecord(String accession, DatabaseRecordConfig config)
     throws ObjectStoreException {
         DatabaseRecordKey key = new DatabaseRecordKey(config.dbName, accession);
@@ -2773 +2773 @@
             dbRecord.setAttribute("database", config.dbName);
             dbRecord.setAttribute("description", config.dbDescrition);
-            if (StringUtil.isEmpty(accession)) {
+            if (StringUtils.isEmpty(accession)) {
                 dbRecord.setAttribute("accession", "To be confirmed");
             } else {
@@ -2786 +2786 @@
         return dbRecordId;
     }
-    
-    
-    private class DatabaseRecordKey 
+
+
+    private class DatabaseRecordKey
     {
         private String db;
         private String accession;
-        
+
         /**
          * Construct with the database and accession
@@ -2802 +2802 @@
             this.accession = accession;
         }
-        
+
         /**
          * {@inheritDoc}
@@ -2809 +2809 @@
             if (o instanceof DatabaseRecordKey) {
                 DatabaseRecordKey otherKey = (DatabaseRecordKey) o;
-                if (!StringUtil.isEmpty(accession) && !StringUtil.isEmpty(otherKey.accession)) {
-                    return this.db.equals(otherKey.db) && this.accession.equals(otherKey.accession); 
+                if (StringUtils.isNotEmpty(accession)
+                        && StringUtils.isNotEmpty(otherKey.accession)) {
+                    return this.db.equals(otherKey.db)
+                    && this.accession.equals(otherKey.accession);
                 }
             }
             return false;
         }
-        
+
         /**
          * {@inheritDoc}
@@ -2823 +2825 @@
         }
     }
-    
+
     //sub -> prot
     private void setSubmissionProtocolsRefs(Connection connection)
@@ -2841 +2843 @@
             Integer thisSubmissionId = subs.next();
             List<Integer> protocolChadoIds = submissionProtocolMap.get(thisSubmissionId);
-            
+
             ReferenceList collection = new ReferenceList();
             collection.setName("protocols");
@@ -2849 +2851 @@
             Integer storedSubmissionId = submissionMap.get(thisSubmissionId).interMineObjectId;
             getChadoDBConverter().store(collection, storedSubmissionId);
-            
+
             // may need protocols from referenced submissions to work out experiment type
             protocolChadoIds.addAll(findProtocolIdsFromReferencedSubmissions(thisSubmissionId));
-            
+
             String piName = submissionProjectMap.get(thisSubmissionId);
             setSubmissionExperimentType(storedSubmissionId, protocolChadoIds, piName);
@@ -2874 +2876 @@
         }
     }
-    
+
     // Fetch protocols used to create reagents that are inputs to this submission, these are
     // found in referenced submissions
     private List<Integer> findProtocolIdsFromReferencedSubmissions(Integer submissionId) {
         List<Integer> protocolIds = new ArrayList<Integer>();
-        
+
         if (submissionRefs == null) {
             throw new RuntimeException("Attempting to access submissionRefs before it has been"
@@ -2885 +2887 @@
                     + " processSubmissionProperties");
         }
-        
+
         SubmissionReference subRef = submissionRefs.get(submissionId);
         if (subRef != null) {
@@ -2892 +2894 @@
             }
         }
-        
+
         return protocolIds;
     }
-    
-    /** 
+
+    /**
      * Work out an experiment type give the combination of protocols used for the
      * submussion.  e.g. *immunoprecipitation + hybridization = chIP-chip
      * @param protocolTypes the protocal types
+     * @param piName name of PI
      * @return a short experiment type
      */
@@ -2915 +2918 @@
             }
         }
-        
+
         // reverse transcription + PCR + RACE = RACE
         // reverse transcription + PCR - RACE = RTPCR
@@ -2926 +2929 @@
             }
         }
-        
+
         // ChIP + hybridization = ChIP-chip
         // ChIP - hybridization = ChIP-seq
@@ -2934 +2937 @@
             } else {
                 return "ChIP-seq";
-            }           
-        }
-        
+            }
+        }
+
         // hybridization - ChIP =
         //    Celniker:  RNA tiling array
@@ -2952 +2955 @@
 
         }
-        
+
         // annotation = Computational annotation
         if (containsMatch(protocolTypes, "annotation")) {
             return "Computational annotation";
         }
-        
+
         // If we haven't found a type yet, and there is a growth protocol, then
         // this is probably an RNA sample creation experiment from Celniker
@@ -2963 +2966 @@
             return "RNA sample creation";
         }
-        
+
         return null;
     }
-    
+
     // utility method for looking up in a set by regular expression
     private boolean containsMatch(Set<String> testSet, String regex) {
@@ -2979 +2982 @@
         return matches;
     }
-    
+
     //sub -> exp
     private void setSubmissionExperimetRefs(Connection connection)
@@ -3030 +3033 @@
             }
         }
-        LOG.info("TIME setting submission-exFactors references: " 
+        LOG.info("TIME setting submission-exFactors references: "
                 + (System.currentTimeMillis() - bT));
     }
@@ -3050 +3053 @@
                     submissionMap.get(thisSubmissionId).interMineObjectId);
             }
-        LOG.info("TIME setting submission-publication references: " 
+        LOG.info("TIME setting submission-publication references: "
                 + (System.currentTimeMillis() - bT));
     }
 
-    
-    
-    
+
+
+
 
     /**
@@ -3088 +3091 @@
             }
         }
-        LOG.info("TIME setting DAG references: " + (System.currentTimeMillis() - bT));        
+        LOG.info("TIME setting DAG references: " + (System.currentTimeMillis() - bT));
     }
 
@@ -3193 +3196 @@
         dataSubmissionMap.put(dataId, submissionId);
     }
-    
+
     /**
      * =====================
@@ -3199 +3202 @@
      * =====================
      */
-    
+
     /**
      * method to wrap the execution of a query, without log info
@@ -3233 +3236 @@
     }
 
-    
+
     /**
      * adds an element to a list which is the value of a map
@@ -3271 +3274 @@
         }
     }
-    
-    
+
+
     /**
      * adds an element to a list which is the value of a map

trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/WormBaseProcessor.java

@@ -17 +17 @@
 import org.apache.commons.collections.keyvalue.MultiKey;
 import org.apache.commons.collections.map.MultiKeyMap;
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.intermine.bio.chado.config.ConfigAction;
 import org.intermine.bio.chado.config.SetFieldConfigAction;
 import org.intermine.objectstore.ObjectStoreException;
-import org.intermine.util.StringUtil;
 import org.intermine.xml.full.Item;
 
@@ -50 +50 @@
         return itemId;
     }
-    
+
     /**
      * Method to add dataSets and DataSources to items before storing
@@ -78 +78 @@
                                      converter.getDataSourceItem().getIdentifier());
     }
-    
-    
+
     /**
      * {@inheritDoc}
@@ -132 +131 @@
     @Override
     protected String fixIdentifier(FeatureData fdat, String identifier) {
-        
+
         String uniqueName = fdat.getChadoFeatureUniqueName();
         String type = fdat.getInterMineType();
 
-        // the function is used without check for null only for uniquename and name 
+        // the function is used without check for null only for uniquename and name
         // in SequenceProcessor.
         // so we assume that uniquename is never null and that if null it is a name.
-        if (StringUtil.isEmpty(identifier)) {
+        if (StringUtils.isEmpty(identifier)) {
                 identifier = uniqueName;
                 LOG.debug("Found NULL name for feature: " + uniqueName);
-            } 
-        
+            }
+
         if (identifier.startsWith(type + ":")) {
             return identifier.substring(type.length() + 1);
-        } else {
-            return identifier;
         }
+        return identifier;
     }
-    
+
     /**
      * Wormbase chado has pmid prefixed to pubmed identifiers
-     * @param string pubmed id fetched from databaase
+     * @param pubmedStr id fetched from databaase
      * @return the pubmed id
      */

trunk/bio/sources/flymine/flyatlas/main/src/org/intermine/bio/dataconversion/FlyAtlasConverter.java

@@ -22 +22 @@
 import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.util.FormattedTextParser;
-import org.intermine.util.StringUtil;
 import org.intermine.xml.full.Item;
 
@@ -67 +66 @@
                 String probeId = line[0];
                 // there seems to be some empty lines at the end of the file
-                if (StringUtil.isEmpty(probeId)) {
+                if (StringUtils.isEmpty(probeId)) {
                     break;
                 }

trunk/intermine/integrate/main/src/org/intermine/xml/full/Item.java

@@ -19 +19 @@
 import java.util.Set;
 
+import org.apache.commons.lang.StringUtils;
 import org.intermine.metadata.ClassDescriptor;
 import org.intermine.metadata.Model;
@@ -414 +415 @@
      */
     public void addToCollection(String name, String refId) {
-        if (StringUtil.isEmpty(refId)) {
+        if (StringUtils.isEmpty(refId)) {
             throw new RuntimeException("empty string added to collection for: " + name);
         }
@@ -613 +614 @@
 
                 for (String clsName : bits) {
-                    if (!StringUtil.isEmpty(clsName)) {
+                    if (!StringUtils.isEmpty(clsName)) {
                         implementationClassDescriptors.add(getClassDescriptorByName(clsName));
                     }

trunk/intermine/objectstore/main/src/org/intermine/util/StringUtil.java

@@ -462 +462 @@
         }
         return "a";
-    }
-
-
-    /**
-     * Returns true if the given String is null or the empty String.
-     *
-     * @param str checked string
-     * @return true if string is null or empty
-     */
-    public static boolean isEmpty(String str) {
-        if (str == null) {
-            return true;
-        }
-        return str.length() == 0;
     }
 

trunk/intermine/pathquery/main/src/org/intermine/pathquery/PathQuery.java

@@ -27 +27 @@
 import java.util.regex.Pattern;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.intermine.metadata.ClassDescriptor;
@@ -35 +36 @@
 import org.intermine.objectstore.query.ConstraintOp;
 import org.intermine.util.CollectionUtil;
-import org.intermine.util.StringUtil;
 
 /**
@@ -820 +820 @@
         }
         for (Iterator<String> iter = codes.iterator(); iter.hasNext(); ) {
-            if (!StringUtil.isEmpty(logic)) {
+            if (StringUtils.isNotEmpty(logic)) {
                 logic += " " + operator + " ";
             }

trunk/intermine/web/main/src/org/intermine/web/logic/session/SessionMethods.java

@@ -446 +446 @@
 
     /**
-     * Get the COLLAPSED map from the session. If the attribute is not present then a new
-     * map will be created.
-     *
-     * @param session the curren session
-     * @return the COLLAPSED map attribute
-     */
-    public static Map getCollapsedMap(HttpSession session) {
-        Map collapsed = (Map) session.getAttribute(Constants.COLLAPSED);
-        if (collapsed == null) {
-            collapsed = new HashMap();
-            session.setAttribute(Constants.COLLAPSED, collapsed);
-        }
-        return collapsed;
-    }
-
-    /**
      * Return the displayObjects Map from the session or create and return it if it doesn't exist.
      *

trunk/intermine/web/main/src/org/intermine/web/struts/HtmlHeadController.java

@@ -15 +15 @@
 import javax.servlet.http.HttpSession;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionForm;
@@ -29 +30 @@
 import org.intermine.objectstore.ObjectStore;
 import org.intermine.util.DynamicUtil;
-import org.intermine.util.StringUtil;
 import org.intermine.web.logic.results.DisplayObject;
 import org.intermine.web.logic.results.DisplayObjectFactory;
@@ -54 +54 @@
      * @exception Exception if an error occurs
      */
-    public ActionForward execute(@SuppressWarnings("unused") ComponentContext context,
-                                 @SuppressWarnings("unused") ActionMapping mapping,
-                                 @SuppressWarnings("unused") ActionForm form,
+    public ActionForward execute(ComponentContext context,
+                                 ActionMapping mapping,
+                                 ActionForm form,
                                  HttpServletRequest request,
-                                 @SuppressWarnings("unused") HttpServletResponse response)
+                                 HttpServletResponse response)
         throws Exception {
 
@@ -116 +116 @@
                 return null;
             }
-            DisplayObject dobj = (DisplayObject) displayObjects.get(object);
+            DisplayObject dobj = displayObjects.get(object);
 
             String className = DynamicUtil.getFriendlyName(dobj.getObject().getClass());
@@ -133 +133 @@
 
             // TODO use the class keys instead of hardcoding which fields should be used
-            if (StringUtil.isEmpty(idForPageTitle)
+            if (StringUtils.isEmpty(idForPageTitle)
                             && dobj.getAttributes().get("secondaryIdentifier") != null) {
                 idForPageTitle = dobj.getAttributes().get("secondaryIdentifier").toString();
             }
-            if (StringUtil.isEmpty(idForPageTitle)
+            if (StringUtils.isEmpty(idForPageTitle)
                             && dobj.getAttributes().get("identifier") != null) {
                 idForPageTitle = dobj.getAttributes().get("identifier").toString();
             }
-            if (StringUtil.isEmpty(idForPageTitle)
+            if (StringUtils.isEmpty(idForPageTitle)
                             && dobj.getAttributes().get("symbol") != null) {
                 idForPageTitle = dobj.getAttributes().get("symbol").toString();
             }
 
-            if (!StringUtil.isEmpty(idForPageTitle)) {
+            if (StringUtils.isNotEmpty(idForPageTitle)) {
                 htmlPageTitle = className + " report for " + idForPageTitle;
             }