Revision: 17671
http://sourceforge.net/p/gate/code/17671
Author: markagreenwood
Date: 2014-03-15 10:03:31 +0000 (Sat, 15 Mar 2014)
Log Message:
-----------
and that's all the G* plugins cleaned up and the compiler warnings enabled
Modified Paths:
--------------
gate/trunk/plugins/GENIA/build.xml
gate/trunk/plugins/GENIA/src/gate/creole/genia/splitter/GENIASentenceSplitter.java
gate/trunk/plugins/Gazetteer_LKB/.classpath
gate/trunk/plugins/Gazetteer_LKB/build.xml
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/AliasCacheImpl.java
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/EntityPriority.java
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/HashRegister.java
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/Options.java
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/test/PrivateRepositoryFeedTest.java
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/util/datastore/GazetteerListFeed.java
gate/trunk/plugins/Gazetteer_Ontology_Based/build.xml
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/OntoRootGaz.java
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/query/serql/SerqlUtils.java
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/regex/ExpressionFinder.java
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/Ontology2Map.java
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/StringUtil.java
gate/trunk/plugins/Groovy/build.xml
gate/trunk/plugins/Groovy/src/gate/groovy/GateGroovyMethods.java
gate/trunk/plugins/Groovy/src/gate/groovy/GroovySupport.java
gate/trunk/plugins/Groovy/src/gate/groovy/ScriptPR.java
gate/trunk/plugins/Groovy/src/gate/groovy/ScriptableController.groovy
gate/trunk/plugins/Groovy/src/gate/groovy/gui/ControllerScriptEditor.java
gate/trunk/plugins/Groovy/src/gate/groovy/gui/ScriptPREditor.java
Modified: gate/trunk/plugins/GENIA/build.xml
===================================================================
--- gate/trunk/plugins/GENIA/build.xml 2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/GENIA/build.xml 2014-03-15 10:03:31 UTC (rev 17671)
@@ -11,6 +11,7 @@
<property name="jar.location" location="GENIA.jar" />
<property name="doc.dir" location="doc" />
<property name="javadoc.dir" location="${doc.dir}/javadoc" />
+ <property name="gate.compile.maxwarnings" value="10000" />
<!-- Path to compile - includes gate.jar and GATE/lib/*.jar -->
<path id="compile.classpath">
@@ -28,7 +29,11 @@
<!-- compile the source -->
<target name="compile" depends="prepare">
- <javac classpathref="compile.classpath" srcdir="${src.dir}"
destdir="${classes.dir}" debug="true" debuglevel="lines,source"
encoding="UTF-8" source="1.5" target="1.5" />
+ <javac classpathref="compile.classpath" srcdir="${src.dir}"
destdir="${classes.dir}" debug="true" debuglevel="lines,source"
encoding="UTF-8" source="1.6" target="1.6">
+ <compilerarg value="-Xmaxwarns" />
+ <compilerarg value="${gate.compile.maxwarnings}" />
+ <compilerarg value="-Xlint:all" />
+ </javac>
</target>
<target name="resources" depends="prepare">
Modified:
gate/trunk/plugins/GENIA/src/gate/creole/genia/splitter/GENIASentenceSplitter.java
===================================================================
---
gate/trunk/plugins/GENIA/src/gate/creole/genia/splitter/GENIASentenceSplitter.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/GENIA/src/gate/creole/genia/splitter/GENIASentenceSplitter.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -29,9 +29,13 @@
import java.io.FileReader;
import java.net.URL;
+import org.apache.commons.io.IOUtils;
+
@CreoleResource(name = "GENIA Sentence Splitter", icon =
"sentence-splitter.png", helpURL =
"http://gate.ac.uk/userguide/sec:domain-creole:biomed:genia";)
public class GENIASentenceSplitter extends AbstractLanguageAnalyser {
+ private static final long serialVersionUID = 142837355544158905L;
+
private boolean debug = false;
private String annotationSetName;
@@ -81,6 +85,9 @@
String docContent =
document.getContent().toString().replace((char)160, ' ');
+ //The reader that brings back the output from the sentence splitter
+ BufferedReader in = null;
+
try {
// create temporary files to use with the external sentence splitter
File tmpIn = File.createTempFile("GENIA", ".txt");
@@ -109,7 +116,7 @@
int end = 0;
// read in the output from the sentence splitter one line at a time
- BufferedReader in = new BufferedReader(new FileReader(tmpOut));
+ in = new BufferedReader(new FileReader(tmpOut));
String sentence = in.readLine();
while(sentence != null) {
@@ -141,5 +148,8 @@
} catch(Exception ioe) {
throw new ExecutionException("An error occured running the splitter",
ioe);
}
+ finally {
+ IOUtils.closeQuietly(in);
+ }
}
}
Modified: gate/trunk/plugins/Gazetteer_LKB/.classpath
===================================================================
--- gate/trunk/plugins/Gazetteer_LKB/.classpath 2014-03-15 09:18:40 UTC (rev
17670)
+++ gate/trunk/plugins/Gazetteer_LKB/.classpath 2014-03-15 10:03:31 UTC (rev
17671)
@@ -7,12 +7,12 @@
<classpathentry exported="true" kind="lib"
path="lib/commons-httpclient-3.1.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/kim-api-3.0-RC5.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/kim-util-3.0-RC5.jar"/>
- <classpathentry exported="true" kind="lib"
path="lib/openrdf-sesame-2.6.10-onejar.jar"/>
- <classpathentry exported="true" kind="lib"
path="lib/owlim-lite-5.3.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/slf4j-api-1.5.11.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/slf4j-log4j12-1.5.11.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/trove4j-2.0.2.jar"/>
<classpathentry kind="con"
path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
<classpathentry combineaccessrules="false" exported="true" kind="src"
path="/GATE"/>
+ <classpathentry kind="lib" path="lib/openrdf-sesame-2.7.9-onejar.jar"/>
+ <classpathentry kind="lib" path="lib/owlim-lite-5.4.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
Modified: gate/trunk/plugins/Gazetteer_LKB/build.xml
===================================================================
--- gate/trunk/plugins/Gazetteer_LKB/build.xml 2014-03-15 09:18:40 UTC (rev
17670)
+++ gate/trunk/plugins/Gazetteer_LKB/build.xml 2014-03-15 10:03:31 UTC (rev
17671)
@@ -49,6 +49,8 @@
<!-- JavaDoc documentation directory -->
<property name="javadoc.dir" location="${doc.dir}/javadoc" />
+ <property name="gate.compile.maxwarnings" value="10000" />
+
<!-- lib directory - put any additional JAR files your plugin requires into
this directory. You will also need to add them as <JAR> entries in
creole.xml -->
@@ -84,8 +86,12 @@
destdir="${classes.dir}"
debug="true"
debuglevel="lines,source"
- source="1.5"
- target="1.5" />
+ source="1.6"
+ target="1.6">
+ <compilerarg value="-Xmaxwarns" />
+ <compilerarg value="${gate.compile.maxwarnings}" />
+ <compilerarg value="-Xlint:all" />
+ </javac>
</target>
<!-- copy resources (anything non-.java) from src to classes -->
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/AliasCacheImpl.java
===================================================================
---
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/AliasCacheImpl.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/AliasCacheImpl.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -4,9 +4,24 @@
import gate.util.profile.Profiler;
import gnu.trove.TIntHashSet;
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
import java.rmi.RemoteException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.apache.commons.collections.Transformer;
import org.apache.commons.io.FileUtils;
@@ -64,9 +79,9 @@
* aliases has been stored in the alias register. */
protected HashRegister aliasInstRegister;
/** Array used for encoding/decoding the instance URI's name-spaces */
- protected ArrayList<String> instNS;
+ protected List<String> instNS;
/** Array used for encoding/decoding the semantic class URIs */
- protected ArrayList<String> classCache;
+ protected List<String> classCache;
/** Additional register containing exactly appointed aliases, which
* must be ignored on storing */
protected HashRegister aliasToIgnore;
@@ -301,6 +316,7 @@
pro.checkPoint("cache loaded");
}
+ @SuppressWarnings("unchecked")
private boolean loadDictionaryFromCacheFile(File fileTCache,
boolean flagTLoaded) {
try {
@@ -310,8 +326,8 @@
ois.close();
aliasRegister = (HashRegister) res[0];
aliasPrefixes = (TIntHashSet) res[1];
- instNS = (ArrayList<String>) res[2];
- classCache = (ArrayList<String>) res[3];
+ instNS = (List<String>) res[2];
+ classCache = (List<String>) res[3];
aliasInstRegister = new HashRegister();
@@ -388,9 +404,9 @@
public void endTableQueryResult() throws IOException {
super.endTableQueryResult();
if (existsClassPriority && allPrioritiesCompetition != null) {
- Iterator it = allPrioritiesCompetition.keySet().iterator();
+ Iterator<String> it = allPrioritiesCompetition.keySet().iterator();
while (it.hasNext()) {
- ArrayList<priorityCompetition> pcList =
+ List<priorityCompetition> pcList =
allPrioritiesCompetition.get(it.next());
int maxPrior = pcList.get(0).maxPriority;
int treshold = m_entPrior.getThreshold();
@@ -571,7 +587,7 @@
* @param alias - the label string of the alias
* @return - array of matching HashedAlias instances
*/
- public ArrayList<KimLookupParser.AliasWrapper> lookup(String alias) {
+ public List<KimLookupParser.AliasWrapper> lookup(String alias) {
ParsingFrame pfm = new ParsingFrame(alias);
pfm.parseAll();
return lookup(pfm, true);
@@ -580,10 +596,10 @@
public Collection<KimLookupParser.AliasWrapper> lookup(ParsingFrame pfm) {
return lookup(pfm, false);
}
- private ArrayList<KimLookupParser.AliasWrapper> lookup(
+ private List<KimLookupParser.AliasWrapper> lookup(
ParsingFrame pfm, boolean exactlySame) {
Stats.markIt(-1);
- ArrayList<KimLookupParser.AliasWrapper> res = new
ArrayList<KimLookupParser.AliasWrapper>();
+ List<KimLookupParser.AliasWrapper> res = new
ArrayList<KimLookupParser.AliasWrapper>();
Object[] tmp = aliasRegister.get(pfm.getAliasHash1());
Stats.markIt(5);
@@ -687,7 +703,7 @@
}
}
- protected HashMap<String, ArrayList<priorityCompetition>>
allPrioritiesCompetition = new HashMap();
+ protected Map<String, List<priorityCompetition>> allPrioritiesCompetition =
new HashMap<String,List<priorityCompetition>>();
protected EntityPriority entPrior;
protected boolean existsClassPriority = false;
@@ -715,13 +731,13 @@
rejectedByPriority =
entPrior.m_hClassPrio.containsKey(priorityClassName);
if (rejectedByPriority) {
- int mp = (Integer) entPrior.m_hClassPrio.get(priorityClassName);
+ int mp = entPrior.m_hClassPrio.get(priorityClassName);
log.info("COMPETITION:" + "\t" + instURI
+ "\t" + classURI + "\t" + alias + "\t" + mp);
if (!allPrioritiesCompetition.containsKey(alias))
allPrioritiesCompetition.put(alias,
new ArrayList<priorityCompetition>());
- ArrayList<priorityCompetition> pcList =
+ List<priorityCompetition> pcList =
allPrioritiesCompetition.get(alias);
boolean foundLesser = false;
for (int i = 0; i < pcList.size(); i++) {
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/EntityPriority.java
===================================================================
---
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/EntityPriority.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/EntityPriority.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -4,6 +4,7 @@
import java.io.FileInputStream;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.Map;
import java.util.Properties;
import com.ontotext.kim.KIMConstants;
@@ -21,9 +22,9 @@
protected int m_nThreshold;
protected boolean m_bFilterLookups;
- protected HashMap m_hClassPrio;
- protected HashMap m_hInstPrio;
- protected HashMap m_hRules;
+ protected Map<String,Integer> m_hClassPrio;
+ protected Map<String,Integer> m_hInstPrio;
+ protected Map<String,Integer> m_hRules;
/**
* read the config file
@@ -31,9 +32,9 @@
* @throws Exception
*/
public EntityPriority() {
- m_hClassPrio = new HashMap(50);
- m_hInstPrio = new HashMap(50);
- m_hRules = new HashMap(100);
+ m_hClassPrio = new HashMap<String,Integer>(50);
+ m_hInstPrio = new HashMap<String,Integer>(50);
+ m_hRules = new HashMap<String,Integer>(100);
m_prop = new Properties();
}
@@ -52,7 +53,7 @@
.getProperty("priority.filterLookups"));
// init class and instance priority
- for (Iterator iter = m_prop.keySet().iterator(); iter.hasNext();) {
+ for (Iterator<Object> iter = m_prop.keySet().iterator();
iter.hasNext();) {
String item = (String) iter.next();
if (item.startsWith(PRIORITY_CLASS_PREFIX))
addClassPriority(item);
@@ -94,17 +95,17 @@
}
public int getInstancePriority(String sInstanceURI) {
- Integer prio = (Integer) m_hInstPrio.get(stripNameSpace(sInstanceURI));
+ Integer prio = m_hInstPrio.get(stripNameSpace(sInstanceURI));
return prio == null ? m_nDefaultInstancePriority : prio.intValue();
}
public int getClassPriority(String sClassURI) {
- Integer prio = (Integer) m_hClassPrio.get(stripNameSpace(sClassURI));
+ Integer prio = m_hClassPrio.get(stripNameSpace(sClassURI));
return prio == null ? m_nDefaultInstancePriority : prio.intValue();
}
public int getPairDelta(String sClass1, String sClass2) {
- Integer nDelta = (Integer) m_hRules.get(stripNameSpace(sClass1) + "_"
+ Integer nDelta = m_hRules.get(stripNameSpace(sClass1) + "_"
+ stripNameSpace(sClass2));
if (nDelta == null)
return 0;
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/HashRegister.java
===================================================================
---
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/HashRegister.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/HashRegister.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -80,7 +80,7 @@
byte elemCountChange = add12(element);
if (elemCountChange < 0) {
if (element instanceof Comparable)
- elemCountChange = addSorted((Comparable) element);
+ elemCountChange = addSorted((Comparable<?>) element);
else
elemCountChange = addUnsorted(element);
}
@@ -117,7 +117,8 @@
return 1;
}
- private static final Comparator<Comparable> nsc = new NullComparator(true);
+ @SuppressWarnings("unchecked")
+ private static final Comparator<Comparable<?>> nsc = new
NullComparator(true);
/** Method adds new element to the container in sorted manner.
* The method is called only if the container already have 2
@@ -126,9 +127,9 @@
* @return number of elements stored: 1 - if stored successfully;
* 0 - element already existed and no duplicates are allowed;
*/
- private byte addSorted(Comparable element) {
- Comparable[] newSubReg;
- Comparable[] oldSubReg = ((Comparable[])elementHolder);
+ private byte addSorted(Comparable<?> element) {
+ Comparable<?>[] newSubReg;
+ Comparable<?>[] oldSubReg = ((Comparable[])elementHolder);
int addPosition = Arrays.binarySearch( oldSubReg, element, nsc);
if (addPosition >= 0) {
return 0; // ignore the new one and retain the old one
@@ -180,8 +181,8 @@
Object[] newSubReg;
if (element instanceof Comparable) {
newSubReg = new Comparable[1 + subRegIncrement];
- if (nsc.compare((Comparable) elementHolder,
- (Comparable) element) < 0) {
+ if (nsc.compare((Comparable<?>) elementHolder,
+ (Comparable<?>) element) < 0) {
newSubReg[0] = elementHolder;
newSubReg[1] = element;
}
@@ -219,8 +220,8 @@
if (element == null)
return (elements == null);
else if (element instanceof Comparable)
- return Arrays.binarySearch( (Comparable[])elements,
- (Comparable) element, nsc) >= 0;
+ return Arrays.binarySearch( (Comparable<?>[])elements,
+ (Comparable<?>) element, nsc) >= 0;
else
return Arrays.asList(elements).contains(element);
}
@@ -234,8 +235,8 @@
int i = -1;
if (element != null) {
if (element instanceof Comparable)
- i = Arrays.binarySearch( (Comparable[])elements,
- (Comparable) element, nsc);
+ i = Arrays.binarySearch( (Comparable<?>[])elements,
+ (Comparable<?>) element, nsc);
else
i = Arrays.asList(elements).indexOf(element);
}
@@ -262,7 +263,7 @@
}
else { // getPoint.elementHolder contains single object
if (elementHolder instanceof Comparable)
- return new Comparable[]{(Comparable) elementHolder};
+ return new Comparable[]{(Comparable<?>) elementHolder};
else
return new Object[]{elementHolder};
}
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/Options.java
===================================================================
--- gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/Options.java
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/model/Options.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -15,7 +15,6 @@
import org.apache.log4j.Logger;
import org.openrdf.model.Graph;
import org.openrdf.model.Statement;
-import org.openrdf.model.impl.GraphImpl;
import org.openrdf.model.impl.URIImpl;
import org.openrdf.rio.RDFFormat;
import org.openrdf.rio.RDFHandlerException;
@@ -50,13 +49,14 @@
* @param dictionaryPath the dictionary path, not null
* @return an Options instance, no null
*/
+ @SuppressWarnings("deprecation")
public static Options load(File dictionaryPath) {
Map<String, String> opts = new HashMap<String, String>();
Reader inp = null;
try {
inp = new FileReader(new File(dictionaryPath, getConfigFileName()));
RDFParser parser =
RDFParserRegistry.getInstance().get(RDFFormat.TURTLE).getParser();
- Graph statements = new GraphImpl();
+ Graph statements = new org.openrdf.model.impl.GraphImpl();
parser.setRDFHandler(new StatementCollector(statements));
parser.parse(inp, "http://www.ontotext.com/lkb_gazetteer#";);
Iterator<Statement> it = statements.match(new
URIImpl("http://www.ontotext.com/lkb_gazetteer#DictionaryConfiguration";), null,
null);
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/test/PrivateRepositoryFeedTest.java
===================================================================
---
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/test/PrivateRepositoryFeedTest.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/test/PrivateRepositoryFeedTest.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -22,7 +22,8 @@
URL configReader =
this.getClass().getClassLoader().getResource("config.ttl");
String query =
IOUtils.toString(this.getClass().getClassLoader().getResourceAsStream("query.txt"));
int settingsHash = new
SettingsHashBuilder().getHash(configReader, query);
- PrivateRepositoryFeed feed = new
PrivateRepositoryFeed(configReader, query, settingsHash, new
Options(Collections.EMPTY_MAP, new File(".")));
+ @SuppressWarnings("unchecked")
+ PrivateRepositoryFeed feed = new PrivateRepositoryFeed(configReader,
query, settingsHash, new Options(Collections.EMPTY_MAP, new File(".")));
QueryResultCounter counter = new QueryResultCounter();
feed.feedTo(counter);
assertEquals(100, counter.getCount());
@@ -33,7 +34,8 @@
URL configReader = configFile.toURI().toURL();
String query = FileUtils.readFileToString(new
File(configFile.getParentFile(), "query.txt"));
int settingsHash = new
SettingsHashBuilder().getHash(configReader, query);
- PrivateRepositoryFeed feed = new
PrivateRepositoryFeed(configReader, query, settingsHash, new
Options(Collections.EMPTY_MAP, new File(".")));
+ @SuppressWarnings("unchecked")
+ PrivateRepositoryFeed feed = new PrivateRepositoryFeed(configReader,
query, settingsHash, new Options(Collections.EMPTY_MAP, new File(".")));
QueryResultCounter counter = new QueryResultCounter();
feed.feedTo(counter);
assertEquals(327, counter.getCount());
Modified:
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/util/datastore/GazetteerListFeed.java
===================================================================
---
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/util/datastore/GazetteerListFeed.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_LKB/src/com/ontotext/kim/util/datastore/GazetteerListFeed.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -8,8 +8,8 @@
import java.io.File;
import java.io.IOException;
+import java.util.Collection;
import java.util.Iterator;
-import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
@@ -70,8 +70,7 @@
private void loadDefinitions(QueryResultListener listener)
throws ResourceInstantiationException, IOException {
- @SuppressWarnings("unchecked")
- List<File> definitionPaths =
(List<File>)FileUtils.listFiles(dictionaryPath,
+ Collection<File> definitionPaths = FileUtils.listFiles(dictionaryPath,
new WildcardFileFilter(DEF_EXTENSION), null);
for(File definitionPath : definitionPaths) {
Modified: gate/trunk/plugins/Gazetteer_Ontology_Based/build.xml
===================================================================
--- gate/trunk/plugins/Gazetteer_Ontology_Based/build.xml 2014-03-15
09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Gazetteer_Ontology_Based/build.xml 2014-03-15
10:03:31 UTC (rev 17671)
@@ -17,6 +17,7 @@
<property name="gate.lib" location="${gate.home}/lib" />
<property name="doc.dir" location="doc" />
<property name="javadoc.dir" location="${doc.dir}/javadoc" />
+ <property name="gate.compile.maxwarnings" value="10000" />
<path id="classpath">
<pathelement location="${gate.jar}" />
@@ -40,8 +41,11 @@
<target name="compile" depends="init"
description="compile the source " >
<!-- Compile the java code from ${src} into ${build} -->
- <javac srcdir="${src}" destdir="${build}" debug="true" source="1.5"
target="1.5">
+ <javac srcdir="${src}" destdir="${build}" debug="true" source="1.6"
target="1.6">
<classpath refid="classpath"/>
+ <compilerarg value="-Xmaxwarns" />
+ <compilerarg value="${gate.compile.maxwarnings}" />
+ <compilerarg value="-Xlint:all" />
</javac>
</target>
Modified:
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/OntoRootGaz.java
===================================================================
---
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/OntoRootGaz.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/OntoRootGaz.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -30,7 +30,6 @@
import gate.creole.morph.Morph;
import gate.creole.ontology.InvalidURIException;
import gate.creole.ontology.Ontology;
-import gate.creole.ontology.URI;
import gate.creole.tokeniser.DefaultTokeniser;
import gate.util.OffsetComparator;
@@ -146,6 +145,8 @@
this.init();
}
+ @Override
+ @SuppressWarnings("deprecation")
public Resource init() throws ResourceInstantiationException {
// list of namespaces to be ignored when creating gazetteer list
List<String> nsToIgnore = new ArrayList<String>();
@@ -188,7 +189,7 @@
typesToConsider.add(CATConstants.TYPE_INSTANCE);
typesToConsider.add(CATConstants.TYPE_PROPERTY);
}
- fsmStates = new HashSet();
+ fsmStates = new HashSet<FSMState>();
initialState = new FSMState(this);
/* set the hidden feature to true */
FeatureMap features = Factory.newFeatureMap();
@@ -256,13 +257,13 @@
/* create uriURI for validation purposes */
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
String classType = "";
if(uri.startsWith("_")) {
- uriUri = new URI(uri, true);
+ uriUri = new gate.creole.ontology.URI(uri, true);
classType = "bNode";
} else {
- uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, false);
classType =
new ArrayList<String>(Ontology2MapManager.getInstance()
.getOntology2Map().getInstanceTypes().get(uri)).get(0);
@@ -328,10 +329,10 @@
try {
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
if(uri.startsWith("_"))
- uriUri = new URI(uri, true);
- else uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, true);
+ else uriUri = new gate.creole.ontology.URI(uri, false);
String propUri = columns[1].trim();
if((propertiesToIncludeList.size() == 0 ||
propertiesToIncludeList
.contains(propUri))
@@ -373,10 +374,10 @@
try {
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
if(uri.startsWith("_"))
- uriUri = new URI(uri, true);
- else uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, true);
+ else uriUri = new gate.creole.ontology.URI(uri, false);
String propUri = columns[1].trim();
if((propertiesToIncludeList.size() == 0 ||
propertiesToIncludeList
.contains(propUri))
@@ -419,10 +420,10 @@
try {
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
if(uri.startsWith("_"))
- uriUri = new URI(uri, true);
- else uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, true);
+ else uriUri = new gate.creole.ontology.URI(uri, false);
String shortName = uriUri.getResourceName();
if(!nsToIgnore.contains(uriUri.getNameSpace())) {
Map<String, Object> lookupFeatures =
@@ -450,10 +451,10 @@
try {
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
if(uri.startsWith("_"))
- uriUri = new URI(uri, true);
- else uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, true);
+ else uriUri = new gate.creole.ontology.URI(uri, false);
String shortName = uriUri.getResourceName();
if(!nsToIgnore.contains(uriUri.getNameSpace())) {
Map<String, Object> lookupFeatures =
@@ -464,7 +465,7 @@
Set<String> l =
Ontology2MapManager.getInstance().getOntology2Map()
.getInstanceTypes().get(uri);
- if(l == null) l = new HashSet();
+ if(l == null) l = new HashSet<String>();
lookupFeatures.put(CATConstants.CLASS_URI_LIST, l);
lookupFeatures.put(CATConstants.CLASS_URI, new ArrayList<String>(
l).get(0));
@@ -490,10 +491,10 @@
try {
// URI uriUri = new URI(uri, false);
// OURI uriUri = ontology.createOURI(uri);
- URI uriUri = null;
+ gate.creole.ontology.URI uriUri = null;
if(uri.startsWith("_"))
- uriUri = new URI(uri, true);
- else uriUri = new URI(uri, false);
+ uriUri = new gate.creole.ontology.URI(uri, true);
+ else uriUri = new gate.creole.ontology.URI(uri, false);
String shortName = uriUri.getResourceName();
if(!nsToIgnore.contains(uriUri.getNameSpace())) {
Map<String, Object> lookupFeatures =
@@ -664,9 +665,9 @@
} catch(ExecutionException ee) {
throw new ResourceInstantiationException(ee);
}
- Iterator it = applicationCorpus.iterator();
+ Iterator<Document> it = applicationCorpus.iterator();
while(it.hasNext()) {
- Document doc = (Document)it.next();
+ Document doc = it.next();
Set<String> tokenTypes = new HashSet<String>();
tokenTypes.add(ANNIEConstants.TOKEN_ANNOTATION_TYPE);
tokenTypes.add(ANNIEConstants.SPACE_TOKEN_ANNOTATION_TYPE);
Modified:
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/query/serql/SerqlUtils.java
===================================================================
---
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/query/serql/SerqlUtils.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/query/serql/SerqlUtils.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -11,19 +11,15 @@
*/
package gate.clone.ql.query.serql;
-import java.io.IOException;
-
-import java.util.HashSet;
-import java.util.Set;
-
import gate.clone.ql.CATConstants;
import gate.creole.ontology.GateOntologyException;
-import gate.creole.ontology.OConstants.QueryLanguage;
-import gate.creole.ontology.Ontology;
-import gate.creole.ontology.OntologyTupleQuery;
+import gate.creole.ontology.OConstants.OWL;
import gate.creole.ontology.OConstants.RDF;
import gate.creole.ontology.OConstants.RDFS;
-import gate.creole.ontology.OConstants.OWL;
+import gate.creole.ontology.Ontology;
+
+import java.util.HashSet;
+import java.util.Set;
//import org.openrdf.model.vocabulary.OWL;
//import org.openrdf.model.vocabulary.RDF;
//import org.openrdf.model.vocabulary.RDFS;
@@ -36,6 +32,7 @@
* @author Danica Damljanovic
*
*/
+@SuppressWarnings("deprecation")
public class SerqlUtils {
// public static Ontology ontology;
@@ -223,10 +220,12 @@
+ " {p} rdf:type {<" + OWL.OBJECTPROPERTY + ">} " + "where y in ("
+ domainClasses + ") and x in (" + domainClasses + ") and x!=y";
+ @SuppressWarnings("unused")
String domainAddition =
" select distinct p, x" + " from {p} rdfs:domain {x}" + " where x=<"
+ firstUri + "> ";
+ @SuppressWarnings("unused")
String rangeAddition =
" select distinct p, x" + " from {p} rdfs:range {x}" + " where x=<"
+ secondUri + "> ";
Modified:
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/regex/ExpressionFinder.java
===================================================================
---
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/regex/ExpressionFinder.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/regex/ExpressionFinder.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -53,7 +53,6 @@
public static String findAndSeparateCamelCases(String inputString,
String regularExpression, String substituteString) {
String afterSubstitution = null;
- int matches = 0;
Pattern pattern = null;
PatternMatcherInput input;
PatternCompiler compiler;
@@ -84,7 +83,7 @@
while(matcher.contains(input, pattern)) {
// Since we're still in the loop, fetch match that was found.
result = matcher.getMatch();
- ++matches;
+
// System.out.println("Match " + matches + ": " + result);
String foundMatch = result.toString();
String[] chars = foundMatch.split("");
Modified:
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/Ontology2Map.java
===================================================================
---
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/Ontology2Map.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/Ontology2Map.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -11,14 +11,13 @@
*/
package gate.clone.ql.utils;
+import gate.clone.ql.query.serql.SerqlUtils;
+import gate.creole.ontology.Ontology;
+
import java.util.HashMap;
-import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import gate.clone.ql.query.serql.SerqlUtils;
-import gate.creole.ontology.Ontology;
-
/**
*
* @author Danica Damljanovic
Modified:
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/StringUtil.java
===================================================================
---
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/StringUtil.java
2014-03-15 09:18:40 UTC (rev 17670)
+++
gate/trunk/plugins/Gazetteer_Ontology_Based/src/gate/clone/ql/utils/StringUtil.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -13,7 +13,6 @@
import gate.clone.ql.CATConstants;
import gate.creole.ontology.InvalidURIException;
-import gate.creole.ontology.URI;
import java.util.HashMap;
import java.util.HashSet;
@@ -40,6 +39,7 @@
* @return a Map with a key taken from the first column of the table and a
* value being a set of values taken from the second column.
*/
+ @SuppressWarnings("deprecation")
public static Map<String, Set<String>> fromStringToMap(String resultsTable) {
Map<String, Set<String>> map = new HashMap<String, Set<String>>();
@@ -55,7 +55,8 @@
}
classes.add(classUri);
try {
- URI uri = new URI(propertyUri, false);
+ @SuppressWarnings("unused")
+ gate.creole.ontology.URI uri = new
gate.creole.ontology.URI(propertyUri, false);
map.put(propertyUri, classes);
}
catch(InvalidURIException e) {
@@ -75,13 +76,15 @@
* @return a Set of Strings from the given table (string separated by new
* lines)
*/
+ @SuppressWarnings("deprecation")
public static Set<String> fromStringToSet(String resultsTable) {
Set<String> set = new HashSet<String>();
String[] rows = resultsTable.split(CATConstants.NEW_LINE);
for(String eachRow : rows) {
String uri = eachRow.trim();
try {
- URI uriUri = new URI(uri, false);
+ @SuppressWarnings("unused")
+ gate.creole.ontology.URI uriUri = new gate.creole.ontology.URI(uri,
false);
set.add(uri);
}
catch(InvalidURIException e) {
Modified: gate/trunk/plugins/Groovy/build.xml
===================================================================
--- gate/trunk/plugins/Groovy/build.xml 2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/build.xml 2014-03-15 10:03:31 UTC (rev 17671)
@@ -56,7 +56,8 @@
<!-- Compile the java and Groovy code from ${src} into ${build} -->
<groovyc srcdir="${src}" destdir="${build}">
<classpath refid="classpath"/>
- <javac debug="true" debuglevel="lines,source" source="1.5" target="1.5"
/>
+ <javac debug="true" debuglevel="lines,source" source="1.6" target="1.6">
+ </javac>
</groovyc>
</target>
Modified: gate/trunk/plugins/Groovy/src/gate/groovy/GateGroovyMethods.java
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/GateGroovyMethods.java
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/GateGroovyMethods.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -47,8 +47,8 @@
* @param closure the closure to call
* @return a list of the return values from each closure call.
*/
- public static List collect(Corpus self, Closure closure) {
- return (List)collect(self, new ArrayList(), closure);
+ public static <T> List<T> collect(Corpus self, Closure<T> closure) {
+ return (List<T>)collect(self, new ArrayList<T>(), closure);
}
/**
@@ -61,11 +61,11 @@
* @param closure the closure to call
* @return a list of the return values from each closure call.
*/
- public static Collection collect(Corpus self, Collection coll,
- Closure closure) {
+ public static <T> Collection<T> collect(Corpus self, Collection<T> coll,
+ Closure<T> closure) {
for(int i = 0; i < self.size(); i++) {
boolean docWasLoaded = self.isDocumentLoaded(i);
- Document doc = (Document)self.get(i);
+ Document doc = self.get(i);
coll.add(closure.call(doc));
if(!docWasLoaded) {
self.unloadDocument(doc);
@@ -85,10 +85,10 @@
* @param closure the closure to call
* @return the corpus.
*/
- public static Object each(Corpus self, Closure closure) {
+ public static <T> Object each(Corpus self, Closure<T> closure) {
for(int i = 0; i < self.size(); i++) {
boolean docWasLoaded = self.isDocumentLoaded(i);
- Document doc = (Document)self.get(i);
+ Document doc = self.get(i);
closure.call(doc);
if(!docWasLoaded) {
self.unloadDocument(doc);
@@ -108,10 +108,10 @@
* @param closure the closure to call
* @return the corpus.
*/
- public static Object eachWithIndex(Corpus self, Closure closure) {
+ public static <T> Object eachWithIndex(Corpus self, Closure<T> closure) {
for(int i = 0; i < self.size(); i++) {
boolean docWasLoaded = self.isDocumentLoaded(i);
- Document doc = (Document)self.get(i);
+ Document doc = self.get(i);
closure.call(new Object[] {doc, i});
if(!docWasLoaded) {
self.unloadDocument(doc);
@@ -129,7 +129,8 @@
* (as start and end return Long).
* @see AnnotationSet#getContained(Long, Long)
*/
- public static AnnotationSet getAt(AnnotationSet self, Range range) {
+ @SuppressWarnings("unchecked")
+ public static AnnotationSet getAt(AnnotationSet self, Range<?> range) {
if(range.getFrom() instanceof Number) {
return self.getContained(
Long.valueOf(((Number)range.getFrom()).longValue()),
@@ -154,7 +155,7 @@
* @param range
* @return
*/
- public static DocumentContent getAt(DocumentContent self, Range range) {
+ public static DocumentContent getAt(DocumentContent self, Range<?> range) {
if(range.getFrom() instanceof Number) {
try {
return self.getContent(
@@ -203,7 +204,7 @@
* @param closure
* @return the value returned from the closure
*/
- public static Object withResource(Resource self, Closure closure) {
+ public static <T> T withResource(Resource self, Closure<T> closure) {
try {
return closure.call(self);
}
Modified: gate/trunk/plugins/Groovy/src/gate/groovy/GroovySupport.java
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/GroovySupport.java
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/GroovySupport.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -54,6 +54,8 @@
@CreoleResource(name = "Groovy support for GATE", isPrivate = true, tool =
true,
autoinstances = @AutoInstance)
public class GroovySupport extends AbstractResource implements
ActionsPublisher {
+
+ private static final long serialVersionUID = 4763983982544551334L;
/**
* Standard list of import statements that are available to any groovy script
* or console in GATE.
@@ -105,7 +107,7 @@
private List<Action> actions;
- public List getActions() {
+ public List<Action> getActions() {
if(actions == null) {
actions = new ArrayList<Action>();
actions.add(new AbstractAction("Groovy Console",
MainFrame.getIcon("groovyConsole")) {
@@ -145,6 +147,7 @@
* of Console. So we have to implement the property setter here,
* delegating to the real private field in the superclass.
*/
+ @SuppressWarnings("unused")
public void setScriptRunning(boolean b) {
try {
Field f =
groovy.ui.Console.class.getDeclaredField("scriptRunning");
Modified: gate/trunk/plugins/Groovy/src/gate/groovy/ScriptPR.java
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/ScriptPR.java 2014-03-15
09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/ScriptPR.java 2014-03-15
10:03:31 UTC (rev 17671)
@@ -53,6 +53,8 @@
ProcessingResource,
ControllerAwarePR {
+ private static final long serialVersionUID = 7563063357390091727L;
+
/**
* Groovy script file
*/
Modified: gate/trunk/plugins/Groovy/src/gate/groovy/ScriptableController.groovy
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/ScriptableController.groovy
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/ScriptableController.groovy
2014-03-15 10:03:31 UTC (rev 17671)
@@ -28,7 +28,7 @@
icon = "/gate/groovy/scriptable-controller")
public class ScriptableController extends SerialController
implements CorpusController, LanguageAnalyser {
-
+
protected static final Logger log = Logger.getLogger(ScriptableController)
/**
@@ -430,7 +430,7 @@
* Yes, this is another typo in the superclass, the method really is called
* getOffendingP(r)ocessingResources.
*/
- public List getOffendingPocessingResources() {
+ public List<ProcessingResource> getOffendingPocessingResources() {
return []
}
Modified:
gate/trunk/plugins/Groovy/src/gate/groovy/gui/ControllerScriptEditor.java
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/gui/ControllerScriptEditor.java
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/gui/ControllerScriptEditor.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -22,6 +22,8 @@
implements DocumentListener,
PropertyChangeListener {
+ private static final long serialVersionUID = -3690719863931044767L;
+
protected ConsoleTextEditor editor;
protected ScriptableController controller;
Modified: gate/trunk/plugins/Groovy/src/gate/groovy/gui/ScriptPREditor.java
===================================================================
--- gate/trunk/plugins/Groovy/src/gate/groovy/gui/ScriptPREditor.java
2014-03-15 09:18:40 UTC (rev 17670)
+++ gate/trunk/plugins/Groovy/src/gate/groovy/gui/ScriptPREditor.java
2014-03-15 10:03:31 UTC (rev 17671)
@@ -46,6 +46,8 @@
ProgressListener,
DocumentListener {
+ private static final long serialVersionUID = -3397858340190887863L;
+
private ConsoleTextEditor editor;
private ScriptPR pr;
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