rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k | meta stringlengths 141 403 |
|---|---|---|---|
return -1; | return 14; | private final int jjStopStringLiteralDfa_0(int pos, long active0){ switch (pos) { case 0: if ((active0 & 0x40000L) != 0L) { jjmatchedKind = 32; return -1; } if ((active0 & 0x40020000L) != 0L) return 10; if ((active0 & 0x80000000L) != 0L) ... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/2e6a5e583cccdc19c543caf9a1fb259181c98cb6/WikiParserTokenManager.java/buggy/wiki/src/org/tcdi/opensource/wiki/parser/WikiParserTokenManager.java |
if ((active0 & 0x80000000L) != 0L) return 49; | if ((active0 & 0x200000000L) != 0L) return 54; | private final int jjStopStringLiteralDfa_0(int pos, long active0){ switch (pos) { case 0: if ((active0 & 0x40000L) != 0L) { jjmatchedKind = 32; return -1; } if ((active0 & 0x40020000L) != 0L) return 10; if ((active0 & 0x80000000L) != 0L) ... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/2e6a5e583cccdc19c543caf9a1fb259181c98cb6/WikiParserTokenManager.java/buggy/wiki/src/org/tcdi/opensource/wiki/parser/WikiParserTokenManager.java |
tree.putClientProperty("JTree.lineStyle", "Angled"); | private TreeViewImageSet createTree(ImageDisplay node) { tree = new JTree(); tree.setShowsRootHandles(true); tree.setCellRenderer(new TreeCellRenderer(true, false)); tree.putClientProperty("JTree.lineStyle", "Angled"); tree.getSelectionModel().setSelectionMode( T... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3b273af3a5320ab0a054540f14a3c299ff01de69/TreeViewUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/hiviewer/treeview/TreeViewUI.java | |
ExperimenterData e = (ExperimenterData) it.next(); g.linkExperimenter((Experimenter) mapper.map(e)); | ExperimenterData ed = (ExperimenterData) it.next(); Experimenter e = (Experimenter) mapper.map( ed ); if ( ! linked( e.findGroupExperimenterMap( g ))) g.linkExperimenter( e ); | public IObject fillIObject( IObject obj, ReverseModelMapper mapper) { if ( obj instanceof ExperimenterGroup) { ExperimenterGroup g = (ExperimenterGroup) obj; if (super.fill(g)) { g.setName(this.getName()); // TODO what to do with DESCRIP... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/b7d44d4a82558acd2336a661072dda1f38cfc0b3/GroupData.java/clean/components/shoola-adapter/src/pojos/GroupData.java |
PixelsService service = PixelsService.getInstance(); | PixelsService service = new PixelsService(PixelsService.ROOT_DEFAULT); | protected void setUp() { pixels = new Pixels(); pixels.setId(1L); pixels.setSizeX(256); pixels.setSizeY(256); pixels.setSizeZ(64); pixels.setSizeC(3); pixels.setSizeT(50); PixelsType type = new PixelsType(); pixels.setPixelsType(type)... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ae0b01fad17fcacba3ec0999ca1ad645f389b5f9/OutOfBoundsUnitTest.java/buggy/components/omeio-nio/test/ome/io/nio/utests/OutOfBoundsUnitTest.java |
return; | throw new NameError(ruby, "undefined method '" + name + "' for " + (isModule() ? "module" : "class") + " '" + toName() + "'"); | public void aliasMethod(String name, String oldName) { testFrozen(); if (oldName.equals(name)) { return; } if (this == getRuby().getClasses().getObjectClass()) { getRuby().secure(4); } MethodNode methodNode = searchMethod(oldName); RubyModule or... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java |
public RubyObject const_get(RubySymbol symbol) { | public RubyObject const_get(RubyObject symbol) { | public RubyObject const_get(RubySymbol symbol) { String name = symbol.toId(); if (!IdUtil.isConstant(name)) { throw new NameError(getRuby(), "wrong constant name " + name); } return getConstant(name); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java |
public RubyObject const_set(RubySymbol symbol, RubyObject value) { | public RubyObject const_set(RubyObject symbol, RubyObject value) { | public RubyObject const_set(RubySymbol symbol, RubyObject value) { String name = symbol.toId(); if (!IdUtil.isConstant(name)) { throw new NameError(getRuby(), "wrong constant name " + name); } setConstant(name, value); return value; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java |
RubyModule origin = body.getMethodOrigin(); | public void exportMethod(String name, int noex) { if (this == getRuby().getClasses().getObjectClass()) { getRuby().secure(4); } MethodNode body = searchMethod(name); RubyModule origin = body.getMethodOrigin(); if (body == null && isModule()) { body = getRuby(... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java | |
origin = body.getMethodOrigin(); | public void exportMethod(String name, int noex) { if (this == getRuby().getClasses().getObjectClass()) { getRuby().secure(4); } MethodNode body = searchMethod(name); RubyModule origin = body.getMethodOrigin(); if (body == null && isModule()) { body = getRuby(... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java | |
if (this == origin) { | if (this == body.getMethodOrigin()) { | public void exportMethod(String name, int noex) { if (this == getRuby().getClasses().getObjectClass()) { getRuby().secure(4); } MethodNode body = searchMethod(name); RubyModule origin = body.getMethodOrigin(); if (body == null && isModule()) { body = getRuby(... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java |
funcall("singleton_added", RubySymbol.newSymbol(getRuby(), name)); | funcall("singleton_method_added", RubySymbol.newSymbol(getRuby(), name)); | public RubyModule module_function(RubyObject[] args) { if (getRuby().getSafeLevel() >= 4 && !isTaint()) { throw new RubySecurityException(getRuby(), "Insecure: can't change method visibility"); } if (args.length == 0) { getRuby().setActMethodScope(Constants.SCOPE_MODFUNC);... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java |
clone.setMethods(new RubyHashMap()); | public RubyObject rbClone() { RubyModule clone = new RubyModule(getRuby(), getRubyClass(), getSuperClass()); clone.setupClone(this); if (getInstanceVariables() != null) { clone.setInstanceVariables(getInstanceVariables().cloneRubyMap()); } // clone the methods. i... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java | |
return; | public void setClassVar(String name, RubyObject value) { RubyModule tmp = this; while (tmp != null) { if (tmp.getInstanceVariables() != null && tmp.getInstanceVariables().get(name) != null) { if (tmp.isTaint() && getRuby().getSafeLevel() >= 4) { throw new R... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/d31a76ee29d5978a9bec41e3ac9134cee024bcab/RubyModule.java/clean/org/jruby/RubyModule.java | |
public static IRubyObject s_digest(IRubyObject recv, RubyString str) { | public static IRubyObject s_digest(IRubyObject recv, IRubyObject str) { | public static IRubyObject s_digest(IRubyObject recv, RubyString str) { String name = ((RubyClass)recv).getClassVar("metadata").toString(); try { MessageDigest md = MessageDigest.getInstance(name); return recv.getRuntime().newString(new String(md.digest(str.toS... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/af3894ea0dfb3e47ce20ec84c999cbcb97567438/RubyDigest.java/clean/src/org/jruby/RubyDigest.java |
public static IRubyObject s_hexdigest(IRubyObject recv, RubyString str) { | public static IRubyObject s_hexdigest(IRubyObject recv, IRubyObject str) { | public static IRubyObject s_hexdigest(IRubyObject recv, RubyString str) { String name = ((RubyClass)recv).getClassVar("metadata").toString(); try { MessageDigest md = MessageDigest.getInstance(name); return recv.getRuntime().newString(toHex(md.digest(str.toStr... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/af3894ea0dfb3e47ce20ec84c999cbcb97567438/RubyDigest.java/clean/src/org/jruby/RubyDigest.java |
cDigestBase.defineSingletonMethod("digest",basecb.getSingletonMethod("s_digest",RubyString.class)); cDigestBase.defineSingletonMethod("hexdigest",basecb.getSingletonMethod("s_hexdigest",RubyString.class)); | cDigestBase.defineSingletonMethod("digest",basecb.getSingletonMethod("s_digest",IRubyObject.class)); cDigestBase.defineSingletonMethod("hexdigest",basecb.getSingletonMethod("s_hexdigest",IRubyObject.class)); | public static void createDigest(IRuby runtime) { RubyModule mDigest = runtime.defineModule("Digest"); RubyClass cDigestBase = mDigest.defineClassUnder("Base",runtime.getObject()); CallbackFactory basecb = runtime.callbackFactory(Base.class); cDigestBase.defineSingletonMethod("new... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/af3894ea0dfb3e47ce20ec84c999cbcb97567438/RubyDigest.java/clean/src/org/jruby/RubyDigest.java |
super(); | public LoadService(Ruby runtime) { super(); this.runtime = runtime; } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java | |
public void init(Ruby runtime, List additionalDirectories) { | public void init(List additionalDirectories) { | public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java |
addPath((String)iter.next()); | addPath((String) iter.next()); | public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java |
public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java | ||
String rubyDir = jrubyHome + File.separatorChar + "lib" + File.separatorChar + "ruby" + File.separatorChar; | char sep = File.separatorChar; String rubyDir = jrubyHome + sep + "lib" + sep + "ruby" + sep; | public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java |
addPath(rubyDir + "site_ruby" + File.separatorChar + Constants.RUBY_MAJOR_VERSION); addPath(rubyDir + "site_ruby" + File.separatorChar + Constants.RUBY_MAJOR_VERSION + File.separatorChar + "java"); | addPath(rubyDir + "site_ruby" + sep + Constants.RUBY_MAJOR_VERSION); addPath(rubyDir + "site_ruby" + sep + Constants.RUBY_MAJOR_VERSION + sep + "java"); | public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java |
addPath(rubyDir + Constants.RUBY_MAJOR_VERSION + File.separatorChar + "java"); | addPath(rubyDir + Constants.RUBY_MAJOR_VERSION + sep + "java"); | public void init(Ruby runtime, List additionalDirectories) { for (Iterator iter = additionalDirectories.iterator(); iter.hasNext();) { addPath((String)iter.next()); } if (runtime.getSafeLevel() == 0) { String jrubyLib = System.getProperty("jruby.lib"); if (jruby... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/61503e7396c70acb6ed9f50922ff044d1fcc4bcc/LoadService.java/clean/src/org/jruby/internal/runtime/load/LoadService.java |
List constantNames = new ArrayList(); | ArrayList constantNames = new ArrayList(); | public RubyArray constants() { List constantNames = new ArrayList(); Iterator iter = getRuby().getClasses().nameIterator(); while (iter.hasNext()) { String name = (String) iter.next(); if (IdUtil.isConstant(name)) { constantNames.add(RubyString.newString(get... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a42a5780d9d19f5b3f27bdc079684319c5596e54/RubyModule.java/clean/org/jruby/RubyModule.java |
rubyClass.defineMethod("each", new JavaEachMethod("hasNext", "next")); | rubyClass.defineMethod("each", new JavaEachMethod(null, "hasNext", "next")); | private void addDefaultModules(RubyClass rubyClass) { if (rubyClass.isMethodDefined("hasNext") && rubyClass.isMethodDefined("next")) { rubyClass.includeModule(ruby.getClasses().getEnumerableModule()); rubyClass.defineMethod("each", new JavaEachMethod("hasNext", "next")); } else i... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/1ceedf02ac15d7325cfcf505ca74f35c5bc4a258/JavaSupport.java/buggy/org/jruby/javasupport/JavaSupport.java |
rubyClass.defineMethod("each", new JavaEachMethod("hasMoreElements", "nextElement")); | rubyClass.defineMethod("each", new JavaEachMethod(null, "hasMoreElements", "nextElement")); } else if (rubyClass.isMethodDefined("iterator")) { rubyClass.includeModule(ruby.getClasses().getEnumerableModule()); rubyClass.defineMethod("each", new JavaEachMethod("iterator", "hasNext", "next")); | private void addDefaultModules(RubyClass rubyClass) { if (rubyClass.isMethodDefined("hasNext") && rubyClass.isMethodDefined("next")) { rubyClass.includeModule(ruby.getClasses().getEnumerableModule()); rubyClass.defineMethod("each", new JavaEachMethod("hasNext", "next")); } else i... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/1ceedf02ac15d7325cfcf505ca74f35c5bc4a258/JavaSupport.java/buggy/org/jruby/javasupport/JavaSupport.java |
model.setNodeForProperty(Browser.SELECTED_DISPLAY_PROPERTY, d); | public void mouseExited(MouseEvent me) { if (model.isRollOver()) return; ImageDisplay d = model.getLastSelectedDisplay(); if (d != null) view.setTitle(model.currentPathString(d)); else view.setTitle(""); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/58be91fb535c971d0bef1fde12344382b140273b/BrowserControl.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/browser/BrowserControl.java | |
kernelModule.getRuby().defineGlobalFunction( "method_missing", CallbackFactory.getOptMethod(RubyObject.class, "method_missing", RubyObject.class)); | Ruby ruby = kernelModule.getRuby(); ruby.defineGlobalFunction("method_missing", CallbackFactory.getOptMethod(RubyObject.class, "method_missing", RubyObject.class)); ruby.defineGlobalFunction("eval", CallbackFactory.getOptMethod(RubyObject.class, "eval", RubyString.class)); | public static void createObjectClass(RubyModule kernelModule) { // TODO: convert to CallbackFactory invokes. Callback clone = new ReflectionCallbackMethod(RubyObject.class, "rbClone"); Callback dup = new ReflectionCallbackMethod(RubyObject.class, "dup"); Callback equal = new ReflectionCa... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b3fad11fe9fed3c3b955874e822c0e093e06dfc8/RubyObject.java/clean/org/jruby/RubyObject.java |
public void show(Component arg0, int arg1, int arg2) { super.show(arg0, arg1, arg2); Point p = arg0.getLocationOnScreen(); final Point displayPoint = new Point(p.x+arg1,p.y+arg2); System.err.println("display="+displayPoin... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/28e98417641b00a2e12a791f10f204dc4562dec1/PopupMenuFactory.java/clean/SRC/org/openmicroscopy/shoola/agents/browser/ui/PopupMenuFactory.java | ||
System.err.println("display="+displayPoint); | public void show(Component arg0, int arg1, int arg2) { super.show(arg0, arg1, arg2); Point p = arg0.getLocationOnScreen(); final Point displayPoint = new Point(p.x+arg1,p.y+arg2); System.err.println("display="+displayPoin... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/28e98417641b00a2e12a791f10f204dc4562dec1/PopupMenuFactory.java/clean/SRC/org/openmicroscopy/shoola/agents/browser/ui/PopupMenuFactory.java | |
public Set findCGCIHierarchies(Set arg0) { /* return null; */ throw new RuntimeException("implement me"); | public Set findCGCIHierarchies(final Set arg0) { if (null == arg0 || arg0.size() == 0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = s... | public Set findCGCIHierarchies(Set arg0) { // TODO Auto-generated method stub /* return null; */ throw new RuntimeException("implement me"); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public Map findDatasetAnnotations(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashMap(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Map) ht.execute(new HibernateCallback() { public Object doInHi... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
if (null == arg0 || arg0.size()==0) { return new HashMap(); } | if (null == arg0 || arg0.size() == 0) { return new HashMap(); } | public Map findDatasetAnnotations(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashMap(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Map) ht.execute(new HibernateCallback() { public Object doInHi... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("findDatasetAnn"); q.setParameterList("ds_list", arg0, new IntegerType()); | Query q = session.getNamedQuery("findImageAnnWithID"); q.setParameterList("img_list", arg0, new IntegerType()); q.setInteger("expId", arg1); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findDatasetAnn"); q.setParameterList("ds_list", arg0, new IntegerType()); Map map = findDatasetAnnotations(q); emptyCache()... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Map map = findDatasetAnnotations(q); | Map map = findImageAnnotations(q); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findDatasetAnn"); q.setParameterList("ds_list", arg0, new IntegerType()); Map map = findDatasetAnnotations(q); emptyCache()... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("findDatasetAnnWithID"); | Query q = session.getNamedQuery("findDatasetAnn"); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findDatasetAnnWithID"); q.setParameterList("ds_list", arg0, new IntegerType()); q.setInteger("expId", arg1); Map map = find... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
q.setInteger("expId", arg1); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findDatasetAnnWithID"); q.setParameterList("ds_list", arg0, new IntegerType()); q.setInteger("expId", arg1); Map map = find... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | |
public Map findImageAnnotations(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashMap(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Map) ht.execute(new HibernateCallback() { public Object doInHibe... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
if (null == arg0 || arg0.size()==0) { return new HashMap(); } | if (null == arg0 || arg0.size() == 0) { return new HashMap(); } | public Map findImageAnnotations(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashMap(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Map) ht.execute(new HibernateCallback() { public Object doInHibe... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("findImageAnn"); | newCache(); Query q = session.getNamedQuery("findCGCI"); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findImageAnn"); q.setParameterList("img_list", arg0, new IntegerType()); Map map = findImageAnnotations(q); emptyCache(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Map map = findImageAnnotations(q); | List result = q.list(); Set imagesAll = new HashSet(result); if (null == imagesAll || imagesAll.size() == 0) { return new HashSet(); } Set hierarchies = new HashSet(); Iterator i = imagesAll.iterator(); while (i.hasNext()) { Image img = (Image) i.next(); ImageData id = go(img, false); Set classifications = img.get... | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findImageAnn"); q.setParameterList("img_list", arg0, new IntegerType()); Map map = findImageAnnotations(q); emptyCache(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
return map; | return hierarchies; | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findImageAnn"); q.setParameterList("img_list", arg0, new IntegerType()); Map map = findImageAnnotations(q); emptyCache(); ... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("findImageAnnWithID"); | Query q = session.getNamedQuery("findImageAnn"); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findImageAnnWithID"); q.setParameterList("img_list", arg0, new IntegerType()); q.setInteger("expId", arg1); Map map = findI... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
q.setInteger("expId", arg1); | public Object doInHibernate(Session session) throws HibernateException { Query q = session.getNamedQuery("findImageAnnWithID"); q.setParameterList("img_list", arg0, new IntegerType()); q.setInteger("expId", arg1); Map map = findI... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | |
if (null == arg0 || arg0.size()==0) { return new HashSet(); } | if (null == arg0 || arg0.size() == 0) { return new HashSet(); } | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
ImageData id = go(img,false); | ImageData id = go(img, false); | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (datasets == null || datasets.size() < 1){ | if (datasets == null || datasets.size() < 1) { | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
} else { | } else { | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
DatasetData dd = go(ds,false); | DatasetData dd = go(ds, false); | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (null == dd.images) dd.images = new HashSet(); | if (null == dd.images) dd.images = new HashSet(); | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
while (p.hasNext()){ | while (p.hasNext()) { | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
ProjectData pd = go(prj,false); if (null == pd.datasets) pd.datasets = new HashSet(); | ProjectData pd = go(prj, false); if (null == pd.datasets) pd.datasets = new HashSet(); | public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public Set findPDIHierarchies(final Set arg0) { // CONTRACT if (null == arg0 || arg0.size()==0) { return new HashSet(); } HibernateTemplate ht = new HibernateTemplate(sessions); return (Set) ht.execute(new HibernateCallback() { public Object doInHibernate(Session session... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
ImageData id = go(img,false); | ImageData id = go(img, false); | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (datasets == null || datasets.size() < 1){ | if (datasets == null || datasets.size() < 1) { | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
} else { | } else { | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
DatasetData dd = go(ds,false); | DatasetData dd = go(ds, false); | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (null == dd.images) dd.images = new HashSet(); | if (null == dd.images) dd.images = new HashSet(); | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
while (p.hasNext()){ | while (p.hasNext()) { | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
ProjectData pd = go(prj,false); if (null == pd.datasets) pd.datasets = new HashSet(); | ProjectData pd = go(prj, false); if (null == pd.datasets) pd.datasets = new HashSet(); | public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public Object doInHibernate(Session session) throws HibernateException { newCache(); //QUERY Query q = session.getNamedQuery("findPDI"); q.setParameterList("img_list", arg0, new IntegerType()); List result = q.list... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
if (! CategoryGroupData.class.equals(arg0) && ! CategoryData.class.equals(arg0)) { | if (!CategoryGroupData.class.equals(arg0) && !CategoryData.class.equals(arg0)) { | public DataObject loadCGCIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! CategoryGroupData.class.equals(arg0) && ! CategoryData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadCGCIHierarchy() must be CategoryGroupData or... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("CGCI_by_"+arg0.getName()); | Query q = session.getNamedQuery("CGCI_by_" + arg0.getName()); | public DataObject loadCGCIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! CategoryGroupData.class.equals(arg0) && ! CategoryData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadCGCIHierarchy() must be CategoryGroupData or... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (arg0.equals(CategoryData.class)){ Category result = (Category) q.uniqueResult(); if (null == result) return null; | if (arg0.equals(CategoryData.class)) { Category result = (Category) q.uniqueResult(); if (null == result) return null; | public DataObject loadCGCIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! CategoryGroupData.class.equals(arg0) && ! CategoryData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadCGCIHierarchy() must be CategoryGroupData or... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
CategoryGroup result = (CategoryGroup) q.uniqueResult(); if (null == result) return null; | CategoryGroup result = (CategoryGroup) q.uniqueResult(); if (null == result) return null; | public DataObject loadCGCIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! CategoryGroupData.class.equals(arg0) && ! CategoryData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadCGCIHierarchy() must be CategoryGroupData or... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("CGCI_by_"+arg0.getName()); | Query q = session.getNamedQuery("CGCI_by_" + arg0.getName()); | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("CGCI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(CategoryData.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (arg0.equals(CategoryData.class)){ Category result = (Category) q.uniqueResult(); if (null == result) return null; | if (arg0.equals(CategoryData.class)) { Category result = (Category) q.uniqueResult(); if (null == result) return null; | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("CGCI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(CategoryData.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
CategoryGroup result = (CategoryGroup) q.uniqueResult(); if (null == result) return null; | CategoryGroup result = (CategoryGroup) q.uniqueResult(); if (null == result) return null; | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("CGCI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(CategoryData.... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { | if (!ProjectData.class.equals(arg0) && !DatasetData.class.equals(arg0)) { | public DataObject loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be ProjectData or DatasetData.")... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
public DataObject loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be ProjectData or DatasetData.")... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
Query q = session.getNamedQuery("PDI_by_"+arg0.getName()); | Query q = session.getNamedQuery("PDI_by_" + arg0.getName()); | public DataObject loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be ProjectData or DatasetData.")... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (arg0.equals(DatasetData.class)){ Dataset result = (Dataset) q.uniqueResult(); if (null == result) return null; | if (arg0.equals(DatasetData.class)) { Dataset result = (Dataset) q.uniqueResult(); if (null == result) return null; | public DataObject loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be ProjectData or DatasetData.")... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Project result = (Project) q.uniqueResult(); if (null == result) return null; | Project result = (Project) q.uniqueResult(); if (null == result) return null; | public DataObject loadPDIHierarchy(final Class arg0, final int arg1) { // CONTRACT if (! ProjectData.class.equals(arg0) && ! DatasetData.class.equals(arg0)) { throw new IllegalArgumentException( "Class parameter for loadPDIHierarchy() must be ProjectData or DatasetData.")... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Query q = session.getNamedQuery("PDI_by_"+arg0.getName()); | Query q = session.getNamedQuery("PDI_by_" + arg0.getName()); | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("PDI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(DatasetData.cl... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
if (arg0.equals(DatasetData.class)){ Dataset result = (Dataset) q.uniqueResult(); if (null == result) return null; | if (arg0.equals(DatasetData.class)) { Dataset result = (Dataset) q.uniqueResult(); if (null == result) return null; | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("PDI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(DatasetData.cl... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
Project result = (Project) q.uniqueResult(); if (null == result) return null; | Project result = (Project) q.uniqueResult(); if (null == result) return null; | public Object doInHibernate(Session session) throws HibernateException { newCache(); Query q = session.getNamedQuery("PDI_by_"+arg0.getName()); q.setLong("id", arg1); DataObject dobj; if (arg0.equals(DatasetData.cl... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java |
void toCache(Object key, Object value) { // FIXME Why are there NULLs in the Cache!!!! ((Map) cache.get()).put(key, value); // TODO return either original value or a new one -- tough. Not when all inherit from a single DataObject!!?? } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/8442e37c365d8ade04f3bf94b6b000049c740d2a/HierarchyBrowsingImpl.java/buggy/components/wars/srv/src/java/org/ome/omero/logic/HierarchyBrowsingImpl.java | ||
if (p == null) { wc.getLog("RecentChanges").error ("WikiPage for " + pageNames[x] + " not found in wiki system. Skipping"); continue; } | public void perform(WikiSystem wiki, WebContext wc, WikiUser user, WikiPage page) throws PageAction.PageActionException { List pages = new ArrayList (); String[] pageNames = wiki.getCurrentPageNames(); double days = 7D; // figure out how many days to show if (wc.getForm ("days") !... | 52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/db4fefa87dec8d716fc2d84cb0b5647665ec65f8/RecentChangesAction.java/buggy/wiki/src/org/tcdi/opensource/wiki/servlet/RecentChangesAction.java | |
if (user == null) return; if (groups == null) return; Experimenter foundUser = iQuery.get(Experimenter.class,user.getId()); for (ExperimenterGroup group : groups) { ExperimenterGroup foundGroup = iQuery.get(ExperimenterGroup.class, group.getId()); foundUser.linkExperimenterGroup(foundGroup); } iUpdate.flush(); | public void addGroups(Experimenter user, ExperimenterGroup[] groups) { // TODO Auto-generated method stub } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/d4a4fd19dcb38c276cd70b93f33ec7f9c4156452/AdminImpl.java/clean/components/server/src/ome/logic/AdminImpl.java | |
if (model.getTreeView() == null) model.createTreeView(); | void showTreeView(boolean b) { Container container = getContentPane(); if (b) { JSplitPane treeViewPane = new JSplitPane(); treeViewPane.setOrientation(JSplitPane.HORIZONTAL_SPLIT); treeViewPane.setOneTouchExpandable(true); treeViewPane.setContinuousLayou... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/df2a60bc22b2182d3cbb3f204d3ec09a6dac6a1d/HiViewerWin.java/buggy/SRC/org/openmicroscopy/shoola/agents/hiviewer/view/HiViewerWin.java | |
channel.close(); | if (channel != null) channel.close(); | public void close() throws IOException { channel.close(); } | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e90cfb321efdaad7f6cf723d38ed886d6dbaf609/FileBuffer.java/buggy/components/romio/src/ome/io/nio/FileBuffer.java |
this.positionFactory = new SourcePositionFactory(); | this.positionFactory = new SourcePositionFactory(this); | public LexerSource(String sourceName, Reader reader) { this.sourceName = sourceName; this.reader = reader; this.positionFactory = new SourcePositionFactory(); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/b1293eda8454686e846e2a9837b348e2983bb423/LexerSource.java/clean/src/org/jruby/lexer/yacc/LexerSource.java |
br = new BufferedReader(new FileReader(sourceFile)); | br = new BufferedReader(new InputStreamReader(new FileInputStream(sourceFile), "UTF-8")); } catch (UnsupportedEncodingException e) { return "<p>Unable to open " + sourceFile.getAbsolutePath() + ": The encoding 'UTF-8' is not supported by your JVM.</p>"; | private String generateHtmlizedJavaSource(SourceFileData sourceFileData) { File sourceFile = null; try { sourceFile = finder.getFileForSource(sourceFileData.getName()); } catch (IOException e) { return "<p>Unable to locate " + sourceFileData.getName() + ". Have you specified the source directory?</p>"; ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/84e7aec08b6ae2534d7a85ebb3c07a0ec1dec0c8/HTMLReport.java/clean/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java |
out = new PrintStream(new FileOutputStream(file)); | out = new PrintStream(new FileOutputStream(file), false, "UTF-8"); | private void generateOverview(PackageData packageData) throws IOException { Iterator iter; String filename; if (packageData == null) { filename = "frame-summary.html"; } else { filename = "frame-summary-" + packageData.getName() + ".html"; } File file = new File(destinationDir, filename); PrintStream out... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/84e7aec08b6ae2534d7a85ebb3c07a0ec1dec0c8/HTMLReport.java/clean/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java |
out = new PrintStream(new FileOutputStream(file)); | out = new PrintStream(new FileOutputStream(file), false, "UTF-8"); | private void generatePackageList() throws IOException { File file = new File(destinationDir, "frame-packages.html"); PrintStream out = null; try { out = new PrintStream(new FileOutputStream(file)); out .println("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\""); out .println(" ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/84e7aec08b6ae2534d7a85ebb3c07a0ec1dec0c8/HTMLReport.java/clean/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java |
out = new PrintStream(new FileOutputStream(file)); | out = new PrintStream(new FileOutputStream(file), false, "UTF-8"); | private void generateSourceFile(SourceFileData sourceFileData) throws IOException { if (!sourceFileData.containsInstrumentationInfo()) { LOGGER.info("Data file does not contain instrumentation " + "information for the file " + sourceFileData.getName() + ". Ensure this class was instrumented, and this " ... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/84e7aec08b6ae2534d7a85ebb3c07a0ec1dec0c8/HTMLReport.java/clean/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java |
out = new PrintStream(new FileOutputStream(file)); | out = new PrintStream(new FileOutputStream(file), false, "UTF-8"); | private void generateSourceFileList(PackageData packageData) throws IOException { String filename; Collection sourceFiles; if (packageData == null) { filename = "frame-sourcefiles.html"; sourceFiles = projectData.getSourceFiles(); } else { filename = "frame-sourcefiles-" + packageData.getName() + ".html... | 50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/84e7aec08b6ae2534d7a85ebb3c07a0ec1dec0c8/HTMLReport.java/clean/cobertura/src/net/sourceforge/cobertura/reporting/html/HTMLReport.java |
args[0] = new RubyFixnum(ruby, 18000000); | args[0] = RubyFixnum.newFixnum(ruby, 18000000); | public void setUp() { ruby = Ruby.getDefaultInstance(null); rubyTime = ruby.getClasses().getTimeClass(); RubyObject[] args = new RubyObject[1]; args[0] = new RubyFixnum(ruby, 18000000); nineTeenSeventy = RubyTime.s_at(ruby, rubyTime, args); } | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/afb67c3765f6466c476317e6bb0c72f6593f05f3/TestRubyTime.java/clean/org/jruby/test/TestRubyTime.java |
registry = control.getRegistry(); pixelsID = control.getCurPixelsID(); | public PlayerManager(Player view, ViewerCtrl control, int max, int index, int s, int e) { this.view = view; this.control = control; setIndex(index, max, s, e); movieType = Player.LOOP; registry = control.getRegistry(); pixelsID = control.getCurPixelsID(); playing = fals... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/480bfd2454ecc542e0e0b43caa0d0de01b218f9f/PlayerManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/viewer/movie/PlayerManager.java | |
control.resetZField(v); } else control.resetTField(v); PlaneDef def = new PlaneDef(PlaneDef.XY, t); def.setZ(z); RenderImage render = new RenderImage(pixelsID, def); registry.getEventBus().post(render); | } control.renderImage(z, t); | private void renderImage(int v) { int t = v, z = curValue; if (index == Player.MOVIE_Z) { t = curValue; z = v; control.resetZField(v); } else control.resetTField(v); PlaneDef def = new PlaneDef(PlaneDef.XY, t); def.setZ(z); RenderImage render = new R... | 54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/480bfd2454ecc542e0e0b43caa0d0de01b218f9f/PlayerManager.java/buggy/SRC/org/openmicroscopy/shoola/agents/viewer/movie/PlayerManager.java |
public RubyObject call(RubyObject recv, RubyId mid, RubyObject[] args, int scope) { | public RubyObject call(RubyObject recv, RubyId mid, RubyPointer args, int scope) { | public RubyObject call(RubyObject recv, RubyId mid, RubyObject[] args, int scope) { RubyMethodCacheEntry ent = RubyMethodCacheEntry.getEntry(getRuby(), this, mid); RubyModule klass = this; RubyId id = mid; int noex; Node body; if (ent != null) { i... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java |
public RubyObject call0(RubyObject recv, RubyId id, RubyObject[] args, Node body, boolean noSuper) { | public RubyObject call0(RubyObject recv, RubyId id, RubyPointer args, Node body, boolean noSuper) { | public RubyObject call0(RubyObject recv, RubyId id, RubyObject[] args, Node body, boolean noSuper) { // ... getRuby().getRubyFrame().push(); // HACK +++ getRuby().getIter().push(RubyIter.ITER_NOT); // HACK --- getRuby().getRubyFrame().setLast... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java |
getRuby().getRubyFrame().push(); | if (getRuby().getIter().getIter() == RubyIter.ITER_PRE) { getRuby().getIter().push(RubyIter.ITER_CUR); } else { getRuby().getIter().push(RubyIter.ITER_NOT); } | public RubyObject call0(RubyObject recv, RubyId id, RubyObject[] args, Node body, boolean noSuper) { // ... getRuby().getRubyFrame().push(); // HACK +++ getRuby().getIter().push(RubyIter.ITER_NOT); // HACK --- getRuby().getRubyFrame().setLast... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java |
getRuby().getIter().push(RubyIter.ITER_NOT); | RubyFrame frame = getRuby().getRubyFrame(); frame.push(); frame.setLastFunc(id); frame.setLastClass(noSuper ? null : this); frame.setSelf(recv); frame.setArgs(args); | public RubyObject call0(RubyObject recv, RubyId id, RubyObject[] args, Node body, boolean noSuper) { // ... getRuby().getRubyFrame().push(); // HACK +++ getRuby().getIter().push(RubyIter.ITER_NOT); // HACK --- getRuby().getRubyFrame().setLast... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java |
getRuby().getRubyFrame().setLastFunc(id); getRuby().getRubyFrame().setLastClass(noSuper ? null : this); getRuby().getRubyFrame().setSelf(recv); getRuby().getRubyFrame().setArgs(new RubyPointer(args)); RubyObject result = getRuby().getNil(); if (body instanceof CallableNode) { result = ((CallableNode)body).call(getRub... | RubyObject result = ((CallableNode)body).call(getRuby(), recv, id, args, noSuper); | public RubyObject call0(RubyObject recv, RubyId id, RubyObject[] args, Node body, boolean noSuper) { // ... getRuby().getRubyFrame().push(); // HACK +++ getRuby().getIter().push(RubyIter.ITER_NOT); // HACK --- getRuby().getRubyFrame().setLast... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java |
RubyMethodCacheEntry.saveEntry(getRuby(), this, id, ent); | public GetMethodBodyResult getMethodBody(RubyId id, int noex) { GetMethodBodyResult result = new GetMethodBodyResult(this, id, noex); MethodNode methodNode = searchMethod(id); if (methodNode == null || methodNode.getBodyNode() == null) { System.out.println("Cant find ... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/f629550c5947df9c1dbe414645f3dc76bcb70df4/RubyModule.java/buggy/org/jruby/RubyModule.java | |
defineMethod("==", Arity.singleArgument(), "equal"); defineAlias("===", "=="); defineMethod("to_s", Arity.noArguments()); defineMethod("nil?", Arity.noArguments(), "nil_p"); defineMethod("to_a", Arity.noArguments()); defineMethod("hash", Arity.noArguments()); defineMethod("id", Arity.noArguments()); defineAlias("__id__... | protected void initializeClass() { defineMethod("==", Arity.singleArgument(), "equal"); defineAlias("===", "=="); defineMethod("to_s", Arity.noArguments()); defineMethod("nil?", Arity.noArguments(), "nil_p"); defineMethod("to_a", Arity.noArguments()); defineMethod("h... | 50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/5e2d21a7295d01b2d891cfc8c8e67af99a3d858e/ObjectMetaClass.java/buggy/src/org/jruby/runtime/builtin/meta/ObjectMetaClass.java |
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