h4iku/coconut_java2006 · Datasets at Hugging Face

return AdapterUtils.go((CategoryGroup) result, new HashMap());

return AdapterUtils.go((CategoryGroup) result, newCache());

static public DataObject adaptLoadedCGCIHierarchy(Class rootNodeType, Object result) { if (rootNodeType.equals(CategoryGroup.class)){ return AdapterUtils.go((CategoryGroup) result, new HashMap()); } else if (rootNodeType.equals(Category.class)){ return AdapterUtils.go((Category) result, new HashMap()); } else { throw new IllegalArgumentException("Method only takes CategoryGroup and Category as argument."); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

return AdapterUtils.go((Category) result, new HashMap());

return AdapterUtils.go((Category) result, newCache());

static public DataObject adaptLoadedCGCIHierarchy(Class rootNodeType, Object result) { if (rootNodeType.equals(CategoryGroup.class)){ return AdapterUtils.go((CategoryGroup) result, new HashMap()); } else if (rootNodeType.equals(Category.class)){ return AdapterUtils.go((Category) result, new HashMap()); } else { throw new IllegalArgumentException("Method only takes CategoryGroup and Category as argument."); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

return AdapterUtils.go((Project) result, new HashMap());

return AdapterUtils.go((Project) result, newCache());

static public DataObject adaptLoadedPDIHierarchy(Class rootNodeType, Object result) { if (rootNodeType.equals(Project.class)){ return AdapterUtils.go((Project) result, new HashMap()); } else if (rootNodeType.equals(Dataset.class)){ return AdapterUtils.go((Dataset) result, new HashMap()); } else { throw new IllegalArgumentException("Method only takes Project and Dataset as argument."); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

return AdapterUtils.go((Dataset) result, new HashMap());

return AdapterUtils.go((Dataset) result, newCache());

static public DataObject adaptLoadedPDIHierarchy(Class rootNodeType, Object result) { if (rootNodeType.equals(Project.class)){ return AdapterUtils.go((Project) result, new HashMap()); } else if (rootNodeType.equals(Dataset.class)){ return AdapterUtils.go((Dataset) result, new HashMap()); } else { throw new IllegalArgumentException("Method only takes Project and Dataset as argument."); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

if (null == p.getProjectId()) {

static public ProjectData go(Project p, Map cache) { if (check(cache,p)) { return (ProjectData) from(cache, p); } ProjectData pd = new ProjectData(); to(cache, p, pd); if (null == p.getProjectId()) { if (log.isDebugEnabled())log.debug(nullId+p); } else { pd.setID(p.getProjectId().intValue()); } pd.setName(p.getName()); pd.setDescription(p.getDescription()); if (null==p.getExperimenter()){ if (log.isDebugEnabled())log.debug(nullExp + p); } else { pd.setOwnerFirstName(p.getExperimenter().getFirstname()); } //TODO if (null==p.getDatasets()){ if (log.isDebugEnabled())log.debug(nullDs + p); } else { Set set = new HashSet(); for (Iterator i = p.getDatasets().iterator(); i.hasNext();) { Dataset d = (Dataset) i.next(); set.add(go(d,cache)); } pd.setDatasets(new ArrayList(set)); } return pd; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

m.put(init_time,new Date());

static Map newCache() { Map m = new HashMap(); m.put(null,null); // This keeps things from getting hairy return m; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/5e29e25bb21b2a51d4b44f9fd80b5b876b782887/AdapterUtils.java/clean/components/shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java

module.defineModuleFunction("select", callbackFactory.getOptSingletonMethod("select"));

public static RubyModule createKernelModule(IRuby runtime) { RubyModule module = runtime.defineModule("Kernel"); CallbackFactory callbackFactory = runtime.callbackFactory(RubyKernel.class); CallbackFactory objectCallbackFactory = runtime.callbackFactory(RubyObject.class); module.defineModuleFunction("Array", callbackFactory.getSingletonMethod("new_array", IRubyObject.class)); module.defineModuleFunction("Float", callbackFactory.getSingletonMethod("new_float", IRubyObject.class)); module.defineModuleFunction("Integer", callbackFactory.getSingletonMethod("new_integer", IRubyObject.class)); module.defineModuleFunction("String", callbackFactory.getSingletonMethod("new_string", IRubyObject.class)); module.defineModuleFunction("`", callbackFactory.getSingletonMethod("backquote", IRubyObject.class)); // TODO: Implement Kernel#abort module.defineModuleFunction("at_exit", callbackFactory.getSingletonMethod("at_exit")); module.defineModuleFunction("autoload", callbackFactory.getSingletonMethod("autoload", IRubyObject.class, IRubyObject.class)); // TODO: Implement Kernel#autoload? module.defineModuleFunction("binding", callbackFactory.getSingletonMethod("binding")); module.defineModuleFunction("block_given?", callbackFactory.getSingletonMethod("block_given")); // TODO: Implement Kernel#callcc module.defineModuleFunction("caller", callbackFactory.getOptSingletonMethod("caller")); module.defineModuleFunction("catch", callbackFactory.getSingletonMethod("rbCatch", IRubyObject.class)); module.defineModuleFunction("chomp", callbackFactory.getOptSingletonMethod("chomp")); module.defineModuleFunction("chomp!", callbackFactory.getOptSingletonMethod("chomp_bang")); module.defineModuleFunction("chop", callbackFactory.getSingletonMethod("chop")); module.defineModuleFunction("chop!", callbackFactory.getSingletonMethod("chop_bang")); module.defineModuleFunction("eval", callbackFactory.getOptSingletonMethod("eval")); // TODO: Implement Kernel#exec module.defineModuleFunction("exit", callbackFactory.getOptSingletonMethod("exit")); module.defineModuleFunction("exit!", callbackFactory.getOptSingletonMethod("exit_bang")); module.defineModuleFunction("fail", callbackFactory.getOptSingletonMethod("raise")); // TODO: Implement Kernel#fork module.defineModuleFunction("format", callbackFactory.getOptSingletonMethod("sprintf")); module.defineModuleFunction("gets", callbackFactory.getOptSingletonMethod("gets")); module.defineModuleFunction("global_variables", callbackFactory.getSingletonMethod("global_variables")); module.defineModuleFunction("gsub", callbackFactory.getOptSingletonMethod("gsub")); module.defineModuleFunction("gsub!", callbackFactory.getOptSingletonMethod("gsub_bang")); // TODO: Add deprecation to Kernel#iterator? (maybe formal deprecation mech.) module.defineAlias("iterator?", "block_given?"); module.defineModuleFunction("lambda", callbackFactory.getSingletonMethod("proc")); module.defineModuleFunction("load", callbackFactory.getOptSingletonMethod("load")); module.defineModuleFunction("local_variables", callbackFactory.getSingletonMethod("local_variables")); module.defineModuleFunction("loop", callbackFactory.getSingletonMethod("loop")); // Note: method_missing is documented as being in Object, but ruby appears to stick it in Kernel. module.defineModuleFunction("method_missing", callbackFactory.getOptSingletonMethod("method_missing")); module.defineModuleFunction("open", callbackFactory.getOptSingletonMethod("open")); module.defineModuleFunction("p", callbackFactory.getOptSingletonMethod("p")); module.defineModuleFunction("print", callbackFactory.getOptSingletonMethod("print")); module.defineModuleFunction("printf", callbackFactory.getOptSingletonMethod("printf")); module.defineModuleFunction("proc", callbackFactory.getSingletonMethod("proc")); // TODO: implement Kernel#putc module.defineModuleFunction("puts", callbackFactory.getOptSingletonMethod("puts")); module.defineAlias("raise", "fail"); module.defineModuleFunction("rand", callbackFactory.getOptSingletonMethod("rand")); module.defineModuleFunction("readline", callbackFactory.getOptSingletonMethod("readline")); module.defineModuleFunction("readlines", callbackFactory.getOptSingletonMethod("readlines")); module.defineModuleFunction("require", callbackFactory.getSingletonMethod("require", IRubyObject.class)); module.defineModuleFunction("scan", callbackFactory.getSingletonMethod("scan", IRubyObject.class)); // TODO: Implement Kernel#select module.defineModuleFunction("set_trace_func", callbackFactory.getSingletonMethod("set_trace_func", IRubyObject.class)); module.defineModuleFunction("sleep", callbackFactory.getSingletonMethod("sleep", IRubyObject.class)); module.defineModuleFunction("split", callbackFactory.getOptSingletonMethod("split")); module.defineAlias("sprintf", "format"); module.defineModuleFunction("srand", callbackFactory.getOptSingletonMethod("srand")); module.defineModuleFunction("sub", callbackFactory.getOptSingletonMethod("sub")); module.defineModuleFunction("sub!", callbackFactory.getOptSingletonMethod("sub_bang")); // Skipping: Kernel#syscall (too system dependent) module.defineModuleFunction("system", callbackFactory.getOptSingletonMethod("system")); // TODO: Implement Kernel#test (partial impl) module.defineModuleFunction("throw", callbackFactory.getOptSingletonMethod("rbThrow")); // TODO: Implement Kernel#trace_var module.defineModuleFunction("trap", callbackFactory.getOptSingletonMethod("trap")); // TODO: Implement Kernel#untrace_var module.defineModuleFunction("warn", callbackFactory.getSingletonMethod("warn", IRubyObject.class)); // Defined p411 Pickaxe 2nd ed. module.defineModuleFunction("singleton_method_added", callbackFactory.getSingletonMethod("singleton_method_added", IRubyObject.class)); // Object methods module.definePublicModuleFunction("==", objectCallbackFactory.getMethod("equal", IRubyObject.class)); module.defineAlias("===", "=="); module.defineAlias("eql?", "=="); module.definePublicModuleFunction("to_s", objectCallbackFactory.getMethod("to_s")); module.definePublicModuleFunction("nil?", objectCallbackFactory.getMethod("nil_p")); module.definePublicModuleFunction("to_a", objectCallbackFactory.getMethod("to_a")); module.definePublicModuleFunction("hash", objectCallbackFactory.getMethod("hash")); module.definePublicModuleFunction("id", objectCallbackFactory.getMethod("id")); module.defineAlias("__id__", "id"); module.defineAlias("object_id", "id"); module.definePublicModuleFunction("is_a?", objectCallbackFactory.getMethod("kind_of", IRubyObject.class)); module.defineAlias("kind_of?", "is_a?"); module.definePublicModuleFunction("dup", objectCallbackFactory.getMethod("dup")); module.definePublicModuleFunction("equal?", objectCallbackFactory.getMethod("same", IRubyObject.class)); module.definePublicModuleFunction("type", objectCallbackFactory.getMethod("type_deprecated")); module.definePublicModuleFunction("class", objectCallbackFactory.getMethod("type")); module.definePublicModuleFunction("inspect", objectCallbackFactory.getMethod("inspect")); module.definePublicModuleFunction("=~", objectCallbackFactory.getMethod("match", IRubyObject.class)); module.definePublicModuleFunction("clone", objectCallbackFactory.getMethod("rbClone")); module.definePublicModuleFunction("display", objectCallbackFactory.getOptMethod("display")); module.definePublicModuleFunction("extend", objectCallbackFactory.getOptMethod("extend")); module.definePublicModuleFunction("freeze", objectCallbackFactory.getMethod("freeze")); module.definePublicModuleFunction("frozen?", objectCallbackFactory.getMethod("frozen")); module.defineModuleFunction("initialize_copy", objectCallbackFactory.getMethod("initialize_copy", IRubyObject.class)); module.definePublicModuleFunction("instance_eval", objectCallbackFactory.getOptMethod("instance_eval")); module.definePublicModuleFunction("instance_of?", objectCallbackFactory.getMethod("instance_of", IRubyObject.class)); module.definePublicModuleFunction("instance_variables", objectCallbackFactory.getMethod("instance_variables")); module.definePublicModuleFunction("instance_variable_get", objectCallbackFactory.getMethod("instance_variable_get", IRubyObject.class)); module.definePublicModuleFunction("instance_variable_set", objectCallbackFactory.getMethod("instance_variable_set", IRubyObject.class, IRubyObject.class)); module.definePublicModuleFunction("method", objectCallbackFactory.getMethod("method", IRubyObject.class)); module.definePublicModuleFunction("methods", objectCallbackFactory.getOptMethod("methods")); module.definePublicModuleFunction("private_methods", objectCallbackFactory.getMethod("private_methods")); module.definePublicModuleFunction("protected_methods", objectCallbackFactory.getMethod("protected_methods")); module.definePublicModuleFunction("public_methods", objectCallbackFactory.getOptMethod("public_methods")); module.definePublicModuleFunction("remove_instance_variable", objectCallbackFactory.getMethod("remove_instance_variable", IRubyObject.class)); module.definePublicModuleFunction("respond_to?", objectCallbackFactory.getOptMethod("respond_to")); module.definePublicModuleFunction("send", objectCallbackFactory.getOptMethod("send")); module.defineAlias("__send__", "send"); module.definePublicModuleFunction("singleton_methods", objectCallbackFactory.getMethod("singleton_methods")); module.definePublicModuleFunction("taint", objectCallbackFactory.getMethod("taint")); module.definePublicModuleFunction("tainted?", objectCallbackFactory.getMethod("tainted")); module.definePublicModuleFunction("untaint", objectCallbackFactory.getMethod("untaint")); return module; }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/54e6b8da799629e0b7db879c45149399878f5f84/RubyKernel.java/clean/src/org/jruby/RubyKernel.java

public NoteTreeNode(NoteTreeNode parent, DisplayedNote data) {

protected NoteTreeNode(NoteTreeNode parent, DisplayedNote data) {

public NoteTreeNode(NoteTreeNode parent, DisplayedNote data) { treeItem = new TreeItem(parent.treeItem, SWT.NONE, data.getNote().getIndex()); init(data); }

57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/d0681c368f8b555700e4ef73b079e6a225f180f2/NoteTreeNode.java/buggy/trunk/src/de/berlios/koalanotes/display/NoteTreeNode.java

if (isSelected() == selected) { return; }

public void setSelected(boolean selected) { List<TreeItem> selectionTemp = Arrays.asList(treeItem.getParent().getSelection()); List<TreeItem> selection = new LinkedList<TreeItem>(selectionTemp); if (selected) { selection.add(treeItem); } else { selection.remove(treeItem); } TreeItem[] newSelection = selection.toArray(new TreeItem[selection.size()]); treeItem.getParent().setSelection(newSelection); }

57508 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57508/d0681c368f8b555700e4ef73b079e6a225f180f2/NoteTreeNode.java/buggy/trunk/src/de/berlios/koalanotes/display/NoteTreeNode.java

super(runtime, null, superClass, runtime.getObject(), "Module", RubyModule.class);

super(runtime, null, superClass, runtime.getObject().getCRef(), "Module", RubyModule.class);

public ModuleMetaClass(IRuby runtime, RubyClass superClass) { super(runtime, null, superClass, runtime.getObject(), "Module", RubyModule.class); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a1b8fc1d456e3d5c6e01579b88773383068aa85c/ModuleMetaClass.java/buggy/src/org/jruby/runtime/builtin/meta/ModuleMetaClass.java

public RubyClass newSubClass(String name, RubyModule parent) { return new ModuleMetaClass(name, this, parent);

public RubyClass newSubClass(String name, SinglyLinkedList parentCRef) { return new ModuleMetaClass(name, this, parentCRef);

public RubyClass newSubClass(String name, RubyModule parent) { return new ModuleMetaClass(name, this, parent); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/a1b8fc1d456e3d5c6e01579b88773383068aa85c/ModuleMetaClass.java/buggy/src/org/jruby/runtime/builtin/meta/ModuleMetaClass.java

if (!currentP.identical(previousP))

Permissions tmpDetails = new Permissions(previousP); if (currentP.isSet(Flag.LOCKED)) { tmpDetails.set(Flag.LOCKED); } else { tmpDetails.unSet(Flag.LOCKED); } if (!currentP.identical(tmpDetails))

protected boolean managedPermissions(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { // setup boolean altered = false; Permissions previousP = previousDetails == null ? null : previousDetails.getPermissions(); Permissions currentP = currentDetails == null ? null : currentDetails .getPermissions(); // ignore newDetails permissions. // If the stored perms are null, then we can't validate anything // TODO : is this alright. Should only happen for system types. // Then can silently ignore ?? if (previousP == null) { if (currentP == null) { newDetails.setPermissions(null); altered |= false; // don't need to update } else { newDetails.setPermissions(currentP); altered = true; } } // WORKAROUND for ticket:307 by checking for SOFT below // see https://trac.openmicroscopy.org.uk/omero/ticket/307 // see // http://opensource.atlassian.com/projects/hibernate/browse/HHH-2027 // Users did not enter permission (normal case) so is null OR // in the workaround permissions is SOFT, then // need to copy whole sale those from database. else if (currentP == null || currentP.isSet(Flag.SOFT)) { newDetails.setPermissions(previousP); altered = true; } // if the user has set the permissions (currentDetails), then we should // try to allow that. if it's identical to the current, then there // is no reason to hit the DB. else { // if we need to filter any permissions, do it here! newDetails.setPermissions(currentP); if (!currentP.identical(previousP)) { if ( ! isOwnerOrSupervisor(obj)) // TODO and privileged? if not, remove from below?? throw new SecurityViolation(String.format( "You are not authorized to change " + "the permissions for %s from %s to %s", obj, previousP, currentP)); altered = true; } } // now we've calculated the desired permissions, throw // a security violation if this instance was locked AND // the read permissions have been lowered or if the lock // was removed. if (locked) { if (previousP == null) // if null it can't have been locked. throw new InternalException("Null permissions cannot be locked"); Permissions calculatedP = newDetails.getPermissions(); if (calculatedP != null) { // can't override if ( ! calculatedP.isSet( Flag.LOCKED )) { calculatedP.set(Flag.LOCKED); altered = true; } if ((previousP.isGranted(USER, READ) && !calculatedP.isGranted(USER, READ)) || (previousP.isGranted(GROUP, READ) && !calculatedP .isGranted(GROUP, READ)) || (previousP.isGranted(WORLD, READ) && !calculatedP .isGranted(WORLD, READ))) throw new SecurityViolation( "Cannot remove READ from locked entity:" + obj); } } // privileged plays no role since everyone can alter their permissions // (within bounds) return altered; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/36bb3b3ff2057894b05b208ab4ef1b9ce950164a/BasicSecuritySystem.java/buggy/components/server/src/ome/security/basic/BasicSecuritySystem.java

&& !source.getOwner().getId().equals( newDetails.getOwner().getId())) {

&& !newDetails.getOwner().getId().equals( source.getOwner().getId())) {

public Details newTransientDetails(IObject obj) { checkReady("transientDetails"); if (obj == null) throw new ApiUsageException("Argument cannot be null."); if (hasPrivilegedToken(obj)) return obj.getDetails(); // EARLY EXIT Details source = obj.getDetails(); Details newDetails = cd.createDetails(); if (source != null) { // PERMISSIONS // users _are_ allowed to alter the permissions of new objects. // this entity may be locked in the same operation, in which case // the READ permissions which are set will not be removable. copyNonNullPermissions(newDetails, source.getPermissions()); applyUmaskIfNecessary(newDetails); // OWNER // users *aren't* allowed to set the owner of an item. if (source.getOwner() != null && !source.getOwner().getId().equals( newDetails.getOwner().getId())) { // but this is root if (currentUserIsAdmin()) { newDetails.setOwner(source.getOwner()); } else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterID" + " for %s to %d", obj, source.getOwner() .getId())); } } // GROUP // users are only allowed to set to another of their groups if (source.getGroup() != null && source.getGroup().getId() != null) { // users can change to their own group if (memberOfGroups().contains(source.getGroup().getId())) { newDetails.setGroup(source.getGroup()); } // and admin can change it too else if (currentUserIsAdmin()) { newDetails.setGroup(source.getGroup()); } // oops. boom! else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterGroupID" + " for %s to %d", obj, source.getGroup() .getId())); } } // EXTERNALINFO // useres _are_ allowed to set the external info on a new object. // subsequent operations, however, will not be able to edit this // value. newDetails.setExternalInfo( source.getExternalInfo() ); // CREATION/UPDATEVENT : currently ignore what users do } return newDetails; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/36bb3b3ff2057894b05b208ab4ef1b9ce950164a/BasicSecuritySystem.java/buggy/components/server/src/ome/security/basic/BasicSecuritySystem.java

"You are not authorized to set the ExperimenterID" + " for %s to %d", obj, source.getOwner() .getId()));

"You are not authorized to set the Experimenter" + " for %s to %s", obj, source.getOwner()));

public Details newTransientDetails(IObject obj) { checkReady("transientDetails"); if (obj == null) throw new ApiUsageException("Argument cannot be null."); if (hasPrivilegedToken(obj)) return obj.getDetails(); // EARLY EXIT Details source = obj.getDetails(); Details newDetails = cd.createDetails(); if (source != null) { // PERMISSIONS // users _are_ allowed to alter the permissions of new objects. // this entity may be locked in the same operation, in which case // the READ permissions which are set will not be removable. copyNonNullPermissions(newDetails, source.getPermissions()); applyUmaskIfNecessary(newDetails); // OWNER // users *aren't* allowed to set the owner of an item. if (source.getOwner() != null && !source.getOwner().getId().equals( newDetails.getOwner().getId())) { // but this is root if (currentUserIsAdmin()) { newDetails.setOwner(source.getOwner()); } else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterID" + " for %s to %d", obj, source.getOwner() .getId())); } } // GROUP // users are only allowed to set to another of their groups if (source.getGroup() != null && source.getGroup().getId() != null) { // users can change to their own group if (memberOfGroups().contains(source.getGroup().getId())) { newDetails.setGroup(source.getGroup()); } // and admin can change it too else if (currentUserIsAdmin()) { newDetails.setGroup(source.getGroup()); } // oops. boom! else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterGroupID" + " for %s to %d", obj, source.getGroup() .getId())); } } // EXTERNALINFO // useres _are_ allowed to set the external info on a new object. // subsequent operations, however, will not be able to edit this // value. newDetails.setExternalInfo( source.getExternalInfo() ); // CREATION/UPDATEVENT : currently ignore what users do } return newDetails; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/36bb3b3ff2057894b05b208ab4ef1b9ce950164a/BasicSecuritySystem.java/buggy/components/server/src/ome/security/basic/BasicSecuritySystem.java

"You are not authorized to set the ExperimenterGroupID" + " for %s to %d", obj, source.getGroup() .getId()));

"You are not authorized to set the ExperimenterGroup" + " for %s to %s", obj, source.getGroup()));

public Details newTransientDetails(IObject obj) { checkReady("transientDetails"); if (obj == null) throw new ApiUsageException("Argument cannot be null."); if (hasPrivilegedToken(obj)) return obj.getDetails(); // EARLY EXIT Details source = obj.getDetails(); Details newDetails = cd.createDetails(); if (source != null) { // PERMISSIONS // users _are_ allowed to alter the permissions of new objects. // this entity may be locked in the same operation, in which case // the READ permissions which are set will not be removable. copyNonNullPermissions(newDetails, source.getPermissions()); applyUmaskIfNecessary(newDetails); // OWNER // users *aren't* allowed to set the owner of an item. if (source.getOwner() != null && !source.getOwner().getId().equals( newDetails.getOwner().getId())) { // but this is root if (currentUserIsAdmin()) { newDetails.setOwner(source.getOwner()); } else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterID" + " for %s to %d", obj, source.getOwner() .getId())); } } // GROUP // users are only allowed to set to another of their groups if (source.getGroup() != null && source.getGroup().getId() != null) { // users can change to their own group if (memberOfGroups().contains(source.getGroup().getId())) { newDetails.setGroup(source.getGroup()); } // and admin can change it too else if (currentUserIsAdmin()) { newDetails.setGroup(source.getGroup()); } // oops. boom! else { throw new SecurityViolation(String.format( "You are not authorized to set the ExperimenterGroupID" + " for %s to %d", obj, source.getGroup() .getId())); } } // EXTERNALINFO // useres _are_ allowed to set the external info on a new object. // subsequent operations, however, will not be able to edit this // value. newDetails.setExternalInfo( source.getExternalInfo() ); // CREATION/UPDATEVENT : currently ignore what users do } return newDetails; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/36bb3b3ff2057894b05b208ab4ef1b9ce950164a/BasicSecuritySystem.java/buggy/components/server/src/ome/security/basic/BasicSecuritySystem.java

private JToolBar buildViewBar() { JToolBar bar = new JToolBar(); bar.setFloatable(false); bar.setRollover(true); bar.setBorder(null); JToggleButton b = new JToggleButton( controller.getAction(HiViewerControl.TREE_VIEW)); bar.add(b); b = new JToggleButton( controller.getAction(HiViewerControl.CLIPBOARD_VIEW)); b.setSelected(true); bar.add(b); bar.add(new JSeparator(SwingConstants.HORIZONTAL)); return bar; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/ea7509babe2344eb702969105eb77096cc5b6bcf/HiViewerToolBar.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/view/HiViewerToolBar.java

Class targetType = (Class) c2c().get(current.getClass());

Class targetType = findClass(current.getClass());

public Object findTarget(Object current){ // IMMUTABLES if (null == current | current instanceof Integer | current instanceof String) // TODO can use findTarget then for these as well. { return current; } else // Special cases TODO put into doFindTarget if (current instanceof Date){ return new Timestamp(((Date)current).getTime()); // FIXME should cache these in model2pojo } Object target = model2target.get(current); if (null == target) { Class targetType = (Class) c2c().get(current.getClass()); if (null != targetType){ try { target = targetType.newInstance(); } catch (Exception e) { throw new RuntimeException("Internal error: could not instantiate object of type "+targetType+" while trying to map "+current,e); } model2target.put(current,target); } } return target; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/afec4b5da2a19f70c897c6d87552b4e998da56cb/ModelMapper.java/clean/components/common/src/ome/util/ModelMapper.java

(Category)controller.getCategories(group).get(i);

(Category)controller.getCategories(group).get(selectedCategory);

private void buildGUI() { Container container = getContentPane(); container.setLayout(new BorderLayout(2,2)); JPanel listPanel = new JPanel(); listPanel.setLayout(new GridLayout(1,2)); JPanel leftPanel = new JPanel(); leftPanel.setLayout(new BorderLayout(2,2)); JPanel leftLabelPanel = new JPanel(); leftLabelPanel.setLayout(new FlowLayout(FlowLayout.LEFT)); leftLabelPanel.add(new JLabel("Groups:")); leftPanel.add(leftLabelPanel,BorderLayout.NORTH); groupList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); groupList.addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { newCategoryButton.setEnabled(true); categoryList.setEnabled(true); if(groupList.getSelectedIndex() != -1) { selectedGroup = groupList.getSelectedIndex(); } CategoryGroup group = (CategoryGroup)controller.getCategoryGroups().get(selectedGroup); buildCategoryList(group); repaint(); } }); groupList.addFocusListener(new FocusAdapter() { public void focusLost(FocusEvent arg0) { if(arg0.getOppositeComponent() != editButton) { editButton.setEnabled(false); } } public void focusGained(FocusEvent arg0) { editButton.setEnabled(true); editButton.setAction(editGroupAction); } }); JScrollPane scrollPane = new JScrollPane(groupList); scrollPane.setPreferredSize(new Dimension(150,225)); leftPanel.add(scrollPane,BorderLayout.CENTER); listPanel.add(leftPanel); JPanel rightPanel = new JPanel(); rightPanel.setLayout(new BorderLayout(2,2)); JPanel rightLabelPanel = new JPanel(); rightLabelPanel.setLayout(new FlowLayout(FlowLayout.LEFT)); rightLabelPanel.add(new JLabel("Phenotypes:")); rightPanel.add(rightLabelPanel,BorderLayout.NORTH); categoryList.setEnabled(false); categoryList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); categoryList.addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { int i = categoryList.getSelectedIndex(); CategoryGroup group = (CategoryGroup)controller.getCategoryGroups().get(selectedGroup); Category cat = (Category)controller.getCategories(group).get(i); repaint(); } }); categoryList.addFocusListener(new FocusAdapter() { public void focusLost(FocusEvent arg0) { if(arg0.getOppositeComponent() != editButton) { editButton.setEnabled(false); } } public void focusGained(FocusEvent arg0) { editButton.setEnabled(true); editButton.setAction(editCategoryAction); } }); JScrollPane rightScrollPane = new JScrollPane(categoryList); rightScrollPane.setPreferredSize(new Dimension(150,225)); rightPanel.add(rightScrollPane,BorderLayout.CENTER); listPanel.add(rightPanel); JPanel detailsPanel = new JPanel(); detailsPanel.setBorder(BorderFactory.createLineBorder(Color.gray)); detailsPanel.setLayout(new BorderLayout(2,2)); detailsPanel.add(listPanel,BorderLayout.CENTER); JPanel buttonPanel = new JPanel(); newGroupButton = new JButton("New Group"); newGroupButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { CategoryEditUI.showCreateGroupDialog(refCopy,controller); } }); buttonPanel.add(newGroupButton); editButton = new JButton("Edit"); buttonPanel.add(editButton); newCategoryButton = new JButton("New Phenotype"); newCategoryButton.setEnabled(false); newCategoryButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { CategoryGroup group = (CategoryGroup)controller.getCategoryGroups().get(selectedGroup); CategoryEditUI.showCreateCategoryDialog(refCopy,controller,group); } }); buttonPanel.add(newCategoryButton); detailsPanel.add(buttonPanel,BorderLayout.SOUTH); container.add(detailsPanel,BorderLayout.CENTER); JPanel savePanel = new JPanel(); savePanel.setLayout(new FlowLayout(FlowLayout.RIGHT)); JButton saveButton = new JButton("Save"); saveButton.setAction(saveAction); savePanel.add(saveButton); savePanel.add(Box.createHorizontalStrut(10)); JButton cancelButton = new JButton("Cancel"); cancelButton.setAction(cancelAction); savePanel.add(cancelButton); container.add(savePanel,BorderLayout.SOUTH); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a47b86cb03a09b865a88769c10a7d57151002bd0/CategoryUI.java/clean/SRC/org/openmicroscopy/shoola/agents/classifier/CategoryUI.java

(Category)controller.getCategories(group).get(i);

(Category)controller.getCategories(group).get(selectedCategory);

public void valueChanged(ListSelectionEvent e) { int i = categoryList.getSelectedIndex(); CategoryGroup group = (CategoryGroup)controller.getCategoryGroups().get(selectedGroup); Category cat = (Category)controller.getCategories(group).get(i); repaint(); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/a47b86cb03a09b865a88769c10a7d57151002bd0/CategoryUI.java/clean/SRC/org/openmicroscopy/shoola/agents/classifier/CategoryUI.java

return _allCategories;

if(_allCategories==null){ return new LinkedHashMap(); } else{ return _allCategories; }

public Map getCategories() { if (_allCategories == null) { Collection cats = CategoryUtil.getCategories(); if(cats!=null && !cats.isEmpty()){ _allCategories = new LinkedHashMap(); _allCategories.put(ArticleUtil.getBundle().getLocalizedText("All categories"), "-1"); Iterator cat = cats.iterator(); while (cat.hasNext()) { String category = (String) cat.next(); _allCategories.put(ArticleUtil.getBundle().getLocalizedText(category),category); } } } return _allCategories; }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/77f6af59c63a9bb06fc5f97887a10f33495a1eb0/SearchArticleBean.java/clean/src/java/com/idega/block/article/bean/SearchArticleBean.java

if(!getSearchCategory().equals("-1")){

if(!("-1").equals(getSearchCategory())){

public SearchRequest getSearchRequest(String scope, Locale locale) throws SearchException { SearchRequest s = new SearchRequest(); s.addSelection(IWSlideConstants.PROPERTY_CREATION_DATE); s.addSelection(IWSlideConstants.PROPERTY_CATEGORY); s.addScope(new SearchScope(scope)); SearchExpression whereExpression = null; //String localeString = ""; //((locale!=null)?locale.getLanguage():""); //TODO create search input for language SearchExpression namePatternExpression = s.compare(CompareOperator.LIKE, IWSlideConstants.PROPERTY_DISPLAY_NAME,"%.article"); //todo search by the content type //SearchExpression contentTypeExpression = s.compare(CompareOperator.LIKE, ArticleItemBean.PROPERTY_CONTENT_TYPE, ArticleItemBean.ARTICLE_FILENAME_SCOPE); whereExpression = namePatternExpression; //whereExpression = contentTypeExpression; SearchExpression creationDateFromExpression = null; if(getSearchPublishedFrom() != null){ Date from = getSearchPublishedFrom(); IWTimestamp stamp = new IWTimestamp(from); //the date's time is at 24:00 so anything from that day will not be found. So be back up a day to 24:00 stamp.addDays(-1); from = stamp.getDate(); creationDateFromExpression = s.compare(CompareOperator.GTE, IWSlideConstants.PROPERTY_CREATION_DATE,from); whereExpression = s.and(whereExpression,creationDateFromExpression); } SearchExpression creationDateToExpression = null; if(getSearchPublishedTo() != null){ creationDateToExpression = s.compare(CompareOperator.LTE, IWSlideConstants.PROPERTY_CREATION_DATE,getSearchPublishedTo()); whereExpression = s.and(whereExpression,creationDateToExpression); } // List categoryExpressions = new ArrayList(); if(!getSearchCategory().equals("-1")){ SearchExpression categoryExpression = s.compare(CompareOperator.LIKE,IWSlideConstants.PROPERTY_CATEGORY,","+getSearchCategory()+","); whereExpression = s.and(whereExpression,categoryExpression); } String author = getSearchAuthor(); if(author!=null && !"".equals(author)){ SearchExpression authorExpression = s.compare(CompareOperator.LIKE,IWSlideConstants.PROPERTY_CREATOR_DISPLAY_NAME,"%"+author+"%"); whereExpression = s.and(whereExpression,authorExpression); } // }// whereExpression = s.and(whereExpression,categoryExpression);// for (Iterator iter = categoryList.iterator(); iter.hasNext();) {// String categoryName = (String) iter.next();// categoryExpressions.add(s.compare(CompareOperator.LIKE,IWSlideConstants.PROPERTY_CATEGORY,"%"+categoryName+"%"));// }// Iterator expr = categoryExpressions.iterator();// if(expr.hasNext()){// SearchExpression categoryExpression = (SearchExpression)expr.next();// while(expr.hasNext()){// categoryExpression = s.or(categoryExpression,(SearchExpression)expr.next());// }// whereExpression = s.and(whereExpression,categoryExpression);// }// } SearchExpression containsExpression = null; if(getSearchText() != null && !"".equals(getSearchText())){ containsExpression = s.contains(getSearchText()); if(whereExpression!=null){ whereExpression = s.and(whereExpression,containsExpression); }else{ whereExpression = containsExpression; } } s.setWhereExpression(whereExpression); System.out.println("------------------------"); System.out.println(s.asString()); System.out.println("------------------------"); return s; }

57000 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/57000/77f6af59c63a9bb06fc5f97887a10f33495a1eb0/SearchArticleBean.java/clean/src/java/com/idega/block/article/bean/SearchArticleBean.java

int n = Integer.parseInt(args[0]);

public static void main(String args[]) throws IOException { //@START int n = Integer.parseInt(args[0]); int i, c; String s = ""; Integer ii; // the original program used: // Hashtable ht = new Hashtable(); // John Olsson points out that Hashtable is for synchronized access // and we should use instead: HashMap ht = new HashMap(); c = 0; for (i = 1; i <= n; i++) ht.put(Integer.toString(i, 16), new Integer(i)); for (i = 1; i <= n; i++) // The original code converted to decimal string this way: // if (ht.containsKey(i+"")) if (ht.containsKey(Integer.toString(i, 10))) c++; System.out.println(c); //@END }

53330 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/53330/eb6c850277407b38bcaefb81155941da0f27b849/hash.java/buggy/tests/shootout/java-start/hash.java

FlowLayout(FlowLayout.LEFT, 0, 0)) {

private void createUI() { setLayout(new BorderLayout()); tabs = new JPanel(new FlowLayout(FlowLayout.LEFT, 0, 0)) { public Dimension getPreferredSize() { if (getParent() == null) return getPreferredSize(); // calculate the preferred size based on the flow of components FlowLayout flow = (FlowLayout)getLayout(); int w = getParent().getWidth(); int h = flow.getVgap(); int x = flow.getHgap(); int rowH = 0; Dimension d; Component[] comps = getComponents(); for (int i = 0; i < comps.length; i++) { if (comps[i].isVisible()) { d = comps[i].getPreferredSize(); if (x + d.width > w && x > flow.getHgap()) { x = flow.getHgap(); h += rowH; rowH = 0; h += flow.getVgap(); } rowH = Math.max(d.height, rowH); x += d.width + flow.getHgap(); } } h += rowH; return new Dimension(w, h); } }; final JPanel topPanel = new JPanel(); topPanel.setLayout(new GridBagLayout()); topPanel.add(new JLabel(), new GridBagConstraints(1, 0, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0)); topPanel.setOpaque(false); // Add Tabs panel to top of panel. if (tabPlacement == JTabbedPane.TOP) { topPanel.add(tabs, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(2, 0, 0, 0), 0, 0)); add(topPanel, BorderLayout.NORTH); } else { topPanel.add(tabs, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 2, 0), 0, 0)); add(topPanel, BorderLayout.SOUTH); } // Create mainPanel mainPanel = new JPanel(new CardLayout()); add(mainPanel, BorderLayout.CENTER); // mainPanel.setBorder(BorderFactory.createLineBorder(Color.lightGray)); // Initialize close button closeInactiveButtonIcon = SparkRes.getImageIcon(SparkRes.CLOSE_WHITE_X_IMAGE); closeActiveButtonIcon = SparkRes.getImageIcon(SparkRes.CLOSE_DARK_X_IMAGE); setOpaque(false); tabs.setOpaque(false); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/93be14b35e2ec723a91a9660ce4217f9947cf7b5/SparkTabbedPane.java/buggy/src/java/org/jivesoftware/spark/component/tabbedPane/SparkTabbedPane.java

if (e.getSource() instanceof SparkTab) { SparkTab tab = (SparkTab)e.getSource(); setSelectedTab(tab); }

public void mouseClicked(MouseEvent e) { }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/93be14b35e2ec723a91a9660ce4217f9947cf7b5/SparkTabbedPane.java/buggy/src/java/org/jivesoftware/spark/component/tabbedPane/SparkTabbedPane.java

if(e.isPopupTrigger()){ return; } if (e.getSource() instanceof SparkTab) { SparkTab tab = (SparkTab)e.getSource(); setSelectedTab(tab); }

public void mousePressed(MouseEvent e) { if(e.isPopupTrigger()){ return; } if (e.getSource() instanceof SparkTab) { SparkTab tab = (SparkTab)e.getSource(); setSelectedTab(tab); } }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/93be14b35e2ec723a91a9660ce4217f9947cf7b5/SparkTabbedPane.java/buggy/src/java/org/jivesoftware/spark/component/tabbedPane/SparkTabbedPane.java

textLabel.setFont(defaultFont);

public void setSelected(boolean selected) { super.setSelected(selected); this.selected = selected; if (boldWhenActive && selected) { textLabel.setFont(textLabel.getFont().deriveFont(Font.BOLD)); } else { textLabel.setFont(defaultFont); } invalidate(); repaint(); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/00fab4f4f794528a2db5b65568d6efec6e2e119d/SparkTab.java/buggy/src/java/org/jivesoftware/spark/component/tabbedPane/SparkTab.java

put(varName,toolType);

put(varName,tool);

WC(final Broker broker) { _broker = broker; try { String tools = (String) _broker.getValue("config","TemplateTools"); Enumeration tenum = new StringTokenizer(tools); while (tenum.hasMoreElements()) { String toolName = (String) tenum.nextElement(); try { Class toolType = Class.forName(toolName); String varName = getToolName(toolName); Object tool = toolType.newInstance(); put(varName,toolType); } catch (ClassNotFoundException ce) { _log.exception(ce); _log.error("Tool class " + toolName + " not found: " + ce); } catch (IllegalAccessException ia) { _log.exception(ia); _log.error("Tool class and methods must be public for " + toolName + ": " + ia); } catch (InstantiationException ie) { _log.exception(ie); _log.error("Tool class " + toolName + " must have a public zero " + "argument or default constructor: " + ie); } } } catch (NotFoundException e) { _log.exception(e); _log.error("Could not locate TemplateTools in config: " + e); } catch (InvalidTypeException e) { _log.exception(e); _log.error("Could not access config: " + e); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/2b733b59c2820d3bfe96a20a52e269bad07b066e/WC.java/buggy/webmacro/src/org/webmacro/servlet/WC.java

" is a " + name.getClass());

" is a " + c + ": " + v);

final public ContextTool getTool(String name) throws InvalidContextException { try { return (ContextTool) getMacro(name); } catch (ClassCastException ce) { throw new InvalidContextException("Not a tool, " + name + " is a " + name.getClass()); } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/2b733b59c2820d3bfe96a20a52e269bad07b066e/WC.java/buggy/webmacro/src/org/webmacro/servlet/WC.java

WebContext wc = (WebContext) clone(null);

WebContext wc = (WebContext) clone();

final public WebContext clone( final HttpServletRequest req, final HttpServletResponse resp) { try { // want: new local vars, both existing tools tables, no bean, // plus store req and resp somewhere, plus existing broker WebContext wc = (WebContext) clone(null); wc._request = req; wc._response = resp; return wc; } catch (Exception e) { _log.error("Clone not supported on WebContext!"); return null; } }

52513 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52513/278b4a35f5c73b37a3381dc75821bfaa4d3aa3d0/WebContext.java/buggy/webmacro/src/org/webmacro/servlet/WebContext.java

this.myName, name, desc, ignoreRegex);

this.myName, name, desc, ignoreRegexs);

public MethodVisitor visitMethod(final int access, final String name, final String desc, final String signature, final String[] exceptions) { MethodVisitor mv = cv.visitMethod(access, name, desc, signature, exceptions); if (!instrument) return mv; return mv == null ? null : new MethodInstrumenter(classData, mv, this.myName, name, desc, ignoreRegex); }

50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8d76b07e3d230fcd0d3b233e7ffc80df6ca3ec82/ClassInstrumenter.java/clean/cobertura/src/net/sourceforge/cobertura/instrument/ClassInstrumenter.java

final String owner, final String myName, final String myDescriptor, final Pattern ignoreRegexp)

final String owner, final String myName, final String myDescriptor, final Collection ignoreRegexs)

public MethodInstrumenter(ClassData classData, final MethodVisitor mv, final String owner, final String myName, final String myDescriptor, final Pattern ignoreRegexp) { super(mv); this.classData = classData; this.ownerClass = owner; this.myName = myName; this.myDescriptor = myDescriptor; this.ignoreRegex = ignoreRegexp; }

50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8d76b07e3d230fcd0d3b233e7ffc80df6ca3ec82/MethodInstrumenter.java/buggy/cobertura/src/net/sourceforge/cobertura/instrument/MethodInstrumenter.java

this.ignoreRegex = ignoreRegexp;

this.ignoreRegexs = ignoreRegexs;

public MethodInstrumenter(ClassData classData, final MethodVisitor mv, final String owner, final String myName, final String myDescriptor, final Pattern ignoreRegexp) { super(mv); this.classData = classData; this.ownerClass = owner; this.myName = myName; this.myDescriptor = myDescriptor; this.ignoreRegex = ignoreRegexp; }

50197 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50197/8d76b07e3d230fcd0d3b233e7ffc80df6ca3ec82/MethodInstrumenter.java/buggy/cobertura/src/net/sourceforge/cobertura/instrument/MethodInstrumenter.java

} else { model.setState(ANNOTATIONS_READY); fireStateChange();

public void manageAnnotationEditing(boolean b) { if (model.getState() != ClipBoard.EDIT_ANNOTATIONS) throw new IllegalStateException("This method can only be invoked " + "in the EDIT_ANNOTATIONS state."); if (b) { view.manageAnnotation(); retrieveAnnotations(model.getAnnotatedObjectID(), model.getAnnotatedObjectIndex()); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/3feec30057da68977528d8509d07bff5c080fb40/ClipBoardComponent.java/clean/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/ClipBoardComponent.java

initListener();

void initialize(ClipBoardControl controller, ClipBoardModel model) { if (controller == null) throw new NullPointerException("No control."); if (model == null) throw new NullPointerException("No model."); this.model = model; this.controller = controller; initComponents(); buildUI(); //Initializes the listener otherwise an event is fired when //components are added to the tabbed pane. initListener(); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/0c7517f5d0ece413452f58f3f0a071be2ccbee2e/ClipBoardUI.java/buggy/SRC/org/openmicroscopy/shoola/agents/hiviewer/clipboard/ClipBoardUI.java

public void composingNotification(final String from, String packetID) { SwingUtilities.invokeLater(new Runnable() { public void run() { String bareAddress = StringUtils.parseBareAddress(from); if (bareAddress.equals(getRoomname())) { String nickname = StringUtils.parseResource(from); String isTypingText = Res.getString("message.is.typing.a.message", nickname); } } }); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/d039de56513c7dd0e3c5c2762f184ca886fb4900/GroupChatRoom.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/GroupChatRoom.java

public void run() { String bareAddress = StringUtils.parseBareAddress(from); if (bareAddress.equals(getRoomname())) { String nickname = StringUtils.parseResource(from); String isTypingText = Res.getString("message.is.typing.a.message", nickname); } }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/d039de56513c7dd0e3c5c2762f184ca886fb4900/GroupChatRoom.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/GroupChatRoom.java

public void setSendAndReceiveTypingNotifications(boolean sendAndReceiveTypingNotifications) { sendNotifications = sendAndReceiveTypingNotifications; if (sendAndReceiveTypingNotifications) { SparkManager.getMessageEventManager().addMessageEventNotificationListener(messageManager); } else { SparkManager.getMessageEventManager().removeMessageEventNotificationListener(messageManager); } }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/d039de56513c7dd0e3c5c2762f184ca886fb4900/GroupChatRoom.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/GroupChatRoom.java

private void setupListeners() { chat.addParticipantStatusListener(new DefaultParticipantStatusListener() { public void kicked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.kicked.from.room", nickname)); } public void voiceGranted(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.given.voice", nickname)); } public void voiceRevoked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.voice.revoked", nickname)); } public void banned(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.banned", nickname)); } public void membershipGranted(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.granted.membership", nickname)); } public void membershipRevoked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.revoked.membership", nickname)); } public void moderatorGranted(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.granted.moderator", nickname)); } public void moderatorRevoked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.revoked.moderator", nickname)); } public void ownershipGranted(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.granted.owner", nickname)); } public void ownershipRevoked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.revoked.owner", nickname)); } public void adminGranted(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.granted.admin", nickname)); } public void adminRevoked(String participant) { String nickname = StringUtils.parseResource(participant); insertText(Res.getString("message.user.revoked.admin", nickname)); } public void nicknameChanged(String participant, String nickname) { insertText(Res.getString("message.user.nickname.changed", StringUtils.parseResource(participant), nickname)); } }); chat.addUserStatusListener(new DefaultUserStatusListener() { public void kicked(String s, String reason) { insertText(Res.getString("message.your.kicked", s)); getChatInputEditor().setEnabled(false); getSplitPane().setRightComponent(null); leaveChatRoom(); } public void voiceGranted() { insertText(Res.getString("message.your.voice.granted")); getChatInputEditor().setEnabled(true); } public void voiceRevoked() { insertText(Res.getString("message.your.voice.revoked")); getChatInputEditor().setEnabled(false); } public void banned(String s, String reason) { insertText(Res.getString("message.your.banned")); } public void membershipGranted() { insertText(Res.getString("message.your.membership.granted")); } public void membershipRevoked() { insertText(Res.getString("message.your.membership.revoked")); } public void moderatorGranted() { insertText(Res.getString("message.your.moderator.granted")); } public void moderatorRevoked() { insertText(Res.getString("message.your.moderator.revoked")); } public void ownershipGranted() { insertText(Res.getString("message.your.ownership.granted")); } public void ownershipRevoked() { insertText(Res.getString("message.your.ownership.revoked")); } public void adminGranted() { insertText(Res.getString("message.your.admin.granted")); } public void adminRevoked() { insertText(Res.getString("message.your.revoked.granted")); } }); chat.addSubjectUpdatedListener(new SubjectListener()); }

52006 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/52006/d039de56513c7dd0e3c5c2762f184ca886fb4900/GroupChatRoom.java/buggy/src/java/org/jivesoftware/spark/ui/rooms/GroupChatRoom.java

public void addLog(String action, Class klass, Long id) {

public void addLog(String action, Class klass, Long id) { Assert.notNull(action); Assert.notNull(klass); Assert.notNull(id); if (Event.class.isAssignableFrom(klass) || EventLog.class.isAssignableFrom(klass) || EventDiff.class.isAssignableFrom(klass)) { log.debug("Not logging creation of logging type:" + klass); } else { checkReady("addLog"); log.info("Adding log:" + action + "," + klass + "," + id); EventLog l = new EventLog(); l.setAction(action); l.setType(klass.getName()); // TODO could be id to Type entity l.setIdList(id.toString()); l.setDetails(CurrentDetails.createDetails()); l.getGraphHolder().setToken(null, token); CurrentDetails.getCreationEvent().addEventLog(l); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

EventLog l = new EventLog(); l.setAction(action); l.setType(klass.getName()); l.setIdList(id.toString()); l.setDetails(CurrentDetails.createDetails()); l.getGraphHolder().setToken(null, token); CurrentDetails.getCreationEvent().addEventLog(l);

CurrentDetails.addLog( action, klass, id );

public void addLog(String action, Class klass, Long id) { Assert.notNull(action); Assert.notNull(klass); Assert.notNull(id); if (Event.class.isAssignableFrom(klass) || EventLog.class.isAssignableFrom(klass) || EventDiff.class.isAssignableFrom(klass)) { log.debug("Not logging creation of logging type:" + klass); } else { checkReady("addLog"); log.info("Adding log:" + action + "," + klass + "," + id); EventLog l = new EventLog(); l.setAction(action); l.setType(klass.getName()); // TODO could be id to Type entity l.setIdList(id.toString()); l.setDetails(CurrentDetails.createDetails()); l.getGraphHolder().setToken(null, token); CurrentDetails.getCreationEvent().addEventLog(l); } }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

Assert.notNull(d); if (isSystemType(klass))

if ( d == null || isSystemType(klass) )

public boolean allowLoad(Class<? extends IObject> klass, Details d) { Assert.notNull(klass); Assert.notNull(d); if (isSystemType(klass)) return true; return SecurityFilter.passesFilter(this, d); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

if ( currentDetails.getCreationEvent() == null ) { newDetails.setCreationEvent( previousDetails.getCreationEvent() ); return true; }

protected boolean managedEvent(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { if (!idEqual(previousDetails.getCreationEvent(), currentDetails .getCreationEvent())) { // no one change them. throw new SecurityViolation(String.format( "You are not authorized to change " + "the creation event for %s from %s to %s", obj, previousDetails.getCreationEvent(), currentDetails .getCreationEvent())); } // they are equal meaning no change was intended but in case other // changes took place, we have to make sure newDetails has the correct // value else { newDetails.setCreationEvent(previousDetails.getCreationEvent()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

if (locked) { throw new SecurityViolation("Cannot change group for entity:" + obj); } else if (currentDetails.getGroup() == null) {

if ( currentDetails.getGroup() == null ) {

protected boolean managedGroup(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { // previous and current have different ids. either change it and return // true if permitted, or throw an exception. if (!idEqual(previousDetails.getGroup(), currentDetails.getGroup())) { if (locked) { throw new SecurityViolation("Cannot change group for entity:" + obj); } // even root can't set them to null. else if (currentDetails.getGroup() == null) { newDetails.setGroup(previousDetails.getGroup()); return true; } // if user is a member of the group or the current user is an admin // or if the entity has been marked as privileged, then use the // current group. else if (memberOfGroups().contains( currentDetails.getGroup().getId()) || currentUserIsAdmin() || privileged) { newDetails.setGroup(currentDetails.getGroup()); return true; } // everyone else can't change them at all. else { throw new SecurityViolation(String.format( "You are not authorized to change " + "the group for %s from %s to %s", obj, previousDetails.getGroup(), currentDetails.getGroup())); } } // previous and current are the same, but we need to set // that value on newDetails. else { // This doesn't need to return true, because it'll only // be used if something else was changed. newDetails.setGroup(previousDetails.getGroup()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

} if (locked) { throw new SecurityViolation("Object locked! " + "Cannot change group for entity:" + obj);

protected boolean managedGroup(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { // previous and current have different ids. either change it and return // true if permitted, or throw an exception. if (!idEqual(previousDetails.getGroup(), currentDetails.getGroup())) { if (locked) { throw new SecurityViolation("Cannot change group for entity:" + obj); } // even root can't set them to null. else if (currentDetails.getGroup() == null) { newDetails.setGroup(previousDetails.getGroup()); return true; } // if user is a member of the group or the current user is an admin // or if the entity has been marked as privileged, then use the // current group. else if (memberOfGroups().contains( currentDetails.getGroup().getId()) || currentUserIsAdmin() || privileged) { newDetails.setGroup(currentDetails.getGroup()); return true; } // everyone else can't change them at all. else { throw new SecurityViolation(String.format( "You are not authorized to change " + "the group for %s from %s to %s", obj, previousDetails.getGroup(), currentDetails.getGroup())); } } // previous and current are the same, but we need to set // that value on newDetails. else { // This doesn't need to return true, because it'll only // be used if something else was changed. newDetails.setGroup(previousDetails.getGroup()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

throw new SecurityViolation("Cannot change owner for:" + obj);

throw new SecurityViolation("Object locked! " + "Cannot change owner for:" + obj);

protected boolean managedOwner(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { if (!idEqual(previousDetails.getOwner(), currentDetails.getOwner())) { if (locked) { throw new SecurityViolation("Cannot change owner for:" + obj); } // if the current user is an admin or if the entity has been // marked privileged, then use the current owner. else if (currentUserIsAdmin() || privileged) { // even root can't set them to null. if (currentDetails.getOwner() == null) { newDetails.setOwner(previousDetails.getOwner()); return true; } } // everyone else can't change them at all. else { throw new SecurityViolation(String.format( "You are not authorized to change " + "the owner for %s from %s to %s", obj, previousDetails.getOwner(), currentDetails.getOwner())); } } else { // values are the same. ensure they are the same for // newDetails as well newDetails.setOwner(previousDetails.getOwner()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

if (currentDetails.getOwner() == null) { newDetails.setOwner(previousDetails.getOwner()); return true; }

protected boolean managedOwner(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { if (!idEqual(previousDetails.getOwner(), currentDetails.getOwner())) { if (locked) { throw new SecurityViolation("Cannot change owner for:" + obj); } // if the current user is an admin or if the entity has been // marked privileged, then use the current owner. else if (currentUserIsAdmin() || privileged) { // even root can't set them to null. if (currentDetails.getOwner() == null) { newDetails.setOwner(previousDetails.getOwner()); return true; } } // everyone else can't change them at all. else { throw new SecurityViolation(String.format( "You are not authorized to change " + "the owner for %s from %s to %s", obj, previousDetails.getOwner(), currentDetails.getOwner())); } } else { // values are the same. ensure they are the same for // newDetails as well newDetails.setOwner(previousDetails.getOwner()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

protected boolean managedOwner(boolean locked, boolean privileged, IObject obj, Details previousDetails, Details currentDetails, Details newDetails) { if (!idEqual(previousDetails.getOwner(), currentDetails.getOwner())) { if (locked) { throw new SecurityViolation("Cannot change owner for:" + obj); } // if the current user is an admin or if the entity has been // marked privileged, then use the current owner. else if (currentUserIsAdmin() || privileged) { // even root can't set them to null. if (currentDetails.getOwner() == null) { newDetails.setOwner(previousDetails.getOwner()); return true; } } // everyone else can't change them at all. else { throw new SecurityViolation(String.format( "You are not authorized to change " + "the owner for %s from %s to %s", obj, previousDetails.getOwner(), currentDetails.getOwner())); } } else { // values are the same. ensure they are the same for // newDetails as well newDetails.setOwner(previousDetails.getOwner()); } return false; }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

if (iObject == null)

if (iObject == null || isSystemType( iObject.getClass() ))

public void markLockedIfNecessary(IObject iObject) { if (iObject == null) return; Set<IObject> s = new HashSet<IObject>(); IObject[] candidates = em.getLockCandidates(iObject); for (IObject object : candidates) { s.add(object); // TODO NEED TO CHECK FOR OWNERSHIP etc. etc. } CurrentDetails.appendLockCandidates(s); }

54698 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/54698/e6b7ac4062ce844e31078de77a00a7ab77e5e5d5/BasicSecuritySystem.java/buggy/components/server/src/ome/security/BasicSecuritySystem.java

if (recv.getRuntime().getLoadService().load(file.toString())) { return recv.getRuntime().getTrue(); } return recv.getRuntime().getFalse();

recv.getRuntime().getLoadService().load(file.toString()); return recv.getRuntime().getTrue();

public static IRubyObject load(IRubyObject recv, IRubyObject[] args) { RubyString file = (RubyString)args[0]; if (recv.getRuntime().getLoadService().load(file.toString())) { return recv.getRuntime().getTrue(); } return recv.getRuntime().getFalse(); }

50661 /local/tlutelli/issta_data/temp/all_java5context/java/2006_temp/2006/50661/ee934b89304925fd623a76285f84cfb31cb3695f/RubyKernel.java/buggy/src/org/jruby/RubyKernel.java

Experimenter foundUser = iQuery.get(Experimenter.class,user.getId());

Experimenter foundUser = internalGetExperimenter(user.getId());

public void addGroups(Experimenter user, ExperimenterGroup[] groups) { if (user == null) return; // Handled by annotations 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(); }