public static void main(String args[]) throws Exception {
// cache the initial set of loggers before this test begins
// to add any loggers
Enumeration<String> e = logMgr.getLoggerNames();
List<String> defaultLoggers = getDefaultLoggerNames();
while (e.hasMoreElements()) {
String logger = e.nextElement();
if (!defaultLoggers.contains(logger)) {
initialLoggerNames.add(logger);
}
}
;
String tstSrc = System.getProperty(TST_SRC_PROP);
File fname = new File(tstSrc, LM_PROP_FNAME);
String prop = fname.getCanonicalPath();
System.setProperty(CFG_FILE_PROP, prop);
logMgr.readConfiguration();
System.out.println();
if (checkLoggers() == PASSED) {
System.out.println(MSG_PASSED);
} else {
System.out.println(MSG_FAILED);
throw new Exception(MSG_FAILED);
}
}
/**
* Commit the contained item to the main archive. The item is associated with the relevant
* collection, added to the search index, and any other tasks such as assigning dates are
* performed.
*
* @return the fully archived item.
*/
@Override
public Item archive(Context context, BasicWorkflowItem workflowItem)
throws SQLException, IOException, AuthorizeException {
// FIXME: Check auth
Item item = workflowItem.getItem();
Collection collection = workflowItem.getCollection();
log.info(
LogManager.getHeader(
context,
"archive_item",
"workflow_item_id="
+ workflowItem.getID()
+ "item_id="
+ item.getID()
+ "collection_id="
+ collection.getID()));
installItemService.installItem(context, workflowItem);
// Log the event
log.info(
LogManager.getHeader(
context,
"install_item",
"workflow_id=" + workflowItem.getID() + ", item_id=" + item.getID() + "handle=FIXME"));
return item;
}
protected void notifyOfReject(
Context context, BasicWorkflowItem workflowItem, EPerson e, String reason) {
try {
// Get the item title
String title = getItemTitle(workflowItem);
// Get the collection
Collection coll = workflowItem.getCollection();
// Get rejector's name
String rejector = getEPersonName(e);
Locale supportedLocale = I18nUtil.getEPersonLocale(e);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "submit_reject"));
email.addRecipient(workflowItem.getSubmitter().getEmail());
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(rejector);
email.addArgument(reason);
email.addArgument(getMyDSpaceLink());
email.send();
} catch (RuntimeException re) {
// log this email error
log.warn(
LogManager.getHeader(
context,
"notify_of_reject",
"cannot email user eperson_id="
+ e.getID()
+ " eperson_email="
+ e.getEmail()
+ " workflow_item_id="
+ workflowItem.getID()
+ ": "
+ re.getMessage()));
throw re;
} catch (Exception ex) {
// log this email error
log.warn(
LogManager.getHeader(
context,
"notify_of_reject",
"cannot email user eperson_id="
+ e.getID()
+ " eperson_email="
+ e.getEmail()
+ " workflow_item_id="
+ workflowItem.getID()
+ ": "
+ ex.getMessage()));
}
}
static void checkDataset() {
Attribute[] outputs = Attributes.getOutputAttributes();
if (outputs.length != 1) {
LogManager.printErr("Only datasets with one output are supported");
System.exit(1);
}
if (outputs[0].getType() != Attribute.NOMINAL) {
LogManager.printErr("Output attribute should be nominal");
System.exit(1);
}
Parameters.numClasses = outputs[0].getNumNominalValues();
Parameters.numAttributes = Attributes.getInputAttributes().length;
}
public static void logInit(boolean force) throws IOException {
if (!IsLogInitialized || force) {
LogManager.getLogManager()
.readConfiguration(
LibRt.class.getClassLoader().getResourceAsStream("cfg.logging.properties"));
String logFile = System.getProperty("CfgLog");
if (logFile != null) {
LogManager.getLogManager().readConfiguration(new FileInputStream(logFile));
}
try {
LogLvlMax = Integer.parseInt(System.getProperty("LogLvlMax", LogLvlMax + ""));
} catch (Exception ex) {
}
; // XXX: mostrar mensaje?
}
}
/* Check: getLoggerNames() must return correct names
* for registered loggers and their parents.
* Returns boolean values: PASSED or FAILED
*/
public static boolean checkLoggers() {
String failMsg = "# checkLoggers: getLoggerNames() returned unexpected loggers";
Vector<String> expectedLoggerNames = new Vector<String>(getDefaultLoggerNames());
// Create the logger LOGGER_NAME_1
Logger.getLogger(LOGGER_NAME_1);
expectedLoggerNames.addElement(PARENT_NAME_1);
expectedLoggerNames.addElement(LOGGER_NAME_1);
// Create the logger LOGGER_NAME_2
Logger.getLogger(LOGGER_NAME_2);
expectedLoggerNames.addElement(PARENT_NAME_2);
expectedLoggerNames.addElement(LOGGER_NAME_2);
Enumeration<String> returnedLoggersEnum = logMgr.getLoggerNames();
Vector<String> returnedLoggerNames = new Vector<String>(0);
while (returnedLoggersEnum.hasMoreElements()) {
String logger = returnedLoggersEnum.nextElement();
if (!initialLoggerNames.contains(logger)) {
// filter out the loggers that have been added before this test runs
returnedLoggerNames.addElement(logger);
}
}
;
return checkNames(expectedLoggerNames, returnedLoggerNames, failMsg);
}
/**
* Return the workflow item to the workspace of the submitter. The workflow item is removed, and a
* workspace item created.
*
* @param c Context
* @param wfi WorkflowItem to be 'dismantled'
* @return the workspace item
*/
protected WorkspaceItem returnToWorkspace(Context c, BasicWorkflowItem wfi)
throws SQLException, IOException, AuthorizeException {
// FIXME: How should this interact with the workflow system?
// FIXME: Remove license
// FIXME: Provenance statement?
// Create the new workspace item row
WorkspaceItem workspaceItem = workspaceItemService.create(c, wfi);
workspaceItem.setMultipleFiles(wfi.hasMultipleFiles());
workspaceItem.setMultipleTitles(wfi.hasMultipleTitles());
workspaceItem.setPublishedBefore(wfi.isPublishedBefore());
workspaceItemService.update(c, workspaceItem);
// myitem.update();
log.info(
LogManager.getHeader(
c,
"return_to_workspace",
"workflow_item_id=" + wfi.getID() + "workspace_item_id=" + workspaceItem.getID()));
// Now remove the workflow object manually from the database
workflowItemService.deleteWrapper(c, wfi);
return workspaceItem;
}
@Override
public WorkspaceItem abort(Context c, XmlWorkflowItem wi, EPerson e)
throws AuthorizeException, SQLException, IOException {
if (!authorizeService.isAdmin(c)) {
throw new AuthorizeException("You must be an admin to abort a workflow");
}
c.turnOffAuthorisationSystem();
// Restore permissions for the submitter
// convert into personal workspace
WorkspaceItem wsi = returnToWorkspace(c, wi);
log.info(
LogManager.getHeader(
c,
"abort_workflow",
"workflow_item_id="
+ wi.getID()
+ "item_id="
+ wsi.getItem().getID()
+ "collection_id="
+ wi.getCollection().getID()
+ "eperson_id="
+ e.getID()));
c.restoreAuthSystemState();
return wsi;
}
@Override
public WorkspaceItem abort(Context context, BasicWorkflowItem workflowItem, EPerson e)
throws SQLException, AuthorizeException, IOException {
// authorize a DSpaceActions.ABORT
if (!authorizeService.isAdmin(context)) {
throw new AuthorizeException("You must be an admin to abort a workflow");
}
// stop workflow regardless of its state
taskListItemService.deleteByWorkflowItem(context, workflowItem);
log.info(
LogManager.getHeader(
context,
"abort_workflow",
"workflow_item_id="
+ workflowItem.getID()
+ "item_id="
+ workflowItem.getItem().getID()
+ "collection_id="
+ workflowItem.getCollection().getID()
+ "eperson_id="
+ e.getID()));
// convert into personal workspace
return returnToWorkspace(context, workflowItem);
}
/**
* Gets the score for a given position from a sgr file
*
* @author elee
*/
public class SgrScoreCalculator extends StoredScoreCalculator {
// class variables
protected static final Logger logger = LogManager.getLogger(SgrScoreCalculator.class);
/**
* Builds a SgrScoreCalculator object
*
* @param data - name of file containing sgr data
* @param winSize - size of display window
* @throws IOException - if the file cannot be accessed
*/
public SgrScoreCalculator(String data, int winSize, CurationSet curation) throws IOException {
super(winSize);
BufferedReader br = new BufferedReader(new FileReader(data));
String line;
double minAbsScore = Double.POSITIVE_INFINITY;
Set<String> unmatchedIds = new HashSet<String>();
while ((line = br.readLine()) != null) {
String[] tokens = line.split("\t");
String refId = curation.getRefSequence().getName();
if (!tokens[0].equals(refId)) {
if (!unmatchedIds.contains(tokens[0])) {
logger.warn(
"Score id "
+ tokens[0]
+ " does not match main sequence id "
+ refId
+ ". Skipping score.");
unmatchedIds.add(tokens[0]);
}
continue;
}
Double score = new Double(Double.parseDouble(tokens[2]));
// chuck out scores outside of the given range
int pos = Integer.parseInt(tokens[1]);
if (pos >= curation.getLow() && pos <= curation.getHigh()) {
scoreMap.put(pos, score);
}
if (Math.abs(score) < minAbsScore) {
minAbsScore = Math.abs(score);
}
if (score.doubleValue() < minScore) {
minScore = score;
}
if (score.doubleValue() > maxScore) {
maxScore = score;
}
}
while (minAbsScore * factor < 1) {
factor *= 10;
}
}
}
/** @param args the command line arguments */
public static void main(String[] args) {
ParserParameters.doParse(args[0]);
LogManager.initLogManager();
InstanceSet is = new InstanceSet();
try {
is.readSet(Parameters.trainInputFile, true);
} catch (Exception e) {
LogManager.printErr(e.toString());
System.exit(1);
}
checkDataset();
Discretizer dis;
String name = Parameters.algorithmName;
dis = new FayyadDiscretizer();
dis.buildCutPoints(is);
dis.applyDiscretization(Parameters.trainInputFile, Parameters.trainOutputFile);
dis.applyDiscretization(Parameters.testInputFile, Parameters.testOutputFile);
LogManager.closeLog();
}
/**
* Commit the contained item to the main archive. The item is associated with the relevant
* collection, added to the search index, and any other tasks such as assigning dates are
* performed.
*
* @param context The relevant DSpace Context.
* @param wfi workflow item
* @return the fully archived item.
* @throws IOException A general class of exceptions produced by failed or interrupted I/O
* operations.
* @throws SQLException An exception that provides information on a database access error or other
* errors.
* @throws AuthorizeException Exception indicating the current user of the context does not have
* permission to perform a particular action.
*/
@Override
public Item archive(Context context, XmlWorkflowItem wfi)
throws SQLException, IOException, AuthorizeException {
// FIXME: Check auth
Item item = wfi.getItem();
Collection collection = wfi.getCollection();
// Remove (if any) the workflowItemroles for this item
workflowItemRoleService.deleteForWorkflowItem(context, wfi);
log.info(
LogManager.getHeader(
context,
"archive_item",
"workflow_item_id="
+ wfi.getID()
+ "item_id="
+ item.getID()
+ "collection_id="
+ collection.getID()));
installItemService.installItem(context, wfi);
// Notify
notifyOfArchive(context, item, collection);
// Clear any remaining workflow metadata
itemService.clearMetadata(
context, item, WorkflowRequirementsService.WORKFLOW_SCHEMA, Item.ANY, Item.ANY, Item.ANY);
itemService.update(context, item);
// Log the event
log.info(
LogManager.getHeader(
context,
"install_item",
"workflow_item_id=" + wfi.getID() + ", item_id=" + item.getID() + "handle=FIXME"));
return item;
}
@Override
public void claim(Context context, BasicWorkflowItem workflowItem, EPerson e)
throws SQLException, IOException, AuthorizeException {
int taskstate = workflowItem.getState();
switch (taskstate) {
case WFSTATE_STEP1POOL:
// authorize DSpaceActions.SUBMIT_REVIEW
doState(context, workflowItem, WFSTATE_STEP1, e);
break;
case WFSTATE_STEP2POOL:
// authorize DSpaceActions.SUBMIT_STEP2
doState(context, workflowItem, WFSTATE_STEP2, e);
break;
case WFSTATE_STEP3POOL:
// authorize DSpaceActions.SUBMIT_STEP3
doState(context, workflowItem, WFSTATE_STEP3, e);
break;
// if we got here, we weren't pooled... error?
// FIXME - log the error?
}
log.info(
LogManager.getHeader(
context,
"claim_task",
"workflow_item_id="
+ workflowItem.getID()
+ "item_id="
+ workflowItem.getItem().getID()
+ "collection_id="
+ workflowItem.getCollection().getID()
+ "newowner_id="
+ workflowItem.getOwner().getID()
+ "old_state="
+ taskstate
+ "new_state="
+ workflowItem.getState()));
}
@Override
public void unclaim(Context context, BasicWorkflowItem workflowItem, EPerson e)
throws SQLException, IOException, AuthorizeException {
int taskstate = workflowItem.getState();
switch (taskstate) {
case WFSTATE_STEP1:
// authorize DSpaceActions.STEP1
doState(context, workflowItem, WFSTATE_STEP1POOL, e);
break;
case WFSTATE_STEP2:
// authorize DSpaceActions.APPROVE
doState(context, workflowItem, WFSTATE_STEP2POOL, e);
break;
case WFSTATE_STEP3:
// authorize DSpaceActions.STEP3
doState(context, workflowItem, WFSTATE_STEP3POOL, e);
break;
// error handling? shouldn't get here
// FIXME - what to do with error - log it?
}
log.info(
LogManager.getHeader(
context,
"unclaim_workflow",
"workflow_item_id="
+ workflowItem.getID()
+ ",item_id="
+ workflowItem.getItem().getID()
+ ",collection_id="
+ workflowItem.getCollection().getID()
+ ",old_state="
+ taskstate
+ ",new_state="
+ workflowItem.getState()));
}
// send notices of curation activity
@Override
public void notifyOfCuration(
Context c,
BasicWorkflowItem wi,
List<EPerson> ePeople,
String taskName,
String action,
String message)
throws SQLException, IOException {
try {
// Get the item title
String title = getItemTitle(wi);
// Get the submitter's name
String submitter = getSubmitterName(wi);
// Get the collection
Collection coll = wi.getCollection();
for (EPerson epa : ePeople) {
Locale supportedLocale = I18nUtil.getEPersonLocale(epa);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "flowtask_notify"));
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(submitter);
email.addArgument(taskName);
email.addArgument(message);
email.addArgument(action);
email.addRecipient(epa.getEmail());
email.send();
}
} catch (MessagingException e) {
log.warn(
LogManager.getHeader(
c,
"notifyOfCuration",
"cannot email users of workflow_item_id " + wi.getID() + ": " + e.getMessage()));
}
}
protected void activateFirstStep(
Context context, Workflow wf, Step firstStep, XmlWorkflowItem wfi)
throws AuthorizeException, IOException, SQLException, WorkflowException,
WorkflowConfigurationException {
WorkflowActionConfig firstActionConfig = firstStep.getUserSelectionMethod();
firstActionConfig.getProcessingAction().activate(context, wfi);
log.info(
LogManager.getHeader(
context,
"start_workflow",
firstActionConfig.getProcessingAction()
+ " workflow_item_id="
+ wfi.getID()
+ "item_id="
+ wfi.getItem().getID()
+ "collection_id="
+ wfi.getCollection().getID()));
// record the start of the workflow w/provenance message
recordStart(context, wfi.getItem(), firstActionConfig.getProcessingAction());
// Fire an event !
logWorkflowEvent(
context,
firstStep.getWorkflow().getID(),
null,
null,
wfi,
null,
firstStep,
firstActionConfig);
// If we don't have a UI activate it
if (!firstActionConfig.requiresUI()) {
ActionResult outcome =
firstActionConfig.getProcessingAction().execute(context, wfi, firstStep, null);
processOutcome(context, null, wf, firstStep, firstActionConfig, outcome, wfi, true);
}
}
private void initLogger() {
ConsoleHandler consoleHandler = null;
Logger rootLogger = LogManager.getLogManager().getLogger("");
Handler[] handlers = rootLogger.getHandlers();
for (Handler handler : handlers) {
if (handler instanceof ConsoleHandler) {
consoleHandler = (ConsoleHandler) handler;
rootLogger.removeHandler(handler);
}
}
logger = Logger.getLogger(contextId);
logger.setLevel(logLevel);
if (!logLevel.equals(Level.OFF)) {
LogFormatter formatter = new LogFormatter();
if (consoleLog) {
if (consoleHandler == null) {
consoleHandler = new ConsoleHandler();
}
consoleHandler.setFormatter(formatter);
consoleHandler.setLevel(logLevel);
logger.addHandler(consoleHandler);
}
String userHomePath = getProperty("user.home", ".");
File logDir = new File(userHomePath, '.' + contextId + "/log");
logDir.mkdirs();
String logFilePattern = new File(logDir, contextId + "-%g.log").getPath();
try {
FileHandler fileHandler = new FileHandler(logFilePattern);
fileHandler.setFormatter(formatter);
fileHandler.setLevel(logLevel);
logger.addHandler(fileHandler);
} catch (IOException e) {
System.err.println("Error: Failed to create log file: " + logFilePattern);
}
}
}
/**
* Return the workflow item to the workspace of the submitter. The workflow item is removed, and a
* workspace item created.
*
* @param c Context
* @param wfi WorkflowItem to be 'dismantled'
* @return the workspace item
* @throws java.io.IOException ...
* @throws java.sql.SQLException ...
* @throws org.dspace.authorize.AuthorizeException ...
*/
protected WorkspaceItem returnToWorkspace(Context c, XmlWorkflowItem wfi)
throws SQLException, IOException, AuthorizeException {
// authorize a DSpaceActions.REJECT
// stop workflow
deleteAllTasks(c, wfi);
c.turnOffAuthorisationSystem();
// Also clear all info for this step
workflowRequirementsService.clearInProgressUsers(c, wfi);
// Remove (if any) the workflowItemroles for this item
workflowItemRoleService.deleteForWorkflowItem(c, wfi);
Item myitem = wfi.getItem();
// Restore permissions for the submitter
grantUserAllItemPolicies(c, myitem, myitem.getSubmitter());
// FIXME: How should this interact with the workflow system?
// FIXME: Remove license
// FIXME: Provenance statement?
// Create the new workspace item row
WorkspaceItem workspaceItem = workspaceItemService.create(c, wfi);
workspaceItem.setMultipleFiles(wfi.hasMultipleFiles());
workspaceItem.setMultipleTitles(wfi.hasMultipleTitles());
workspaceItem.setPublishedBefore(wfi.isPublishedBefore());
workspaceItemService.update(c, workspaceItem);
// myitem.update();
log.info(
LogManager.getHeader(
c,
"return_to_workspace",
"workflow_item_id=" + wfi.getID() + "workspace_item_id=" + workspaceItem.getID()));
// Now remove the workflow object manually from the database
xmlWorkflowItemService.deleteWrapper(c, wfi);
return workspaceItem;
}
@Override
public BasicWorkflowItem start(Context context, WorkspaceItem wsi)
throws SQLException, AuthorizeException, IOException {
// FIXME Check auth
Item myitem = wsi.getItem();
Collection collection = wsi.getCollection();
log.info(
LogManager.getHeader(
context,
"start_workflow",
"workspace_item_id="
+ wsi.getID()
+ "item_id="
+ myitem.getID()
+ "collection_id="
+ collection.getID()));
// record the start of the workflow w/provenance message
recordStart(context, myitem);
// create the WorkflowItem
BasicWorkflowItem wfi = workflowItemService.create(context, myitem, collection);
wfi.setMultipleFiles(wsi.hasMultipleFiles());
wfi.setMultipleTitles(wsi.hasMultipleTitles());
wfi.setPublishedBefore(wsi.isPublishedBefore());
// remove the WorkspaceItem
workspaceItemService.deleteWrapper(context, wsi);
// now get the workflow started
wfi.setState(WFSTATE_SUBMIT);
advance(context, wfi, null);
// Return the workflow item
return wfi;
}
/**
* notify the submitter that the item is archived
*
* @param context The relevant DSpace Context.
* @param item which item was archived
* @param coll collection name to display in template
* @throws SQLException An exception that provides information on a database access error or other
* errors.
* @throws IOException A general class of exceptions produced by failed or interrupted I/O
* operations.
*/
protected void notifyOfArchive(Context context, Item item, Collection coll)
throws SQLException, IOException {
try {
// Get submitter
EPerson ep = item.getSubmitter();
// Get the Locale
Locale supportedLocale = I18nUtil.getEPersonLocale(ep);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "submit_archive"));
// Get the item handle to email to user
String handle = handleService.findHandle(context, item);
// Get title
List<MetadataValue> titles =
itemService.getMetadata(item, MetadataSchema.DC_SCHEMA, "title", null, Item.ANY);
String title = "";
try {
title = I18nUtil.getMessage("org.dspace.workflow.WorkflowManager.untitled");
} catch (MissingResourceException e) {
title = "Untitled";
}
if (titles.size() > 0) {
title = titles.iterator().next().getValue();
}
email.addRecipient(ep.getEmail());
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(handleService.getCanonicalForm(handle));
email.send();
} catch (MessagingException e) {
log.warn(
LogManager.getHeader(
context, "notifyOfArchive", "cannot email user" + " item_id=" + item.getID()));
}
}
/** notify the submitter that the item is archived */
protected void notifyOfArchive(Context context, Item item, Collection coll)
throws SQLException, IOException {
try {
// Get submitter
EPerson ep = item.getSubmitter();
// Get the Locale
Locale supportedLocale = I18nUtil.getEPersonLocale(ep);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "submit_archive"));
// Get the item handle to email to user
String handle = handleService.findHandle(context, item);
// Get title
String title = item.getName();
if (StringUtils.isBlank(title)) {
try {
title = I18nUtil.getMessage("org.dspace.workflow.WorkflowManager.untitled");
} catch (MissingResourceException e) {
title = "Untitled";
}
}
email.addRecipient(ep.getEmail());
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(handleService.getCanonicalForm(handle));
email.send();
} catch (MessagingException e) {
log.warn(
LogManager.getHeader(
context,
"notifyOfArchive",
"cannot email user; item_id=" + item.getID() + ": " + e.getMessage()));
}
}
/*
* Executes an action and returns the next.
*/
@Override
public WorkflowActionConfig doState(
Context c,
EPerson user,
HttpServletRequest request,
int workflowItemId,
Workflow workflow,
WorkflowActionConfig currentActionConfig)
throws SQLException, AuthorizeException, IOException, MessagingException, WorkflowException {
try {
XmlWorkflowItem wi = xmlWorkflowItemService.find(c, workflowItemId);
Step currentStep = currentActionConfig.getStep();
if (currentActionConfig.getProcessingAction().isAuthorized(c, request, wi)) {
ActionResult outcome =
currentActionConfig.getProcessingAction().execute(c, wi, currentStep, request);
return processOutcome(
c, user, workflow, currentStep, currentActionConfig, outcome, wi, false);
} else {
throw new AuthorizeException("You are not allowed to to perform this task.");
}
} catch (WorkflowConfigurationException e) {
log.error(
LogManager.getHeader(
c,
"error while executing state",
"workflow: "
+ workflow.getID()
+ " action: "
+ currentActionConfig.getId()
+ " workflowItemId: "
+ workflowItemId),
e);
WorkflowUtils.sendAlert(request, e);
throw new WorkflowException(e);
}
}
protected void notifyOfReject(Context c, XmlWorkflowItem wi, EPerson e, String reason) {
try {
// Get the item title
String title = wi.getItem().getName();
// Get the collection
Collection coll = wi.getCollection();
// Get rejector's name
String rejector = getEPersonName(e);
Locale supportedLocale = I18nUtil.getEPersonLocale(e);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "submit_reject"));
email.addRecipient(wi.getSubmitter().getEmail());
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(rejector);
email.addArgument(reason);
email.addArgument(ConfigurationManager.getProperty("dspace.url") + "/mydspace");
email.send();
} catch (Exception ex) {
// log this email error
log.warn(
LogManager.getHeader(
c,
"notify_of_reject",
"cannot email user"
+ " eperson_id"
+ e.getID()
+ " eperson_email"
+ e.getEmail()
+ " workflow_item_id"
+ wi.getID()));
}
}
/**
* FXML Controller class
*
* @author Mostafa
*/
public class LocalDeleteObjectInstanceServiceController implements Initializable {
// Logger
private static final Logger logger = LogManager.getLogger();
@FXML private TextField ObjectInstanceDesignator;
@FXML private Button OkButton;
/** Initializes the controller class. */
@Override
public void initialize(URL url, ResourceBundle rb) {
logger.entry();
OkButton.disableProperty().bind(ObjectInstanceDesignator.textProperty().isEmpty());
logger.exit();
}
@FXML
private void Cancel_click(ActionEvent event) {
logger.entry();
((Stage) OkButton.getScene().getWindow()).close();
logger.exit();
}
@FXML
private void Ok_click(ActionEvent event) {
logger.entry();
LogEntry log = new LogEntry("6.16", "Local Delete Object Instance service");
try {
ObjectInstanceHandle instanceHandle =
rtiAmb
.getObjectInstanceHandleFactory()
.decode(
ByteBuffer.allocate(4)
.putInt(Integer.parseInt(ObjectInstanceDesignator.getText()))
.array(),
0);
log.getSuppliedArguments()
.add(
new ClassValuePair(
"Object instance designator",
ObjectInstanceHandle.class,
instanceHandle.toString()));
rtiAmb.localDeleteObjectInstance(instanceHandle);
log.setDescription("Local Object instance deleted successfully");
log.setLogType(LogEntryType.REQUEST);
} catch (FederateNotExecutionMember
| NotConnected
| NumberFormatException
| CouldNotDecode
| RTIinternalError
| OwnershipAcquisitionPending
| FederateOwnsAttributes
| ObjectInstanceNotKnown
| SaveInProgress
| RestoreInProgress ex) {
log.setException(ex);
log.setLogType(LogEntryType.ERROR);
logger.log(Level.ERROR, ex.getMessage(), ex);
} catch (Exception ex) {
log.setException(ex);
log.setLogType(LogEntryType.FATAL);
logger.log(Level.FATAL, ex.getMessage(), ex);
}
logEntries.add(log);
((Stage) OkButton.getScene().getWindow()).close();
logger.exit();
}
}
/**
* The instance is stored in a place directly accessible through the Java SE API, so that it can
* be recovered from any class loader.
*/
protected MockingBridge(Class<? extends MockingBridge> subclass) {
super("mockit." + subclass.hashCode(), null);
LogManager.getLogManager().addLogger(this);
}
protected void notifyGroupOfTask(
Context c, BasicWorkflowItem wi, Group mygroup, List<EPerson> epa)
throws SQLException, IOException {
// check to see if notification is turned off
// and only do it once - delete key after notification has
// been suppressed for the first time
UUID myID = wi.getItem().getID();
if (noEMail.containsKey(myID)) {
// suppress email, and delete key
noEMail.remove(myID);
} else {
try {
// Get the item title
String title = getItemTitle(wi);
// Get the submitter's name
String submitter = getSubmitterName(wi);
// Get the collection
Collection coll = wi.getCollection();
String message = "";
for (EPerson anEpa : epa) {
Locale supportedLocale = I18nUtil.getEPersonLocale(anEpa);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "submit_task"));
email.addArgument(title);
email.addArgument(coll.getName());
email.addArgument(submitter);
ResourceBundle messages = ResourceBundle.getBundle("Messages", supportedLocale);
switch (wi.getState()) {
case WFSTATE_STEP1POOL:
message = messages.getString("org.dspace.workflow.WorkflowManager.step1");
break;
case WFSTATE_STEP2POOL:
message = messages.getString("org.dspace.workflow.WorkflowManager.step2");
break;
case WFSTATE_STEP3POOL:
message = messages.getString("org.dspace.workflow.WorkflowManager.step3");
break;
}
email.addArgument(message);
email.addArgument(getMyDSpaceLink());
email.addRecipient(anEpa.getEmail());
email.send();
}
} catch (MessagingException e) {
String gid = (mygroup != null) ? String.valueOf(mygroup.getID()) : "none";
log.warn(
LogManager.getHeader(
c,
"notifyGroupofTask",
"cannot email user group_id="
+ gid
+ " workflow_item_id="
+ wi.getID()
+ ": "
+ e.getMessage()));
}
}
}
@Override
public WorkspaceItem sendWorkflowItemBackSubmission(
Context context,
BasicWorkflowItem workflowItem,
EPerson ePerson,
String provenancePrefix,
String rejection_message)
throws SQLException, AuthorizeException, IOException {
int oldState = workflowItem.getState();
// authorize a DSpaceActions.REJECT
// stop workflow
taskListItemService.deleteByWorkflowItem(context, workflowItem);
// rejection provenance
Item myitem = workflowItem.getItem();
// Get current date
String now = DCDate.getCurrent().toString();
// Get user's name + email address
String usersName = getEPersonName(ePerson);
// Here's what happened
String provDescription =
"Rejected by " + usersName + ", reason: " + rejection_message + " on " + now + " (GMT) ";
// Add to item as a DC field
itemService.addMetadata(
context,
myitem,
MetadataSchema.DC_SCHEMA,
"description",
"provenance",
"en",
provDescription);
itemService.update(context, myitem);
// convert into personal workspace
WorkspaceItem wsi = returnToWorkspace(context, workflowItem);
// notify that it's been rejected
notifyOfReject(context, workflowItem, ePerson, rejection_message);
log.info(
LogManager.getHeader(
context,
"reject_workflow",
"workflow_item_id="
+ workflowItem.getID()
+ "item_id="
+ workflowItem.getItem().getID()
+ "collection_id="
+ workflowItem.getCollection().getID()
+ "eperson_id="
+ ePerson.getID()));
logWorkflowEvent(
context,
wsi.getItem(),
workflowItem,
ePerson,
WFSTATE_SUBMIT,
null,
wsi.getCollection(),
oldState,
null);
return wsi;
}
@Override
public boolean advance(
Context context, BasicWorkflowItem workflowItem, EPerson e, boolean curate, boolean record)
throws SQLException, IOException, AuthorizeException {
int taskstate = workflowItem.getState();
boolean archived = false;
// perform curation tasks if needed
if (curate && workflowCuratorService.needsCuration(workflowItem)) {
if (!workflowCuratorService.doCuration(context, workflowItem)) {
// don't proceed - either curation tasks queued, or item rejected
log.info(
LogManager.getHeader(
context,
"advance_workflow",
"workflow_item_id="
+ workflowItem.getID()
+ ",item_id="
+ workflowItem.getItem().getID()
+ ",collection_id="
+ workflowItem.getCollection().getID()
+ ",old_state="
+ taskstate
+ ",doCuration=false"));
return false;
}
}
switch (taskstate) {
case WFSTATE_SUBMIT:
archived = doState(context, workflowItem, WFSTATE_STEP1POOL, e);
break;
case WFSTATE_STEP1:
// authorize DSpaceActions.SUBMIT_REVIEW
// Record provenance
if (record) {
recordApproval(context, workflowItem, e);
}
archived = doState(context, workflowItem, WFSTATE_STEP2POOL, e);
break;
case WFSTATE_STEP2:
// authorize DSpaceActions.SUBMIT_STEP2
// Record provenance
if (record) {
recordApproval(context, workflowItem, e);
}
archived = doState(context, workflowItem, WFSTATE_STEP3POOL, e);
break;
case WFSTATE_STEP3:
// authorize DSpaceActions.SUBMIT_STEP3
// We don't record approval for editors, since they can't reject,
// and thus didn't actually make a decision
archived = doState(context, workflowItem, WFSTATE_ARCHIVE, e);
break;
// error handling? shouldn't get here
}
log.info(
LogManager.getHeader(
context,
"advance_workflow",
"workflow_item_id="
+ workflowItem.getID()
+ ",item_id="
+ workflowItem.getItem().getID()
+ ",collection_id="
+ workflowItem.getCollection().getID()
+ ",old_state="
+ taskstate
+ ",new_state="
+ workflowItem.getState()));
return archived;
}
/**
* Return the global LogManager object.
*/
public static LogManager getLogManager() {
if (manager != null) {
manager.readPrimordialConfiguration();
}
return manager;
}
/**
* FXML Controller class
*
* @author Mostafa Ali <*****@*****.**>
*/
public class InteractionsListController extends VBox {
// Logger
private static final Logger logger = LogManager.getLogger();
@FXML private TableView<InteractionState> InteractionTableView;
@FXML private TableColumn<InteractionState, String> InteractionTableColumn;
@FXML private TableColumn CheckTableColumn;
CheckBox cb = new CheckBox();
ObservableList<InteractionState> interactions = FXCollections.observableArrayList();
public InteractionsListController() {
logger.entry();
FXMLLoader fxmlLoader =
new FXMLLoader(getClass().getResource("/fxml/customcontrol/InteractionsList.fxml"));
fxmlLoader.setController(this);
fxmlLoader.setRoot(this);
try {
fxmlLoader.load();
} catch (IOException ex) {
logger.log(Level.FATAL, ex.getMessage(), ex);
}
logger.exit();
}
public void setFddObjectModel(FddObjectModel fddObjectModel) {
logger.entry();
if (fddObjectModel != null) {
fddObjectModel
.getInteractionClasses()
.values()
.stream()
.forEach(
(value) -> {
interactions.add(new InteractionState(value));
});
InteractionTableView.setItems(interactions);
interactions.forEach(
(interaction) -> {
interaction
.onProperty()
.addListener(
(observable, oldValue, newValue) -> {
if (!newValue) {
cb.setSelected(false);
} else if (interactions.stream().allMatch(a -> a.isOn())) {
cb.setSelected(true);
}
});
});
InteractionTableColumn.setCellValueFactory(new PropertyValueFactory<>("interactionName"));
CheckTableColumn.setCellValueFactory(
new Callback<
TableColumn.CellDataFeatures<InteractionState, Boolean>, ObservableValue<Boolean>>() {
@Override
public ObservableValue<Boolean> call(
TableColumn.CellDataFeatures<InteractionState, Boolean> param) {
return param.getValue().onProperty();
}
});
CheckTableColumn.setCellFactory(CheckBoxTableCell.forTableColumn(CheckTableColumn));
cb.setUserData(CheckTableColumn);
cb.setOnAction(
(ActionEvent event) -> {
CheckBox cb1 = (CheckBox) event.getSource();
TableColumn tc = (TableColumn) cb1.getUserData();
InteractionTableView.getItems()
.stream()
.forEach(
(item) -> {
item.setOn(cb1.isSelected());
});
});
CheckTableColumn.setGraphic(cb);
}
logger.exit();
}
public List<InteractionClassFDD> getInteractions() {
return interactions
.stream()
.filter(a -> a.isOn())
.map(a -> a.interaction)
.collect(Collectors.toList());
}
public static class InteractionState {
private final ReadOnlyStringWrapper interactionName = new ReadOnlyStringWrapper();
private final BooleanProperty on = new SimpleBooleanProperty();
private final InteractionClassFDD interaction;
public InteractionState(InteractionClassFDD interaction) {
this.interaction = interaction;
interactionName.set(interaction.getFullName());
}
public String getInteractionName() {
return interactionName.get();
}
public ReadOnlyStringProperty interactionNameProperty() {
return interactionName.getReadOnlyProperty();
}
public boolean isOn() {
return on.get();
}
public void setOn(boolean value) {
on.set(value);
}
public BooleanProperty onProperty() {
return on;
}
@Override
public String toString() {
return interaction.getFullName();
}
}
}