/**
* Generate code corresponding to the given classes. The classes must have previously been
* returned from {@link #enter}. If there are classes outstanding to be analyzed, that will be
* done before any classes are generated. If null is specified, code will be generated for all
* outstanding classes.
*
* @param classes a list of class elements
*/
public Iterable<? extends JavaFileObject> generate(Iterable<? extends TypeElement> classes)
throws IOException {
final ListBuffer<JavaFileObject> results = new ListBuffer<JavaFileObject>();
try {
analyze(null); // ensure all classes have been parsed, entered, and analyzed
if (classes == null) {
compiler.generate(compiler.desugar(genList), results);
genList.clear();
} else {
Filter f =
new Filter() {
public void process(Env<AttrContext> env) {
compiler.generate(compiler.desugar(ListBuffer.of(env)), results);
}
};
f.run(genList, classes);
}
if (genList.isEmpty()) {
compiler.reportDeferredDiagnostics();
cleanup();
}
} finally {
if (compiler != null) compiler.log.flush();
}
return results;
}
public static void filtersToParameters(
Collection<Filter> filters, List<String> parameters, Collection<VirtualFile> paths) {
for (Filter filter : filters) {
filter.getCommandParametersFilter().applyToCommandLine(parameters);
filter.getCommandParametersFilter().applyToPaths(paths);
}
}
private DirFilter getDirFilter() {
DirFilter deepestDirFilter = new DirFilter(Operator.EQ, preferences.get(Keys.MEDIA_DIR));
for (Filter<? super Tables.Tracks> filter : getFilters()) {
final DirFilter finalDeepestDirFilter = deepestDirFilter;
deepestDirFilter =
filter.accept(
new TurtleFilterVisitor<Tables.Tracks, DirFilter>() {
public DirFilter visit(DirFilter dirFilter) {
return finalDeepestDirFilter
.getValue()
.contains(dirFilter.getValueWithoutWildcards())
? finalDeepestDirFilter
: new DirFilter(Operator.EQ, dirFilter.getValueWithoutWildcards());
}
public DirFilter visit(NotFilter<? super Tables.Tracks> notFilter) {
return finalDeepestDirFilter;
}
public <T, Z> DirFilter visit(
FieldFilter<? super Tables.Tracks, Z, T> fieldFilter) {
return finalDeepestDirFilter;
}
public DirFilter visit(FilterSet<? super Tables.Tracks> filterSet) {
return finalDeepestDirFilter;
}
});
}
return deepestDirFilter;
}
public static List<MemoryFilter> combineFilters(final Collection<Filter> filters) {
final Merger[] mergers = {new UsersMerger()};
if (filters.isEmpty()) return Collections.emptyList();
final List<MemoryFilter> result = new ArrayList<MemoryFilter>();
for (Filter filter : filters) {
boolean taken = false;
for (Merger combiner : mergers) {
if (combiner.accept(filter.getMemoryFilter())) {
taken = true;
break;
}
}
if (!taken) {
result.add(filter.getMemoryFilter());
}
}
for (Merger combiner : mergers) {
final MemoryFilter combined = combiner.getResult();
if (combined != null) {
result.add(combined);
}
}
return result;
}
private Filter toFilter(List<String> filterList) {
Filter filter = new Filter();
if (filterList == null) return filter;
for (String pattern : filterList) {
filter.add(new IgnoredFiles(pattern));
}
return filter;
}
/**
* Main method for testing this class.
*
* @param argv should contain arguments to the filter: use -h for help
*/
public static void main(String[] argv) {
try {
if (Utils.getFlag('b', argv)) {
Filter.batchFilterFile(new AllFilter(), argv);
} else {
Filter.filterFile(new AllFilter(), argv);
}
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
}
public Filter createBaseFilter() {
if (auxiliaryClasses.length == 0) {
return Filter.createEqualityFilter("objectClass", structuralClass);
} else {
final ArrayList<Filter> comps = new ArrayList<Filter>(1 + auxiliaryClasses.length);
comps.add(Filter.createEqualityFilter("objectClass", structuralClass));
for (final String s : auxiliaryClasses) {
comps.add(Filter.createEqualityFilter("objectClass", s));
}
return Filter.createANDFilter(comps);
}
}
/** Helper method for the above. */
private <T> boolean setOrUnsetOrdering(
final Class<T> category, final boolean set, final Filter service1, final Filter service2) {
boolean done = false;
T impl1 = null;
T impl2 = null;
for (final Iterator<? extends T> it = getServiceProviders(category, false); it.hasNext(); ) {
final T factory = it.next();
if (service1.filter(factory)) impl1 = factory;
if (service2.filter(factory)) impl2 = factory;
if (impl1 != null && impl2 != null && impl1 != impl2) {
if (set) done |= setOrdering(category, impl1, impl2);
else done |= unsetOrdering(category, impl1, impl2);
}
}
return done;
}
/**
* Returns {@code true} is the specified {@code factory} meets the requirements specified by a map
* of {@code hints} and the filter. This method is the entry point for the following public
* methods:
*
* <ul>
* <li>Singleton {@link #getServiceProvider (Class category, Filter, Hints, Hints.Key)}
* <li>Iterator {@link #getServiceProviders(Class category, Filter, Hints)}
* </ul>
*
* @param candidate The factory to checks.
* @param category The factory category. Usually an interface.
* @param hints The optional user requirements, or {@code null}.
* @param filter The optional filter, or {@code null}.
* @return {@code true} if the {@code factory} meets the user requirements.
*/
final <T> boolean isAcceptable(
final T candidate, final Class<T> category, final Hints hints, final Filter filter) {
if (filter != null && !filter.filter(candidate)) {
return false;
}
/*
* Note: isAvailable(...) must be tested before checking the hints, because in current
* Geotools implementation (especially DeferredAuthorityFactory), some hints computation
* are deferred until a connection to the database is etablished (which 'isAvailable'
* does in order to test the connection).
*/
if (!isAvailable(candidate)) {
return false;
}
if (hints != null) {
if (candidate instanceof Factory) {
if (!usesAcceptableHints((Factory) candidate, category, hints, (Set<Factory>) null)) {
return false;
}
}
}
/*
* Checks for optional user conditions supplied in FactoryRegistry subclasses.
*/
return isAcceptable(candidate, category, hints);
}
/**
* Merges expensive descendant-or-self::node() steps.
*
* @param qc query context
* @return original or new expression
*/
private Expr mergeSteps(final QueryContext qc) {
boolean opt = false;
final int sl = steps.length;
final ExprList stps = new ExprList(sl);
for (int s = 0; s < sl; s++) {
final Expr step = steps[s];
// check for simple descendants-or-self step with succeeding step
if (s < sl - 1 && step instanceof Step) {
final Step curr = (Step) step;
if (curr.simple(DESCORSELF, false)) {
// check succeeding step
final Expr next = steps[s + 1];
// descendant-or-self::node()/child::X -> descendant::X
if (simpleChild(next)) {
((Step) next).axis = DESC;
opt = true;
continue;
}
// descendant-or-self::node()/(X, Y) -> (descendant::X | descendant::Y)
Expr e = mergeList(next);
if (e != null) {
steps[s + 1] = e;
opt = true;
continue;
}
// //(X, Y)[text()] -> (/descendant::X | /descendant::Y)[text()]
if (next instanceof Filter && !next.has(Flag.FCS)) {
final Filter f = (Filter) next;
e = mergeList(f.root);
if (e != null) {
f.root = e;
opt = true;
continue;
}
}
}
}
stps.add(step);
}
if (opt) {
qc.compInfo(OPTDESC);
return get(info, root, stps.finish());
}
return this;
}
public Document processRecord(Document record, int position) throws Exception {
for (HashMap<String, String> map : check_fields) {
String fieldXpath = map.get("Field Name");
String regexp = map.get("Field Value");
Filter.apply(record, new OpDelete(), fieldXpath, new TextMatches(regexp));
}
return record;
}
public boolean include(Object object) {
if (object instanceof IResource) {
IResource resource = (IResource) object;
IPath path =
IResource.FILE == resource.getType()
? resource.getFullPath()
: resource.getFullPath().addTrailingSeparator();
object = path.toPortableString();
}
for (Iterator iter = filters.iterator(); iter.hasNext(); ) {
Filter filter = (Filter) iter.next();
if (filter.matches(object)) {
return filter.inclusive();
}
}
return default_;
}
XmlNode[] getMatchingChildren(Filter filter) {
ArrayList rv = new ArrayList();
NodeList nodes = this.dom.getChildNodes();
for (int i = 0; i < nodes.getLength(); i++) {
Node node = nodes.item(i);
if (filter.accept(node)) {
rv.add(createImpl(node));
}
}
return (XmlNode[]) rv.toArray(new XmlNode[0]);
}
@Override
protected void doOKAction() {
mySelectedClass = calcSelectedClass();
if (mySelectedClass == null) return;
if (!myClassFilter.isAccepted(mySelectedClass)) {
Messages.showErrorDialog(
myTabbedPane.getComponent(),
SymbolPresentationUtil.getSymbolPresentableText(mySelectedClass) + " is not acceptable");
return;
}
super.doOKAction();
}
@Override
public Set<String> retrieveUserGroups(LdapUserContext userContext) throws LdapException {
Set<String> groups = new HashSet<String>();
try {
Filter groupClassFilter;
if (groupObjectClass != null && !groupObjectClass.isEmpty()) {
groupClassFilter = Filter.createEqualityFilter("objectClass", groupObjectClass);
} else {
groupClassFilter = Filter.createPresenceFilter("objectClass");
}
Filter filter =
Filter.createANDFilter(
groupClassFilter,
Filter.createEqualityFilter(groupMemberAttribute, userContext.getDn()));
LOGGER.debug(filter.toString());
SearchResult searchResult =
ldapConnectionPool.search(
StringUtils.join(groupBase, ','), SearchScope.SUB, filter, "cn");
for (SearchResultEntry entry : searchResult.getSearchEntries()) {
groups.add(entry.getAttributeValue("cn"));
}
return groups;
} catch (com.unboundid.ldap.sdk.LDAPException e) {
throw new LdapException(e);
}
}
// This implementation requires that we open up privileges on JavaCompiler.
// An alternative implementation would be to move this code to JavaCompiler and
// wrap it here
public Iterable<? extends Element> analyze(Iterable<? extends TypeElement> classes)
throws IOException {
enter(null); // ensure all classes have been entered
final ListBuffer<Element> results = new ListBuffer<Element>();
try {
if (classes == null) {
handleFlowResults(compiler.flow(compiler.attribute(compiler.todo)), results);
} else {
Filter f =
new Filter() {
public void process(Env<AttrContext> env) {
handleFlowResults(compiler.flow(compiler.attribute(env)), results);
}
};
f.run(compiler.todo, classes);
}
} finally {
compiler.log.flush();
}
return results;
}
public void init(final ServletContext servletContext, Injector injector) throws ServletException {
// this may or may not be a singleton, but is only initialized once
final Filter filter = injector.getInstance(filterKey);
// initialize our filter with the configured context params and servlet context
//noinspection OverlyComplexAnonymousInnerClass,AnonymousInnerClassWithTooManyMethods
filter.init(
new FilterConfig() {
public String getFilterName() {
return filterKey.toString();
}
public ServletContext getServletContext() {
return servletContext;
}
public String getInitParameter(String s) {
return initParams.get(s);
}
public Enumeration getInitParameterNames() {
//noinspection InnerClassTooDeeplyNested,AnonymousInnerClassWithTooManyMethods
return new Enumeration() {
private final Iterator<String> paramNames = initParams.keySet().iterator();
public boolean hasMoreElements() {
return paramNames.hasNext();
}
public Object nextElement() {
return paramNames.next();
}
};
}
});
}
public Collection matches(Message message, NodeDescriptor senderID) {
List matchingNeighbors = new ArrayList();
// iterates over the subscribed neighbors
Set keys = data.keySet();
synchronized (data) {
Iterator it = keys.iterator();
NodeDescriptor currentNeighbor;
while (it.hasNext()) {
currentNeighbor = (NodeDescriptor) it.next();
// Check if currentNeighbor is subscribed to the message
// iterates over the set of filters for currentNeighbor
if (senderID.equals(currentNeighbor)) continue;
Iterator it1 = ((Collection) data.get(currentNeighbor)).iterator();
while (it1.hasNext()) {
Filter f = (Filter) it1.next();
if (f.matches(message)) {
matchingNeighbors.add(currentNeighbor);
break;
}
}
}
}
return matchingNeighbors;
}
@Override
public boolean hasNext() {
canremove = false;
if (nextObject != null) {
return true;
}
while (iterator.hasNext()) {
final Object obj = iterator.next();
final T f = filter.filter(obj);
if (f != null) {
nextObject = f;
return true;
}
}
return false;
}
@Test
public void testSODA() {
// should say fieldsTypes, maybe with object/component prefix
Map<String, Object> eventTypes = new HashMap<>();
eventTypes.put(LITERAL_SYMBOL, String.class);
eventTypes.put(LITERAL_PRICE, Integer.class);
EPStatementObjectModel model = new EPStatementObjectModel();
model.setInsertInto(InsertIntoClause.create(LITERAL_RETURN_OBJ));
model.setSelectClause(
SelectClause.create().add(Expressions.avg(LITERAL_PRICE), LITERAL_AVG).add(LITERAL_PRICE));
Filter filter = Filter.create("quotes_default", Expressions.eq(LITERAL_SYMBOL, "A"));
model.setFromClause(
FromClause.create(
FilterStream.create(filter).addView("win", "length", Expressions.constant(2))));
model.setHavingClause(
Expressions.gt(Expressions.avg(LITERAL_PRICE), Expressions.constant(60.0)));
TopologyBuilder builder = new TopologyBuilder();
builder.setSpout(LITERAL_QUOTES, new RandomSentenceSpout());
builder
.setBolt(
LITERAL_ESPER,
(new EsperBolt())
.addEventTypes(eventTypes)
.addOutputTypes(
Collections.singletonMap(
LITERAL_RETURN_OBJ, Arrays.asList(LITERAL_AVG, LITERAL_PRICE)))
.addObjectStatemens(Collections.singleton(model)))
.shuffleGrouping(LITERAL_QUOTES);
builder.setBolt("print", new PrinterBolt()).shuffleGrouping(LITERAL_ESPER, LITERAL_RETURN_OBJ);
Config conf = new Config();
LocalCluster cluster = new LocalCluster();
cluster.submitTopology("test", conf, builder.createTopology());
Utils.sleep(10000);
cluster.shutdown();
assertEquals(resultSODA.get(100), new Double(75.0));
assertEquals(resultSODA.get(50), new Double(75.0));
}
@Override
public LdapUserContext findUser(String identityAttributeValue) throws LdapException {
try {
Filter userClassFilter;
if (userObjectClass != null && !userObjectClass.isEmpty()) {
userClassFilter = Filter.createEqualityFilter("objectClass", userObjectClass);
} else {
userClassFilter = Filter.createPresenceFilter("objectClass");
}
Filter filter =
Filter.createANDFilter(
userClassFilter,
Filter.createEqualityFilter(userIdentityAttribute, identityAttributeValue));
LOGGER.debug(filter.toString());
String[] attributesToRetrieve;
if (userAdditionalAttributes != null) {
attributesToRetrieve = userAdditionalAttributes;
if (!ArrayUtils.contains(attributesToRetrieve, "cn")
|| !ArrayUtils.contains(attributesToRetrieve, "CN")) {
ArrayUtils.add(attributesToRetrieve, "cn");
}
} else {
attributesToRetrieve = new String[] {"cn"};
}
SearchResult searchResult =
ldapConnectionPool.search(
StringUtils.join(userBase, ','), SearchScope.SUB, filter, attributesToRetrieve);
if (searchResult.getEntryCount() != 1) {
throw new UnknownAccountException();
}
SearchResultEntry searchResultEntry = searchResult.getSearchEntries().get(0);
String dn = searchResultEntry.getDN();
DefaultLdapUserContext ldapUserContext = internalCreateUser(dn);
ldapUserContext.getKnownAttributes().put("cn", searchResultEntry.getAttributeValue("cn"));
return ldapUserContext;
} catch (com.unboundid.ldap.sdk.LDAPException e) {
throw new LdapException(e);
}
}
private Filter createFilter(final T o, final AtomicBoolean addedRequiredOrAllowed)
throws LDAPPersistException {
final ArrayList<Attribute> attrs = new ArrayList<Attribute>(5);
attrs.add(objectClassAttribute);
for (final FieldInfo i : requiredFilterFields) {
final Attribute a = i.encode(o, true);
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_FILTER_MISSING_REQUIRED_FIELD.get(i.getField().getName()));
} else {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final GetterInfo i : requiredFilterGetters) {
final Attribute a = i.encode(o);
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_FILTER_MISSING_REQUIRED_GETTER.get(i.getMethod().getName()));
} else {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final FieldInfo i : alwaysAllowedFilterFields) {
final Attribute a = i.encode(o, true);
if (a != null) {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final GetterInfo i : alwaysAllowedFilterGetters) {
final Attribute a = i.encode(o);
if (a != null) {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final FieldInfo i : conditionallyAllowedFilterFields) {
final Attribute a = i.encode(o, true);
if (a != null) {
attrs.add(a);
}
}
for (final GetterInfo i : conditionallyAllowedFilterGetters) {
final Attribute a = i.encode(o);
if (a != null) {
attrs.add(a);
}
}
final ArrayList<Filter> comps = new ArrayList<Filter>(attrs.size());
for (final Attribute a : attrs) {
for (final ASN1OctetString v : a.getRawValues()) {
comps.add(Filter.createEqualityFilter(a.getName(), v.getValue()));
}
}
if (superclassHandler != null) {
final Filter f = superclassHandler.createFilter(o, addedRequiredOrAllowed);
if (f.getFilterType() == Filter.FILTER_TYPE_AND) {
comps.addAll(Arrays.asList(f.getComponents()));
} else {
comps.add(f);
}
}
return Filter.createANDFilter(comps);
}
boolean filterIncludesItem(T graphObject) {
return filter == null || filter.includeItem(graphObject);
}
/** @throws Exception */
private void loadWorkload() throws Exception {
final boolean debug = LOG.isDebugEnabled();
// Workload Trace
if (this.params.containsKey(PARAM_WORKLOAD)) {
assert (this.catalog_db != null) : "Missing catalog!";
String path = new File(this.params.get(PARAM_WORKLOAD)).getAbsolutePath();
boolean weightedTxns = this.getBooleanParam(PARAM_WORKLOAD_XACT_WEIGHTS, false);
if (debug) LOG.debug("Use Transaction Weights in Limits: " + weightedTxns);
// This will prune out duplicate trace records...
if (params.containsKey(PARAM_WORKLOAD_REMOVE_DUPES)) {
DuplicateTraceFilter filter = new DuplicateTraceFilter();
this.workload_filter =
(this.workload_filter != null ? filter.attach(this.workload_filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// TRANSACTION OFFSET
if (params.containsKey(PARAM_WORKLOAD_XACT_OFFSET)) {
this.workload_xact_offset = Long.parseLong(params.get(PARAM_WORKLOAD_XACT_OFFSET));
ProcedureLimitFilter filter =
new ProcedureLimitFilter(-1l, this.workload_xact_offset, weightedTxns);
// Important! The offset should go in the front!
this.workload_filter =
(this.workload_filter != null ? filter.attach(this.workload_filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// BASE PARTITIONS
if (params.containsKey(PARAM_WORKLOAD_RANDOM_PARTITIONS)
|| params.containsKey(PARAM_WORKLOAD_BASE_PARTITIONS)) {
BasePartitionTxnFilter filter =
new BasePartitionTxnFilter(new PartitionEstimator(catalog_db));
// FIXED LIST
if (params.containsKey(PARAM_WORKLOAD_BASE_PARTITIONS)) {
for (String p_str : this.getParam(PARAM_WORKLOAD_BASE_PARTITIONS).split(",")) {
workload_base_partitions.add(Integer.valueOf(p_str));
} // FOR
// RANDOM
} else {
double factor = this.getDoubleParam(PARAM_WORKLOAD_RANDOM_PARTITIONS);
List<Integer> all_partitions =
new ArrayList<Integer>(CatalogUtil.getAllPartitionIds(catalog_db));
Collections.shuffle(all_partitions, new Random());
workload_base_partitions.addAll(
all_partitions.subList(0, (int) (all_partitions.size() * factor)));
}
filter.addPartitions(workload_base_partitions);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// Txn Limit
this.workload_xact_limit = this.getLongParam(PARAM_WORKLOAD_XACT_LIMIT);
Histogram<String> proc_histogram = null;
// Include/exclude procedures from the traces
if (params.containsKey(PARAM_WORKLOAD_PROC_INCLUDE)
|| params.containsKey(PARAM_WORKLOAD_PROC_EXCLUDE)) {
Filter filter = new ProcedureNameFilter(weightedTxns);
// INCLUDE
String temp = params.get(PARAM_WORKLOAD_PROC_INCLUDE);
if (temp != null && !temp.equals(ProcedureNameFilter.INCLUDE_ALL)) {
// We can take the counts for PROC_INCLUDE and scale them
// with the multiplier
double multiplier = 1.0d;
if (this.hasDoubleParam(PARAM_WORKLOAD_PROC_INCLUDE_MULTIPLIER)) {
multiplier = this.getDoubleParam(PARAM_WORKLOAD_PROC_INCLUDE_MULTIPLIER);
if (debug) LOG.debug("Workload Procedure Multiplier: " + multiplier);
}
// Default Txn Frequencies
String procinclude = params.get(PARAM_WORKLOAD_PROC_INCLUDE);
if (procinclude.equalsIgnoreCase("default")) {
procinclude =
AbstractProjectBuilder.getProjectBuilder(catalog_type)
.getTransactionFrequencyString();
}
Map<String, Integer> limits = new HashMap<String, Integer>();
int total_unlimited = 0;
int total = 0;
for (String proc_name : procinclude.split(",")) {
int limit = -1;
// Check if there is a limit for this procedure
if (proc_name.contains(":")) {
String pieces[] = proc_name.split(":");
proc_name = pieces[0];
limit = (int) Math.round(Integer.parseInt(pieces[1]) * multiplier);
}
if (limit < 0) {
if (proc_histogram == null) {
if (debug) LOG.debug("Generating procedure histogram from workload file");
proc_histogram = WorkloadUtil.getProcedureHistogram(new File(path));
}
limit = (int) proc_histogram.get(proc_name, 0);
total_unlimited += limit;
} else {
total += limit;
}
limits.put(proc_name, limit);
} // FOR
// If we have a workload limit and some txns that we want
// to get unlimited
// records from, then we want to modify the other txns so
// that we fill in the "gap"
if (this.workload_xact_limit != null && total_unlimited > 0) {
int remaining = this.workload_xact_limit.intValue() - total - total_unlimited;
if (remaining > 0) {
for (Entry<String, Integer> e : limits.entrySet()) {
double ratio = e.getValue() / (double) total;
e.setValue((int) Math.ceil(e.getValue() + (ratio * remaining)));
} // FOR
}
}
Histogram<String> proc_multiplier_histogram = null;
if (debug) {
if (proc_histogram != null) LOG.debug("Full Workload Histogram:\n" + proc_histogram);
proc_multiplier_histogram = new Histogram<String>();
}
total = 0;
for (Entry<String, Integer> e : limits.entrySet()) {
if (debug) proc_multiplier_histogram.put(e.getKey(), e.getValue());
((ProcedureNameFilter) filter).include(e.getKey(), e.getValue());
total += e.getValue();
} // FOR
if (debug)
LOG.debug("Multiplier Histogram [total=" + total + "]:\n" + proc_multiplier_histogram);
}
// EXCLUDE
temp = params.get(PARAM_WORKLOAD_PROC_EXCLUDE);
if (temp != null) {
for (String proc_name : params.get(PARAM_WORKLOAD_PROC_EXCLUDE).split(",")) {
((ProcedureNameFilter) filter).exclude(proc_name);
} // FOR
}
// Sampling!!
if (this.getBooleanParam(PARAM_WORKLOAD_PROC_SAMPLE, false)) {
if (debug) LOG.debug("Attaching sampling filter");
if (proc_histogram == null)
proc_histogram = WorkloadUtil.getProcedureHistogram(new File(path));
Map<String, Integer> proc_includes = ((ProcedureNameFilter) filter).getProcIncludes();
SamplingFilter sampling_filter = new SamplingFilter(proc_includes, proc_histogram);
filter = sampling_filter;
if (debug) LOG.debug("Workload Procedure Histogram:\n" + proc_histogram);
}
// Attach our new filter to the chain (or make it the head if
// it's the first one)
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// TRANSACTION LIMIT
if (this.workload_xact_limit != null) {
ProcedureLimitFilter filter =
new ProcedureLimitFilter(this.workload_xact_limit, weightedTxns);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// QUERY LIMIT
if (params.containsKey(PARAM_WORKLOAD_QUERY_LIMIT)) {
this.workload_query_limit = Long.parseLong(params.get(PARAM_WORKLOAD_QUERY_LIMIT));
QueryLimitFilter filter = new QueryLimitFilter(this.workload_query_limit);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
}
if (this.workload_filter != null && debug)
LOG.debug("Workload Filters: " + this.workload_filter.toString());
this.workload = new Workload(this.catalog);
this.workload.load(path, this.catalog_db, this.workload_filter);
this.workload_path = new File(path).getAbsolutePath();
if (this.workload_filter != null) this.workload_filter.reset();
}
// Workload Statistics
if (this.catalog_db != null) {
this.stats = new WorkloadStatistics(this.catalog_db);
if (this.params.containsKey(PARAM_STATS)) {
String path = this.params.get(PARAM_STATS);
if (debug) LOG.debug("Loading in workload statistics from '" + path + "'");
this.stats_path = new File(path).getAbsolutePath();
try {
this.stats.load(path, this.catalog_db);
} catch (Throwable ex) {
throw new RuntimeException("Failed to load stats file '" + this.stats_path + "'", ex);
}
}
// Scaling
if (this.params.containsKey(PARAM_STATS_SCALE_FACTOR)) {
double scale_factor = this.getDoubleParam(PARAM_STATS_SCALE_FACTOR);
LOG.info("Scaling TableStatistics: " + scale_factor);
AbstractTableStatisticsGenerator generator =
AbstractTableStatisticsGenerator.factory(
this.catalog_db, this.catalog_type, scale_factor);
generator.apply(this.stats);
}
}
}
public long getCardinality(Filter filter, BindingSet bindings) {
long card = getCardinality(filter.getArg(), bindings);
return (long) (card * 0.5);
}
/**
* This frame shows an input record's XML in the form of a tree, with an added ability to copy the
* values from any node for other purposes. There are controls to create selection criteria for
* choosing particular records as the scan proceeds, and buttons for going to the first or the next
* record.
*
* @author Gerald de Jong <*****@*****.**>
*/
public class InputFrame extends FrameBase {
private static final DefaultTreeModel EMPTY_MODEL =
new DefaultTreeModel(new DefaultMutableTreeNode("No input"));
private JTree recordTree;
private JComboBox filterBox = new JComboBox(Filter.values());
private JTextField filterField = new JTextField();
private enum Filter {
REGEX("Regex"),
MODULO("Modulo");
private String name;
private Filter(String name) {
this.name = name;
}
@Override
public String toString() {
return name;
}
}
public InputFrame(SipModel sipModel) {
super(Which.INPUT, sipModel, "Input");
sipModel.addParseListener(
new SipModel.ParseListener() {
@Override
public void updatedRecord(MetadataRecord metadataRecord) {
exec(new RecordSetter(metadataRecord));
}
});
recordTree =
new JTree(EMPTY_MODEL) {
@Override
public String getToolTipText(MouseEvent evt) {
TreePath treePath = recordTree.getPathForLocation(evt.getX(), evt.getY());
return treePath != null
? ((GroovyTreeNode) treePath.getLastPathComponent()).toolTip
: "";
}
};
recordTree.setToolTipText("Input Record");
recordTree.setCellRenderer(new Renderer());
recordTree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
recordTree.setTransferHandler(new TreeTransferHandler());
filterField.addActionListener(rewind);
}
@Override
protected void buildContent(Container content) {
content.add(scrollVH(recordTree), BorderLayout.CENTER);
content.add(createRecordButtonPanel(), BorderLayout.SOUTH);
}
private JPanel createRecordButtonPanel() {
JPanel p = new JPanel(new BorderLayout());
p.setBorder(BorderFactory.createTitledBorder("Filter"));
p.add(filterBox, BorderLayout.WEST);
p.add(filterField, BorderLayout.CENTER);
p.add(createButtonPanel(), BorderLayout.SOUTH);
return p;
}
private JPanel createButtonPanel() {
JPanel p = new JPanel(new GridLayout(1, 0));
p.add(new JButton(rewind));
p.add(new JButton(play));
return p;
}
private class RecordSetter implements Swing {
private MetadataRecord metadataRecord;
private RecordSetter(MetadataRecord metadataRecord) {
this.metadataRecord = metadataRecord;
}
@Override
public void run() {
if (metadataRecord == null) {
recordTree.setModel(EMPTY_MODEL);
} else {
GroovyTreeNode root = new GroovyTreeNode(metadataRecord);
recordTree.setModel(new DefaultTreeModel(root));
root.expand();
}
}
}
private class GroovyTreeNode implements TreeNode, Comparable<GroovyTreeNode> {
private static final int MAX_LENGTH = 40;
private MetadataRecord metadataRecord;
private GroovyTreeNode parent;
private String attrKey, attrValue;
private GroovyNode node;
private Vector<GroovyTreeNode> children = new Vector<GroovyTreeNode>();
private String string;
private String toolTip;
private GroovyTreeNode(MetadataRecord metadataRecord) {
this(null, metadataRecord.getRootNode());
this.metadataRecord = metadataRecord;
}
private GroovyTreeNode(GroovyTreeNode parent, String attrKey, String attrValue) {
this.parent = parent;
this.attrKey = attrKey;
this.attrValue = attrValue;
string = String.format("<html><b>%s</b> = %s</html>", attrKey, attrValue);
toolTip = string; // todo
}
private GroovyTreeNode(GroovyTreeNode parent, GroovyNode node) {
this.parent = parent;
this.node = node;
for (Map.Entry<String, String> entry : node.attributes().entrySet()) {
children.add(new GroovyTreeNode(this, entry.getKey(), entry.getValue()));
}
if (node.getNodeValue() instanceof List) {
string = node.getNodeName();
toolTip = String.format("Size: %d", ((List) node.getNodeValue()).size());
} else {
String truncated = node.text();
if (truncated.contains("\n") || truncated.length() >= MAX_LENGTH) {
int index = truncated.indexOf('\n');
if (index > 0) truncated = truncated.substring(0, index);
if (truncated.length() >= MAX_LENGTH) truncated = truncated.substring(0, MAX_LENGTH);
string = String.format("<html><b>%s</b> = %s ...</html>", node.getNodeName(), truncated);
toolTip = tameTooltipText(node.text());
} else {
string = String.format("<html><b>%s</b> = %s</html>", node.getNodeName(), truncated);
toolTip = truncated;
}
}
if (this.node.getNodeValue() instanceof List) {
for (Object sub : ((List) this.node.getNodeValue())) {
GroovyNode subnode = (GroovyNode) sub;
children.add(new GroovyTreeNode(this, subnode));
}
Collections.sort(children);
}
}
@Override
public TreeNode getChildAt(int i) {
return children.elementAt(i);
}
@Override
public int getChildCount() {
return children.size();
}
@Override
public TreeNode getParent() {
return parent;
}
@Override
public int getIndex(TreeNode treeNode) {
return children.indexOf(treeNode);
}
@Override
public boolean getAllowsChildren() {
return !children.isEmpty();
}
@Override
public boolean isLeaf() {
return children.isEmpty();
}
@Override
public Enumeration children() {
return children.elements();
}
@Override
public String toString() {
return metadataRecord != null
? String.format("record %d", metadataRecord.getRecordNumber())
: string;
}
public void expand() {
if (!isLeaf()) {
Timer timer =
new Timer(
50,
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
recordTree.expandPath(getTreePath());
for (TreeNode sub : children) {
((GroovyTreeNode) sub).expand();
}
}
});
timer.setRepeats(false);
timer.start();
}
}
public TreePath getTreePath() {
List<TreeNode> list = new ArrayList<TreeNode>();
compilePathList(list);
return new TreePath(list.toArray());
}
private void compilePathList(List<TreeNode> list) {
if (parent != null) parent.compilePathList(list);
list.add(this);
}
private String tameTooltipText(String text) {
List<String> lines = new ArrayList<String>();
while (text.length() > MAX_LENGTH) {
int pos = text.indexOf(' ', MAX_LENGTH - 10);
if (pos < 0) break;
if (pos > MAX_LENGTH + 5) pos = MAX_LENGTH;
lines.add(text.substring(0, pos).trim());
text = text.substring(pos).trim();
}
if (!text.trim().isEmpty()) lines.add(text);
StringBuilder html = new StringBuilder("<html>");
for (String line : lines) html.append(line).append("<br/>\n");
return html.toString();
}
@Override
public int compareTo(GroovyTreeNode gtn) {
if (attrKey != null && gtn.attrKey == null) return -1;
if (attrKey == null && gtn.attrKey != null) return 1;
if (attrKey != null && gtn.attrKey != null) return attrKey.compareTo(gtn.attrKey);
return node.getNodeName().compareTo(gtn.node.getNodeName());
}
}
public static class Renderer extends DefaultTreeCellRenderer {
@Override
public Component getTreeCellRendererComponent(
JTree tree,
Object value,
boolean sel,
boolean expanded,
boolean leaf,
int row,
boolean hasFocus) {
Component component =
super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
if (value instanceof GroovyTreeNode) {
GroovyTreeNode node = (GroovyTreeNode) value;
if (node.attrKey != null) {
setIcon(SwingHelper.ICON_ATTRIBUTE);
} else if (!node.isLeaf()) {
setIcon(SwingHelper.ICON_COMPOSITE);
} else {
setIcon(SwingHelper.ICON_VALUE);
}
} else {
setIcon(SwingHelper.ICON_COMPOSITE);
}
return component;
}
}
private RewindAction rewind = new RewindAction();
private class RewindAction extends AbstractAction {
private RewindAction() {
super("First");
putValue(Action.SMALL_ICON, SwingHelper.ICON_REWIND);
}
@Override
public void actionPerformed(ActionEvent actionEvent) {
sipModel.seekReset();
play.actionPerformed(actionEvent);
}
}
private PlayAction play = new PlayAction();
private class PlayAction extends AbstractAction {
private PlayAction() {
super("Next");
putValue(Action.SMALL_ICON, SwingHelper.ICON_PLAY);
}
@Override
public void actionPerformed(ActionEvent actionEvent) {
setEnabled(false);
sipModel.seekRecord(
createPredicate(),
new Swing() {
@Override
public void run() {
setEnabled(true);
}
});
}
}
private SipModel.ScanPredicate createPredicate() {
final String filterString = filterField.getText().trim();
switch ((Filter) filterBox.getSelectedItem()) {
case REGEX:
return new SipModel.ScanPredicate() {
@Override
public boolean accept(MetadataRecord record) {
return record.contains(Pattern.compile(filterString));
}
};
case MODULO:
int modulo;
try {
modulo = Integer.parseInt(filterString);
} catch (NumberFormatException e) {
modulo = 1;
}
if (modulo <= 0) modulo = 1;
final int recordNumberModulo = modulo;
return new SipModel.ScanPredicate() {
@Override
public boolean accept(MetadataRecord record) {
return recordNumberModulo == 1 || record.getRecordNumber() % recordNumberModulo == 0;
}
};
default:
throw new RuntimeException();
}
}
private static class TreeTransferHandler extends TransferHandler {
protected Transferable createTransferable(JComponent c) {
JTree tree = (JTree) c;
TreePath[] paths = tree.getSelectionPaths();
if (paths == null || paths.length != 1) return null;
TreePath path = tree.getSelectionPath();
GroovyTreeNode groovyTreeNode = (GroovyTreeNode) path.getLastPathComponent();
return new StringTransferable((String) (groovyTreeNode.node.getNodeValue()));
}
public int getSourceActions(JComponent c) {
return COPY;
}
}
private static class StringTransferable implements Transferable {
private String string;
private static final DataFlavor[] flavors = {DataFlavor.stringFlavor};
private StringTransferable(String string) {
this.string = string;
}
@Override
public DataFlavor[] getTransferDataFlavors() {
return flavors;
}
@Override
public boolean isDataFlavorSupported(DataFlavor flavor) {
return flavor.equals(flavors[0]);
}
@Override
public Object getTransferData(DataFlavor flavor)
throws UnsupportedFlavorException, IOException {
return string;
}
}
}
/**
* Constructs an image information class based on the 5D image source, and the individual set of
* pixels desired in that image. Needs Factory to query the database about statistics. (this might
* not be a good thing)
*
* @param imageSource The image to store information about.
* @param pixels The pixel source of the image.
* @param dataSource The factory used to access the OME database. Is there a better way to do
* this?
*/
public ImageInformation(Image imageSource, ImagePixels pixels, Factory dataSource) {
this.imageSource = imageSource;
this.pixels = pixels;
this.pixelsAttribute = pixels.getPixelsAttribute();
this.dataSource = dataSource;
Map imageSourceMap = new HashMap();
imageSourceMap.put("target", imageSource);
// extract the channel/wavelength information for this image.
List channelComponents = dataSource.findAttributes("PixelChannelComponent", imageSourceMap);
final int pixelsID = pixelsAttribute.getID();
// this taken straight out of the SVG viewer code
// might be a faster/better/less OME-call-intensive way to do it
channelComponents =
Filter.grep(
channelComponents,
new GrepOperator() {
public boolean eval(Object o) {
Attribute attribute = (Attribute) o;
Attribute pixels = attribute.getAttributeElement("Pixels");
return pixels.getID() == pixelsID;
}
});
channelInfo = new Wavelength[channelComponents.size()];
for (int i = 0; i < channelComponents.size(); i++) {
Attribute channel = (Attribute) channelComponents.get(i);
channelInfo[i] = new Wavelength(channel.getIntElement("Index"));
}
CBS = ChannelBlackScaleData.getDefaultChannelScale(channelInfo);
cbsMap = new HashMap();
// hopefully this doesn't break right here
// extract the proper stack statistics for this image,
// this might be done the hard way (I dunno)
Map moduleConstraints = new HashMap();
moduleConstraints.put("name", "Fast Stack statistics");
Module stackModule = (Module) dataSource.findObject("OME::Module", moduleConstraints);
Map formalInputConstraints = new HashMap();
formalInputConstraints.put("module_id", new Integer(stackModule.getID()));
formalInputConstraints.put("name", "Pixels");
Module.FormalInput formalInput =
(Module.FormalInput)
dataSource.findObject("OME::Module::FormalInput", formalInputConstraints);
RemoteModuleExecution moduleExecution =
(RemoteModuleExecution) pixelsAttribute.getModuleExecution();
Map actualInputConstraints = new HashMap();
actualInputConstraints.put("formal_input_id", new Integer(formalInput.getID()));
actualInputConstraints.put("input_module_execution_id", new Integer(moduleExecution.getID()));
ModuleExecution.ActualInput actualInput =
(ModuleExecution.ActualInput)
dataSource.findObject("OME::ModuleExecution::ActualInput", actualInputConstraints);
final int stackAnalysisID = actualInput.getModuleExecution().getID();
// retrieve statistics
List stackMins = dataSource.findAttributes("StackMinimum", imageSourceMap);
List stackMaxes = dataSource.findAttributes("StackMaximum", imageSourceMap);
List stackMeans = dataSource.findAttributes("StackMean", imageSourceMap);
List stackSigmas = dataSource.findAttributes("StackSigma", imageSourceMap);
List stackGeomeans = dataSource.findAttributes("StackGeometricMean", imageSourceMap);
List stackGeosigmas = dataSource.findAttributes("StackGeometricSigma", imageSourceMap);
GrepOperator stackIDOperator =
new GrepOperator() {
public boolean eval(Object o) {
Attribute attribute = (Attribute) o;
RemoteModuleExecution execution =
(RemoteModuleExecution) attribute.getModuleExecution();
if (execution.getID() == stackAnalysisID) {
return true;
} else return false;
}
};
List usableMins = Filter.grep(stackMins, stackIDOperator);
List usableMaxes = Filter.grep(stackMaxes, stackIDOperator);
List usableMeans = Filter.grep(stackMeans, stackIDOperator);
List usableSigmas = Filter.grep(stackSigmas, stackIDOperator);
List usableGeomeans = Filter.grep(stackGeomeans, stackIDOperator);
List usableGeosigmas = Filter.grep(stackGeosigmas, stackIDOperator);
sizeX = pixelsAttribute.getIntElement("SizeX");
sizeY = pixelsAttribute.getIntElement("SizeY");
sizeZ = pixelsAttribute.getIntElement("SizeZ");
sizeC = pixelsAttribute.getIntElement("SizeC");
sizeT = pixelsAttribute.getIntElement("SizeT");
bitsPerPixel = pixelsAttribute.getIntElement("BitsPerPixel");
stackStats = new StackStatistics[sizeC][sizeT];
// initialize array
for (int i = 0; i < sizeC; i++) {
for (int j = 0; j < sizeT; j++) {
stackStats[i][j] = new StackStatistics();
}
}
// populate internal data structures
for (Iterator iter = usableMins.iterator(); iter.hasNext(); ) {
Attribute stackMin = (Attribute) iter.next();
int theC = stackMin.getIntElement("TheC");
int theT = stackMin.getIntElement("TheT");
stackStats[theC][theT].setMin(stackMin.getIntElement("Minimum"));
}
for (Iterator iter = usableMaxes.iterator(); iter.hasNext(); ) {
Attribute stackMax = (Attribute) iter.next();
int theC = stackMax.getIntElement("TheC");
int theT = stackMax.getIntElement("TheT");
stackStats[theC][theT].setMax(stackMax.getIntElement("Maximum"));
}
for (Iterator iter = usableMeans.iterator(); iter.hasNext(); ) {
Attribute stackMean = (Attribute) iter.next();
int theC = stackMean.getIntElement("TheC");
int theT = stackMean.getIntElement("TheT");
stackStats[theC][theT].setMean(stackMean.getFloatElement("Mean"));
}
for (Iterator iter = usableSigmas.iterator(); iter.hasNext(); ) {
Attribute stackSigma = (Attribute) iter.next();
int theC = stackSigma.getIntElement("TheC");
int theT = stackSigma.getIntElement("TheT");
stackStats[theC][theT].setSigma(stackSigma.getFloatElement("Sigma"));
}
for (Iterator iter = usableGeomeans.iterator(); iter.hasNext(); ) {
Attribute stackMean = (Attribute) iter.next();
int theC = stackMean.getIntElement("TheC");
int theT = stackMean.getIntElement("TheT");
stackStats[theC][theT].setGeoMean(stackMean.getFloatElement("GeometricMean"));
}
for (Iterator iter = usableGeosigmas.iterator(); iter.hasNext(); ) {
Attribute stackSigma = (Attribute) iter.next();
int theC = stackSigma.getIntElement("TheC");
int theT = stackSigma.getIntElement("TheT");
stackStats[theC][theT].setGeoSigma(stackSigma.getFloatElement("GeometricSigma"));
}
}
public void destroy(Injector injector) {
// may or may not be singleton, upto user to work out properly
final Filter filter = injector.getInstance(filterKey);
filter.destroy();
}
/**
* Sets the format of the input instances.
*
* @param instanceInfo an Instances object containing the input instance structure (any instances
* contained in the object are ignored - only the structure is required).
* @return true if the outputFormat may be collected immediately
*/
public boolean setInputFormat(Instances instanceInfo) throws Exception {
super.setInputFormat(instanceInfo);
setOutputFormat(instanceInfo);
return true;
}