/**
* Loads markup from a resource stream.
*
* @param container The original requesting markup container
* @param markupResourceStream The markup resource stream to load
* @param enforceReload The cache will be ignored and all, including inherited markup files, will
* be reloaded. Whatever is in the cache, it will be ignored
* @return The markup. Markup.NO_MARKUP, if not found.
*/
private final Markup loadMarkup(
final MarkupContainer container,
final MarkupResourceStream markupResourceStream,
final boolean enforceReload) {
String cacheKey = markupResourceStream.getCacheKey();
String locationString = markupResourceStream.locationAsString();
if (locationString == null) {
// set the cache key as location string, because location string
// couldn't be resolved.
locationString = cacheKey;
}
Markup markup = MarkupFactory.get().loadMarkup(container, markupResourceStream, enforceReload);
if (markup != null) {
if (cacheKey != null) {
String temp = markup.locationAsString();
if (temp != null) {
locationString = temp;
}
// add the markup to the cache.
markupKeyCache.put(cacheKey, locationString);
return putIntoCache(locationString, container, markup);
}
return markup;
}
// In case the markup could not be loaded (without exception) then ..
if (cacheKey != null) {
removeMarkup(cacheKey);
}
return Markup.NO_MARKUP;
}
private void removeMarkupWhereBaseMarkupIsNoLongerInTheCache() {
// Repeat until all dependent resources have been removed (count == 0)
int count = 1;
while (count > 0) {
// Reset prior to next round
count = 0;
// Iterate though all entries of the cache
Iterator<Markup> iter = markupCache.getValues().iterator();
while (iter.hasNext()) {
Markup markup = iter.next();
if ((markup != null) && (markup != Markup.NO_MARKUP)) {
// Check if the markup associated with key has a base markup. And if yes, test
// if that is cached. If the base markup has been removed, than remove the
// derived markup as well.
MarkupResourceStream resourceStream = markup.getMarkupResourceStream();
if (resourceStream != null) {
resourceStream = resourceStream.getBaseMarkupResourceStream();
}
// Is the base markup available in the cache?
if ((resourceStream != null) && !isMarkupCached(resourceStream)) {
iter.remove();
count++;
if (log.isDebugEnabled()) {
log.debug("Removed derived markup from cache: " + markup.getMarkupResourceStream());
}
}
}
}
}
}
@Test
public void testWithMarkups() {
Markup markup = new Markup();
markup.setStart(13);
Sequence withMarkups = sequence.withMarkups(ImmutableList.of(markup));
assertNotNull(withMarkups.getMarkups());
assertEquals(2, withMarkups.getMarkups().size());
for (Markup m : withMarkups.getMarkups()) {
assertTrue(m.getStart() == 13 || m.getStart() == 24);
}
}
@Before
public void setUp() {
sequence = new Sequence();
sequence.setLength(42);
Options options = new Options();
options.setBaseUrl("baseUrl");
sequence.setOptions(options);
Markup markup = new Markup();
markup.setStart(24);
sequence.setMarkups(ImmutableList.of(markup));
Map<String, Object> metadata = newHashMap();
metadata.put("key", "value");
sequence.setMetadata(metadata);
Motif motif = new Motif();
motif.setStart(24);
sequence.setMotifs(ImmutableList.of(motif));
Region region = new Region();
region.setStart(24);
sequence.setRegions(ImmutableList.of(region));
}
public int compareTo(Markup markup) {
long pk = markup.getPrimaryKey();
if (getPrimaryKey() < pk) {
return -1;
} else if (getPrimaryKey() > pk) {
return 1;
} else {
return 0;
}
}
public IMarkupFragment getMarkup() {
IMarkupFragment enclosureMarkup = null;
if (this.enclosureMarkupAsString == null) {
final IMarkupFragment markup = super.getMarkup();
if (markup != null && markup != Markup.NO_MARKUP) {
enclosureMarkup = markup;
this.enclosureMarkupAsString = markup.toString(true);
}
} else {
enclosureMarkup = Markup.of(this.enclosureMarkupAsString);
}
return enclosureMarkup;
}
