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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/inline/InlineRendition.java | InlineRendition.isMatchingFileExtension | private boolean isMatchingFileExtension() {
String[] fileExtensions = mediaArgs.getFileExtensions();
if (fileExtensions == null || fileExtensions.length == 0) {
return true;
}
for (String fileExtension : fileExtensions) {
if (StringUtils.equalsIgnoreCase(fileExtension, getFileExtension())) {
return true;
}
}
return false;
} | java | private boolean isMatchingFileExtension() {
String[] fileExtensions = mediaArgs.getFileExtensions();
if (fileExtensions == null || fileExtensions.length == 0) {
return true;
}
for (String fileExtension : fileExtensions) {
if (StringUtils.equalsIgnoreCase(fileExtension, getFileExtension())) {
return true;
}
}
return false;
} | [
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/inline/InlineRendition.java | InlineRendition.getRequestedDimension | private Dimension getRequestedDimension() {
// check for fixed dimensions from media args
if (mediaArgs.getFixedWidth() > 0 || mediaArgs.getFixedHeight() > 0) {
return new Dimension(mediaArgs.getFixedWidth(), mediaArgs.getFixedHeight());
}
// check for dimensions from mediaformat (evaluate only first media format)
MediaFormat[] mediaFormats = mediaArgs.getMediaFormats();
if (mediaFormats != null && mediaFormats.length > 0) {
Dimension dimension = mediaFormats[0].getMinDimension();
if (dimension != null) {
return dimension;
}
}
// fallback to 0/0 - no specific dimension requested
return new Dimension(0, 0);
} | java | private Dimension getRequestedDimension() {
// check for fixed dimensions from media args
if (mediaArgs.getFixedWidth() > 0 || mediaArgs.getFixedHeight() > 0) {
return new Dimension(mediaArgs.getFixedWidth(), mediaArgs.getFixedHeight());
}
// check for dimensions from mediaformat (evaluate only first media format)
MediaFormat[] mediaFormats = mediaArgs.getMediaFormats();
if (mediaFormats != null && mediaFormats.length > 0) {
Dimension dimension = mediaFormats[0].getMinDimension();
if (dimension != null) {
return dimension;
}
}
// fallback to 0/0 - no specific dimension requested
return new Dimension(0, 0);
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/suffix/SuffixParser.java | SuffixParser.getResources | public @NotNull List<Resource> getResources() {
return getResources((Predicate<Resource>)null, (Resource)null);
} | java | public @NotNull List<Resource> getResources() {
return getResources((Predicate<Resource>)null, (Resource)null);
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/suffix/SuffixBuilder.java | SuffixBuilder.build | public @NotNull String build() {
SortedMap<String, Object> sortedParameterMap = new TreeMap<>(parameterMap);
// gather resource paths in a treeset (having them in a defined order helps with caching)
SortedSet<String> resourcePathsSet = new TreeSet<>();
// iterate over all parts that should be kept from the current request
for (String nextPart : initialSuffixParts) {
// if this is a key-value-part:
if (nextPart.indexOf(KEY_VALUE_DELIMITER) > 0) {
String key = decodeKey(nextPart);
// decode and keep the part if it is not overridden in the given parameter-map
if (!sortedParameterMap.containsKey(key)) {
String value = decodeValue(nextPart);
sortedParameterMap.put(key, value);
}
}
else {
// decode and keep the resource paths (unless they are specified again in resourcePaths)
String path = decodeResourcePathPart(nextPart);
if (!resourcePaths.contains(path)) {
resourcePathsSet.add(path);
}
}
}
// copy the resources specified as parameters to the sorted set of paths
if (resourcePaths != null) {
resourcePathsSet.addAll(ImmutableList.copyOf(resourcePaths));
}
// gather all suffix parts in this list
List<String> suffixParts = new ArrayList<>();
// now encode all resource paths
for (String path : resourcePathsSet) {
suffixParts.add(encodeResourcePathPart(path));
}
// now encode all entries from the parameter map
for (Entry<String, Object> entry : sortedParameterMap.entrySet()) {
Object value = entry.getValue();
if (value == null) {
// don't add suffix part if value is null
continue;
}
String encodedKey = encodeKeyValuePart(entry.getKey());
String encodedValue = encodeKeyValuePart(value.toString());
suffixParts.add(encodedKey + KEY_VALUE_DELIMITER + encodedValue);
}
// finally join these parts to a single string
return StringUtils.join(suffixParts, SUFFIX_PART_DELIMITER);
} | java | public @NotNull String build() {
SortedMap<String, Object> sortedParameterMap = new TreeMap<>(parameterMap);
// gather resource paths in a treeset (having them in a defined order helps with caching)
SortedSet<String> resourcePathsSet = new TreeSet<>();
// iterate over all parts that should be kept from the current request
for (String nextPart : initialSuffixParts) {
// if this is a key-value-part:
if (nextPart.indexOf(KEY_VALUE_DELIMITER) > 0) {
String key = decodeKey(nextPart);
// decode and keep the part if it is not overridden in the given parameter-map
if (!sortedParameterMap.containsKey(key)) {
String value = decodeValue(nextPart);
sortedParameterMap.put(key, value);
}
}
else {
// decode and keep the resource paths (unless they are specified again in resourcePaths)
String path = decodeResourcePathPart(nextPart);
if (!resourcePaths.contains(path)) {
resourcePathsSet.add(path);
}
}
}
// copy the resources specified as parameters to the sorted set of paths
if (resourcePaths != null) {
resourcePathsSet.addAll(ImmutableList.copyOf(resourcePaths));
}
// gather all suffix parts in this list
List<String> suffixParts = new ArrayList<>();
// now encode all resource paths
for (String path : resourcePathsSet) {
suffixParts.add(encodeResourcePathPart(path));
}
// now encode all entries from the parameter map
for (Entry<String, Object> entry : sortedParameterMap.entrySet()) {
Object value = entry.getValue();
if (value == null) {
// don't add suffix part if value is null
continue;
}
String encodedKey = encodeKeyValuePart(entry.getKey());
String encodedValue = encodeKeyValuePart(value.toString());
suffixParts.add(encodedKey + KEY_VALUE_DELIMITER + encodedValue);
}
// finally join these parts to a single string
return StringUtils.join(suffixParts, SUFFIX_PART_DELIMITER);
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/integrator/impl/IntegratorHandlerImpl.java | IntegratorHandlerImpl.detectIntegratorTemplateModes | private void detectIntegratorTemplateModes() {
// integrator mode cannot be active if no modes defined
if (urlHandlerConfig.getIntegratorModes().isEmpty()) {
return;
}
if (request != null && RequestPath.hasSelector(request, SELECTOR_INTEGRATORTEMPLATE_SECURE)) {
integratorTemplateSecureMode = true;
}
else if (request != null && RequestPath.hasSelector(request, SELECTOR_INTEGRATORTEMPLATE)) {
integratorTemplateMode = true;
}
} | java | private void detectIntegratorTemplateModes() {
// integrator mode cannot be active if no modes defined
if (urlHandlerConfig.getIntegratorModes().isEmpty()) {
return;
}
if (request != null && RequestPath.hasSelector(request, SELECTOR_INTEGRATORTEMPLATE_SECURE)) {
integratorTemplateSecureMode = true;
}
else if (request != null && RequestPath.hasSelector(request, SELECTOR_INTEGRATORTEMPLATE)) {
integratorTemplateMode = true;
}
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/integrator/impl/IntegratorHandlerImpl.java | IntegratorHandlerImpl.getIntegratorTemplateSelector | @Override
public @NotNull String getIntegratorTemplateSelector() {
if (currentPage != null && urlHandlerConfig.isIntegrator(currentPage)) {
if (isResourceUrlSecure(currentPage)) {
return SELECTOR_INTEGRATORTEMPLATE_SECURE;
}
else {
return SELECTOR_INTEGRATORTEMPLATE;
}
}
if (integratorTemplateSecureMode) {
return SELECTOR_INTEGRATORTEMPLATE_SECURE;
}
else {
return SELECTOR_INTEGRATORTEMPLATE;
}
} | java | @Override
public @NotNull String getIntegratorTemplateSelector() {
if (currentPage != null && urlHandlerConfig.isIntegrator(currentPage)) {
if (isResourceUrlSecure(currentPage)) {
return SELECTOR_INTEGRATORTEMPLATE_SECURE;
}
else {
return SELECTOR_INTEGRATORTEMPLATE;
}
}
if (integratorTemplateSecureMode) {
return SELECTOR_INTEGRATORTEMPLATE_SECURE;
}
else {
return SELECTOR_INTEGRATORTEMPLATE;
}
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In HTTPS mode the secure selector is returned, otherwise the default selector.
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/integrator/impl/IntegratorHandlerImpl.java | IntegratorHandlerImpl.getIntegratorMode | @SuppressWarnings("null")
private @NotNull IntegratorMode getIntegratorMode(ValueMap properties) {
IntegratorMode mode = null;
Collection<IntegratorMode> integratorModes = urlHandlerConfig.getIntegratorModes();
String modeString = properties.get(IntegratorNameConstants.PN_INTEGRATOR_MODE, String.class);
if (StringUtils.isNotEmpty(modeString)) {
for (IntegratorMode candidate : integratorModes) {
if (StringUtils.equals(modeString, candidate.getId())) {
mode = candidate;
break;
}
}
}
// fallback to first mode defined in configuration
if (mode == null && !integratorModes.isEmpty()) {
mode = integratorModes.iterator().next();
}
return mode;
} | java | @SuppressWarnings("null")
private @NotNull IntegratorMode getIntegratorMode(ValueMap properties) {
IntegratorMode mode = null;
Collection<IntegratorMode> integratorModes = urlHandlerConfig.getIntegratorModes();
String modeString = properties.get(IntegratorNameConstants.PN_INTEGRATOR_MODE, String.class);
if (StringUtils.isNotEmpty(modeString)) {
for (IntegratorMode candidate : integratorModes) {
if (StringUtils.equals(modeString, candidate.getId())) {
mode = candidate;
break;
}
}
}
// fallback to first mode defined in configuration
if (mode == null && !integratorModes.isEmpty()) {
mode = integratorModes.iterator().next();
}
return mode;
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/integrator/impl/IntegratorHandlerImpl.java | IntegratorHandlerImpl.getIntegratorProtocol | @SuppressWarnings("null")
private IntegratorProtocol getIntegratorProtocol(ValueMap properties) {
IntegratorProtocol protocol = IntegratorProtocol.AUTO;
try {
String protocolString = properties.get(IntegratorNameConstants.PN_INTEGRATOR_PROTOCOL, String.class);
if (StringUtils.isNotEmpty(protocolString)) {
protocol = IntegratorProtocol.valueOf(protocolString.toUpperCase());
}
}
catch (IllegalArgumentException ex) {
// ignore
}
return protocol;
} | java | @SuppressWarnings("null")
private IntegratorProtocol getIntegratorProtocol(ValueMap properties) {
IntegratorProtocol protocol = IntegratorProtocol.AUTO;
try {
String protocolString = properties.get(IntegratorNameConstants.PN_INTEGRATOR_PROTOCOL, String.class);
if (StringUtils.isNotEmpty(protocolString)) {
protocol = IntegratorProtocol.valueOf(protocolString.toUpperCase());
}
}
catch (IllegalArgumentException ex) {
// ignore
}
return protocol;
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wcm-io/wcm-io-handler | url/src/main/java/io/wcm/handler/url/integrator/impl/IntegratorHandlerImpl.java | IntegratorHandlerImpl.isResourceUrlSecure | private boolean isResourceUrlSecure(Page page) {
ValueMap props = getPagePropertiesNullSafe(page);
IntegratorMode mode = getIntegratorMode(props);
if (mode.isDetectProtocol()) {
IntegratorProtocol integratorProtocol = getIntegratorProtocol(props);
if (integratorProtocol == IntegratorProtocol.HTTPS) {
return true;
}
else if (integratorProtocol == IntegratorProtocol.AUTO) {
return RequestPath.hasSelector(request, IntegratorHandler.SELECTOR_INTEGRATORTEMPLATE_SECURE);
}
}
return false;
} | java | private boolean isResourceUrlSecure(Page page) {
ValueMap props = getPagePropertiesNullSafe(page);
IntegratorMode mode = getIntegratorMode(props);
if (mode.isDetectProtocol()) {
IntegratorProtocol integratorProtocol = getIntegratorProtocol(props);
if (integratorProtocol == IntegratorProtocol.HTTPS) {
return true;
}
else if (integratorProtocol == IntegratorProtocol.AUTO) {
return RequestPath.hasSelector(request, IntegratorHandler.SELECTOR_INTEGRATORTEMPLATE_SECURE);
}
}
return false;
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wcm-io/wcm-io-handler | link/src/main/java/io/wcm/handler/link/type/helpers/InternalLinkResolver.java | InternalLinkResolver.getTargetPage | private Page getTargetPage(String targetPath, InternalLinkResolverOptions options) {
if (StringUtils.isEmpty(targetPath)) {
return null;
}
// Rewrite target to current site context
String rewrittenPath;
if (options.isRewritePathToContext() && !useTargetContext(options)) {
rewrittenPath = urlHandler.rewritePathToContext(SyntheticNavigatableResource.get(targetPath, resourceResolver));
}
else {
rewrittenPath = targetPath;
}
if (StringUtils.isEmpty(rewrittenPath)) {
return null;
}
// Get target page referenced by target path and check for acceptance
Page targetPage = pageManager.getPage(rewrittenPath);
if (acceptPage(targetPage, options)) {
return targetPage;
}
else {
return null;
}
} | java | private Page getTargetPage(String targetPath, InternalLinkResolverOptions options) {
if (StringUtils.isEmpty(targetPath)) {
return null;
}
// Rewrite target to current site context
String rewrittenPath;
if (options.isRewritePathToContext() && !useTargetContext(options)) {
rewrittenPath = urlHandler.rewritePathToContext(SyntheticNavigatableResource.get(targetPath, resourceResolver));
}
else {
rewrittenPath = targetPath;
}
if (StringUtils.isEmpty(rewrittenPath)) {
return null;
}
// Get target page referenced by target path and check for acceptance
Page targetPage = pageManager.getPage(rewrittenPath);
if (acceptPage(targetPage, options)) {
return targetPage;
}
else {
return null;
}
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@param targetPath Repository path
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wcm-io/wcm-io-handler | link/src/main/java/io/wcm/handler/link/type/helpers/InternalLinkResolver.java | InternalLinkResolver.useTargetContext | private boolean useTargetContext(InternalLinkResolverOptions options) {
if (options.isUseTargetContext() && !options.isRewritePathToContext()) {
return true;
}
// even is use target context is not activated use it if current page is an experience fragment
// otherwise it will be always impossible to resolve internal links
else if (currentPage != null && Path.isExperienceFragmentPath(currentPage.getPath())) {
return true;
}
return false;
} | java | private boolean useTargetContext(InternalLinkResolverOptions options) {
if (options.isUseTargetContext() && !options.isRewritePathToContext()) {
return true;
}
// even is use target context is not activated use it if current page is an experience fragment
// otherwise it will be always impossible to resolve internal links
else if (currentPage != null && Path.isExperienceFragmentPath(currentPage.getPath())) {
return true;
}
return false;
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/HtmlElement.java | HtmlElement.addCssClass | public final T addCssClass(String value) {
if (StringUtils.isNotEmpty(value)) {
return setCssClass(StringUtils.isNotEmpty(getCssClass()) ? getCssClass() + " " + value : value);
}
else {
return (T)this;
}
} | java | public final T addCssClass(String value) {
if (StringUtils.isNotEmpty(value)) {
return setCssClass(StringUtils.isNotEmpty(getCssClass()) ? getCssClass() + " " + value : value);
}
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/HtmlElement.java | HtmlElement.getStyles | public final Map<String, String> getStyles() {
Map<String, String> styleMap = new HashMap<String, String>();
// de-serialize style string, fill style map
String styleString = getStyleString();
if (styleString != null) {
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String[] styleParts = StringUtils.split(styleSubString, ":");
if (styleParts.length > 1) {
styleMap.put(styleParts[0].trim(), styleParts[1].trim());
}
}
}
return styleMap;
} | java | public final Map<String, String> getStyles() {
Map<String, String> styleMap = new HashMap<String, String>();
// de-serialize style string, fill style map
String styleString = getStyleString();
if (styleString != null) {
String[] styles = StringUtils.split(styleString, ";");
for (String styleSubString : styles) {
String[] styleParts = StringUtils.split(styleSubString, ":");
if (styleParts.length > 1) {
styleMap.put(styleParts[0].trim(), styleParts[1].trim());
}
}
}
return styleMap;
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/HtmlElement.java | HtmlElement.setStyle | public final T setStyle(String styleAttribute, String styleValue) {
// Add style to style map
Map<String, String> styleMap = getStyles();
styleMap.put(styleAttribute, styleValue);
// Serialize style string
StringBuilder styleString = new StringBuilder();
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styleString.append(':');
styleString.append(style.getValue());
styleString.append(';');
}
setStyleString(styleString.toString());
return (T)this;
} | java | public final T setStyle(String styleAttribute, String styleValue) {
// Add style to style map
Map<String, String> styleMap = getStyles();
styleMap.put(styleAttribute, styleValue);
// Serialize style string
StringBuilder styleString = new StringBuilder();
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/format/MediaFormat.java | MediaFormat.guessHumanReadableRatioString | private static String guessHumanReadableRatioString(double ratio, NumberFormat numberFormat) {
for (long width = 1; width <= 50; width++) {
double height = width / ratio;
if (isLong(height)) {
return numberFormat.format(width) + ":" + numberFormat.format(height);
}
}
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double height = width / 2d / ratio;
if (isHalfLong(height)) {
return numberFormat.format(width / 2d) + ":" + numberFormat.format(height);
}
}
return null;
} | java | private static String guessHumanReadableRatioString(double ratio, NumberFormat numberFormat) {
for (long width = 1; width <= 50; width++) {
double height = width / ratio;
if (isLong(height)) {
return numberFormat.format(width) + ":" + numberFormat.format(height);
}
}
for (long width = 1; width <= 200; width++) {
double height = width / 2d / ratio;
if (isHalfLong(height)) {
return numberFormat.format(width / 2d) + ":" + numberFormat.format(height);
}
}
return null;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/format/MediaFormat.java | MediaFormat.getMinDimension | public Dimension getMinDimension() {
long effWithMin = getEffectiveMinWidth();
long effHeightMin = getEffectiveMinHeight();
double effRatio = getRatio();
if (effWithMin == 0 && effHeightMin > 0 && effRatio > 0) {
effWithMin = Math.round(effHeightMin * effRatio);
}
if (effWithMin > 0 && effHeightMin == 0 && effRatio > 0) {
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}
if (effWithMin > 0 || effHeightMin > 0) {
return new Dimension(effWithMin, effHeightMin);
}
else {
return null;
}
} | java | public Dimension getMinDimension() {
long effWithMin = getEffectiveMinWidth();
long effHeightMin = getEffectiveMinHeight();
double effRatio = getRatio();
if (effWithMin == 0 && effHeightMin > 0 && effRatio > 0) {
effWithMin = Math.round(effHeightMin * effRatio);
}
if (effWithMin > 0 && effHeightMin == 0 && effRatio > 0) {
effHeightMin = Math.round(effWithMin / effRatio);
}
if (effWithMin > 0 || effHeightMin > 0) {
return new Dimension(effWithMin, effHeightMin);
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/impl/MediaFormatResolver.java | MediaFormatResolver.resolveByNames | private boolean resolveByNames(MediaArgs mediaArgs) {
// resolved media formats already set? done.
if (mediaArgs.getMediaFormats() != null) {
return true;
}
// no media format names present? done.
if (mediaArgs.getMediaFormatNames() == null) {
return true;
}
String[] mediaFormatNames = mediaArgs.getMediaFormatNames();
MediaFormat[] mediaFormats = new MediaFormat[mediaFormatNames.length];
boolean resolutionSuccessful = true;
for (int i = 0; i < mediaFormatNames.length; i++) {
mediaFormats[i] = mediaFormatHandler.getMediaFormat(mediaFormatNames[i]);
if (mediaFormats[i] == null) {
log.warn("Media format name '" + mediaFormatNames[i] + "' is invalid.");
resolutionSuccessful = false;
}
}
mediaArgs.mediaFormats(mediaFormats);
mediaArgs.mediaFormatNames((String[])null);
return resolutionSuccessful;
} | java | private boolean resolveByNames(MediaArgs mediaArgs) {
// resolved media formats already set? done.
if (mediaArgs.getMediaFormats() != null) {
return true;
}
// no media format names present? done.
if (mediaArgs.getMediaFormatNames() == null) {
return true;
}
String[] mediaFormatNames = mediaArgs.getMediaFormatNames();
MediaFormat[] mediaFormats = new MediaFormat[mediaFormatNames.length];
boolean resolutionSuccessful = true;
for (int i = 0; i < mediaFormatNames.length; i++) {
mediaFormats[i] = mediaFormatHandler.getMediaFormat(mediaFormatNames[i]);
if (mediaFormats[i] == null) {
log.warn("Media format name '" + mediaFormatNames[i] + "' is invalid.");
resolutionSuccessful = false;
}
}
mediaArgs.mediaFormats(mediaFormats);
mediaArgs.mediaFormatNames((String[])null);
return resolutionSuccessful;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/impl/MediaFormatResolver.java | MediaFormatResolver.addResponsiveImageMediaFormats | private boolean addResponsiveImageMediaFormats(MediaArgs mediaArgs) {
Map<String, MediaFormat> additionalMediaFormats = new LinkedHashMap<>();
// check if additional on-the-fly generated media formats needs to be added for responsive image handling
if (!resolveForImageSizes(mediaArgs, additionalMediaFormats)) {
return false;
}
if (!resolveForResponsivePictureSources(mediaArgs, additionalMediaFormats)) {
return false;
}
// if additional media formats where found add them to the media format list in media args
if (!additionalMediaFormats.isEmpty()) {
List<MediaFormat> allMediaFormats = new ArrayList<>();
if (mediaArgs.getMediaFormats() != null) {
allMediaFormats.addAll(Arrays.asList(mediaArgs.getMediaFormats()));
}
allMediaFormats.addAll(additionalMediaFormats.values());
mediaArgs.mediaFormats(allMediaFormats.toArray(new MediaFormat[allMediaFormats.size()]));
}
return true;
} | java | private boolean addResponsiveImageMediaFormats(MediaArgs mediaArgs) {
Map<String, MediaFormat> additionalMediaFormats = new LinkedHashMap<>();
// check if additional on-the-fly generated media formats needs to be added for responsive image handling
if (!resolveForImageSizes(mediaArgs, additionalMediaFormats)) {
return false;
}
if (!resolveForResponsivePictureSources(mediaArgs, additionalMediaFormats)) {
return false;
}
// if additional media formats where found add them to the media format list in media args
if (!additionalMediaFormats.isEmpty()) {
List<MediaFormat> allMediaFormats = new ArrayList<>();
if (mediaArgs.getMediaFormats() != null) {
allMediaFormats.addAll(Arrays.asList(mediaArgs.getMediaFormats()));
}
allMediaFormats.addAll(additionalMediaFormats.values());
mediaArgs.mediaFormats(allMediaFormats.toArray(new MediaFormat[allMediaFormats.size()]));
}
return true;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/inline/InlineMediaSource.java | InlineMediaSource.getInlineAsset | private Asset getInlineAsset(Resource ntResourceResource, Media media, String fileName) {
return new InlineAsset(ntResourceResource, media, fileName, adaptable);
} | java | private Asset getInlineAsset(Resource ntResourceResource, Media media, String fileName) {
return new InlineAsset(ntResourceResource, media, fileName, adaptable);
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/inline/InlineMediaSource.java | InlineMediaSource.detectFileName | private String detectFileName(Resource referencedResource, Resource ntFileResource,
Resource ntResourceResource) {
// detect file name
String fileName = null;
// if referenced resource is not the nt:file node check for <nodename>Name property
if (ntFileResource != null && !referencedResource.equals(ntFileResource)) {
fileName = referencedResource.getValueMap().get(ntFileResource.getName() + "Name", String.class);
}
// if not nt:file node exists and the referenced resource is not the nt:resource node check for <nodename>Name property
else if (ntFileResource == null && !referencedResource.equals(ntResourceResource)) {
fileName = referencedResource.getValueMap().get(ntResourceResource.getName() + "Name", String.class);
}
// otherwise use node name of nt:file resource if it exists
else if (ntFileResource != null) {
fileName = ntFileResource.getName();
}
// make sure filename has an extension, otherwise build virtual file name
if (!StringUtils.contains(fileName, ".")) {
fileName = null;
}
// if no filename found detect extension from mime type and build virtual filename
if (StringUtils.isBlank(fileName)) {
String fileExtension = null;
if (ntResourceResource != null) {
String mimeType = ntResourceResource.getValueMap().get(JcrConstants.JCR_MIMETYPE, String.class);
if (StringUtils.isNotEmpty(mimeType) && mimeTypeService != null) {
fileExtension = mimeTypeService.getExtension(mimeType);
}
}
if (StringUtils.isEmpty(fileExtension)) {
fileExtension = "bin";
}
fileName = "file." + fileExtension;
}
return fileName;
} | java | private String detectFileName(Resource referencedResource, Resource ntFileResource,
Resource ntResourceResource) {
// detect file name
String fileName = null;
// if referenced resource is not the nt:file node check for <nodename>Name property
if (ntFileResource != null && !referencedResource.equals(ntFileResource)) {
fileName = referencedResource.getValueMap().get(ntFileResource.getName() + "Name", String.class);
}
// if not nt:file node exists and the referenced resource is not the nt:resource node check for <nodename>Name property
else if (ntFileResource == null && !referencedResource.equals(ntResourceResource)) {
fileName = referencedResource.getValueMap().get(ntResourceResource.getName() + "Name", String.class);
}
// otherwise use node name of nt:file resource if it exists
else if (ntFileResource != null) {
fileName = ntFileResource.getName();
}
// make sure filename has an extension, otherwise build virtual file name
if (!StringUtils.contains(fileName, ".")) {
fileName = null;
}
// if no filename found detect extension from mime type and build virtual filename
if (StringUtils.isBlank(fileName)) {
String fileExtension = null;
if (ntResourceResource != null) {
String mimeType = ntResourceResource.getValueMap().get(JcrConstants.JCR_MIMETYPE, String.class);
if (StringUtils.isNotEmpty(mimeType) && mimeTypeService != null) {
fileExtension = mimeTypeService.getExtension(mimeType);
}
}
if (StringUtils.isEmpty(fileExtension)) {
fileExtension = "bin";
}
fileName = "file." + fileExtension;
}
return fileName;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/inline/InlineMediaSource.java | InlineMediaSource.cleanupFileName | private String cleanupFileName(String fileName) {
String processedFileName = fileName;
// strip off path parts
if (StringUtils.contains(processedFileName, "/")) {
processedFileName = StringUtils.substringAfterLast(processedFileName, "/");
}
if (StringUtils.contains(processedFileName, "\\")) {
processedFileName = StringUtils.substringAfterLast(processedFileName, "\\");
}
// make sure filename does not contain any invalid characters
processedFileName = Escape.validFilename(processedFileName);
return processedFileName;
} | java | private String cleanupFileName(String fileName) {
String processedFileName = fileName;
// strip off path parts
if (StringUtils.contains(processedFileName, "/")) {
processedFileName = StringUtils.substringAfterLast(processedFileName, "/");
}
if (StringUtils.contains(processedFileName, "\\")) {
processedFileName = StringUtils.substringAfterLast(processedFileName, "\\");
}
// make sure filename does not contain any invalid characters
processedFileName = Escape.validFilename(processedFileName);
return processedFileName;
} | [
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/format/impl/MediaFormatHandlerImpl.java | MediaFormatHandlerImpl.isRenditionMatchSizeSameBigger | private boolean isRenditionMatchSizeSameBigger(MediaFormat mediaFormat, MediaFormat mediaFormatRequested) {
long widthRequested = mediaFormatRequested.getEffectiveMinWidth();
long heightRequested = mediaFormatRequested.getEffectiveMinHeight();
long widthMax = mediaFormat.getEffectiveMaxWidth();
long heightMax = mediaFormat.getEffectiveMaxHeight();
return ((widthMax >= widthRequested) || (widthMax == 0))
&& ((heightMax >= heightRequested) || (heightMax == 0));
} | java | private boolean isRenditionMatchSizeSameBigger(MediaFormat mediaFormat, MediaFormat mediaFormatRequested) {
long widthRequested = mediaFormatRequested.getEffectiveMinWidth();
long heightRequested = mediaFormatRequested.getEffectiveMinHeight();
long widthMax = mediaFormat.getEffectiveMaxWidth();
long heightMax = mediaFormat.getEffectiveMaxHeight();
return ((widthMax >= widthRequested) || (widthMax == 0))
&& ((heightMax >= heightRequested) || (heightMax == 0));
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/format/impl/MediaFormatHandlerImpl.java | MediaFormatHandlerImpl.isRenditionMatchSizeSameSmaller | private boolean isRenditionMatchSizeSameSmaller(MediaFormat mediaFormat, MediaFormat mediaFormatRequested) {
long widthRequested = mediaFormatRequested.getEffectiveMinWidth();
long heightRequested = mediaFormatRequested.getEffectiveMinHeight();
long widthMin = mediaFormat.getEffectiveMinWidth();
long heightMin = mediaFormat.getEffectiveMinHeight();
return widthMin <= widthRequested && heightMin <= heightRequested;
} | java | private boolean isRenditionMatchSizeSameSmaller(MediaFormat mediaFormat, MediaFormat mediaFormatRequested) {
long widthRequested = mediaFormatRequested.getEffectiveMinWidth();
long heightRequested = mediaFormatRequested.getEffectiveMinHeight();
long widthMin = mediaFormat.getEffectiveMinWidth();
long heightMin = mediaFormat.getEffectiveMinHeight();
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/format/impl/MediaFormatHandlerImpl.java | MediaFormatHandlerImpl.isRenditionMatchExtension | private boolean isRenditionMatchExtension(MediaFormat mediaFormat) {
for (String extension : mediaFormat.getExtensions()) {
if (FileExtension.isImage(extension)) {
return true;
}
}
return false;
} | java | private boolean isRenditionMatchExtension(MediaFormat mediaFormat) {
for (String extension : mediaFormat.getExtensions()) {
if (FileExtension.isImage(extension)) {
return true;
}
}
return false;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/dam/impl/TransformedRenditionHandler.java | TransformedRenditionHandler.rotateSourceRenditions | private NavigableSet<RenditionMetadata> rotateSourceRenditions(Set<RenditionMetadata> candidates) {
if (rotation == null) {
return new TreeSet<>(candidates);
}
return candidates.stream()
.map(rendition -> new VirtualTransformedRenditionMetadata(rendition.getRendition(),
rotateMapWidth(rendition.getWidth(), rendition.getHeight()),
rotateMapHeight(rendition.getWidth(), rendition.getHeight()),
null, rotation))
.collect(Collectors.toCollection(TreeSet::new));
} | java | private NavigableSet<RenditionMetadata> rotateSourceRenditions(Set<RenditionMetadata> candidates) {
if (rotation == null) {
return new TreeSet<>(candidates);
}
return candidates.stream()
.map(rendition -> new VirtualTransformedRenditionMetadata(rendition.getRendition(),
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rotateMapHeight(rendition.getWidth(), rendition.getHeight()),
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/dam/impl/TransformedRenditionHandler.java | TransformedRenditionHandler.getCropRendition | private VirtualTransformedRenditionMetadata getCropRendition(NavigableSet<RenditionMetadata> candidates) {
RenditionMetadata original = getOriginalRendition();
if (original == null) {
return null;
}
Double scaleFactor = getCropScaleFactor();
CropDimension scaledCropDimension = new CropDimension(
Math.round(cropDimension.getLeft() * scaleFactor),
Math.round(cropDimension.getTop() * scaleFactor),
Math.round(cropDimension.getWidth() * scaleFactor),
Math.round(cropDimension.getHeight() * scaleFactor));
return new VirtualTransformedRenditionMetadata(original.getRendition(),
rotateMapWidth(scaledCropDimension.getWidth(), scaledCropDimension.getHeight()),
rotateMapHeight(scaledCropDimension.getWidth(), scaledCropDimension.getHeight()),
scaledCropDimension, rotation);
} | java | private VirtualTransformedRenditionMetadata getCropRendition(NavigableSet<RenditionMetadata> candidates) {
RenditionMetadata original = getOriginalRendition();
if (original == null) {
return null;
}
Double scaleFactor = getCropScaleFactor();
CropDimension scaledCropDimension = new CropDimension(
Math.round(cropDimension.getLeft() * scaleFactor),
Math.round(cropDimension.getTop() * scaleFactor),
Math.round(cropDimension.getWidth() * scaleFactor),
Math.round(cropDimension.getHeight() * scaleFactor));
return new VirtualTransformedRenditionMetadata(original.getRendition(),
rotateMapWidth(scaledCropDimension.getWidth(), scaledCropDimension.getHeight()),
rotateMapHeight(scaledCropDimension.getWidth(), scaledCropDimension.getHeight()),
scaledCropDimension, rotation);
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/mediasource/dam/impl/TransformedRenditionHandler.java | TransformedRenditionHandler.getCropScaleFactor | private double getCropScaleFactor() {
RenditionMetadata original = getOriginalRendition();
RenditionMetadata webEnabled = AutoCropping.getWebRenditionForCropping(getAsset());
if (original == null || webEnabled == null || original.getWidth() == 0 || webEnabled.getWidth() == 0) {
return 1d;
}
return (double)original.getWidth() / (double)webEnabled.getWidth();
} | java | private double getCropScaleFactor() {
RenditionMetadata original = getOriginalRendition();
RenditionMetadata webEnabled = AutoCropping.getWebRenditionForCropping(getAsset());
if (original == null || webEnabled == null || original.getWidth() == 0 || webEnabled.getWidth() == 0) {
return 1d;
}
return (double)original.getWidth() / (double)webEnabled.getWidth();
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wcm-io/wcm-io-handler | link/src/main/java/io/wcm/handler/link/type/helpers/SyntheticNavigatableResource.java | SyntheticNavigatableResource.get | static @NotNull Resource get(String path, ResourceResolver resolver) {
Resource resource = resolver.getResource(path);
if (resource != null) {
return resource;
}
return new SyntheticNavigatableResource(path, resolver);
} | java | static @NotNull Resource get(String path, ResourceResolver resolver) {
Resource resource = resolver.getResource(path);
if (resource != null) {
return resource;
}
return new SyntheticNavigatableResource(path, resolver);
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/MediaArgs.java | MediaArgs.dragDropSupport | public @NotNull MediaArgs dragDropSupport(DragDropSupport value) {
if (value == null) {
throw new IllegalArgumentException("No null value allowed for drag&drop support.");
}
this.dragDropSupport = value;
return this;
} | java | public @NotNull MediaArgs dragDropSupport(DragDropSupport value) {
if (value == null) {
throw new IllegalArgumentException("No null value allowed for drag&drop support.");
}
this.dragDropSupport = value;
return this;
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wcm-io/wcm-io-handler | media/src/main/java/io/wcm/handler/media/impl/ImageFileServlet.java | ImageFileServlet.getImageFileName | public static String getImageFileName(String originalFilename) {
String namePart = StringUtils.substringBeforeLast(originalFilename, ".");
String extensionPart = StringUtils.substringAfterLast(originalFilename, ".");
// use PNG format if original image is PNG, otherwise always use JPEG
if (StringUtils.equalsIgnoreCase(extensionPart, FileExtension.PNG)) {
extensionPart = FileExtension.PNG;
}
else {
extensionPart = FileExtension.JPEG;
}
return namePart + "." + extensionPart;
} | java | public static String getImageFileName(String originalFilename) {
String namePart = StringUtils.substringBeforeLast(originalFilename, ".");
String extensionPart = StringUtils.substringAfterLast(originalFilename, ".");
// use PNG format if original image is PNG, otherwise always use JPEG
if (StringUtils.equalsIgnoreCase(extensionPart, FileExtension.PNG)) {
extensionPart = FileExtension.PNG;
}
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extensionPart = FileExtension.JPEG;
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wcm-io/wcm-io-handler | richtext/src/main/java/io/wcm/handler/richtext/impl/DataPropertyUtil.java | DataPropertyUtil.toHtml5DataName | public static String toHtml5DataName(String headlessCamelCaseName) {
if (StringUtils.isEmpty(headlessCamelCaseName)) {
throw new IllegalArgumentException("Property name is empty.");
}
if (!isHeadlessCamelCaseName(headlessCamelCaseName)) {
throw new IllegalArgumentException("This is not a valid headless camel case property name: " + headlessCamelCaseName);
}
StringBuilder html5DataName = new StringBuilder(HTML5_DATA_PREFIX);
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if (CharUtils.isAsciiAlphaUpper(c)) {
html5DataName.append('-');
}
html5DataName.append(Character.toLowerCase(c));
}
return html5DataName.toString();
} | java | public static String toHtml5DataName(String headlessCamelCaseName) {
if (StringUtils.isEmpty(headlessCamelCaseName)) {
throw new IllegalArgumentException("Property name is empty.");
}
if (!isHeadlessCamelCaseName(headlessCamelCaseName)) {
throw new IllegalArgumentException("This is not a valid headless camel case property name: " + headlessCamelCaseName);
}
StringBuilder html5DataName = new StringBuilder(HTML5_DATA_PREFIX);
for (int i = 0; i < headlessCamelCaseName.length(); i++) {
char c = headlessCamelCaseName.charAt(i);
if (CharUtils.isAsciiAlphaUpper(c)) {
html5DataName.append('-');
}
html5DataName.append(Character.toLowerCase(c));
}
return html5DataName.toString();
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wcm-io/wcm-io-handler | richtext/src/main/java/io/wcm/handler/richtext/impl/DataPropertyUtil.java | DataPropertyUtil.toHeadlessCamelCaseName | public static String toHeadlessCamelCaseName(String html5DataName) {
if (StringUtils.isEmpty(html5DataName)) {
throw new IllegalArgumentException("Property name is empty.");
}
if (!isHtml5DataName(html5DataName)) {
throw new IllegalArgumentException("This is not a valid HTML5 data property name: " + html5DataName);
}
String html5DataNameWithoutSuffix = StringUtils.substringAfter(html5DataName, HTML5_DATA_PREFIX);
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char c = html5DataNameWithoutSuffix.charAt(i);
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headlessCamelCaseName.append(Character.toUpperCase(c));
upperCaseNext = false;
}
else {
headlessCamelCaseName.append(c);
}
}
return headlessCamelCaseName.toString();
} | java | public static String toHeadlessCamelCaseName(String html5DataName) {
if (StringUtils.isEmpty(html5DataName)) {
throw new IllegalArgumentException("Property name is empty.");
}
if (!isHtml5DataName(html5DataName)) {
throw new IllegalArgumentException("This is not a valid HTML5 data property name: " + html5DataName);
}
String html5DataNameWithoutSuffix = StringUtils.substringAfter(html5DataName, HTML5_DATA_PREFIX);
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char c = html5DataNameWithoutSuffix.charAt(i);
if (c == '-') {
upperCaseNext = true;
}
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headlessCamelCaseName.append(Character.toUpperCase(c));
upperCaseNext = false;
}
else {
headlessCamelCaseName.append(c);
}
}
return headlessCamelCaseName.toString();
} | [
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.setName | @Override
@Deprecated
public final org.jdom2.Element setName(String value) {
return super.setName(value);
} | java | @Override
@Deprecated
public final org.jdom2.Element setName(String value) {
return super.setName(value);
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.getAttributeValueAsInteger | public final int getAttributeValueAsInteger(String attributeName) {
Attribute attribute = getAttribute(attributeName);
if (attribute == null) {
return 0;
}
else {
try {
return attribute.getIntValue();
}
catch (DataConversionException ex) {
return 0;
}
}
} | java | public final int getAttributeValueAsInteger(String attributeName) {
Attribute attribute = getAttribute(attributeName);
if (attribute == null) {
return 0;
}
else {
try {
return attribute.getIntValue();
}
catch (DataConversionException ex) {
return 0;
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.setAttributeValueAsLong | public final T setAttributeValueAsLong(String name, long value) {
setAttribute(name, Long.toString(value));
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} | java | public final T setAttributeValueAsLong(String name, long value) {
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.getAttributeValueAsLong | public final long getAttributeValueAsLong(String attributeName) {
Attribute attribute = getAttribute(attributeName);
if (attribute == null) {
return 0;
}
else {
try {
return attribute.getLongValue();
}
catch (DataConversionException ex) {
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}
} | java | public final long getAttributeValueAsLong(String attributeName) {
Attribute attribute = getAttribute(attributeName);
if (attribute == null) {
return 0;
}
else {
try {
return attribute.getLongValue();
}
catch (DataConversionException ex) {
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.setAttributeValueAsInteger | public final T setAttributeValueAsInteger(String name, int value) {
setAttribute(name, Integer.toString(value));
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} | java | public final T setAttributeValueAsInteger(String name, int value) {
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.addContent | @Override
public final org.jdom2.Element addContent(Content content) {
// ignore empty elements
if (content == null) {
return null;
}
return super.addContent(content);
} | java | @Override
public final org.jdom2.Element addContent(Content content) {
// ignore empty elements
if (content == null) {
return null;
}
return super.addContent(content);
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wcm-io/wcm-io-handler | commons/src/main/java/io/wcm/handler/commons/dom/AbstractElement.java | AbstractElement.addContent | @Override
public final org.jdom2.Element addContent(Collection collection) {
// ignore empty elements
if (collection == null) {
return null;
}
return super.addContent(collection);
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public final org.jdom2.Element addContent(Collection collection) {
// ignore empty elements
if (collection == null) {
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return super.addContent(collection);
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wcm-io/wcm-io-handler | richtext/src/main/java/io/wcm/handler/richtext/util/XHtmlEntityResolver.java | XHtmlEntityResolver.resolveEntity | @Override
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String filename = xhtmlResourceMap.get(publicId);
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throw new IOException("Resource '" + resourceName + "' not found in class path.");
}
return new InputSource(is);
}
return null;
} | java | @Override
public InputSource resolveEntity(String publicId, String systemId) throws SAXException, IOException {
String filename = xhtmlResourceMap.get(publicId);
if (filename != null) {
String resourceName = resourceFolder + "/" + filename;
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jenkinsci/favorite-plugin | src/main/java/hudson/plugins/favorite/user/FavoriteUserProperty.java | FavoriteUserProperty.readResolve | Object readResolve() {
if (favorites != null) {
data = Maps.newConcurrentMap();
for (String job : favorites) {
data.put(job, true);
}
favorites = null;
}
return this;
} | java | Object readResolve() {
if (favorites != null) {
data = Maps.newConcurrentMap();
for (String job : favorites) {
data.put(job, true);
}
favorites = null;
}
return this;
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/index/IndexerWorkItemQueue.java | IndexerWorkItemQueue.stop | @Nonnull
@ReturnsMutableCopy
public ICommonsList <IIndexerWorkItem> stop ()
{
// don't take any more actions
m_aImmediateCollector.stopQueuingNewObjects ();
// Get all remaining objects and save them for late reuse
final ICommonsList <IIndexerWorkItem> aRemainingItems = m_aImmediateCollector.drainQueue ();
// Shutdown the thread pool afterwards
ExecutorServiceHelper.shutdownAndWaitUntilAllTasksAreFinished (m_aSenderThreadPool);
return aRemainingItems;
} | java | @Nonnull
@ReturnsMutableCopy
public ICommonsList <IIndexerWorkItem> stop ()
{
// don't take any more actions
m_aImmediateCollector.stopQueuingNewObjects ();
// Get all remaining objects and save them for late reuse
final ICommonsList <IIndexerWorkItem> aRemainingItems = m_aImmediateCollector.drainQueue ();
// Shutdown the thread pool afterwards
ExecutorServiceHelper.shutdownAndWaitUntilAllTasksAreFinished (m_aSenderThreadPool);
return aRemainingItems;
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/index/IndexerWorkItemQueue.java | IndexerWorkItemQueue.queueObject | public void queueObject (@Nonnull final IIndexerWorkItem aItem)
{
ValueEnforcer.notNull (aItem, "Item");
m_aImmediateCollector.queueObject (aItem);
} | java | public void queueObject (@Nonnull final IIndexerWorkItem aItem)
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ValueEnforcer.notNull (aItem, "Item");
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/reindex/ReIndexWorkItemList.java | ReIndexWorkItemList.addItem | public void addItem (@Nonnull final ReIndexWorkItem aItem) throws IllegalStateException
{
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m_aRWLock.writeLocked ( () -> {
internalCreateItem (aItem);
});
LOGGER.info ("Added " + aItem.getLogText () + " to re-try list for retry #" + (aItem.getRetryCount () + 1));
} | java | public void addItem (@Nonnull final ReIndexWorkItem aItem) throws IllegalStateException
{
ValueEnforcer.notNull (aItem, "Item");
m_aRWLock.writeLocked ( () -> {
internalCreateItem (aItem);
});
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/mgr/PDIndexerManager.java | PDIndexerManager._queueUniqueWorkItem | @Nonnull
private EChange _queueUniqueWorkItem (@Nonnull final IIndexerWorkItem aWorkItem)
{
ValueEnforcer.notNull (aWorkItem, "WorkItem");
// Check for duplicate
m_aRWLock.writeLock ().lock ();
try
{
if (!m_aUniqueItems.add (aWorkItem))
{
LOGGER.info ("Ignoring work item " +
aWorkItem.getLogText () +
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return EChange.UNCHANGED;
}
}
finally
{
m_aRWLock.writeLock ().unlock ();
}
// Queue it
m_aIndexerWorkQueue.queueObject (aWorkItem);
LOGGER.info ("Queued work item " + aWorkItem.getLogText ());
// Remove the entry from the dead list to avoid spamming the dead list
if (m_aDeadList.getAndRemoveEntry (x -> x.getWorkItem ().equals (aWorkItem)) != null)
LOGGER.info ("Removed the new work item " + aWorkItem.getLogText () + " from the dead list");
return EChange.CHANGED;
} | java | @Nonnull
private EChange _queueUniqueWorkItem (@Nonnull final IIndexerWorkItem aWorkItem)
{
ValueEnforcer.notNull (aWorkItem, "WorkItem");
// Check for duplicate
m_aRWLock.writeLock ().lock ();
try
{
if (!m_aUniqueItems.add (aWorkItem))
{
LOGGER.info ("Ignoring work item " +
aWorkItem.getLogText () +
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return EChange.UNCHANGED;
}
}
finally
{
m_aRWLock.writeLock ().unlock ();
}
// Queue it
m_aIndexerWorkQueue.queueObject (aWorkItem);
LOGGER.info ("Queued work item " + aWorkItem.getLogText ());
// Remove the entry from the dead list to avoid spamming the dead list
if (m_aDeadList.getAndRemoveEntry (x -> x.getWorkItem ().equals (aWorkItem)) != null)
LOGGER.info ("Removed the new work item " + aWorkItem.getLogText () + " from the dead list");
return EChange.CHANGED;
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/mgr/PDIndexerManager.java | PDIndexerManager.queueWorkItem | @Nonnull
public EChange queueWorkItem (@Nonnull final IParticipantIdentifier aParticipantID,
@Nonnull final EIndexerWorkItemType eType,
@Nonnull @Nonempty final String sOwnerID,
@Nonnull @Nonempty final String sRequestingHost)
{
// Build item
final IIndexerWorkItem aWorkItem = new IndexerWorkItem (aParticipantID, eType, sOwnerID, sRequestingHost);
// And queue it
return _queueUniqueWorkItem (aWorkItem);
} | java | @Nonnull
public EChange queueWorkItem (@Nonnull final IParticipantIdentifier aParticipantID,
@Nonnull final EIndexerWorkItemType eType,
@Nonnull @Nonempty final String sOwnerID,
@Nonnull @Nonempty final String sRequestingHost)
{
// Build item
final IIndexerWorkItem aWorkItem = new IndexerWorkItem (aParticipantID, eType, sOwnerID, sRequestingHost);
// And queue it
return _queueUniqueWorkItem (aWorkItem);
} | [
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Participant ID to use.
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Action type.
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Owner of this action
@param sRequestingHost
Requesting host (IP address)
@return {@link EChange#UNCHANGED} if the item was queued,
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/mgr/PDIndexerManager.java | PDIndexerManager.expireOldEntries | public void expireOldEntries ()
{
// Expire old entries
final ICommonsList <IReIndexWorkItem> aExpiredItems = m_aReIndexList.getAndRemoveAllEntries (IReIndexWorkItem::isExpired);
if (aExpiredItems.isNotEmpty ())
{
LOGGER.info ("Expiring " + aExpiredItems.size () + " re-index work items and move them to the dead list");
for (final IReIndexWorkItem aItem : aExpiredItems)
{
// remove them from the overall list but move to dead item list
m_aRWLock.writeLocked ( () -> m_aUniqueItems.remove (aItem.getWorkItem ()));
// move all to the dead item list
m_aDeadList.addItem ((ReIndexWorkItem) aItem);
LOGGER.info ("Added " + aItem.getLogText () + " to the dead list");
}
}
} | java | public void expireOldEntries ()
{
// Expire old entries
final ICommonsList <IReIndexWorkItem> aExpiredItems = m_aReIndexList.getAndRemoveAllEntries (IReIndexWorkItem::isExpired);
if (aExpiredItems.isNotEmpty ())
{
LOGGER.info ("Expiring " + aExpiredItems.size () + " re-index work items and move them to the dead list");
for (final IReIndexWorkItem aItem : aExpiredItems)
{
// remove them from the overall list but move to dead item list
m_aRWLock.writeLocked ( () -> m_aUniqueItems.remove (aItem.getWorkItem ()));
// move all to the dead item list
m_aDeadList.addItem ((ReIndexWorkItem) aItem);
LOGGER.info ("Added " + aItem.getLogText () + " to the dead list");
}
}
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/mgr/PDIndexerManager.java | PDIndexerManager.reIndexParticipantData | public void reIndexParticipantData ()
{
final LocalDateTime aNow = PDTFactory.getCurrentLocalDateTime ();
// Get and remove all items to re-index "now"
final List <IReIndexWorkItem> aReIndexNowItems = m_aReIndexList.getAndRemoveAllEntries (aWorkItem -> aWorkItem.isRetryPossible (aNow));
if (LOGGER.isDebugEnabled ())
LOGGER.debug ("Re-indexing " + aReIndexNowItems.size () + " work items");
for (final IReIndexWorkItem aReIndexItem : aReIndexNowItems)
{
LOGGER.info ("Try to re-index " + aReIndexItem.getLogText ());
PDIndexExecutor.executeWorkItem (m_aStorageMgr,
aReIndexItem.getWorkItem (),
1 + aReIndexItem.getRetryCount (),
aSuccessItem -> _onReIndexSuccess (aSuccessItem),
aFailureItem -> _onReIndexFailure (aReIndexItem));
}
} | java | public void reIndexParticipantData ()
{
final LocalDateTime aNow = PDTFactory.getCurrentLocalDateTime ();
// Get and remove all items to re-index "now"
final List <IReIndexWorkItem> aReIndexNowItems = m_aReIndexList.getAndRemoveAllEntries (aWorkItem -> aWorkItem.isRetryPossible (aNow));
if (LOGGER.isDebugEnabled ())
LOGGER.debug ("Re-indexing " + aReIndexNowItems.size () + " work items");
for (final IReIndexWorkItem aReIndexItem : aReIndexNowItems)
{
LOGGER.info ("Try to re-index " + aReIndexItem.getLogText ());
PDIndexExecutor.executeWorkItem (m_aStorageMgr,
aReIndexItem.getWorkItem (),
1 + aReIndexItem.getRetryCount (),
aSuccessItem -> _onReIndexSuccess (aSuccessItem),
aFailureItem -> _onReIndexFailure (aReIndexItem));
}
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/clientcert/ClientCertificateValidator.java | ClientCertificateValidator.verifyClientCertificate | @Nonnull
public static ClientCertificateValidationResult verifyClientCertificate (@Nonnull final HttpServletRequest aHttpRequest,
@Nonnull final String sLogPrefix)
{
if (s_bIsCheckDisabled.get ())
{
if (LOGGER.isDebugEnabled ())
LOGGER.debug (sLogPrefix + "Client certificate is considered valid because the 'allow all' for tests is set!");
return ClientCertificateValidationResult.createSuccess (INSECURE_DEBUG_CLIENT);
}
// This is how to get client certificate from request
final Object aValue = aHttpRequest.getAttribute ("javax.servlet.request.X509Certificate");
if (aValue == null)
{
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "No client certificates present in the request");
return ClientCertificateValidationResult.createFailure ();
}
// type check
if (!(aValue instanceof X509Certificate []))
throw new IllegalStateException ("Request value is not of type X509Certificate[] but of " + aValue.getClass ());
// Main checking
final X509Certificate [] aRequestCerts = (X509Certificate []) aValue;
if (ArrayHelper.isEmpty (aRequestCerts))
{
// Empty array
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "No client certificates passed for validation");
return ClientCertificateValidationResult.createFailure ();
}
// OK, we have a non-empty, type checked Certificate array
// TODO: determine CRLs
final ICommonsList <CRL> aCRLs = new CommonsArrayList <> ();
// Verify for "now"
final LocalDateTime aVerificationDate = PDTFactory.getCurrentLocalDateTime ();
// Search the certificate from the request matching our required issuers
X509Certificate aClientCertToVerify = null;
{
for (final X509Certificate aCert : aRequestCerts)
{
final X500Principal aIssuer = aCert.getIssuerX500Principal ();
if (s_aSearchIssuers.contains (aIssuer))
{
if (LOGGER.isInfoEnabled ())
LOGGER.info (sLogPrefix +
" Using the following client certificate issuer for verification: '" +
aIssuer +
"'");
aClientCertToVerify = aCert;
break;
}
}
// Do we have a certificate to verify?
if (aClientCertToVerify == null)
{
throw new IllegalStateException ("Found no client certificate that was issued by one of the " +
s_aSearchIssuers.size () +
" required issuers. Provided certs are: " +
Arrays.toString (aRequestCerts));
}
}
final String sClientID = getClientUniqueID (aClientCertToVerify);
// This is the main verification process against the PEPPOL SMP root
// certificate
for (final X509Certificate aRootCert : s_aPeppolSMPRootCerts)
{
final String sVerifyErrorMsg = _verifyCertificate (aClientCertToVerify, aRootCert, aCRLs, aVerificationDate);
if (sVerifyErrorMsg == null)
{
if (LOGGER.isInfoEnabled ())
LOGGER.info (sLogPrefix + " Passed client certificate is valid");
return ClientCertificateValidationResult.createSuccess (sClientID);
}
}
if (LOGGER.isWarnEnabled ())
LOGGER.warn ("Client certificate is invalid: " + sClientID);
return ClientCertificateValidationResult.createFailure ();
} | java | @Nonnull
public static ClientCertificateValidationResult verifyClientCertificate (@Nonnull final HttpServletRequest aHttpRequest,
@Nonnull final String sLogPrefix)
{
if (s_bIsCheckDisabled.get ())
{
if (LOGGER.isDebugEnabled ())
LOGGER.debug (sLogPrefix + "Client certificate is considered valid because the 'allow all' for tests is set!");
return ClientCertificateValidationResult.createSuccess (INSECURE_DEBUG_CLIENT);
}
// This is how to get client certificate from request
final Object aValue = aHttpRequest.getAttribute ("javax.servlet.request.X509Certificate");
if (aValue == null)
{
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "No client certificates present in the request");
return ClientCertificateValidationResult.createFailure ();
}
// type check
if (!(aValue instanceof X509Certificate []))
throw new IllegalStateException ("Request value is not of type X509Certificate[] but of " + aValue.getClass ());
// Main checking
final X509Certificate [] aRequestCerts = (X509Certificate []) aValue;
if (ArrayHelper.isEmpty (aRequestCerts))
{
// Empty array
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "No client certificates passed for validation");
return ClientCertificateValidationResult.createFailure ();
}
// OK, we have a non-empty, type checked Certificate array
// TODO: determine CRLs
final ICommonsList <CRL> aCRLs = new CommonsArrayList <> ();
// Verify for "now"
final LocalDateTime aVerificationDate = PDTFactory.getCurrentLocalDateTime ();
// Search the certificate from the request matching our required issuers
X509Certificate aClientCertToVerify = null;
{
for (final X509Certificate aCert : aRequestCerts)
{
final X500Principal aIssuer = aCert.getIssuerX500Principal ();
if (s_aSearchIssuers.contains (aIssuer))
{
if (LOGGER.isInfoEnabled ())
LOGGER.info (sLogPrefix +
" Using the following client certificate issuer for verification: '" +
aIssuer +
"'");
aClientCertToVerify = aCert;
break;
}
}
// Do we have a certificate to verify?
if (aClientCertToVerify == null)
{
throw new IllegalStateException ("Found no client certificate that was issued by one of the " +
s_aSearchIssuers.size () +
" required issuers. Provided certs are: " +
Arrays.toString (aRequestCerts));
}
}
final String sClientID = getClientUniqueID (aClientCertToVerify);
// This is the main verification process against the PEPPOL SMP root
// certificate
for (final X509Certificate aRootCert : s_aPeppolSMPRootCerts)
{
final String sVerifyErrorMsg = _verifyCertificate (aClientCertToVerify, aRootCert, aCRLs, aVerificationDate);
if (sVerifyErrorMsg == null)
{
if (LOGGER.isInfoEnabled ())
LOGGER.info (sLogPrefix + " Passed client certificate is valid");
return ClientCertificateValidationResult.createSuccess (sClientID);
}
}
if (LOGGER.isWarnEnabled ())
LOGGER.warn ("Client certificate is invalid: " + sClientID);
return ClientCertificateValidationResult.createFailure ();
} | [
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@param aHttpRequest
The HTTP request to use. May not be <code>null</code>.
@param sLogPrefix
The context - for logging only. May not be <code>null</code>.
@return Never <code>null</code>. | [
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] | 98da26da29fb7178371d6b029516cbf01be223fb | https://github.com/phax/peppol-directory/blob/98da26da29fb7178371d6b029516cbf01be223fb/peppol-directory-indexer/src/main/java/com/helger/pd/indexer/clientcert/ClientCertificateValidator.java#L264-L351 | train |
phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/storage/PDStorageManager.java | PDStorageManager.getGroupedByParticipantID | @Nonnull
@ReturnsMutableCopy
public static IMultiMapListBased <IParticipantIdentifier, PDStoredBusinessEntity> getGroupedByParticipantID (@Nonnull final Iterable <PDStoredBusinessEntity> aDocs)
{
final MultiLinkedHashMapArrayListBased <IParticipantIdentifier, PDStoredBusinessEntity> ret = new MultiLinkedHashMapArrayListBased <> ();
for (final PDStoredBusinessEntity aDoc : aDocs)
ret.putSingle (aDoc.getParticipantID (), aDoc);
return ret;
} | java | @Nonnull
@ReturnsMutableCopy
public static IMultiMapListBased <IParticipantIdentifier, PDStoredBusinessEntity> getGroupedByParticipantID (@Nonnull final Iterable <PDStoredBusinessEntity> aDocs)
{
final MultiLinkedHashMapArrayListBased <IParticipantIdentifier, PDStoredBusinessEntity> ret = new MultiLinkedHashMapArrayListBased <> ();
for (final PDStoredBusinessEntity aDoc : aDocs)
ret.putSingle (aDoc.getParticipantID (), aDoc);
return ret;
} | [
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/rest/IndexerResource.java | IndexerResource._checkClientCertificate | @Nonnull
private static ClientCertificateValidationResult _checkClientCertificate (@Nonnull final HttpServletRequest aHttpServletRequest,
@Nonnull final String sLogPrefix)
{
try
{
return ClientCertificateValidator.verifyClientCertificate (aHttpServletRequest, sLogPrefix);
}
catch (final RuntimeException ex)
{
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "Error validating client certificate", ex);
}
return ClientCertificateValidationResult.createFailure ();
} | java | @Nonnull
private static ClientCertificateValidationResult _checkClientCertificate (@Nonnull final HttpServletRequest aHttpServletRequest,
@Nonnull final String sLogPrefix)
{
try
{
return ClientCertificateValidator.verifyClientCertificate (aHttpServletRequest, sLogPrefix);
}
catch (final RuntimeException ex)
{
if (LOGGER.isWarnEnabled ())
LOGGER.warn (sLogPrefix + "Error validating client certificate", ex);
}
return ClientCertificateValidationResult.createFailure ();
} | [
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@param aHttpServletRequest
The current servlet request. May not be <code>null</code>.
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The context - for logging only. May not be <code>null</code>.
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/reindex/ReIndexWorkItem.java | ReIndexWorkItem.incRetryCount | public void incRetryCount ()
{
m_nRetries++;
m_aPreviousRetryDT = PDTFactory.getCurrentLocalDateTime ();
m_aNextRetryDT = m_aPreviousRetryDT.plusMinutes (PDServerConfiguration.getReIndexRetryMinutes ());
} | java | public void incRetryCount ()
{
m_nRetries++;
m_aPreviousRetryDT = PDTFactory.getCurrentLocalDateTime ();
m_aNextRetryDT = m_aPreviousRetryDT.plusMinutes (PDServerConfiguration.getReIndexRetryMinutes ());
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/lucene/PDLucene.java | PDLucene.getSearcher | @Nullable
public IndexSearcher getSearcher () throws IOException
{
_checkClosing ();
final IndexReader aReader = getReader ();
if (aReader == null)
{
// Index not readable
LOGGER.warn ("Index not readable");
return null;
}
if (m_aSearchReader == aReader)
{
// Reader did not change - use cached searcher
assert m_aSearcher != null;
}
else
{
// Create new searcher only if necessary
m_aSearchReader = aReader;
m_aSearcher = new IndexSearcher (aReader);
}
return m_aSearcher;
} | java | @Nullable
public IndexSearcher getSearcher () throws IOException
{
_checkClosing ();
final IndexReader aReader = getReader ();
if (aReader == null)
{
// Index not readable
LOGGER.warn ("Index not readable");
return null;
}
if (m_aSearchReader == aReader)
{
// Reader did not change - use cached searcher
assert m_aSearcher != null;
}
else
{
// Create new searcher only if necessary
m_aSearchReader = aReader;
m_aSearcher = new IndexSearcher (aReader);
}
return m_aSearcher;
} | [
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/lucene/PDLucene.java | PDLucene.updateDocuments | @MustBeLocked (ELockType.WRITE)
public void updateDocuments (@Nullable final Term aDelTerm,
@Nonnull final Iterable <? extends Iterable <? extends IndexableField>> aDocs) throws IOException
{
long nSeqNum;
if (false)
{
// Delete and than add
nSeqNum = _getWriter ().deleteDocuments (aDelTerm);
nSeqNum = _getWriter ().updateDocuments (null, aDocs);
}
else
{
// Update directly
nSeqNum = _getWriter ().updateDocuments (aDelTerm, aDocs);
}
if (LOGGER.isDebugEnabled ())
LOGGER.debug ("Last seq# after updateDocuments is " + nSeqNum);
m_aWriterChanges.incrementAndGet ();
} | java | @MustBeLocked (ELockType.WRITE)
public void updateDocuments (@Nullable final Term aDelTerm,
@Nonnull final Iterable <? extends Iterable <? extends IndexableField>> aDocs) throws IOException
{
long nSeqNum;
if (false)
{
// Delete and than add
nSeqNum = _getWriter ().deleteDocuments (aDelTerm);
nSeqNum = _getWriter ().updateDocuments (null, aDocs);
}
else
{
// Update directly
nSeqNum = _getWriter ().updateDocuments (aDelTerm, aDocs);
}
if (LOGGER.isDebugEnabled ())
LOGGER.debug ("Last seq# after updateDocuments is " + nSeqNum);
m_aWriterChanges.incrementAndGet ();
} | [
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reader will see all or none of the documents.
@param aDelTerm
the term to identify the document(s) to be deleted. May be
<code>null</code>.
@param aDocs
the documents to be added. May not be <code>null</code>.
@throws CorruptIndexException
if the index is corrupt
@throws IOException
if there is a low-level IO error | [
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/lucene/PDLucene.java | PDLucene.writeLockedAtomic | @Nonnull
public ESuccess writeLockedAtomic (@Nonnull final IThrowingRunnable <IOException> aRunnable) throws IOException
{
m_aRWLock.writeLock ().lock ();
try
{
if (isClosing ())
{
LOGGER.info ("Cannot executed something write locked, because Lucene is shutting down");
return ESuccess.FAILURE;
}
aRunnable.run ();
}
finally
{
m_aRWLock.writeLock ().unlock ();
}
return ESuccess.SUCCESS;
} | java | @Nonnull
public ESuccess writeLockedAtomic (@Nonnull final IThrowingRunnable <IOException> aRunnable) throws IOException
{
m_aRWLock.writeLock ().lock ();
try
{
if (isClosing ())
{
LOGGER.info ("Cannot executed something write locked, because Lucene is shutting down");
return ESuccess.FAILURE;
}
aRunnable.run ();
}
finally
{
m_aRWLock.writeLock ().unlock ();
}
return ESuccess.SUCCESS;
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/storage/field/AbstractPDField.java | AbstractPDField.getDocValue | @Nullable
public final NATIVE_TYPE getDocValue (@Nonnull final Document aDoc)
{
final IndexableField aField = getDocField (aDoc);
if (aField != null)
return getFieldNativeValue (aField);
return null;
} | java | @Nullable
public final NATIVE_TYPE getDocValue (@Nonnull final Document aDoc)
{
final IndexableField aField = getDocField (aDoc);
if (aField != null)
return getFieldNativeValue (aField);
return null;
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phax/peppol-directory | peppol-directory-businesscard/src/main/java/com/helger/pd/businesscard/helper/PDBusinessCardHelper.java | PDBusinessCardHelper.parseBusinessCard | @Nullable
public static PDBusinessCard parseBusinessCard (@Nonnull final byte [] aData, @Nullable final Charset aCharset)
{
ValueEnforcer.notNull (aData, "Data");
{
// Read version 1
final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ();
aMarshaller1.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller1.setCharset (aCharset);
final PD1BusinessCardType aBC1 = aMarshaller1.read (aData);
if (aBC1 != null)
try
{
return PD1APIHelper.createBusinessCard (aBC1);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 2
final PD2BusinessCardMarshaller aMarshaller2 = new PD2BusinessCardMarshaller ();
aMarshaller2.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller2.setCharset (aCharset);
final PD2BusinessCardType aBC2 = aMarshaller2.read (aData);
if (aBC2 != null)
try
{
return PD2APIHelper.createBusinessCard (aBC2);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 3
final PD3BusinessCardMarshaller aMarshaller3 = new PD3BusinessCardMarshaller ();
aMarshaller3.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller3.setCharset (aCharset);
final PD3BusinessCardType aBC3 = aMarshaller3.read (aData);
if (aBC3 != null)
try
{
return PD3APIHelper.createBusinessCard (aBC3);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
// Unsupported version
return null;
} | java | @Nullable
public static PDBusinessCard parseBusinessCard (@Nonnull final byte [] aData, @Nullable final Charset aCharset)
{
ValueEnforcer.notNull (aData, "Data");
{
// Read version 1
final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ();
aMarshaller1.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller1.setCharset (aCharset);
final PD1BusinessCardType aBC1 = aMarshaller1.read (aData);
if (aBC1 != null)
try
{
return PD1APIHelper.createBusinessCard (aBC1);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 2
final PD2BusinessCardMarshaller aMarshaller2 = new PD2BusinessCardMarshaller ();
aMarshaller2.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller2.setCharset (aCharset);
final PD2BusinessCardType aBC2 = aMarshaller2.read (aData);
if (aBC2 != null)
try
{
return PD2APIHelper.createBusinessCard (aBC2);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 3
final PD3BusinessCardMarshaller aMarshaller3 = new PD3BusinessCardMarshaller ();
aMarshaller3.readExceptionCallbacks ().removeAll ();
if (aCharset != null)
aMarshaller3.setCharset (aCharset);
final PD3BusinessCardType aBC3 = aMarshaller3.read (aData);
if (aBC3 != null)
try
{
return PD3APIHelper.createBusinessCard (aBC3);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
// Unsupported version
return null;
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phax/peppol-directory | peppol-directory-businesscard/src/main/java/com/helger/pd/businesscard/helper/PDBusinessCardHelper.java | PDBusinessCardHelper.parseBusinessCard | @Nullable
public static PDBusinessCard parseBusinessCard (@Nonnull final Node aNode)
{
ValueEnforcer.notNull (aNode, "Node");
{
// Read version 1
final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ();
aMarshaller1.readExceptionCallbacks ().removeAll ();
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}
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{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
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aMarshaller2.readExceptionCallbacks ().removeAll ();
final PD2BusinessCardType aBC2 = aMarshaller2.read (aNode);
if (aBC2 != null)
try
{
return PD2APIHelper.createBusinessCard (aBC2);
}
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// Happens if e.g. name is null
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{
// Read as version 3
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if (aBC3 != null)
try
{
return PD3APIHelper.createBusinessCard (aBC3);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
// Unsupported version
return null;
} | java | @Nullable
public static PDBusinessCard parseBusinessCard (@Nonnull final Node aNode)
{
ValueEnforcer.notNull (aNode, "Node");
{
// Read version 1
final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ();
aMarshaller1.readExceptionCallbacks ().removeAll ();
final PD1BusinessCardType aBC1 = aMarshaller1.read (aNode);
if (aBC1 != null)
try
{
return PD1APIHelper.createBusinessCard (aBC1);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 2
final PD2BusinessCardMarshaller aMarshaller2 = new PD2BusinessCardMarshaller ();
aMarshaller2.readExceptionCallbacks ().removeAll ();
final PD2BusinessCardType aBC2 = aMarshaller2.read (aNode);
if (aBC2 != null)
try
{
return PD2APIHelper.createBusinessCard (aBC2);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
{
// Read as version 3
final PD3BusinessCardMarshaller aMarshaller3 = new PD3BusinessCardMarshaller ();
aMarshaller3.readExceptionCallbacks ().removeAll ();
final PD3BusinessCardType aBC3 = aMarshaller3.read (aNode);
if (aBC3 != null)
try
{
return PD3APIHelper.createBusinessCard (aBC3);
}
catch (final IllegalArgumentException ex)
{
// If the BC does not adhere to the XSD
// Happens if e.g. name is null
return null;
}
}
// Unsupported version
return null;
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phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/clientcert/ClientCertificateValidationResult.java | ClientCertificateValidationResult.createSuccess | @Nonnull
public static ClientCertificateValidationResult createSuccess (@Nonnull @Nonempty final String sClientID)
{
ValueEnforcer.notEmpty (sClientID, "ClientID");
return new ClientCertificateValidationResult (true, sClientID);
} | java | @Nonnull
public static ClientCertificateValidationResult createSuccess (@Nonnull @Nonempty final String sClientID)
{
ValueEnforcer.notEmpty (sClientID, "ClientID");
return new ClientCertificateValidationResult (true, sClientID);
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Client ID to use. May neither be <code>null</code> nor empty.
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phax/peppol-directory | peppol-directory-client/src/main/java/com/helger/pd/client/PDClient.java | PDClient.executeRequest | @Nonnull
@OverrideOnDemand
protected <T> T executeRequest (@Nonnull final HttpRequestBase aRequest,
@Nonnull final ResponseHandler <T> aHandler) throws IOException
{
// Contextual attributes set the local context level will take
// precedence over those set at the client level.
final HttpContext aContext = HttpClientHelper.createHttpContext (m_aProxy, m_aProxyCredentials);
return m_aHttpClientMgr.execute (aRequest, aContext, aHandler);
} | java | @Nonnull
@OverrideOnDemand
protected <T> T executeRequest (@Nonnull final HttpRequestBase aRequest,
@Nonnull final ResponseHandler <T> aHandler) throws IOException
{
// Contextual attributes set the local context level will take
// precedence over those set at the client level.
final HttpContext aContext = HttpClientHelper.createHttpContext (m_aProxy, m_aProxyCredentials);
return m_aHttpClientMgr.execute (aRequest, aContext, aHandler);
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phax/peppol-directory | peppol-directory-client/src/main/java/com/helger/pd/client/PDClient.java | PDClient.isServiceGroupRegistered | @Nonnull
public boolean isServiceGroupRegistered (@Nonnull final IParticipantIdentifier aParticipantID)
{
ValueEnforcer.notNull (aParticipantID, "ParticipantID");
final HttpGet aGet = new HttpGet (m_sPDIndexerURL + aParticipantID.getURIPercentEncoded ());
try
{
return executeRequest (aGet, new PDClientResponseHandler ()).isSuccess ();
}
catch (final Throwable t)
{
m_aExceptionHdl.onException (aParticipantID, "isServiceGroupRegistered", t);
}
return false;
} | java | @Nonnull
public boolean isServiceGroupRegistered (@Nonnull final IParticipantIdentifier aParticipantID)
{
ValueEnforcer.notNull (aParticipantID, "ParticipantID");
final HttpGet aGet = new HttpGet (m_sPDIndexerURL + aParticipantID.getURIPercentEncoded ());
try
{
return executeRequest (aGet, new PDClientResponseHandler ()).isSuccess ();
}
catch (final Throwable t)
{
m_aExceptionHdl.onException (aParticipantID, "isServiceGroupRegistered", t);
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return false;
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Participant ID to query for existence. May not be <code>null</code>.
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phax/peppol-directory | peppol-directory-publisher/src/main/java/com/helger/pd/publisher/exportall/ExportAllManager.java | ExportAllManager.streamFileXMLTo | public static void streamFileXMLTo (@Nonnull final UnifiedResponse aUR)
{
// Do it in a read lock!
s_aRWLock.readLock ().lock ();
try
{
final File f = _getFileXML ();
// setContent(IReadableResource) is lazy
aUR.setContent (new FileSystemResource (f));
}
finally
{
s_aRWLock.readLock ().unlock ();
}
} | java | public static void streamFileXMLTo (@Nonnull final UnifiedResponse aUR)
{
// Do it in a read lock!
s_aRWLock.readLock ().lock ();
try
{
final File f = _getFileXML ();
// setContent(IReadableResource) is lazy
aUR.setContent (new FileSystemResource (f));
}
finally
{
s_aRWLock.readLock ().unlock ();
}
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phax/peppol-directory | peppol-directory-publisher/src/main/java/com/helger/pd/publisher/exportall/ExportAllManager.java | ExportAllManager.streamFileExcelTo | public static void streamFileExcelTo (@Nonnull final UnifiedResponse aUR)
{
// Do it in a read lock!
s_aRWLock.readLock ().lock ();
try
{
final File f = _getFileExcel ();
// setContent(IReadableResource) is lazy
aUR.setContent (new FileSystemResource (f));
}
finally
{
s_aRWLock.readLock ().unlock ();
}
} | java | public static void streamFileExcelTo (@Nonnull final UnifiedResponse aUR)
{
// Do it in a read lock!
s_aRWLock.readLock ().lock ();
try
{
final File f = _getFileExcel ();
// setContent(IReadableResource) is lazy
aUR.setContent (new FileSystemResource (f));
}
finally
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s_aRWLock.readLock ().unlock ();
}
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] | 98da26da29fb7178371d6b029516cbf01be223fb | https://github.com/phax/peppol-directory/blob/98da26da29fb7178371d6b029516cbf01be223fb/peppol-directory-publisher/src/main/java/com/helger/pd/publisher/exportall/ExportAllManager.java#L246-L260 | train |
phax/peppol-directory | peppol-directory-indexer/src/main/java/com/helger/pd/indexer/mgr/PDIndexExecutor.java | PDIndexExecutor.executeWorkItem | @Nonnull
public static ESuccess executeWorkItem (@Nonnull final IPDStorageManager aStorageMgr,
@Nonnull final IIndexerWorkItem aWorkItem,
@Nonnegative final int nRetryCount,
@Nonnull final Consumer <? super IIndexerWorkItem> aSuccessHandler,
@Nonnull final Consumer <? super IIndexerWorkItem> aFailureHandler)
{
LOGGER.info ("Execute work item " +
aWorkItem.getLogText () +
" - " +
(nRetryCount > 0 ? "retry #" + nRetryCount : "initial try"));
try
{
final IParticipantIdentifier aParticipantID = aWorkItem.getParticipantID ();
ESuccess eSuccess;
switch (aWorkItem.getType ())
{
case CREATE_UPDATE:
{
// Get BI from participant (e.g. from SMP)
final PDExtendedBusinessCard aBI = PDMetaManager.getBusinessCardProvider ().getBusinessCard (aParticipantID);
if (aBI == null)
{
// No/invalid extension present - no need to try again
eSuccess = ESuccess.FAILURE;
}
else
{
// Got data - put in storage
eSuccess = aStorageMgr.createOrUpdateEntry (aParticipantID, aBI, aWorkItem.getAsMetaData ());
}
break;
}
case DELETE:
{
// Only mark as deleted
eSuccess = aStorageMgr.markEntryDeleted (aParticipantID, aWorkItem.getAsMetaData ());
break;
}
case SYNC:
{
// Get BI from participant (e.g. from SMP)
final PDExtendedBusinessCard aBI = PDMetaManager.getBusinessCardProvider ().getBusinessCard (aParticipantID);
if (aBI == null)
{
// No/invalid extension present - delete from index
eSuccess = aStorageMgr.markEntryDeleted (aParticipantID, aWorkItem.getAsMetaData ());
}
else
{
// Got data - put in storage
eSuccess = aStorageMgr.createOrUpdateEntry (aParticipantID, aBI, aWorkItem.getAsMetaData ());
}
break;
}
default:
throw new IllegalStateException ("Unsupported work item type: " + aWorkItem);
}
if (eSuccess.isSuccess ())
{
// Item handled - remove from overall list
aSuccessHandler.accept (aWorkItem);
// And we're done
return ESuccess.SUCCESS;
}
// else error storing data
}
catch (final Exception ex)
{
LOGGER.error ("Error in executing work item " + aWorkItem.getLogText (), ex);
// Fall through
}
// Invoke failure handler
aFailureHandler.accept (aWorkItem);
return ESuccess.FAILURE;
} | java | @Nonnull
public static ESuccess executeWorkItem (@Nonnull final IPDStorageManager aStorageMgr,
@Nonnull final IIndexerWorkItem aWorkItem,
@Nonnegative final int nRetryCount,
@Nonnull final Consumer <? super IIndexerWorkItem> aSuccessHandler,
@Nonnull final Consumer <? super IIndexerWorkItem> aFailureHandler)
{
LOGGER.info ("Execute work item " +
aWorkItem.getLogText () +
" - " +
(nRetryCount > 0 ? "retry #" + nRetryCount : "initial try"));
try
{
final IParticipantIdentifier aParticipantID = aWorkItem.getParticipantID ();
ESuccess eSuccess;
switch (aWorkItem.getType ())
{
case CREATE_UPDATE:
{
// Get BI from participant (e.g. from SMP)
final PDExtendedBusinessCard aBI = PDMetaManager.getBusinessCardProvider ().getBusinessCard (aParticipantID);
if (aBI == null)
{
// No/invalid extension present - no need to try again
eSuccess = ESuccess.FAILURE;
}
else
{
// Got data - put in storage
eSuccess = aStorageMgr.createOrUpdateEntry (aParticipantID, aBI, aWorkItem.getAsMetaData ());
}
break;
}
case DELETE:
{
// Only mark as deleted
eSuccess = aStorageMgr.markEntryDeleted (aParticipantID, aWorkItem.getAsMetaData ());
break;
}
case SYNC:
{
// Get BI from participant (e.g. from SMP)
final PDExtendedBusinessCard aBI = PDMetaManager.getBusinessCardProvider ().getBusinessCard (aParticipantID);
if (aBI == null)
{
// No/invalid extension present - delete from index
eSuccess = aStorageMgr.markEntryDeleted (aParticipantID, aWorkItem.getAsMetaData ());
}
else
{
// Got data - put in storage
eSuccess = aStorageMgr.createOrUpdateEntry (aParticipantID, aBI, aWorkItem.getAsMetaData ());
}
break;
}
default:
throw new IllegalStateException ("Unsupported work item type: " + aWorkItem);
}
if (eSuccess.isSuccess ())
{
// Item handled - remove from overall list
aSuccessHandler.accept (aWorkItem);
// And we're done
return ESuccess.SUCCESS;
}
// else error storing data
}
catch (final Exception ex)
{
LOGGER.error ("Error in executing work item " + aWorkItem.getLogText (), ex);
// Fall through
}
// Invoke failure handler
aFailureHandler.accept (aWorkItem);
return ESuccess.FAILURE;
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vorburger/ch.vorburger.exec | src/main/java/ch/vorburger/exec/ManagedProcess.java | ManagedProcess.buffer | protected BufferedInputStream buffer(final InputStream inputStream) {
// reject null early on rather than waiting for IO operation to fail
if (inputStream == null) { // not checked by BufferedInputStream
throw new NullPointerException("inputStream == null");
}
return inputStream instanceof BufferedInputStream ? (BufferedInputStream) inputStream
: new BufferedInputStream(inputStream);
} | java | protected BufferedInputStream buffer(final InputStream inputStream) {
// reject null early on rather than waiting for IO operation to fail
if (inputStream == null) { // not checked by BufferedInputStream
throw new NullPointerException("inputStream == null");
}
return inputStream instanceof BufferedInputStream ? (BufferedInputStream) inputStream
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vorburger/ch.vorburger.exec | src/main/java/ch/vorburger/exec/ManagedProcess.java | ManagedProcess.exitValue | @Override
public int exitValue() throws ManagedProcessException {
try {
return resultHandler.getExitValue();
} catch (IllegalStateException e) {
throw new ManagedProcessException("Exit Value not (yet) available for "
+ getProcLongName(), e);
}
} | java | @Override
public int exitValue() throws ManagedProcessException {
try {
return resultHandler.getExitValue();
} catch (IllegalStateException e) {
throw new ManagedProcessException("Exit Value not (yet) available for "
+ getProcLongName(), e);
}
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milaboratory/milib | src/main/java/com/milaboratory/core/io/sequence/fastq/FastqRecordsReader.java | FastqRecordsReader.close | @Override
public void close() {
if (!closed.compareAndSet(false, true))
return;
//is synchronized with itself and _next calls,
//so no synchronization on inner reader is needed
try {
synchronized (inputStream) {
inputStream.close();
}
} catch (IOException ex) {
throw new RuntimeException(ex);
}
} | java | @Override
public void close() {
if (!closed.compareAndSet(false, true))
return;
//is synchronized with itself and _next calls,
//so no synchronization on inner reader is needed
try {
synchronized (inputStream) {
inputStream.close();
}
} catch (IOException ex) {
throw new RuntimeException(ex);
}
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/FileIndex.java | FileIndex.write | public void write(OutputStream stream) throws IOException {
//Creating buffer
ByteArrayOutputStream bos = new ByteArrayOutputStream();
//Creating compressed output data stream
DeflaterOutputStream deflate = new DeflaterOutputStream(bos);
DataOutputStream dataStream = new DataOutputStream(deflate);
//Writing index step
dataStream.writeLong(step);
//Writing boundaries of index
dataStream.writeLong(getStartingRecordNumber());
dataStream.writeLong(getLastRecordNumber());
//Writing number of meta-records
dataStream.writeInt(metadata.size());
//Writing meta records
for (Map.Entry<String, String> e : metadata.entrySet()) {
dataStream.writeUTF(e.getKey());
dataStream.writeUTF(e.getValue());
}
//Writing number of entries
dataStream.writeInt(index.size());
//Writing index
long lastValue = 0, v;
for (int i = 0; i < index.size(); ++i) {
IOUtil.writeRawVarint64(dataStream, (v = index.get(i)) - lastValue);
lastValue = v;
}
//Flushing gzip output stream to underlying stream
deflate.finish();
//Creating raw output stream
DataOutputStream raw = new DataOutputStream(stream);
//Writing non-compressed magic number
raw.writeInt(MAGIC);
//Writing index size
raw.writeInt(bos.size());
//Writes index
raw.write(bos.toByteArray());
} | java | public void write(OutputStream stream) throws IOException {
//Creating buffer
ByteArrayOutputStream bos = new ByteArrayOutputStream();
//Creating compressed output data stream
DeflaterOutputStream deflate = new DeflaterOutputStream(bos);
DataOutputStream dataStream = new DataOutputStream(deflate);
//Writing index step
dataStream.writeLong(step);
//Writing boundaries of index
dataStream.writeLong(getStartingRecordNumber());
dataStream.writeLong(getLastRecordNumber());
//Writing number of meta-records
dataStream.writeInt(metadata.size());
//Writing meta records
for (Map.Entry<String, String> e : metadata.entrySet()) {
dataStream.writeUTF(e.getKey());
dataStream.writeUTF(e.getValue());
}
//Writing number of entries
dataStream.writeInt(index.size());
//Writing index
long lastValue = 0, v;
for (int i = 0; i < index.size(); ++i) {
IOUtil.writeRawVarint64(dataStream, (v = index.get(i)) - lastValue);
lastValue = v;
}
//Flushing gzip output stream to underlying stream
deflate.finish();
//Creating raw output stream
DataOutputStream raw = new DataOutputStream(stream);
//Writing non-compressed magic number
raw.writeInt(MAGIC);
//Writing index size
raw.writeInt(bos.size());
//Writes index
raw.write(bos.toByteArray());
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/FileIndex.java | FileIndex.read | public static FileIndex read(InputStream stream) throws IOException {
//Creating raw input stream
DataInputStream raw = new DataInputStream(stream);
//Reading magic number
int magic = raw.readInt();
if (magic != MAGIC)
throw new IOException("Wrong magic number");
//Reading length
int length = raw.readInt();
//Reading whole index
byte[] buffer = new byte[length];
raw.read(buffer);
//Creating uncompressed stream
InflaterInputStream inflater = new InflaterInputStream(new ByteArrayInputStream(buffer));
DataInputStream dataStream = new DataInputStream(inflater);
//Reading step
long step = dataStream.readLong();
long startingRecordNumner = dataStream.readLong();
long lastRecordNumber = dataStream.readLong();
//Reading meta record count
int metaRecordsCount = dataStream.readInt();
//Reading meta records
Map<String, String> metadata = new HashMap<>();
String key, value;
while (--metaRecordsCount >= 0) {
key = dataStream.readUTF();
value = dataStream.readUTF();
metadata.put(key, value);
}
//Reading entries number
int size = dataStream.readInt();
//Creating array for index
TLongArrayList index = new TLongArrayList(size);
//Reading index
long last = 0, val;
for (int i = 0; i < size; ++i) {
val = IOUtil.readRawVarint64(dataStream, -1);
if (val == -1)
throw new IOException("Wrong file format");
last += val;
index.add(last);
}
return new FileIndex(step, metadata, index, startingRecordNumner, lastRecordNumber);
} | java | public static FileIndex read(InputStream stream) throws IOException {
//Creating raw input stream
DataInputStream raw = new DataInputStream(stream);
//Reading magic number
int magic = raw.readInt();
if (magic != MAGIC)
throw new IOException("Wrong magic number");
//Reading length
int length = raw.readInt();
//Reading whole index
byte[] buffer = new byte[length];
raw.read(buffer);
//Creating uncompressed stream
InflaterInputStream inflater = new InflaterInputStream(new ByteArrayInputStream(buffer));
DataInputStream dataStream = new DataInputStream(inflater);
//Reading step
long step = dataStream.readLong();
long startingRecordNumner = dataStream.readLong();
long lastRecordNumber = dataStream.readLong();
//Reading meta record count
int metaRecordsCount = dataStream.readInt();
//Reading meta records
Map<String, String> metadata = new HashMap<>();
String key, value;
while (--metaRecordsCount >= 0) {
key = dataStream.readUTF();
value = dataStream.readUTF();
metadata.put(key, value);
}
//Reading entries number
int size = dataStream.readInt();
//Creating array for index
TLongArrayList index = new TLongArrayList(size);
//Reading index
long last = 0, val;
for (int i = 0; i < size; ++i) {
val = IOUtil.readRawVarint64(dataStream, -1);
if (val == -1)
throw new IOException("Wrong file format");
last += val;
index.add(last);
}
return new FileIndex(step, metadata, index, startingRecordNumner, lastRecordNumber);
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/Alphabets.java | Alphabets.register | public static void register(Alphabet alphabet) {
if (alphabetsByName.put(alphabet.getAlphabetName(), alphabet) != null)
throw new IllegalStateException("Alphabet with this name is already registered.");
if (alphabetsById.put(alphabet.getId(), alphabet) != null)
throw new IllegalStateException("Alphabet with this id is already registered.");
} | java | public static void register(Alphabet alphabet) {
if (alphabetsByName.put(alphabet.getAlphabetName(), alphabet) != null)
throw new IllegalStateException("Alphabet with this name is already registered.");
if (alphabetsById.put(alphabet.getId(), alphabet) != null)
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milaboratory/milib | src/main/java/com/milaboratory/util/Sorter.java | Sorter.sort | public static <T> OutputPortCloseable<T> sort(
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int chunkSize,
Class<T> clazz,
File tempFile) throws IOException {
return sort(initialSource, comparator, chunkSize,
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} | java | public static <T> OutputPortCloseable<T> sort(
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Comparator<T> comparator,
int chunkSize,
Class<T> clazz,
File tempFile) throws IOException {
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milaboratory/milib | src/main/java/com/milaboratory/core/tree/BranchingEnumerator.java | BranchingEnumerator.move1 | private void move1() {
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if (position >= reference.size()) {
node = null;
return;
}
node = node.links[reference.codeAt(position++)];
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node = node.links[reference.codeAt(position++)];
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/AbstractRandomAccessReader.java | AbstractRandomAccessReader.seekToRecord | public void seekToRecord(long recordNumber) throws IOException {
if (currentRecordNumber == recordNumber)
return;
long skip;
if (recordNumber < fileIndex.getStartingRecordNumber()) {
if (currentRecordNumber < recordNumber)
skip = recordNumber - currentRecordNumber;
else {
skip = recordNumber;
seek0(0);
}
} else if (recordNumber > fileIndex.getLastRecordNumber()) {
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skip = recordNumber - currentRecordNumber;
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long record = fileIndex.getLastRecordNumber();
skip = recordNumber - record;
seek0(fileIndex.getNearestPosition(record));
}
} else if (recordNumber > currentRecordNumber && recordNumber - currentRecordNumber < fileIndex.getStep()) {
skip = recordNumber - currentRecordNumber;
} else {
seek0(fileIndex.getNearestPosition(recordNumber));
skip = recordNumber - fileIndex.getNearestRecordNumber(recordNumber);
}
for (; skip > 0; --skip)
skip();
currentRecordNumber = recordNumber;
} | java | public void seekToRecord(long recordNumber) throws IOException {
if (currentRecordNumber == recordNumber)
return;
long skip;
if (recordNumber < fileIndex.getStartingRecordNumber()) {
if (currentRecordNumber < recordNumber)
skip = recordNumber - currentRecordNumber;
else {
skip = recordNumber;
seek0(0);
}
} else if (recordNumber > fileIndex.getLastRecordNumber()) {
if (currentRecordNumber < recordNumber)
skip = recordNumber - currentRecordNumber;
else {
long record = fileIndex.getLastRecordNumber();
skip = recordNumber - record;
seek0(fileIndex.getNearestPosition(record));
}
} else if (recordNumber > currentRecordNumber && recordNumber - currentRecordNumber < fileIndex.getStep()) {
skip = recordNumber - currentRecordNumber;
} else {
seek0(fileIndex.getNearestPosition(recordNumber));
skip = recordNumber - fileIndex.getNearestRecordNumber(recordNumber);
}
for (; skip > 0; --skip)
skip();
currentRecordNumber = recordNumber;
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/AbstractRandomAccessReader.java | AbstractRandomAccessReader.take | @Override
public T take() {
T t = take0();
if (t != null)
++currentRecordNumber;
return t;
} | java | @Override
public T take() {
T t = take0();
if (t != null)
++currentRecordNumber;
return t;
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/Mutations.java | Mutations.getLengthDelta | public int getLengthDelta() {
int delta = 0;
for (int mut : mutations)
switch (mut & MUTATION_TYPE_MASK) {
case RAW_MUTATION_TYPE_DELETION:
--delta;
break;
case RAW_MUTATION_TYPE_INSERTION:
++delta;
break;
}
return delta;
} | java | public int getLengthDelta() {
int delta = 0;
for (int mut : mutations)
switch (mut & MUTATION_TYPE_MASK) {
case RAW_MUTATION_TYPE_DELETION:
--delta;
break;
case RAW_MUTATION_TYPE_INSERTION:
++delta;
break;
}
return delta;
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/Mutations.java | Mutations.concat | public Mutations<S> concat(final Mutations<S> other) {
return new MutationsBuilder<>(alphabet, false)
.ensureCapacity(this.size() + other.size())
.append(this)
.append(other)
.createAndDestroy();
} | java | public Mutations<S> concat(final Mutations<S> other) {
return new MutationsBuilder<>(alphabet, false)
.ensureCapacity(this.size() + other.size())
.append(this)
.append(other)
.createAndDestroy();
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/Mutations.java | Mutations.move | public Mutations<S> move(int offset) {
int[] newMutations = new int[mutations.length];
for (int i = 0; i < mutations.length; ++i)
newMutations[i] = Mutation.move(mutations[i], offset);
return new Mutations<S>(alphabet, newMutations, true);
} | java | public Mutations<S> move(int offset) {
int[] newMutations = new int[mutations.length];
for (int i = 0; i < mutations.length; ++i)
newMutations[i] = Mutation.move(mutations[i], offset);
return new Mutations<S>(alphabet, newMutations, true);
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/Mutations.java | Mutations.removeMutationsInRange | public Mutations<S> removeMutationsInRange(int from, int to) {
if (to < from)
throw new IllegalArgumentException("Reversed ranges are not supported.");
// If range is empty return untouched mutations object
if (from == to)
return this;
// Determine range in mutations to remove
long indexRange = getIndexRange(from, to);
// Unpacking
int fromIndex = (int) (indexRange >>> 32),
toIndex = (int) (indexRange & 0xFFFFFFFF);
if (fromIndex == 0 && toIndex == mutations.length)
return empty(alphabet);
// Creating result
int[] result = new int[mutations.length - (toIndex - fromIndex)];
// Constant to move positions in the output array
int offset = (from - to) << POSITION_OFFSET; // Negative value
// Copy and move mutations
int i = 0;
for (int j = 0; j < fromIndex; ++j)
result[i++] = mutations[j];
for (int j = toIndex; j < mutations.length; ++j)
result[i++] = mutations[j] + offset;
assert i == result.length;
return new Mutations<>(alphabet, result, true);
} | java | public Mutations<S> removeMutationsInRange(int from, int to) {
if (to < from)
throw new IllegalArgumentException("Reversed ranges are not supported.");
// If range is empty return untouched mutations object
if (from == to)
return this;
// Determine range in mutations to remove
long indexRange = getIndexRange(from, to);
// Unpacking
int fromIndex = (int) (indexRange >>> 32),
toIndex = (int) (indexRange & 0xFFFFFFFF);
if (fromIndex == 0 && toIndex == mutations.length)
return empty(alphabet);
// Creating result
int[] result = new int[mutations.length - (toIndex - fromIndex)];
// Constant to move positions in the output array
int offset = (from - to) << POSITION_OFFSET; // Negative value
// Copy and move mutations
int i = 0;
for (int j = 0; j < fromIndex; ++j)
result[i++] = mutations[j];
for (int j = toIndex; j < mutations.length; ++j)
result[i++] = mutations[j] + offset;
assert i == result.length;
return new Mutations<>(alphabet, result, true);
} | [
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<p>
<b>Important:</b> to remove leftmost insertions (left trailing insertions) use {@code from = -1}. E.g.
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@param from left bound of range, inclusive. Use -1 to extract leftmost insertions.
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milaboratory/milib | src/main/java/com/milaboratory/util/ArraysUtils.java | ArraysUtils.getSortedDistinct | public static long[] getSortedDistinct(long[] values) {
if (values.length == 0)
return values;
Arrays.sort(values);
int shift = 0;
int i = 0;
while (i + shift + 1 < values.length)
if (values[i + shift] == values[i + shift + 1])
++shift;
else {
values[i] = values[i + shift];
++i;
}
values[i] = values[i + shift];
return Arrays.copyOf(values, i + 1);
} | java | public static long[] getSortedDistinct(long[] values) {
if (values.length == 0)
return values;
Arrays.sort(values);
int shift = 0;
int i = 0;
while (i + shift + 1 < values.length)
if (values[i + shift] == values[i + shift + 1])
++shift;
else {
values[i] = values[i + shift];
++i;
}
values[i] = values[i + shift];
return Arrays.copyOf(values, i + 1);
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceWithQuality.java | SequenceWithQuality.toPrettyString | public String toPrettyString() {
String seq = sequence.toString();
String qual = quality.toString();
return seq + '\n' + qual;
} | java | public String toPrettyString() {
String seq = sequence.toString();
String qual = quality.toString();
return seq + '\n' + qual;
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/tree/NeighborhoodIterator.java | NeighborhoodIterator.ensureCapacity | private void ensureCapacity(int newSize) {
int oldSize;
if ((oldSize = branchingEnumerators.length) < newSize) {
branchingEnumerators = Arrays.copyOfRange(branchingEnumerators, 0, newSize);
for (int i = oldSize; i < newSize; ++i)
branchingEnumerators[i] = new BranchingEnumerator<>(reference, guide);
}
} | java | private void ensureCapacity(int newSize) {
int oldSize;
if ((oldSize = branchingEnumerators.length) < newSize) {
branchingEnumerators = Arrays.copyOfRange(branchingEnumerators, 0, newSize);
for (int i = oldSize; i < newSize; ++i)
branchingEnumerators[i] = new BranchingEnumerator<>(reference, guide);
}
} | [
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milaboratory/milib | src/main/java/com/milaboratory/core/tree/NeighborhoodIterator.java | NeighborhoodIterator.setupBranchingEnumerators | private void setupBranchingEnumerators() {
//Getting required sequence of differences (mutations)
final byte[] bSequence = branchingSequences[branchingSequenceIndex];
//Ensure number of branching enumerators
ensureCapacity(bSequence.length);
//Setting up initial branching enumerators
byte previous = -1, current;
for (int i = 0; i < bSequence.length; ++i) {
current = bSequence[i];
boolean autoMove1 = (previous == 1 && current == 2); // prevents insertion right after deletion
if (parameters.isGreedy()) {
// prevent some other 'redundant' cases
autoMove1 = autoMove1 || (previous == 2 && current == 1) || // prevents deletion right after insertion
(previous == 2 && current == 0); // prevents mismatch right after insertion
}
branchingEnumerators[i].setup(current, autoMove1);
previous = bSequence[i];
}
branchingEnumerators[0].reset(0, root);
lastEnumerator = bSequence.length - 1;
} | java | private void setupBranchingEnumerators() {
//Getting required sequence of differences (mutations)
final byte[] bSequence = branchingSequences[branchingSequenceIndex];
//Ensure number of branching enumerators
ensureCapacity(bSequence.length);
//Setting up initial branching enumerators
byte previous = -1, current;
for (int i = 0; i < bSequence.length; ++i) {
current = bSequence[i];
boolean autoMove1 = (previous == 1 && current == 2); // prevents insertion right after deletion
if (parameters.isGreedy()) {
// prevent some other 'redundant' cases
autoMove1 = autoMove1 || (previous == 2 && current == 1) || // prevents deletion right after insertion
(previous == 2 && current == 0); // prevents mismatch right after insertion
}
branchingEnumerators[i].setup(current, autoMove1);
previous = bSequence[i];
}
branchingEnumerators[0].reset(0, root);
lastEnumerator = bSequence.length - 1;
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/LinearGapAlignmentScoring.java | LinearGapAlignmentScoring.getAminoAcidBLASTScoring | public static LinearGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapPenalty) {
return new LinearGapAlignmentScoring<>(AminoAcidSequence.ALPHABET,
matrix.getMatrix(),
gapPenalty);
} | java | public static LinearGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapPenalty) {
return new LinearGapAlignmentScoring<>(AminoAcidSequence.ALPHABET,
matrix.getMatrix(),
gapPenalty);
} | [
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@param matrix BLAST substitution matrix
@param gapPenalty penalty for gap, must be < 0
@return standard amino acid BLAST scoring | [
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milaboratory/milib | src/main/java/com/milaboratory/core/io/sequence/fasta/RandomAccessFastaIndex.java | RandomAccessFastaIndex.index | public static RandomAccessFastaIndex index(Path file, int indexStep, boolean save, LongProcessReporter reporter) {
Path indexFile = file.resolveSibling(file.getFileName() + INDEX_SUFFIX);
if (Files.exists(indexFile))
try (FileInputStream fis = new FileInputStream(indexFile.toFile())) {
RandomAccessFastaIndex index = RandomAccessFastaIndex.read(new BufferedInputStream(fis));
if (index.getIndexStep() != indexStep)
throw new IllegalArgumentException("Mismatched index step in " + indexFile + ". Remove the file to recreate the index.");
return index;
} catch (IOException e) {
throw new RuntimeException(e);
}
try (LongProcess lp = reporter.start("Indexing " + file.getFileName());
FileChannel fc = FileChannel.open(file, StandardOpenOption.READ)) {
// Requesting file size to correctly report status
long size = Files.size(file);
// Allocating buffer
ByteBuffer buffer = ByteBuffer.allocate(65536);
// Extracting backing byte array
byte[] bufferArray = buffer.array();
// Creating builder
StreamIndexBuilder builder = new StreamIndexBuilder(indexStep);
// Indexing file
int read;
long done = 0;
while ((read = fc.read((ByteBuffer) buffer.clear())) > 0) {
builder.processBuffer(bufferArray, 0, read);
lp.reportStatus(1.0 * (done += read) / size);
}
// Build index
RandomAccessFastaIndex index = builder.build();
if (save)
try (FileOutputStream fos = new FileOutputStream(indexFile.toFile())) {
index.write(new BufferedOutputStream(fos));
}
return index;
} catch (IOException ioe) {
throw new RuntimeException(ioe);
}
} | java | public static RandomAccessFastaIndex index(Path file, int indexStep, boolean save, LongProcessReporter reporter) {
Path indexFile = file.resolveSibling(file.getFileName() + INDEX_SUFFIX);
if (Files.exists(indexFile))
try (FileInputStream fis = new FileInputStream(indexFile.toFile())) {
RandomAccessFastaIndex index = RandomAccessFastaIndex.read(new BufferedInputStream(fis));
if (index.getIndexStep() != indexStep)
throw new IllegalArgumentException("Mismatched index step in " + indexFile + ". Remove the file to recreate the index.");
return index;
} catch (IOException e) {
throw new RuntimeException(e);
}
try (LongProcess lp = reporter.start("Indexing " + file.getFileName());
FileChannel fc = FileChannel.open(file, StandardOpenOption.READ)) {
// Requesting file size to correctly report status
long size = Files.size(file);
// Allocating buffer
ByteBuffer buffer = ByteBuffer.allocate(65536);
// Extracting backing byte array
byte[] bufferArray = buffer.array();
// Creating builder
StreamIndexBuilder builder = new StreamIndexBuilder(indexStep);
// Indexing file
int read;
long done = 0;
while ((read = fc.read((ByteBuffer) buffer.clear())) > 0) {
builder.processBuffer(bufferArray, 0, read);
lp.reportStatus(1.0 * (done += read) / size);
}
// Build index
RandomAccessFastaIndex index = builder.build();
if (save)
try (FileOutputStream fos = new FileOutputStream(indexFile.toFile())) {
index.write(new BufferedOutputStream(fos));
}
return index;
} catch (IOException ioe) {
throw new RuntimeException(ioe);
}
} | [
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@param file file to index
@param indexStep index step
@param save whether to save index to {input_file_name}.mifdx file
@param reporter reporter
@return index | [
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java | KAlignerParameters.getByName | public static KAlignerParameters getByName(String name) {
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return null;
return params.clone();
} | java | public static KAlignerParameters getByName(String name) {
KAlignerParameters params = knownParameters.get(name);
if (params == null)
return null;
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milaboratory/milib | src/main/java/com/milaboratory/core/io/sequence/fasta/FastaReader.java | FastaReader.asRawRecordsPort | public OutputPortCloseable<RawFastaRecord> asRawRecordsPort() {
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librato/metrics-librato | src/main/java/com/librato/metrics/reporter/SourceInformation.java | SourceInformation.from | public static SourceInformation from(Pattern sourceRegex, String name) {
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milaboratory/milib | src/main/java/com/milaboratory/core/clustering/Clustering.java | Clustering.performClustering | public static <T, S extends Sequence<S>> List<Cluster<T>> performClustering(Collection<T> inputObjects,
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Alignment.java | Alignment.calculateScore | public int calculateScore(AlignmentScoring<S> scoring) {
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Alignment.java | Alignment.convertToSeq1Range | public Range convertToSeq1Range(Range rangeInSeq2) {
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Alignment.java | Alignment.convertToSeq2Range | public Range convertToSeq2Range(Range rangeInSeq1) {
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int from = aabs(convertToSeq2Position(rangeInSeq1.getFrom()));
int to = aabs(convertToSeq2Position(rangeInSeq1.getTo()));
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Alignment.java | Alignment.invert | public Alignment<S> invert(S sequence2) {
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} | java | public Alignment<S> invert(S sequence2) {
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Alignment.java | Alignment.similarity | public float similarity() {
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librato/metrics-librato | src/main/java/com/librato/metrics/reporter/DeltaTracker.java | DeltaTracker.peekDelta | public Long peekDelta(String name, long count) {
Long previous = lookup.get(name);
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librato/metrics-librato | src/main/java/com/librato/metrics/reporter/DeltaTracker.java | DeltaTracker.getDelta | public Long getDelta(String name, long count) {
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java | QualityTrimmer.extendRange | public static Range extendRange(SequenceQuality quality, QualityTrimmerParameters parameters, Range initialRange) {
int lower = pabs(trim(quality, 0, initialRange.getLower(), -1, false, parameters));
int upper = pabs(trim(quality, initialRange.getUpper(), quality.size(), +1, false, parameters)) + 1;
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int lower = pabs(trim(quality, 0, initialRange.getLower(), -1, false, parameters));
int upper = pabs(trim(quality, initialRange.getUpper(), quality.size(), +1, false, parameters)) + 1;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java | QualityTrimmer.trim | public static Range trim(SequenceQuality quality, QualityTrimmerParameters parameters) {
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java | QualityTrimmer.trim | public static Range trim(SequenceQuality quality, QualityTrimmerParameters parameters, Range initialRange) {
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The criteria of QualityTrimmer may not be fulfilled for the resulting range. This method detects
beginning of the region with stably high quality, once the beginning of the region is detected the algorithm
stops. Detected stop positions are "from" and "to" of the output range.
@param quality quality values
@param parameters trimming parameters
@param initialRange initial range to trim
@return trimmed range, or null in case the whole sequence should be trimmed | [
"Trims",
"the",
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"by",
"cutting",
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"low",
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"on",
"both",
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"."
] | 2349b3dccdd3c7948643760e570238d6e30d5a34 | https://github.com/milaboratory/milib/blob/2349b3dccdd3c7948643760e570238d6e30d5a34/src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java#L191-L201 | train |
milaboratory/milib | src/main/java/com/milaboratory/core/sequence/AminoAcidSequence.java | AminoAcidSequence.translate | public static AminoAcidSequence translate(NucleotideSequence sequence) {
if (sequence.size() % 3 != 0)
throw new IllegalArgumentException("Only nucleotide sequences with size multiple " +
"of three are supported (in-frame).");
byte[] aaData = new byte[sequence.size() / 3];
GeneticCode.translate(aaData, 0, sequence, 0, sequence.size());
return new AminoAcidSequence(aaData, true);
} | java | public static AminoAcidSequence translate(NucleotideSequence sequence) {
if (sequence.size() % 3 != 0)
throw new IllegalArgumentException("Only nucleotide sequences with size multiple " +
"of three are supported (in-frame).");
byte[] aaData = new byte[sequence.size() / 3];
GeneticCode.translate(aaData, 0, sequence, 0, sequence.size());
return new AminoAcidSequence(aaData, true);
} | [
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@param sequence nucleotide sequence
@return translated amino acid sequence | [
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] | 2349b3dccdd3c7948643760e570238d6e30d5a34 | https://github.com/milaboratory/milib/blob/2349b3dccdd3c7948643760e570238d6e30d5a34/src/main/java/com/milaboratory/core/sequence/AminoAcidSequence.java#L145-L152 | train |
milaboratory/milib | src/main/java/com/milaboratory/cli/ACommand.java | ACommand.validate | public void validate() {
for (String in : getInputFiles()) {
if (!new File(in).exists())
throwValidationException("ERROR: input file \"" + in + "\" does not exist.", false);
validateInfo(in);
}
} | java | public void validate() {
for (String in : getInputFiles()) {
if (!new File(in).exists())
throwValidationException("ERROR: input file \"" + in + "\" does not exist.", false);
validateInfo(in);
}
} | [
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"\"ERROR: input file \\\"\"",... | Validate injected parameters and options | [
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"parameters",
"and",
"options"
] | 2349b3dccdd3c7948643760e570238d6e30d5a34 | https://github.com/milaboratory/milib/blob/2349b3dccdd3c7948643760e570238d6e30d5a34/src/main/java/com/milaboratory/cli/ACommand.java#L70-L76 | train |
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