id
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public void newSegment() { getData().newSegment(); graphicsState.lineWidth = 0; //Looks like a new segment invalidates the graphics state } @Override <BUG>public void setComplete(boolean complete) { Iterator<GraphicsData> it = objects.iterator(); while (it.hasNext()) { Completable completedObject = it.next();</BUG> com...
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Map<Integer, Integer> akpx = new HashMap<Integer, Integer>(); Map<Integer, Integer> ckpx = e1.getValue(); for (Map.Entry<Integer, Integer> e : ckpx.entrySet()) { Integer unicodeKey2 = e.getKey(); Integer cidKey2 = unicodeToGlyph(unicodeKey2); <BUG>Integer kern = e.getValue(); Iterator uniMap = mtxTab[cidKey2].getUnicod...
for (Object o : mtxTab[cidKey2].getUnicodeIndex()) { Integer unicodeKey = (Integer) o;
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for (Integer ansiKey : ansiKeys) { akpx.put(ansiKey, kern); } } } <BUG>if (akpx.size() > 0) { Iterator uniMap = mtxTab[cidKey1].getUnicodeIndex().listIterator(); while (uniMap.hasNext()) { Integer unicodeKey = (Integer)uniMap.next(); </BUG> Integer[] ansiKeys = unicodeToWinAnsi(unicodeKey);
for (Object o : mtxTab[cidKey1].getUnicodeIndex()) { Integer unicodeKey = (Integer) o;
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cgl.setLexicalvalue(valueEdit); cgl.setIdgroup(idDomaine); cgl.setIdthesaurus(idTheso); cgl.setLang(langueEdit); GroupHelper cgh = new GroupHelper(); <BUG>if (!cgh.isDomainExist(connect.getPoolConnexion(), cgl.getLexicalvalue(),</BUG> cgl.getIdthesaurus(), cgl.getLang())) { FacesContext.getCurrentInstance().addMessage(...
if (cgh.isDomainExist(connect.getPoolConnexion(), cgl.getLexicalvalue(),
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Term terme = new Term(); terme.setId_thesaurus(idTheso); terme.setLang(langueEdit); terme.setLexical_value(valueEdit); terme.setId_term(idT); <BUG>if (new TermHelper().isTermExist(connect.getPoolConnexion(), </BUG> terme.getLexical_value(), terme.getId_thesaurus(), terme.getLang())) { FacesContext.getCurrentInstance()....
if (termHelper.isTermExist(connect.getPoolConnexion(),
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Term terme = new Term(); terme.setId_thesaurus(idTheso); terme.setLang(langueEdit); terme.setLexical_value(valueEdit); terme.setId_term(idT); <BUG>if (new TermHelper().isTermExist(connect.getPoolConnexion(), </BUG> terme.getLexical_value(), terme.getId_thesaurus(), terme.getLang())) { FacesContext.getCurrentInstance()....
if (termHelper.isTermExist(connect.getPoolConnexion(),
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langues = new ArrayList<>(); HashMap<String, String> tempMapL = new HashMap<>(); for (NodeTermTraduction ntt : tempNTT) { tempMapL.put(ntt.getLang(), ntt.getLexicalValue()); } <BUG>langues.addAll(tempMapL.entrySet()); }</BUG> langueEdit = ""; valueEdit = ""; if (!tradExist) {
if(newTraduction) { nom = termHelper.getThisTerm(connect.getPoolConnexion(),idC, idTheso, idlangue).getLexical_value();
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if (n.getTitle().trim().isEmpty()) { dynamicTreeNode = (TreeNode) new MyTreeNode(1, n.getIdConcept(), idTheso, idlangue, "", "", "dossier", n.getIdConcept(), root); } else { dynamicTreeNode = (TreeNode) new MyTreeNode(1, n.getIdConcept(), idTheso, idlangue, "", "", "dossier", n.getTitle(), root); } <BUG>new DefaultTree...
DefaultTreeNode defaultTreeNode = new DefaultTreeNode("fake", dynamicTreeNode); defaultTreeNode.setExpanded(true);
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SKOSXmlDocument sxd = new ReadFileSKOS().readStringBuffer(sb); for (SKOSResource resource : sxd.getResourcesList()) { NodeAlignment na = new NodeAlignment(); na.setInternal_id_concept(idC); na.setInternal_id_thesaurus(idTheso); <BUG>na.setThesaurus_target("OpenTheso"); </BUG> na.setUri_target(resource.getUri()); for(SK...
na.setThesaurus_target("Pactols");
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this.queryLogger = Loggers.getLogger(logger, ".query"); this.fetchLogger = Loggers.getLogger(logger, ".fetch"); queryLogger.setLevel(level); fetchLogger.setLevel(level); indexSettingsService.addListener(new ApplySettings()); <BUG>} private long parseTimeSetting(String name, long defaultNanos) { try { return componentSe...
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Bundle savedInstanceState) { final View rootView = inflater.inflate(R.layout.tab_qibla, container, false); final QiblaCompassView qiblaCompassView = (QiblaCompassView)rootView.findViewById(R.id.qibla_compass); qiblaCompassView.setConstants(((TextView)rootView.findViewById(R.id.bearing_north)), getText(R.string.bearing_...
sOrientationListener = new android.hardware.SensorListener() {
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if(worldIn.getTileEntity(pos) != null){ TileEntity te = worldIn.getTileEntity(pos); if(te.hasCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null) && te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).getTemp() >= -273D + mult){ te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).addHeat(-mult); } <...
if(te.hasCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null)){ te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).addHeat(mult);
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public static double betterRound(double numIn, int decPlac){ double opOn = Math.round(numIn * Math.pow(10, decPlac)) / Math.pow(10D, decPlac); return opOn; } public static double centerCeil(double numIn, int tiers){ <BUG>return ((numIn > 0) ? Math.ceil(numIn * tiers) : Math.floor(numIn * tiers)) / tiers; </BUG> } publi...
return ((numIn > 0) ? Math.ceil(numIn * (double) tiers) : Math.floor(numIn * (double) tiers)) / (double) tiers;
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package com.Da_Technomancer.crossroads.API; import com.Da_Technomancer.crossroads.API.DefaultStorageHelper.DefaultStorage; import com.Da_Technomancer.crossroads.API.heat.DefaultHeatHandler; import com.Da_Technomancer.crossroads.API.heat.IHeatHandler; import com.Da_Technomancer.crossroads.API.magic.DefaultMagicHandler; ...
import com.Da_Technomancer.crossroads.API.rotary.DefaultAxleHandler; import com.Da_Technomancer.crossroads.API.rotary.DefaultCogHandler; import com.Da_Technomancer.crossroads.API.rotary.IAxleHandler; import com.Da_Technomancer.crossroads.API.rotary.ICogHandler;
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import net.minecraftforge.common.capabilities.Capability; import net.minecraftforge.common.capabilities.CapabilityInject; import net.minecraftforge.common.capabilities.CapabilityManager; public class Capabilities{ @CapabilityInject(IHeatHandler.class) <BUG>public static Capability<IHeatHandler> HEAT_HANDLER_CAPABILITY ...
@CapabilityInject(IAxleHandler.class) public static Capability<IAxleHandler> AXLE_HANDLER_CAPABILITY = null; @CapabilityInject(ICogHandler.class) public static Capability<ICogHandler> COG_HANDLER_CAPABILITY = null;
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public IEffect getMixEffect(Color col){ if(col == null){ return effect; } int top = Math.max(col.getBlue(), Math.max(col.getRed(), col.getGreen())); <BUG>if(top < rand.nextInt(128) + 128){ return voidEffect;</BUG> } return effect; }
if(top != 255){ return voidEffect;
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import java.util.Locale; import java.util.Map; import java.util.TreeMap; public class DependencyConvergenceReport extends AbstractProjectInfoReport <BUG>{ private List reactorProjects; private static final int PERCENTAGE = 100;</BUG> public String getOutputName() {
private static final int PERCENTAGE = 100; private static final List SUPPORTED_FONT_FAMILY_NAMES = Arrays.asList( GraphicsEnvironment .getLocalGraphicsEnvironment().getAvailableFontFamilyNames() );
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sink.section1(); sink.sectionTitle1(); sink.text( getI18nString( locale, "title" ) ); sink.sectionTitle1_(); Map dependencyMap = getDependencyMap(); <BUG>generateLegend( locale, sink ); generateStats( locale, sink, dependencyMap ); generateConvergence( locale, sink, dependencyMap ); sink.section1_();</BUG> sink.body_()...
sink.lineBreak(); sink.section1_();
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Iterator it = artifactMap.keySet().iterator(); while ( it.hasNext() ) { String version = (String) it.next(); sink.tableRow(); <BUG>sink.tableCell(); sink.text( version );</BUG> sink.tableCell_(); sink.tableCell(); generateVersionDetails( sink, artifactMap, version );
sink.tableCell( String.valueOf( cellWidth ) + "px" ); sink.text( version );
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sink.tableCell(); sink.text( getI18nString( locale, "legend.shared" ) ); sink.tableCell_(); sink.tableRow_(); sink.tableRow(); <BUG>sink.tableCell(); iconError( sink );</BUG> sink.tableCell_(); sink.tableCell(); sink.text( getI18nString( locale, "legend.different" ) );
sink.tableCell( "15px" ); // according /images/icon_error_sml.gif iconError( sink );
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sink.tableCaption(); sink.text( getI18nString( locale, "stats.caption" ) ); sink.tableCaption_();</BUG> sink.tableRow(); <BUG>sink.tableHeaderCell(); sink.text( getI18nString( locale, "stats.subprojects" ) + ":" ); sink.tableHeaderCell_();</BUG> sink.tableCell(); sink.text( String.valueOf( reactorProjects.size() ) ); s...
sink.bold(); sink.bold_(); sink.tableCaption_(); sink.tableHeaderCell( headerCellWidth ); sink.text( getI18nString( locale, "stats.subprojects" ) ); sink.tableHeaderCell_();
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sink.tableCell(); sink.text( String.valueOf( reactorProjects.size() ) ); sink.tableCell_(); sink.tableRow_(); sink.tableRow(); <BUG>sink.tableHeaderCell(); sink.text( getI18nString( locale, "stats.dependencies" ) + ":" ); sink.tableHeaderCell_();</BUG> sink.tableCell(); sink.text( String.valueOf( depCount ) );
sink.tableHeaderCell( headerCellWidth ); sink.text( getI18nString( locale, "stats.dependencies" ) ); sink.tableHeaderCell_();
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sink.text( String.valueOf( convergence ) + "%" ); sink.bold_(); sink.tableCell_(); sink.tableRow_(); sink.tableRow(); <BUG>sink.tableHeaderCell(); sink.text( getI18nString( locale, "stats.readyrelease" ) + ":" ); sink.tableHeaderCell_();</BUG> sink.tableCell(); if ( convergence >= PERCENTAGE && snapshotCount <= 0 )
sink.tableHeaderCell( headerCellWidth ); sink.text( getI18nString( locale, "stats.readyrelease" ) ); sink.tableHeaderCell_();
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{ ReverseDependencyLink p1 = (ReverseDependencyLink) o1; ReverseDependencyLink p2 = (ReverseDependencyLink) o2; return p1.getProject().getId().compareTo( p2.getProject().getId() ); } <BUG>else {</BUG> return 0; } }
iconError( sink );
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package com.rackspace.papi.filter; import javax.servlet.Filter; <BUG>public class FilterContext { private final ClassLoader filterClassLoader;</BUG> private final Filter filter; public FilterContext(Filter filter, ClassLoader filterClassLoader) { this.filter = filter;
import com.rackspace.papi.commons.util.Destroyable; public class FilterContext implements Destroyable { private final ClassLoader filterClassLoader;
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import com.rackspace.papi.commons.util.http.CommonHttpHeader; import com.rackspace.papi.commons.util.http.HttpStatusCode; import com.rackspace.papi.commons.util.servlet.filter.ApplicationContextAwareFilter; import com.rackspace.papi.commons.util.servlet.http.HttpServletHelper; import com.rackspace.papi.commons.util.ser...
import com.rackspace.papi.commons.util.thread.DestroyableThreadWrapper; import com.rackspace.papi.filter.resource.PowerFilterChainReclaimer; import com.rackspace.papi.filter.resource.PowerFilterChainGarbageCollector; import com.rackspace.papi.model.PowerProxy;
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import javax.servlet.ServletResponse; public class PowerFilter extends ApplicationContextAwareFilter { private static final Logger LOG = LoggerFactory.getLogger(PowerFilter.class); private final EventListener<ApplicationDeploymentEvent, String> applicationDeploymentListener; private final UpdateListener<PowerProxy> sys...
private PowerFilterChainBuilder powerFilterChainBuilder; private PowerFilterChainGarbageCollector filterChainGarbageCollector; private DestroyableThreadWrapper filterChainGarbageCollectorThread; private List<FilterContext> filterChain;
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applicationDeploymentListener = new EventListener<ApplicationDeploymentEvent, String>() { @Override public void onEvent(Event<ApplicationDeploymentEvent, String> e) { LOG.info("Application collection has been modified. Application that changed: " + e.payload()); if (currentSystemModel != null) { <BUG>final List<FilterC...
final List<FilterContext> newFilterChain = new FilterContextInitializer(filterConfig).buildFilterContexts(papiContext.classLoader(), currentSystemModel); updateFilterChainBuilder(newFilterChain);
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final byte[] expectedBytes = new byte[16]; for (int i = 0; i < expectedBytes.length; i++) { expectedBytes[i] = 1; } final UUID uuid = UUIDHelper.bytesToUUID(expectedBytes); <BUG>System.out.println(uuid.toString());</BUG> final byte[] actualBytes = UUIDHelper.stringToUUIDBytes(uuid.toString()); assertTrue(new ByteArrayC...
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new InetSocketAddress(InetAddress.getLocalHost(), 2103), new InetSocketAddress(InetAddress.getLocalHost(), 2104)}); final String myKey = "mykey"; final int finishTotal = 9700, sleep1 = 1000, <BUG>sleep2 = 100000, sleep3 = 200000, sleep4 = 100250; </BUG> total = 0;
sleep2 = 2000, sleep3 = 1200, sleep4 = 3000;
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import org.slf4j.Logger; import org.slf4j.LoggerFactory; import javax.servlet.FilterConfig; import java.util.Collection; public class FilterContextManagerImpl implements FilterContextManager { <BUG>private static final Logger LOG = LoggerFactory.getLogger(PowerFilterChainBuilder.class); </BUG> private final FilterConfi...
private static final Logger LOG = LoggerFactory.getLogger(FilterContextInitializer.class);
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import org.netbeans.lib.cvsclient.event.IEntryListener; import org.netbeans.lib.cvsclient.event.IEventSender; import org.netbeans.lib.cvsclient.file.FileObject; import org.netbeans.lib.cvsclient.file.ICvsFileSystem; import org.netbeans.lib.cvsclient.util.BugLog; <BUG>import org.jetbrains.annotations.NonNls; public fina...
import java.util.regex.Matcher; import java.util.regex.Pattern; public final class UpdateMessageParser extends AbstractMessageParser implements IEntryListener {
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customTokens.put("%%mlFinalForestsPerHost%%", hubConfig.finalForestsPerHost.toString()); customTokens.put("%%mlTraceAppserverName%%", hubConfig.traceHttpName); customTokens.put("%%mlTracePort%%", hubConfig.tracePort.toString()); customTokens.put("%%mlTraceDbName%%", hubConfig.traceDbName); customTokens.put("%%mlTraceFo...
customTokens.put("%%mlTriggersDbName%%", hubConfig.triggersDbName); customTokens.put("%%mlSchemasDbName%%", hubConfig.schemasDbName); }
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@Override public String toString() { return "desc"; } }; <BUG>public static final SortOrder DEFAULT = DESC; private static final SortOrder PROTOTYPE = DEFAULT; </BUG> @Override public SortOrder readFrom(StreamInput in) throws IOException {
return "asc"; }, DESC { private static final SortOrder PROTOTYPE = ASC;
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GeoDistance geoDistance = GeoDistance.DEFAULT; boolean reverse = false; MultiValueMode sortMode = null; NestedInnerQueryParseSupport nestedHelper = null; final boolean indexCreatedBeforeV2_0 = context.indexShard().getIndexSettings().getIndexVersionCreated().before(Version.V_2_0_0); <BUG>boolean coerce = false; boolean ...
boolean coerce = GeoDistanceSortBuilder.DEFAULT_COERCE; boolean ignoreMalformed = GeoDistanceSortBuilder.DEFAULT_IGNORE_MALFORMED; XContentParser.Token token;
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String currentName = parser.currentName(); while ((token = parser.nextToken()) != XContentParser.Token.END_OBJECT) { if (token == XContentParser.Token.FIELD_NAME) { currentName = parser.currentName(); } else if (token == XContentParser.Token.START_ARRAY) { <BUG>parseGeoPoints(parser, geoPoints); </BUG> fieldName = curr...
GeoDistanceSortBuilder.parseGeoPoints(parser, geoPoints);
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package org.elasticsearch.search.sort; <BUG>import org.elasticsearch.script.Script; public class SortBuilders {</BUG> public static ScoreSortBuilder scoreSort() { return new ScoreSortBuilder(); }
import org.elasticsearch.common.geo.GeoPoint; import java.util.Arrays; public class SortBuilders {
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public GeoDistanceSortBuilder ignoreMalformed(boolean ignoreMalformed) { this.ignoreMalformed = ignoreMalformed; return this; }</BUG> @Override <BUG>public XContentBuilder toXContent(XContentBuilder builder, Params params) throws IOException { builder.startObject("_geo_distance"); if (geohashes.size() == 0 && points.si...
if (coerce == false) { } } public boolean ignoreMalformed() { return this.ignoreMalformed; } builder.startObject(NAME);
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System.out.println(change); } } }; @Override <BUG>protected Callback<VChild, Void> copyChildCallback() </BUG> { return (child) -> {
protected Callback<VChild, Void> copyIntoCallback()
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package jfxtras.labs.icalendarfx.components; import jfxtras.labs.icalendarfx.properties.component.descriptive.Comment; <BUG>import jfxtras.labs.icalendarfx.properties.component.misc.IANAProperty; import jfxtras.labs.icalendarfx.properties.component.misc.UnknownProperty;</BUG> import jfxtras.labs.icalendarfx.properties...
import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty;
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VEVENT ("VEVENT", Arrays.asList(PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.CATEGORIES, PropertyType.CLASSIFICATION, PropertyType.COMMENT, PropertyType.CONTACT, PropertyType.DATE_TIME_CREATED, PropertyType.DATE_TIME_END, PropertyType.DATE_TIME_STAMP, PropertyType.DATE_TIME_START, PropertyType.DESCRIPTI...
PropertyType.GEOGRAPHIC_POSITION, PropertyType.LAST_MODIFIED, PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER, PropertyType.PRIORITY,
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VTODO ("VTODO", Arrays.asList(PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.CATEGORIES, PropertyType.CLASSIFICATION, PropertyType.COMMENT, PropertyType.CONTACT, PropertyType.DATE_TIME_COMPLETED, PropertyType.DATE_TIME_CREATED, PropertyType.DATE_TIME_DUE, PropertyType.DATE_TIME_STAMP, PropertyType.DATE_TI...
PropertyType.EXCEPTION_DATE_TIMES, PropertyType.GEOGRAPHIC_POSITION, PropertyType.LAST_MODIFIED, PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER,
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throw new RuntimeException("not implemented"); } }, DAYLIGHT_SAVING_TIME ("DAYLIGHT", Arrays.asList(PropertyType.COMMENT, PropertyType.DATE_TIME_START, <BUG>PropertyType.IANA_PROPERTY, PropertyType.NON_STANDARD, PropertyType.RECURRENCE_DATE_TIMES, PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType....
PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType.TIME_ZONE_OFFSET_FROM,
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throw new RuntimeException("not implemented"); } }, VALARM ("VALARM", Arrays.asList(PropertyType.ACTION, PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.DESCRIPTION, <BUG>PropertyType.DURATION, PropertyType.IANA_PROPERTY, PropertyType.NON_STANDARD, PropertyType.REPEAT_COUNT, PropertyType.SUMMARY, PropertyT...
DAYLIGHT_SAVING_TIME ("DAYLIGHT", Arrays.asList(PropertyType.COMMENT, PropertyType.DATE_TIME_START, PropertyType.NON_STANDARD, PropertyType.RECURRENCE_DATE_TIMES, PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType.TIME_ZONE_OFFSET_FROM, PropertyType.TIME_ZONE_OFFSET_TO), DaylightSavingTime.class)
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private ContentLineStrategy contentLineGenerator; protected void setContentLineGenerator(ContentLineStrategy contentLineGenerator) { this.contentLineGenerator = contentLineGenerator; } <BUG>protected Callback<VChild, Void> copyChildCallback() </BUG> { throw new RuntimeException("Can't copy children. copyChildCallback ...
protected Callback<VChild, Void> copyIntoCallback()
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import jfxtras.labs.icalendarfx.properties.calendar.Version; import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty; public enum CalendarProperty { CALENDAR_SCALE ("CALSCALE", <BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER), CalendarSca...
Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD), CalendarScale.class)
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CalendarScale calendarScale = (CalendarScale) child; destination.setCalendarScale(calendarScale); } }, METHOD ("METHOD", <BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER), Method.class)</BUG> { @Override public VChild parse(VCalendar vCalendar, String contentLi...
Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD), Method.class)
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} list.add(new NonStandardProperty((NonStandardProperty) child)); } }, PRODUCT_IDENTIFIER ("PRODID", <BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER), ProductIdentifier.class)</BUG> { @Override public VChild parse(VCalendar vCalendar, String contentLine)
public void copyChild(VChild child, VCalendar destination) CalendarScale calendarScale = (CalendarScale) child; destination.setCalendarScale(calendarScale); METHOD ("METHOD", Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD), Method.class)
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ProductIdentifier productIdentifier = (ProductIdentifier) child; destination.setProductIdentifier(productIdentifier); } }, VERSION ("VERSION", <BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER), Version.class)</BUG> { @Override public VChild parse(VCalendar vCal...
Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD), Version.class)
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package jfxtras.labs.icalendarfx.components; import jfxtras.labs.icalendarfx.properties.component.descriptive.Comment; <BUG>import jfxtras.labs.icalendarfx.properties.component.misc.IANAProperty; import jfxtras.labs.icalendarfx.properties.component.misc.UnknownProperty;</BUG> import jfxtras.labs.icalendarfx.properties...
import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty;
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import uk.ac.ebi.pride.utilities.data.utils.MzTabUtils; import uk.ac.ebi.pride.utilities.term.CvTermReference; import javax.xml.bind.JAXBException; import java.net.MalformedURLException; import java.net.URL; <BUG>import java.util.*; public class MzIdentMLMzTabConverter extends AbstractMzTabConverter {</BUG> public stat...
import static uk.ac.ebi.pride.utilities.data.utils.MzTabUtils.removeNewLineAndTab; public class MzIdentMLMzTabConverter extends AbstractMzTabConverter {
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for (int index = 0; index < peptides.size(); index++) { Peptide oldPSM = peptides.get(index); PSM psm = new PSM(psmColumnFactory, metadata); psm.setSequence(oldPSM.getPeptideSequence().getSequence()); psm.setPSM_ID(oldPSM.getSpectrumIdentification().getId().toString()); <BUG>psm.setAccession(generateAccession(oldPSM));...
psm.setAccession(removeNewLineAndTab(generateAccession(oldPSM)));
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if (ptm.getCvParams().get(0).getAccession() == null) { continue; } Modification mod = MZTabUtils.parseModification(Section.PSM, ptm.getCvParams().get(0).getAccession()); if (mod != null) { <BUG>if (peptideEvidence.getStartPosition() != null && ptm.getLocation() != -1) { </BUG> Integer position = peptideEvidence.getStar...
if (peptideEvidence.getStartPosition() != null && peptideEvidence.getStartPosition() >= 0 && ptm.getLocation() >= 0) {
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import java.net.URI; import java.net.URISyntaxException; import java.util.*; import java.util.regex.Matcher; import java.util.regex.Pattern; <BUG>import static uk.ac.ebi.pride.jmztab.model.MZTabUtils.isEmpty; public abstract class AbstractMzTabConverter extends ConvertProvider<DataAccessController, Void> {</BUG> protec...
import static uk.ac.ebi.pride.utilities.data.utils.MzTabUtils.removeNewLineAndTab; public abstract class AbstractMzTabConverter extends ConvertProvider<DataAccessController, Void> {
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int i = 1; for(Reference ref: references){ List<PublicationItem> items = new ArrayList<PublicationItem>(); String doi = ref.getDoi(); if(doi != null && !doi.isEmpty()){ <BUG>items.add(new PublicationItem(PublicationItem.Type.DOI, doi)); </BUG> } if(ref.getCvParams() != null){ String pubmed = getPublicationAccession(ref...
items.add(new PublicationItem(PublicationItem.Type.DOI, removeNewLineAndTab(doi)));
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ParamGroup params = (rawIdent.getAdditional()==null)?new ParamGroup():transformParamGroup(rawIdent.getAdditional()); Double seqConverage = rawIdent.getSequenceCoverage(); double seqConverageVal = seqConverage == null ? -1 : seqConverage; Double threshold = rawIdent.getThreshold(); double thresholdVal = threshold == nul...
Number scoreValue = rawIdent.getScore(); SearchEngineScoreCvTermReference searchEngineScoreParam = SearchEngineScoreCvTermReference.getSearchEngineScoreParamByName(searchEngineName); if (searchEngineScoreParam != null) {
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Score score = new Score(); if(scoreValue != null){ SearchEngineScoreCvTermReference searchEngineScoreParam = SearchEngineScoreCvTermReference.getSearchEngineScoreParamByName(searchEngineName);</BUG> score.addScore(searchEngineScoreParam.getSearchEngineParam(), searchEngineScoreParam, scoreValue); <BUG>} else { score.a...
if (searchEngineScoreParam != null) { } else { score.addScore(SearchEngineScoreCvTermReference.MS_SEARCH_ENGINE_SPECIFIC_SCORE.getSearchEngineParam(), SearchEngineScoreCvTermReference.MS_SEARCH_ENGINE_SPECIFIC_SCORE, scoreValue);
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import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.security.DigestOutputStream; import java.security.MessageDigest; <BUG>import java.security.NoSuchAlgorithmException; import java.util.ArrayList; import java.util.Collections; import java.util.List;</BUG> public final class ...
import java.text.DateFormat; import java.util.Date; import java.util.List;
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package org.jboss.as.patching.runner; <BUG>import org.jboss.as.boot.DirectoryStructure; import org.jboss.as.patching.LocalPatchInfo;</BUG> import org.jboss.as.patching.PatchInfo; import org.jboss.as.patching.PatchLogger; import org.jboss.as.patching.PatchMessages;
import static org.jboss.as.patching.runner.PatchUtils.generateTimestamp; import org.jboss.as.patching.CommonAttributes; import org.jboss.as.patching.LocalPatchInfo;
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private static final String PATH_DELIMITER = "/"; public static final byte[] NO_CONTENT = PatchingTask.NO_CONTENT; enum Element { ADDED_BUNDLE("added-bundle"), ADDED_MISC_CONTENT("added-misc-content"), <BUG>ADDED_MODULE("added-module"), BUNDLES("bundles"),</BUG> CUMULATIVE("cumulative"), DESCRIPTION("description"), MIS...
APPLIES_TO_VERSION("applies-to-version"), BUNDLES("bundles"),
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final int count = reader.getAttributeCount(); for (int i = 0; i < count; i++) { final String value = reader.getAttributeValue(i); final Attribute attribute = Attribute.forName(reader.getAttributeLocalName(i)); switch (attribute) { <BUG>case APPLIES_TO_VERSION: builder.addAppliesTo(value); break;</BUG> case RESULTING_VE...
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final StringBuilder path = new StringBuilder(); for(final String p : item.getPath()) { path.append(p).append(PATH_DELIMITER); } path.append(item.getName()); <BUG>writer.writeAttribute(Attribute.PATH.name, path.toString()); if(type != ModificationType.REMOVE) {</BUG> writer.writeAttribute(Attribute.HASH.name, bytesToHex...
if (item.isDirectory()) { writer.writeAttribute(Attribute.DIRECTORY.name, "true"); if(type != ModificationType.REMOVE) {
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package org.jboss.as.patching; import org.jboss.as.controller.OperationFailedException; import org.jboss.as.patching.runner.PatchingException; import org.jboss.logging.Messages; import org.jboss.logging.annotations.Message; <BUG>import org.jboss.logging.annotations.MessageBundle; import java.io.IOException;</BUG> impor...
import org.jboss.logging.annotations.Cause; import java.io.IOException;
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import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.LocalFileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.permission.FsPermission; import org.apache.hadoop.util.Progressable; <BUG>import static org.apache.hadoop.fs.s3a.S3AConstants.*; public class S3AFileSystem extends FileSyste...
import static org.apache.hadoop.fs.s3a.Constants.*; public class S3AFileSystem extends FileSystem {
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public void initialize(URI name, Configuration conf) throws IOException { super.initialize(name, conf); uri = URI.create(name.getScheme() + "://" + name.getAuthority()); workingDir = new Path("/user", System.getProperty("user.name")).makeQualified(this.uri, this.getWorkingDirectory()); <BUG>String accessKey = conf.get(...
String accessKey = conf.get(NEW_ACCESS_KEY, conf.get(OLD_ACCESS_KEY, null)); String secretKey = conf.get(NEW_SECRET_KEY, conf.get(OLD_SECRET_KEY, null));
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} else { accessKey = userInfo; } } AWSCredentialsProviderChain credentials = new AWSCredentialsProviderChain( <BUG>new S3ABasicAWSCredentialsProvider(accessKey, secretKey), new InstanceProfileCredentialsProvider(), new S3AAnonymousAWSCredentialsProvider() );</BUG> bucket = name.getHost();
new BasicAWSCredentialsProvider(accessKey, secretKey), new AnonymousAWSCredentialsProvider()
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awsConf.setSocketTimeout(conf.getInt(SOCKET_TIMEOUT, DEFAULT_SOCKET_TIMEOUT)); </BUG> s3 = new AmazonS3Client(credentials, awsConf); <BUG>maxKeys = conf.getInt(MAX_PAGING_KEYS, DEFAULT_MAX_PAGING_KEYS); partSize = conf.getLong(MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE); partSizeThreshold = conf.getInt(MIN_MULTIPART_THR...
new InstanceProfileCredentialsProvider(), new AnonymousAWSCredentialsProvider() bucket = name.getHost(); ClientConfiguration awsConf = new ClientConfiguration(); awsConf.setMaxConnections(conf.getInt(NEW_MAXIMUM_CONNECTIONS, conf.getInt(OLD_MAXIMUM_CONNECTIONS, DEFAULT_MAXIMUM_CONNECTIONS))); awsConf.setProtocol(conf.g...
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cannedACL = null; } if (!s3.doesBucketExist(bucket)) { throw new IOException("Bucket " + bucket + " does not exist"); } <BUG>boolean purgeExistingMultipart = conf.getBoolean(PURGE_EXISTING_MULTIPART, DEFAULT_PURGE_EXISTING_MULTIPART); long purgeExistingMultipartAge = conf.getLong(PURGE_EXISTING_MULTIPART_AGE, DEFAULT_...
boolean purgeExistingMultipart = conf.getBoolean(NEW_PURGE_EXISTING_MULTIPART, conf.getBoolean(OLD_PURGE_EXISTING_MULTIPART, DEFAULT_PURGE_EXISTING_MULTIPART)); long purgeExistingMultipartAge = conf.getLong(NEW_PURGE_EXISTING_MULTIPART_AGE, conf.getLong(OLD_PURGE_EXISTING_MULTIPART_AGE, DEFAULT_PURGE_EXISTING_MULTIPART...
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import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; <BUG>import static org.apache.hadoop.fs.s3a.S3AConstants.*; public class S3AOutputStream extends OutputStream {</BUG> private OutputStream backupStream; private File backup...
import static org.apache.hadoop.fs.s3a.Constants.*; public class S3AOutputStream extends OutputStream {
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this.client = client; this.progress = progress; this.fs = fs; this.cannedACL = cannedACL; this.statistics = statistics; <BUG>partSize = conf.getLong(MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE); partSizeThreshold = conf.getInt(MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD); </BUG> if (conf.get(BUFFER_DIR, null) ...
partSize = conf.getLong(OLD_MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE); partSizeThreshold = conf.getInt(OLD_MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD);
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import de.vanita5.twittnuker.receiver.NotificationReceiver; import de.vanita5.twittnuker.service.LengthyOperationsService; import de.vanita5.twittnuker.util.ActivityTracker; import de.vanita5.twittnuker.util.AsyncTwitterWrapper; import de.vanita5.twittnuker.util.DataStoreFunctionsKt; <BUG>import de.vanita5.twittnuker.u...
import de.vanita5.twittnuker.util.DebugLog; import de.vanita5.twittnuker.util.ImagePreloader;
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final List<InetAddress> addresses = mDns.lookup(host); for (InetAddress address : addresses) { c.addRow(new String[]{host, address.getHostAddress()}); } } catch (final IOException ignore) { <BUG>if (BuildConfig.DEBUG) { Log.w(LOGTAG, ignore); }</BUG> }
DebugLog.w(LOGTAG, null, ignore);
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@Override public void afterExecute(Bus handler, SingleResponse<Relationship> result) { if (result.hasData()) { handler.post(new FriendshipUpdatedEvent(accountKey, userKey, result.getData())); } else if (result.hasException()) { <BUG>if (BuildConfig.DEBUG) { Log.w(LOGTAG, "Unable to update friendship", result.getExcepti...
public UserKey[] getAccountKeys() { return DataStoreUtils.getActivatedAccountKeys(context);
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MicroBlog microBlog = MicroBlogAPIFactory.getInstance(context, accountId); if (!Utils.isOfficialCredentials(context, accountId)) continue; try { microBlog.setActivitiesAboutMeUnread(cursor); } catch (MicroBlogException e) { <BUG>if (BuildConfig.DEBUG) { Log.w(LOGTAG, e); }</BUG> }
DebugLog.w(LOGTAG, null, e);
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FileBody fileBody = null; try { fileBody = getFileBody(context, imageUri); twitter.updateProfileBannerImage(fileBody); } finally { <BUG>Utils.closeSilently(fileBody); if (deleteImage && "file".equals(imageUri.getScheme())) { final File file = new File(imageUri.getPath()); if (!file.delete()) { Log.w(LOGTAG, String.form...
if (deleteImage) { Utils.deleteMedia(context, imageUri);
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FileBody fileBody = null; try { fileBody = getFileBody(context, imageUri); twitter.updateProfileBackgroundImage(fileBody, tile); } finally { <BUG>Utils.closeSilently(fileBody); if (deleteImage && "file".equals(imageUri.getScheme())) { final File file = new File(imageUri.getPath()); if (!file.delete()) { Log.w(LOGTAG, S...
twitter.updateProfileBannerImage(fileBody); if (deleteImage) { Utils.deleteMedia(context, imageUri);
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FileBody fileBody = null; try { fileBody = getFileBody(context, imageUri); return twitter.updateProfileImage(fileBody); } finally { <BUG>Utils.closeSilently(fileBody); if (deleteImage && "file".equals(imageUri.getScheme())) { final File file = new File(imageUri.getPath()); if (!file.delete()) { Log.w(LOGTAG, String.for...
twitter.updateProfileBannerImage(fileBody); if (deleteImage) { Utils.deleteMedia(context, imageUri);
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import de.vanita5.twittnuker.annotation.CustomTabType; import de.vanita5.twittnuker.library.MicroBlog; import de.vanita5.twittnuker.library.MicroBlogException; import de.vanita5.twittnuker.library.twitter.model.RateLimitStatus; import de.vanita5.twittnuker.library.twitter.model.Status; <BUG>import de.vanita5.twittnuker...
import org.mariotaku.pickncrop.library.PNCUtils; import org.mariotaku.sqliteqb.library.AllColumns;
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context.getApplicationContext().sendBroadcast(intent); } } @Nullable public static Location getCachedLocation(Context context) { <BUG>if (BuildConfig.DEBUG) { Log.v(LOGTAG, "Fetching cached location", new Exception()); }</BUG> Location location = null;
DebugLog.v(LOGTAG, "Fetching cached location", new Exception());
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import java.util.List; import java.util.Map.Entry; import javax.inject.Singleton; import okhttp3.Dns; @Singleton <BUG>public class TwidereDns implements Constants, Dns { </BUG> private static final String RESOLVER_LOGTAG = "TwittnukerDns"; private final SharedPreferences mHostMapping; private final SharedPreferencesWra...
public class TwidereDns implements Dns, Constants {
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for (Location location : twitter.getAvailableTrends()) { map.put(location); } return map.pack(); } catch (final MicroBlogException e) { <BUG>if (BuildConfig.DEBUG) { Log.w(LOGTAG, e); }</BUG> }
DebugLog.w(LOGTAG, null, e);
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import com.mongodb.client.MongoDatabase; import com.mongodb.client.model.BulkWriteOptions; import com.mongodb.client.model.InsertOneModel; import com.mongodb.client.model.WriteModel; public class ReplicaSetTimeout { <BUG>private static final WriteConcern WRITE_CONCERN = new WriteConcern() </BUG> .withW("majority") .wit...
private static final WriteConcern WRITE_CONCERN = WriteConcern.ACKNOWLEDGED
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new ServerAddress("localhost", 27001), // new ServerAddress("localhost", 27002), // new ServerAddress("localhost", 27003))); try { MongoDatabase db = mongo.getDatabase("test"); <BUG>MongoCollection<Document> collection = db.getCollection("foo"); collection = collection.withWriteConcern(WRITE_CONCERN);</BUG> System.out...
MongoCollection<Document> collection = db.getCollection("foo").withWriteConcern(WRITE_CONCERN);
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customTokens.put("%%mlFinalForestsPerHost%%", hubConfig.finalForestsPerHost.toString()); customTokens.put("%%mlTraceAppserverName%%", hubConfig.traceHttpName); customTokens.put("%%mlTracePort%%", hubConfig.tracePort.toString()); customTokens.put("%%mlTraceDbName%%", hubConfig.traceDbName); customTokens.put("%%mlTraceFo...
customTokens.put("%%mlTriggersDbName%%", hubConfig.triggersDbName); customTokens.put("%%mlSchemasDbName%%", hubConfig.schemasDbName); }
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package com.cronutils.model.time.generator; import java.util.Collections; <BUG>import java.util.List; import org.apache.commons.lang3.Validate;</BUG> import com.cronutils.model.field.CronField; import com.cronutils.model.field.expression.FieldExpression; public abstract class FieldValueGenerator {
import org.apache.commons.lang3.Validate; import org.apache.commons.lang3.Validate;
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import java.util.ResourceBundle; import java.util.function.Function;</BUG> class DescriptionStrategyFactory { private DescriptionStrategyFactory() {} public static DescriptionStrategy daysOfWeekInstance(final ResourceBundle bundle, final FieldExpression expression) { <BUG>final Function<Integer, String> nominal = integ...
import java.util.function.Function; import com.cronutils.model.field.expression.FieldExpression; import com.cronutils.model.field.expression.On; final Function<Integer, String> nominal = integer -> DayOfWeek.of(integer).getDisplayName(TextStyle.FULL, bundle.getLocale());
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return dom; } public static DescriptionStrategy monthsInstance(final ResourceBundle bundle, final FieldExpression expression) { return new NominalDescriptionStrategy( bundle, <BUG>integer -> new DateTime().withMonthOfYear(integer).monthOfYear().getAsText(bundle.getLocale()), expression</BUG> ); } public static Descript...
integer -> Month.of(integer).getDisplayName(TextStyle.FULL, bundle.getLocale()), expression
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<BUG>package com.cronutils.model.time.generator; import com.cronutils.mapper.WeekDay;</BUG> import com.cronutils.model.field.CronField; import com.cronutils.model.field.CronFieldName; import com.cronutils.model.field.constraint.FieldConstraintsBuilder;
import java.time.LocalDate; import java.util.Collections; import java.util.List; import java.util.Set; import org.apache.commons.lang3.Validate; import com.cronutils.mapper.WeekDay;
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import com.cronutils.model.field.expression.Between; import com.cronutils.model.field.expression.FieldExpression; import com.cronutils.parser.CronParserField; import com.google.common.collect.Lists; import com.google.common.collect.Sets; <BUG>import org.apache.commons.lang3.Validate; import org.joda.time.DateTime; impo...
[DELETED]
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<BUG>package com.cronutils.model.time.generator; import com.cronutils.model.field.CronField;</BUG> import com.cronutils.model.field.CronFieldName; import com.cronutils.model.field.expression.FieldExpression; import com.cronutils.model.field.expression.On;
import java.time.DayOfWeek; import java.time.LocalDate; import java.util.List; import org.apache.commons.lang3.Validate; import com.cronutils.model.field.CronField;
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import com.cronutils.model.field.CronField;</BUG> import com.cronutils.model.field.CronFieldName; import com.cronutils.model.field.expression.FieldExpression; import com.cronutils.model.field.expression.On; import com.google.common.collect.Lists; <BUG>import org.apache.commons.lang3.Validate; import org.joda.time.DateT...
package com.cronutils.model.time.generator; import java.time.DayOfWeek; import java.time.LocalDate; import java.util.List; import com.cronutils.model.field.CronField;
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class OnDayOfMonthValueGenerator extends FieldValueGenerator { private int year; private int month; public OnDayOfMonthValueGenerator(CronField cronField, int year, int month) { super(cronField); <BUG>Validate.isTrue(CronFieldName.DAY_OF_MONTH.equals(cronField.getField()), "CronField does not belong to day of month"); ...
Validate.isTrue(CronFieldName.DAY_OF_MONTH.equals(cronField.getField()), "CronField does not belong to day of" + " month"); this.year = year;
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package com.cronutils.mapper; public class ConstantsMapper { private ConstantsMapper() {} public static final WeekDay QUARTZ_WEEK_DAY = new WeekDay(2, false); <BUG>public static final WeekDay JODATIME_WEEK_DAY = new WeekDay(1, false); </BUG> public static final WeekDay CRONTAB_WEEK_DAY = new WeekDay(1, true); public st...
public static final WeekDay JAVA8 = new WeekDay(1, false);
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return nextMatch; } catch (NoSuchValueException e) { throw new IllegalArgumentException(e); } } <BUG>DateTime nextClosestMatch(DateTime date) throws NoSuchValueException { </BUG> List<Integer> year = yearsValueGenerator.generateCandidates(date.getYear(), date.getYear()); TimeNode days = null; int lowestMonth = months.g...
ZonedDateTime nextClosestMatch(ZonedDateTime date) throws NoSuchValueException {
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boolean questionMarkSupported = cronDefinition.getFieldDefinition(DAY_OF_WEEK).getConstraints().getSpecialChars().contains(QUESTION_MARK); if(questionMarkSupported){ return new TimeNode( generateDayCandidatesQuestionMarkSupported( <BUG>date.getYear(), date.getMonthOfYear(), </BUG> ((DayOfWeekFieldDefinition) cronDefini...
date.getYear(), date.getMonthValue(),
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) ); }else{ return new TimeNode( generateDayCandidatesQuestionMarkNotSupported( <BUG>date.getYear(), date.getMonthOfYear(), </BUG> ((DayOfWeekFieldDefinition) cronDefinition.getFieldDefinition(DAY_OF_WEEK) ).getMondayDoWValue()
date.getYear(), date.getMonthValue(),
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} public DateTime lastExecution(DateTime date){ </BUG> Validate.notNull(date); try { <BUG>DateTime previousMatch = previousClosestMatch(date); </BUG> if(previousMatch.equals(date)){ previousMatch = previousClosestMatch(date.minusSeconds(1)); }
public java.time.Duration timeToNextExecution(ZonedDateTime date){ return java.time.Duration.between(date, nextExecution(date)); public ZonedDateTime lastExecution(ZonedDateTime date){ ZonedDateTime previousMatch = previousClosestMatch(date);
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return previousMatch; } catch (NoSuchValueException e) { throw new IllegalArgumentException(e); } } <BUG>public Duration timeFromLastExecution(DateTime date){ return new Interval(lastExecution(date), date).toDuration(); } public boolean isMatch(DateTime date){ </BUG> return nextExecution(lastExecution(date)).equals(da...
[DELETED]
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<BUG>package com.cronutils.model.time.generator; import com.cronutils.model.field.CronField;</BUG> import com.cronutils.model.field.expression.Every; import com.cronutils.model.field.expression.FieldExpression; import com.google.common.annotations.VisibleForTesting;
import java.time.ZonedDateTime; import java.util.List; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.cronutils.model.field.CronField;
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import com.cronutils.model.field.CronField;</BUG> import com.cronutils.model.field.expression.Every; import com.cronutils.model.field.expression.FieldExpression; import com.google.common.annotations.VisibleForTesting; import com.google.common.collect.Lists; <BUG>import org.joda.time.DateTime; import org.slf4j.Logger; i...
package com.cronutils.model.time.generator; import java.time.ZonedDateTime; import java.util.List; import com.cronutils.model.field.CronField;