A custom Trigger implementation for Flink 1.1.3 which triggers 1) a window computation on every element 2) doesn't emit duplicate window outputs 3) sends out a special -1 element when a timeout occurs.

CustomTrigger.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
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import org.apache.flink.api.common.functions.MapFunction;
import org.apache.flink.api.common.state.ValueState;
import org.apache.flink.api.common.state.ValueStateDescriptor;
import org.apache.flink.api.java.tuple.Tuple;
import org.apache.flink.api.java.tuple.Tuple2;
import org.apache.flink.configuration.Configuration;
import org.apache.flink.streaming.api.TimeCharacteristic;
import org.apache.flink.streaming.api.environment.StreamExecutionEnvironment;
import org.apache.flink.streaming.api.functions.AssignerWithPunctuatedWatermarks;
import org.apache.flink.streaming.api.functions.windowing.RichWindowFunction;
import org.apache.flink.streaming.api.watermark.Watermark;
import org.apache.flink.streaming.api.windowing.assigners.EventTimeSessionWindows;
import org.apache.flink.streaming.api.windowing.time.Time;
import org.apache.flink.streaming.api.windowing.triggers.Trigger;
import org.apache.flink.streaming.api.windowing.triggers.TriggerResult;
import org.apache.flink.streaming.api.windowing.windows.TimeWindow;
import org.apache.flink.util.Collector;

import javax.annotation.Nullable;
import java.io.IOException;


public class CustomTrigger {


	public static void main(String[] args) throws Exception {

		// timeout after which to sent a 0 element
		final Time timeout = Time.milliseconds(5);

		StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment();
		env.setParallelism(1);

		env.setStreamTimeCharacteristic(TimeCharacteristic.EventTime);
		
		env
				.generateSequence(0, 100)
				.assignTimestampsAndWatermarks(new CustomAssigner())
				.map(new MapFunction<Long, Tuple2<Long, Long>>() {
					@Override
					public Tuple2<Long, Long> map(Long value) throws Exception {
						return new Tuple2<>(1L, value);
					}
				})
				.keyBy(0)
				.window(EventTimeSessionWindows.withGap(timeout))
				.allowedLateness(timeout)
				.trigger(new CustomEventTrigger(timeout))
				.apply(new CustomWindowFunction())
				.print();


		env.execute();
	}


	private static class CustomAssigner implements AssignerWithPunctuatedWatermarks<Long> {

		private long lastWaterMark = Long.MIN_VALUE;

		@Nullable
		@Override
		public Watermark checkAndGetNextWatermark(Long lastElement, long extractedTimestamp) {
			if (extractedTimestamp % 10 == 0) {
				lastWaterMark = lastElement;
			}
			System.out.println("watermark: " + lastWaterMark);
			return new Watermark(lastWaterMark);
		}

		@Override
		public long extractTimestamp(Long element, long previousElementTimestamp) {
			if (element > 50) {
				return element + 10;
			}
			return element;
		}
	}

	private static class CustomEventTrigger extends EventTimeTrigger {

		private final long timeout;

		private final ValueStateDescriptor<Boolean> cleanupStateDescriptor =
				new ValueStateDescriptor<>("cleanupState", Boolean.class, false);

		private CustomEventTrigger(Time timeout) {
			this.timeout = timeout.toMilliseconds();
		}

		@Override
		public TriggerResult onElement(Object element, long timestamp, TimeWindow window, TriggerContext ctx) throws Exception {

			// Check if we already triggered the cleanup (in this case we don't want to fire)
			ValueState<Boolean> cleanupState = ctx.getPartitionedState(cleanupStateDescriptor);
			if(cleanupState.value()) {
				return TriggerResult.CONTINUE;
			}

			// register a time at the end of the window
			if (ctx.getCurrentWatermark() < window.maxTimestamp()) {
				ctx.registerEventTimeTimer(window.maxTimestamp());
			}

			// fire on every element
			return TriggerResult.FIRE;
		}

		@Override
		public TriggerResult onEventTime(long time, TimeWindow window, TriggerContext ctx) {
			if (time == window.maxTimestamp()) {
				ctx.registerEventTimeTimer(window.maxTimestamp() + timeout);
				return TriggerResult.FIRE;
			} else if (time > window.maxTimestamp()){
				System.out.println("time: " + time);
				System.out.println("maxTimeStamp: " + window.maxTimestamp());
				// purging and sending out 0 element
				try {
					ValueState<Boolean> cleanupState = ctx.getPartitionedState(cleanupStateDescriptor);
					cleanupState.update(true);
				} catch (IOException e) {
					throw new RuntimeException("Failed to update state", e);
				}
				return TriggerResult.FIRE_AND_PURGE;
			} else {
				return TriggerResult.CONTINUE;
			}
		}
	}

	private static class CustomWindowFunction extends RichWindowFunction<Tuple2<Long, Long>, Long, Tuple, TimeWindow> {

		/** State to check if we should cleanup and send the zero element */
		private transient ValueState<Boolean> cleanupState;

		/** State to keep track of our current count */
		private transient ValueState<Long> countState;

		private final ValueStateDescriptor<Boolean> cleanupStateDescriptor =
				new ValueStateDescriptor<>("cleanupState", Boolean.class, false);

		private final ValueStateDescriptor<Long> counterStateDescriptor =
				new ValueStateDescriptor<>("counterState", Long.class, 0L);

		@Override
		public void open(Configuration parameters) throws Exception {
			cleanupState = getRuntimeContext().getState(cleanupStateDescriptor);
			countState = getRuntimeContext().getState(counterStateDescriptor);
		}

		@Override
		public void apply(Tuple tuple, TimeWindow window, Iterable<Tuple2<Long, Long>> input, Collector<Long> out) throws Exception {
			if (cleanupState.value()) {
				// we should clean up and send out the zero element
				out.collect(-1L);
			} else {
				// regular window function
				// do some computation
				long newCount = 0;
				for (Tuple2<Long, Long> elem : input) {
					newCount = elem.f1;
				}

				// check if state was updated and only emit then
				if (countState.value() != newCount) {
					countState.update(newCount);
					out.collect(newCount);
				}


			}
		}

	}

	private static class EventTimeTrigger extends Trigger<Object, TimeWindow> {
		private static final long serialVersionUID = 1L;

		private EventTimeTrigger() {}

		@Override
		public TriggerResult onElement(Object element, long timestamp, TimeWindow window, TriggerContext ctx) throws Exception {
			if (window.maxTimestamp() <= ctx.getCurrentWatermark()) {
				// if the watermark is already past the window fire immediately
				return TriggerResult.FIRE;
			} else {
				ctx.registerEventTimeTimer(window.maxTimestamp());
				return TriggerResult.CONTINUE;
			}
		}

		@Override
		public TriggerResult onEventTime(long time, TimeWindow window, TriggerContext ctx) {
			return time == window.maxTimestamp() ?
					TriggerResult.FIRE :
					TriggerResult.CONTINUE;
		}

		@Override
		public TriggerResult onProcessingTime(long time, TimeWindow window, TriggerContext ctx) throws Exception {
			return TriggerResult.CONTINUE;
		}

		@Override
		public void clear(TimeWindow window, TriggerContext ctx) throws Exception {
			ctx.deleteEventTimeTimer(window.maxTimestamp());
		}

		@Override
		public boolean canMerge() {
			return true;
		}

		@Override
		public TriggerResult onMerge(TimeWindow window,
									 OnMergeContext ctx) {
			ctx.registerEventTimeTimer(window.maxTimestamp());
			return TriggerResult.CONTINUE;
		}

		@Override
		public String toString() {
			return "EventTimeTrigger()";
		}

	}

}