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Java command-line application somehow retains state

Foreword: I apologise if this is a very silly error or something that is in fact well-documented. To me right now it seems very strange and makes absolutely no sense.
The Application
I have a Java command-line application built in IntelliJ IDEA Ultimate on macOS 10.13.4 that makes use of four Maven libraries listed below. Its purpose is to download files from a website, and navigates across paginated results in doing so.
One of this application's features is the ability to keep running in a loop, checking for new results if enough time has passed by the time it finishes its current scan. To do this, it calls Thread.sleep(remainingMillis) as part of the while condition in a do-while block.
The Problem
The application worked without any issues, but after introducing the Thread.sleep() call (I suspect this is the troublesome line anyways), some very strange behaviour occurs: The application performs the first run without issues, fetching three items from the configured website; it is then configured to ensure that 60 seconds have passed before running again. However upon consequent runs, rather than scan the first page of results, logs indicate that it starts looking at page 31 (as an example), where it finds no results. Having failed to find anything, attempt two of three looks at page 32, and the final attempt looks at page 33; it then once again waits until 60 seconds have passed since the scan iteration began.
I can't confirm this, but it seems as though it then continues this count in subsequent scans: 34, 35, then 36, and waiting again. However, the code would suggest that this should have started at 1 again when another iteration of the while starts up.
This could have been IntelliJ or Java playing up, and it may have simply required cleaning out the bin/obj folders, but if this is something due to my code, I would much rather know about it so I don't encounter the same silly issue in the future.
The Observations
Having just run the application a few days later with the current configuration means that it doesn't call Thread.sleep(), as more than 60 seconds pass so it continues with the next iteration immediately; when this happens, the weird page index incrementing issue doesn't rear its head - instead the next iteration continues from page 1 as it should.
Afterwards, running it such that it did Thread.sleep() for several seconds before starting the next iteration didn't cause a problem either... very strange. Was this a dream?
The Code
Sidenote: I added Thread.currentThread().interrupt() to try and fix this issue, but it didn't seem to have an effect.
public static void main(String[] args) {
do {
startMillis = System.currentTimeMillis();
int itemsFetched = startFetching(agent, config, record, 1, 0);
} while (shouldRepeat(config.getRepeatSeconds(), startMillis));
}
private static boolean shouldRepeat(int repeatSeconds, long startMillis) {
long passedMillis = System.currentTimeMillis() - startMillis;
int repeatMillis = repeatSeconds * 1000;
boolean repeatSecondsReached = passedMillis >= repeatMillis;
if (repeatSeconds < 0) {
return false;
} else if (repeatSecondsReached) {
return true;
}
long remainingMillis = repeatMillis - passedMillis;
int remainingSeconds = (int) (remainingMillis / 1000);
try {
Thread.sleep(remainingMillis);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
throw new RuntimeException(e);
}
return true;
}
private static int startFetching(Agenter agent, MyApplicationConfig config, MyApplicationRecord record, int pageIndex, int itemsFetched) {
String categoryCode = config.getCategoryCode();
List<Item> items = agent.getPageOfItems(categoryCode, pageIndex, config);
if (items == null) {
return itemsFetched;
}
int maxItems = config.getMaxItems();
try {
for (Item item : items) {
String itemURL = item.getURL();
agent.downloadItem(itemURL, config, item.getItemCount());
itemsFetched++;
if (maxItems > 0 && itemsFetched >= maxItems) {
return itemsFetched;
}
}
} catch (IOException e) {
// Log
}
return startFetching(agent, config, record, pageIndex + 1, itemsFetched);
}
}
Maven Libraries
commons-cli:commons-cli:1.4
org.apache.logging.log4j:log4j-api:2.11.0
org.apache.logging.log4j:log4j-core:2.11.0
org.jsoup:jsoup:1.11.2

Check your Agenter implementation, in the call of
agent.getPageOfItems the pageIndex is supplied but could be stored there in an instance variable or something like that. The error itself might be that on additional calls it probably didn't get reset (correctly).

How to create a single thread cooldown

I'm finding the way to make a Single thread cooldown but get stuck.
In the class who manages the cooldown I created a:
private HashMap<UUID,Integer> players = new HashMap<>();
//UUID = Player UUID
//Integer = Time in cooldown (Seconds)
public void run(){
for(UUID player : players){
//WHAT I NEED TO DO HERE?
if(//Time == 0){
players.remove(player);
}
}
}
Didn't use an IDE hopefully I didn't miss an error that eclipse would have picked up.
But how I can get the integer and save it with a second less?

TimeUnit is used for delaying a process, as it could be used as followed:
TimeUnit.SECONDS.sleep(1);
This will delay the current thread by one second.
I won't suggest using it, because your situation sounds more like a thread is working in the background and you want to wait till it has finished! Therefore use the new feature isAlive, which could be used in a (while) loop.
Edit
If you do want to delay a thread from another thread over the instance, then I'd suggest using the sleep method.
Example:
myThread.sleep(1000);
This will delay myThread by one second.
Edit #2
To change a value for a certain key of a HashMap, use the put and get method.
Example:
// Get the time of a player and subtract it by one
Integer value = players.get(player) - 1;
// Update the value
players.put(player, value);
// If the time runs out, than delete the player
if (value == 0){
players.remove(player);
}

Java: First iteration of for loop takes longer

I am writing some code to test using the MIDI libraries in Java, and have run across a problem. The pause between notes is much longer (almost twice as long, in fact) after the very first note than after all the others. I can't see any reason why, as the sequence of notes has already been generated (hence it is not also having to perform those calculations within the first iteration of the loop, it is only playing notes).
I think I may have also had this problem in the past with a simulation which, without any explanation I could find, took almost 100% of its tick length to perform calculations on the first tick only, and then used only about 2% on all successive iterations.
Main code (extract):
public void play() {
MidiPlayer player = new MidiPlayer();
for (int i = 0; i < NUMNOTES; i++) {
long tic = System.currentTimeMillis();
player.playNote(10, notes[i]);
try {
Thread.sleep(200);
} catch (InterruptedException e) {
e.printStackTrace();
}
long toc = System.currentTimeMillis();
System.out.println(toc - tic);
}
try {
Thread.sleep(500);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
Code for playNote():
public void playNote(int channel, int note) {
channels[channel].allNotesOff();
channels[channel].noteOn(note + 60, volume);
}
There are no 'if' statements that specify the first loop, so surely the delay should be uniform for all notes, as the number of calculations being performed should be the same for all iterations. Please note that the timing variables are just for testing purposes, and the effect was audibly noticeable before I included those.
EDIT: I should also mention that the output produced shows each iteration of the loop taking the expected 200 (occasionally 201) milliseconds. It seems to suggest that there is no gap - yet I clearly hear a gap every time I run the code.

Since you have sleeps, you should calculate how long you should sleep instead of trying to sleep the same amount of time each time - calculate how much more time you actually need to the next note to be played and sleep that much amount. i.e.
long tic = System.currentTimeMillis();
player.playNote(10, notes[i]);
long time_spent = System.currentTimeMillis() - tic;
Thread.sleep(200 - time_spent);

Simulating a Grocery Store Line Queue using Java

So I have a problem I've been wracking my brain over for about a week now. The situation is:
Consider a checkout line at the grocery store. During any given
second, the probability that a new customer joins the line is 0.02 (no
more than one customer joins the line during any given second). The
checkout clerk takes a random amount of time between 20 seconds to 75
seconds to serve each customer. Write a program to simulate this
scenario for about ten million seconds and print out the average
number of seconds that a customer spends waiting in line before the
clerk begins to serve the customer. Note that since you do not know
the maximum number of customers that may be in line at any given time,
you should use an ArrayList and not an array.
The expected average wait time is supposed to be between 500 and 600 seconds. However, I have not gotten an answer anywhere close to this range. Given that the probability of a new customer in the line is only 2%, I would expect the line to never have more than 1 person in it, so the average wait time would be about 45-50 secs. I have asked a friend (who is a math major) what his view on this problem, and he agreed that 45 seconds is a reasonable average given the 2% probability. My code so far is:
package grocerystore;
import java.util.ArrayList;
import java.util.Random;
public class GroceryStore {
private static ArrayList<Integer> line = new ArrayList();
private static Random r = new Random();
public static void addCustomer() {
int timeToServe = r.nextInt(56) + 20;
line.add(timeToServe);
}
public static void removeCustomer() {
line.remove(0);
}
public static int sum(ArrayList<Integer> a) {
int sum = 0;
for (int i = 0; i < a.size(); i++) {
sum += a.get(i);
}
return sum;
}
public static void main(String[] args) {
int waitTime = 0;
int duration = 10000;
for (int i = 0; i < duration; i++) {
double newCust = r.nextDouble();
if (newCust < .02) {
addCustomer();
}
try {
for (int j = 0; j < line.get(0); j++) {
waitTime = waitTime + sum(line);
}
} catch (IndexOutOfBoundsException e) {}
if (line.isEmpty()) {}
else {
removeCustomer();
}
}
System.out.println(waitTime/duration);
}
}
Any advice about this would be appreciated.

Here's some pseudocode to help you plan it out
for each second that goes by:
generate probability
if probability <= 0.02
add customer
if wait time is 0
if line is not empty
remove customer
generate a new wait time
else
decrement wait time

There's actually a very easy implementation of single server queueing systems where you don't need an ArrayList or Queue to stash customers who are in line. It's based on a simple recurrence relation described below.
You need to know the inter-arrival times' distribution, i.e., the distribution of times between one arrival and the next. Yours was described in time-stepped fashion as a probability of 0.02 of having a new arrival in a given tick of the clock. That equates to a Geometric distribution with p = 0.02. You already know the service time distribution - Uniform(20,75).
With those two pieces of info, and a bit of thought, you can deduce that for any given customer the arrival time is the previous customer's arrival-time plus a (generated) interarrival time; this customer can begin being served at either their arrival-time or the departure-time of the prior customer, whichever comes later; and they finish up with the server and depart at their begin-service time plus a (generated) service-time. You'll need to initialize the arrival-time and departure time of an imaginary zeroth customer to kick-start the whole thing, but then it's a simple loop to calculate the recurrence.
Since this looks like homework I'm giving you an implementation in Ruby. If you don't know Ruby, think of this as pseudo-code. It should be very straightforward for you to translate to Java. I've left out details such as how to generate the distributions, but I have actually run the complete implementation of this, replacing the commented lines with statistical tallies, and it gives average wait times around 500.
interarrival_time = Geometric.new(p_value)
service_time = Uniform.new(service_min, service_max)
arrival_time = depart_time = 0.0 # initialize zeroth customer
loop do
arrival_time += interarrival_time.generate
break if arrival_time > 10_000_000
start_time = [arrival_time, depart_time].max
depart_time = start_time + service_time.generate
delay_in_queue = start_time - arrival_time
# do anything you want with the delay_in_queue value:
# print it, tally it for averaging, whatever...
end
Note that this approach skips over the large swathes of time where nothing is happening, so it's a quite efficient little program compared to time-stepping through every tick of the simulated clock and storing things in dynamically sized containers.
One final note - you may want to ignore the first few hundred or thousand observations due to initialization bias. Simulation models usually need a "warm-up" period to remove the effect of the programmatically necessary initialization of variables to arbitrary values.

Instead of using an ArrayList, a Queue might be better suited for managing the customers. Also, remove the try/catch clause and a throws IndexOutOfBoundsException to the main function definition.

Java - add time delay to a cycle flow

I need to add time delay between cycle flow like this:
public boolean timeDelay(int seconds) {
// 1000000000 ns = 1 s
if (/* some system method to start calculate time in seconds*/ == seconds) {
return true;
} else {
return false;
}
}
public void renderEnemies() {
for (int w = 0; w < wave.size(); w++) {
while(timeDelay(2)){
(wave.get(w)).render();
}
}
}
Maybe my thinking isn't good, but I need to do like this...
wave --> ArrayList of enemies in my game
Render enemies is in game loop after pressing button "NextWave" and I need to spawn them with delay between them like a --> 2s * 2s * 2s * 2s * 2s *
where * is enemy...
Can you help me?

Try:
Thread.sleep(1000);
and use a try-catch.

You should probably thread it and use sleep as #curiosu mentions.
However, if you don't want to use sleeps/multiple threads but do want it to be pseudo real time (not turn based) you'll need a driving loop at the top of your game like so:
boolean keepPlaying = true;
while(keepPlaying) {
doNpcStep()
doPlayerStep()
keepPlaying = !isGameOver()
}
Each of these steps needs to run in a very small time slice, then in the doNpcStep function you get the current time, find the offset from a start time and run any action that should happen by now.
You could, for example, do this by keeping a min priority queue where priority is equal to the time they should execute by (in ms since start of java epoch). Then take all elements off the queue that are less than or equal to current time and run them, placing new occurrences onto the queue as necessary.
In essence this is a simulation of running a player and npc thread, where you are in charge of how much time each gets to run for.

try putting an infinite while loop
while(1)
{
if(/*method to calc time*/ == seconds)
return true;
}
return false;
I'm assuming that you want to start spawning enemies after 'seconds' time, so always a 'true' should be returned after 'seconds' time has passed. Your method should keep track from what time it has to start counting the seconds. You can call that function when 'NextWave' button is pressed where a variable can increment itself in multiples of 'seconds' so that you can keep track of elapsed time.
Hope this helps.