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What is the best way for softcoding schedule tasks in Spring Boot?

In my Spring program, I have a Scheduled task.
#Scheduled(cron = "0 0 0 2 * *") // hardcoded schedule
public void executeBatchJob() {
batchJob.execute();
}
I have a specification change and now have to let the user freely configure the date and time of execution via an API.
One way I came up was to run a scheduled task every morning at 0:00 and check if the date is indeed the date of execution. If true, check the time of execution and schedule the batch job to run at that time of the day.
Is there a "Spring" way of achieving this?

Triggers can be used to configure the scheduled jobs.
From the docs
The basic idea of the Trigger is that execution times may be determined based on past execution outcomes or even arbitrary conditions.
Check out this answer for detailed explanation.

Confused Between Task Queue and Cron Jobs

I have around 1000 entries in my datastore and this is likely to increase with time to around 10,000 entries. My task is to update each row's certain properties and save it back and this task has to be performed every 24 hours.
So, what should I use?

First, you create a cron job that runs every 24 hours.
Second, you need to decide what this cron job will do. The simplest option is to update all 1,000 records. You can retrieve and save all entities in large batches (i.e. 500 per call). If this is a simple update of values, it will take just a few seconds.
Since cron jobs are not retried if they fail, a better option is to create a task and add it to the queue. All updates will happen within that task.
NB: Make sure that if your task is retried, it won't mess the data. If this is not possible, you will have to use some kind of flag (i.e. timestamp of last update) to separate updated entities from those that still need updates.
As your data set grows, your cron job can start multiple tasks to update, for example, 1,000 records in each task.

In the task queue the tasks have to be added to the queue manually though code. If you want to do this task automatically every x time, what you need is a cron job.

You need both,
Cron job to start your batch update job every 24 hours
Task-queues to process you records.

Execute MySQL statement in the background automatically

I want to delete records from MySQL table which were not updated for longer than 3 minutes. How can I set the timer in the background to manage it without being invoked by events or methods in java? Is that possible?
DELETE FROM bus WHERE created_at < (NOW() - INTERVAL 5 MINUTE)

As #abhishek-ghosh correctly pointed out, you can use CREATE EVENT.
CREATE EVENT event_bus_delete
EVERY 5 MINUTE
DO
DELETE FROM bus WHERE created_at < (NOW() - INTERVAL 5 MINUTE);
Event support was added in MySQL 5.1.6. However MySQL Event Scheduler is not running by default and needs to be enabled in order for events to work.
See this StackOverflow answer or How to Configure MySQL Event Scheduler article on how to enable MySQL Event Scheduler and make sure it's running.
You can ensure the scheduler starts when MySQL is launched with the command-line option --event-scheduler=ON or setting event_scheduler=ON in your MySQL configuration file (my.cnf or my.ini on Windows).
Alternatively, you can start the scheduler from the MySQL command line:
SET GLOBAL event_scheduler = ON;

Edit
Misread your question - the following describes how you can use Java to schedule the task rather than doing it independently of the Java layer
You can achieve this by using a combination of Timer and TimerTask. Together they form quite a simple scheduling facility. The Timer schedules TimerTasks that occur periodically.
There are a number of good tutorials on the web : for example

Java Executor in timerange at specific time

I need to call a task every x hour in a defined time range and repeat this every day.
My only idea is to calculate the executions times as delay from current time and start each in a seperated thread via scheduleAtFixedRate and a rate of 24 hours.
Do anyone has a better idea?
Regards

Use your machines in built task schedule to call a script and call your java program from that script.

You can use a library dedicated to schedule code: quartz
It use cron like syntax and can schedule Job implementations.

How to configure a thread that execute on a given time

I am making a meeting broadcast application which will broadcast the message to the participant of meeting.
There is a meeting data checker thread which execute after 5 minute.
I have done this using this code :
ScheduledExecutorService scheduledExecutorService = Executors.newScheduledThreadPool(1);
scheduledExecutorService.scheduleWithFixedDelay(new DataAccessSchedule(), 0, 5,TimeUnit.MINUTES);
Now the in DataAccessScedule the query get the data of meeting which are expected to be started after 15 minutes,so I get the data before 15 minutes and the time in table are: 01:45 ,... 01:50 , ... 01:52 ,..
so i have calculated the time of all in millisecond by taking difference from current time so now the time in milis are x,y and z.
I want to fire the thread on x , y and z time and these thread destroy itself after execution.I do not want to run scheduler here like above did using Executors.
Please tell me how should i do that ?

You need a scheduler library for that, for example Quartz Scheduler, that supports cron expressions to specify exactly when the task should be launched.
You can also configure it to run the task finite number of times.
An alternative for writing sheduler library would be to write the similar functionality yourself. You'll need one task running periodically, with the precision you require (it could be 1 minute, but also 1 second) and checking all entries in the data structure, if their start condition matches current date (for example, by matching the date/time against cron expression). It would be, however, reinventing the wheel so don't do as long if you don't want some extra funktionality the existing libraries doesn't provide.