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Should I use Instant or DateTime or LocalDateTime in Java entities?

In my Java (with Spring Boot and Spring Data JPA) applications, I generally use Instant. On the other hand, I would like to use the most proper data type for time values.
Could you please clarify me about these issues? What data type should I prefer for keeping date and time when:
1. To keep time precisely as timestamp (I am not sure if Instant is the best option)?
2. For normal cases when I just need date and time (as far as I know, the old library was obsolete, but not sure which library should I use).
I also consider the TimeZone, but not sure if using LocalDateTime with UTC solves my problem.
Any help would be appreciated.

Let's assume we need to cover the full span of date and time concerns. If there is a certain concern you don't have, that either collapses various types into 'well then they are interchangible' or simply means you don't need to use a certain part of the API. The point is, you need to understand what these types represent, and once you know that, you know which one to apply. Because even if various different java.time types all technically do what you want, code is more flexible and a lot simpler to read if the types you use represent the things you want them to. For the same reason String[] student = new String[] {"Joe McPringle", "56"}; is perhaps mechanically a way to represent a student's name and age, but things are just a lot simpler if you write a class Student { String name; int age; } and use that instead.
Local alarm clock
Imagine you want to wake up at 07:00 in the morning. Not because you have an appointment, you just like to be a fairly early riser.
So you set your alarm for 07:00 in the morning, go to sleep, and your alarm promptly goes off at 7. So far, so good. However, you then hop in a plane and fly from Amsterdam to New York. (it is 6 hours earlier in new york). You then go to sleep again. Should the alarm go off at 01:00 at night, or at 07:00 in the morning?
Both answers are correct. The question is, how do you 'store' that alarm, and to answer that question, you need to figure out what the alarm is attempting to represent.
If the intent is '07:00, whereever I might be at the time the alarm is supposed to go off', the correct data storage mechanism is java.time.LocalDateTime, which stores time in human terms (years, months, days, hours, minutes, and seconds) and not in computery terms (we'll get there later), and does not include a time zone at all. If the alarm is supposed to go off every day, then you don't want that either, as LDT stores date and time, hence the name, you'd use LocalTime instead.
That's because you wanted to store the concept of 'the alarm should go off at 7 o'clock' and nothing more than that. You had no intention of saying: "The alarm should go off when people in Amsterdam would agree it is currently 07:00", nor did you have the intent of saying: "When the universe arrives at this exact moment in time, sound the alarm". You had the intent of saying: "When it is 07:00 where-ever you are now, sound the alarm", so store that, which is a LocalTime.
The same principle applies to LocalDate: It stores a year/month/day tuple with no notion of where.
This does draw some perhaps wonky conclusions: Given a LocalDateTime object, it is not possible to ask how long it'll take until that LDT arrives. It is also not possible for any given moment in time to be compared to an LDT, because these things are apples and oranges. The notion 'Feb 18th, 2023, 7 in the morning on the dot' isn't a singular time. After all, in New York that 'moment' occurs a full 6 hours earlier than it would in Amsterdam. You can only compare 2 LocalDateTimes.
Instead, you would have to first 'place' your LDT somewhere, by converting it to one of the other types (ZonedDateTime or even Instant) by asking the java.time API: Okay, I want this particular LDT in a certain time zone.
Hence, if you are writing your alarm app, you would have to take the stored alarm (a LocalTime object), convert it to an Instant (which is what the nature of 'what time is it now, i.e. System.currentTimeMillis()' works on), by saying: That LocalTime, on the current day in the current local timezone, as an instant, and THEN comparing those two results.
Human appointments
Imagine that, just before jetting off to New York, you made an appointment at your local (in Amsterdam) barber. Their agenda was kinda busy so the appointment was set for June 20th, 2025, at 11:00.
If you stay in New York for a few years, the correct time for your calendar to remind you that you have an appointment with your barber's in an hour is certainly not at 10:00 on june 20th 2025 in New York. You'd have missed the appointment by then. Instead, your phone should chirp at you that you have an hour left to get to your barber's (a bit tricky, from New York, sure) at 04:00 in the middle of the night.
It sure sounds like we can say that the barber's appointment is a specific instant in time. However, this is not correct. The EU has already adopted legislation, agreed upon by all member states, that all EU countries shall abolish daylight savings time. However, this law does not provide a deadline, and crucially, does not provide a time zone that each EU member state needs to pick. The Netherlands is therefore going to change time zones at some point. They will likely choose to stick either to permanent summer time (in which case they'd be at UTC+2 permanently, vs. their current situation where they are at UTC+2 in summer and UTC+1 in winter, with, notably, different dates when the switch happens vs. New York!), or stay on winter time, i.e. UTC+1 forever.
Let's say they choose to stick to winter time forever.
The day the gavel slams down in the dutch parliament building enshrining into law that the dutch will no longer advance the clocks in march is the day your appointment shifts by one hour. After all, your barber is not going to go into their appointment book and shift all appointments by an hour. No, your appointment will remain on June 20th, 2025, at 11:00. If you have a running clock ticking down the seconds until your barber appointment, when that gavel comes down it should jump by 3600 seconds.
This belies the point: That barber appointment truly is not a singular moment in time. It's a human/political agreement that your appointment is when Amsterdam universally agrees it is currently June 20th, 2025, 11:00 – and who knows when that moment will actually occur; it depends on political choices.
So, you cannot 'solve' this by storing an instant in time, and it shows how the concept 'instant in time' and 'year/month/day hour:minute:second in a certain timezone' are not quite interchangible.
The correct data type for this concept is a ZonedDateTime. This represents a date time in human terms: year/month/day hour:second:minute, and the timezone. It doesn't shortcut by storing a moment in time in epochmillis or some such. If the gavel comes down and your JDK updates its timezone definitions, asking "how many seconds until my appointment" will correctly shift by 3600 seconds, which is what you want.
Because this is for appointments and it doesn't make sense to store just the time of an appointment but not the date, there is no such thing as a ZonedDate or a ZonedTime. Unlike the first thing which comes in 3 flavours (LocalDateTime, LocalDate, and LocalTime), there's only ZonedDateTime.
The universe/log time
Imagine you are writing a computer system that logs that an event occurred.
That event, naturally, has a timestamp associated with it. Turns out that due to severe political upheaval, the laws of the land decide that retrospectively the country has been in a different timezone than what you thought when the event occurred. Applying the same logic as the barber's case (where the actual moment in time jumps by 3600 seconds when the gavel comes down) is incorrect. The timestamp represents a moment in time when a thing happened, not an appointment in a ledger. It should not jump by 3600.
Timezone really has no purpose here. The point of storing 'timestamp' for a log event is so you know when it happened, it doesn't matter where it happened (or if it does, that is fundamentally a separate notion).
The correct data type for this is java.time.Instant. An instant doesn't even know about time zones at all, and isn't a human concept. This is 'computery time' - stored as millis since an agreed upon epoch (midnight, UTC, 1970, new years), no timezone information is necessary or sane here. Naturally there is no time-only or date-only variant, this thing doesn't even really know what 'date' is - some fancypants human concept that computery time is not concerned with in the slightest.
Conversions
You can trivially go from a ZonedDateTime to an Instant. There's a no-args method that does it. But note:
Create a ZonedDateTime.
Store it someplace.
Convert it to an Instant, store that too.
Update your JDK and get new time zone info
Load the ZDT.
Convert it to an Instant a second time.
Compare the 2 ZDTs and the 2 instants.
Results in different results: The 2 instants would not be the same, but the ZDTs are the same. The ZDT represents the appointment line in the barber's book (which never changed - 2025 june 20th, 11:00), the instant represents the moment in time that you are supposed to show up which did change.
If you store your barber's appointment as a java.time.Instant object, you will be an hour late to your barber's appointment. That's why it's important to store things as what they are. A barber's appointment is a ZonedDateTime. storing it as anything else would be wrong.
Conversions are rarely truly simple. There is no one way to convert one thing to another - you need to think of what these things represent, what the conversion implies, and then follow suit.
Example: You are writing a logging system. The backend parts store log events into a database of some sort, and the frontend parts read this database and show the log events to an admin user for review. Because the admin user is a human being, they want to see it in terms they understand, say, the time and date according to UTC (it's a programmer, they tend to like that sort of thing).
The logging system's storage should be storing the Instant concept: Epoch millis, and without timezone because that is irrelevant.
The frontend should read these as Instant (it is always a bad idea to do silent conversions!) - then consider how to render this to the user, figure out that the user wants these as local-to-UTC, and thus you would then on the fly, for each event to be printed to screen, convert the Instant to a ZonedDateTime in the zone the user wants, and from there to a LocalDateTime which you then render (because the user probably does not want to see UTC on every line, their screen estate is limited).
It would be incorrect to store the timestamps as UTC ZonedDateTimes, and even more wrong to store them as LocalDateTimes derived by asking for the current LocalDT in UTC as the event happens and then storing that. Mechanically all these things would work but the data types are all wrong. And that will complicate matters. Imagine the user actually wants to see the log event in Europe/Amsterdam time.
A note about timezones
The world is more complicated than a handful of timezones. For example, almost all of mainland europe is currently 'CET' (Central European Time), but some think that refers to european winter time (UTC+1), some thing that refers to the current state in central europe: UTC+1 in winter, UTC+2 in summer. (There's also CEST, Central European Summer Time, which means UTC+2 and isn't ambiguous). When EU countries start applying the new law to get rid of daylight savings, its likely e.g. The Netherlands on the west edge of the CET zone picks a different time than Poland on the eastern edge. Hence, 'all of central europe' is far too broad. 3-letter acronyms also are by no means unique. Various countries use 'EST' to mean 'eastern standard time', it's not just the eastern USA for example.
Hence, the only proper way to represent timezone names is using strings like Europe/Amsterdam or Asia/Singapore. If you need to render these as 09:00 PST for residents of the west coast of the USA, that's a rendering issue, so, write a rendering method that turns America/Los_Angeles into PST, which is an issue of localization, and has nothing to do with time.

The Answer by rzwitserloot is correct and wise. In addition, here is a summary of the various types. For more info, see my Answer on a similar Question.
To keep time precisely as timestamp (I am not sure if Instant is the best option)?
If you want to track a moment, a specific point on the timeline:
InstantA moment as seen with an offset-from-UTC of zero hours-minutes-seconds. This class is the basic building-block of the java.time framework.
OffsetDateTimeA moment as seen with a particular offset, some number of hours-minutes-seconds ahead of, or behind, the temporal meridian of UTC.
ZonedDateTimeA moment as seen with a particular time zone. A time zone is a named history of the past, present, and future changes to the offset used by the people of a particular region, as decided by their politicians.
If you want to track just the date and time-of-day, without the context of an offset or time zone, use LocalDateTime. This class does not represent a moment, is not a point on the timeline.
For normal cases when I just need date and time
If you are absolutely sure that you want only a date with time-of-day, but do not need the context of an offset or time zone, use LocalDateTime.
using LocalDateTime with UTC
That is a contradiction, and makes no sense. A LocalDateTime class has no concept of UTC, nor any concept of offset-from-UTC or time zone.
Spring Data JPA
The JDBC 4.2+ specification maps SQL standard data types to Java classes.
TIMESTAMP WITH TIME ZONE columns map to OffsetDateTime in Java.
TIMESTAMP WITHOUT TIME ZONE columns map to LocalDateTime in Java.
DATE columns map to LocalDate.
TIME WITHOUT TIME ZONE columns map to LocalTime.
The SQL standard also mentions TIME WITH TIME ZONE, but this type is meaningless (just think about it!). The SQL committee has never explained what they had in mind, as far as I know. If you must use this type, Java defines the ZoneOffset class to match.
Note that JDBC does not map any SQL types to Instant nor ZonedDateTime. You can easily convert to/from the mapped type OffsetDateTime.
Instant instant = myOffsetDateTime.toInstant() ;
OffsetDateTime myOffsetDateTime = instant.atOffset( ZoneOffset.UTC ) ;
… and:
ZonedDateTime zdt = myOffsetDateTime.atZoneSameInstant( myZoneId ) ;
OffsetDateTime odt = zdt.toOffsetDateTime() ; // The offset in use at that moment in that zone.
OffsetDateTime odt = zdt.toInstant().atOffset( ZoneOffset.UTC ) ; // Offset of zero hours-minutes-seconds from UTC.
I also consider the TimeZone
The TimeZone class is part of the terrible legacy date-time classes that were years ago supplanted by the modern java.time classes. Replaced by ZoneId and ZoneOffset.

You should take a look at the Java Date and Time API introduced with Java 8. Each class like Instant, LocalDateTime, ZonedDateTime etc. has a documentation as JavaDoc. If you have problems understanding the documentation, please provide a more specific question.

Getting the UTC timestamp in Java

An old Stack Overflow posting suggests that the way to get the UTC timestamp in Java is the following:
Instant.now() // Capture the current moment in UTC.
Unfortunately this does not work for me. I have a very simple program (reproduced below) which demonstrates different behavior.
On Windows: the time is the local time and it is labeled with the offset with GMT
On Linux: the time is again the local time, and it is labeled correctly for the local timezone
Question: How do we display the UTC timestamp in a Java program?
My sample source code is as follows:
import java.time.Instant;
import java.util.Date;
public class UTCTimeDisplayer {
public static void main(String[] args) {
System.out.println(System.getProperty("os.name"));
Date currentUtcTime = Date.from(Instant.now());
System.out.println("Current UTC time is " + currentUtcTime);
}
}
Windows Output:
C:\tmp>java UTCTimeDisplayer
Windows 10
Current UTC time is Fri Jan 22 14:28:59 GMT-06:00 2021
Linux Output:
/tmp> java UTCTimeDisplayer
Linux
Current UTC time is Fri Jan 22 14:31:10 MST 2021

Your code:
Date.from(Instant.now())
You are mixing the terrible legacy classes with their replacement, the modern java.time classes.
Don’t.
Never use Date. Certainly no need to mix with java.time.Instant.
To explain your particular example, understand that among the Date class’ many poor design choices is the anti-feature of its Date#toString method implicitly applying the JVM’s current default time zone while generating its text.
You ran your code on two different JVMs that had different current default time zones. So you got different outputs.
Sun, Oracle, and the JCP gave up on the legacy date-time classes. So should we all. I recommend you not spend time trying understand Date, Calendar, SimpleDateFormat, and such.
You asked:
Question: How do we display the UTC timestamp in a Java program?
Instant.now().toString()
See that code run live at IdeOne.com.
2021-01-22T21:50:18.887335Z
You said:
On Windows: …
On Linux: …
You’ll get the same consistent results from Instant.now().toString() across Windows, Linux, BSD, macOS, iOS, Android, AIX, and so on.
Here is a table I made to guide you in transitioning from the legacy classes.

The java.util.Date object is not a real date-time object like the modern date-time types; rather, it represents the number of milliseconds since the standard base time known as "the epoch", namely January 1, 1970, 00:00:00 GMT (or UTC). When you print an object of java.util.Date, its toString method returns the date-time in the JVM's timezone, calculated from this milliseconds value. If you need to print the date-time in a different timezone, you will need to set the timezone to SimpleDateFormat and obtain the formatted string from it.
I would suggest you simply use Instant.now() which you can convert to other java.time type.
The date-time API of java.util and their formatting API, SimpleDateFormat are outdated and error-prone. It is recommended to stop using them completely and switch to the modern date-time API.
For any reason, if you have to stick to Java 6 or Java 7, you can use ThreeTen-Backport which backports most of the java.time functionality to Java 6 & 7.
If you are working for an Android project and your Android API level is still not compliant with Java-8, check Java 8+ APIs available through desugaring and How to use ThreeTenABP in Android Project.
However, if you still want to use java.util.Date, use SimpleDateFormat as mentioned above.
Demo:
import java.text.SimpleDateFormat;
import java.time.Instant;
import java.util.Date;
import java.util.TimeZone;
public class Main {
public static void main(String[] args) {
Date currentUtcTime = Date.from(Instant.now());
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss z");
sdf.setTimeZone(TimeZone.getTimeZone("Etc/UTC"));
System.out.println("Current UTC time is " + sdf.format(currentUtcTime));
}
}
Output:
Current UTC time is 2021-01-22 21:53:07 UTC

suggests that the way to get the UTC timestamp in Java is the following:
Instant.now() // Capture the current moment in UTC.
This, and most answers in this thread, are misleading.
Instant represents an instant in time. It's 'solarflares' time: Absolutely not one iota about it represents anything that is invented by human brains, and UTC is a timezone: A human invention. The cosmos, the sun, astronomy - they have no idea what UTC is, and don't care - and that's what Instant is all about. Instants are devoid of such human concepts as 'hours' or 'days' or 'timezones'. It makes no sense to ask an instant what day it happened on. It cannot tell you; some event occurred: If I ask a russian from the 19th century when that happened, they'll likely give a completely different answer vs. if I ask someone living a mere 100 miles west, for example. Instant doesn't know which localization to apply and thus doesn't let you ask it this question - that's a good thing, objects should not expose methods to which any answer it gives is either gobbledygook or at least requires knowing about all sorts of surprising caveats.
Crucially, if you tell me '... in UTC', you surely can tell with exacting detail which month, which day, etcetera. And Instant does not do this, which is why it is misleading to say that a java.time.Instant represents a moment of time in UTC. It doesn't. It represents a moment in time (not in any particular timezone).
Yeah, internally Instant, just like Date, is just a light wrapper around what System.currentTimeMillis() returns: "millis since epoch", but the crucial thing to understand about it, is that 'UTC' is not part of what it means, and therefore, when you give an Instant instance to some other method (such as System.out.println, to a database via JDBC, etc), that method is under absolutely no obligation to assume that UTC is semantically relevant.
When you want to mix human notions of time keeping (years, days, months, hours, minutes, milliseconds, and, yeah, timezones) with the notion of a more or less absolute* time, the right answer is java.time.ZonedDateTime. Note that any representation of time in something that isn't java.time.* based is by definition broken, as it is in most programming languages - turns out time is a lot more complex than most takes on a library to represent it realize. The fact that java.time is in effect the 4th attempt at writing a time library should be ample indication that it's hard to get it right.
ZonedDateTime zdt = ZonedDateTime.now(ZoneOffset.UTC);
THAT is what you want - that isn't just implementation-detail-wise what you want, but it is code that exactly describes what you mean: Right now, at the UTC time zone, stored in an object that semantically doesn't just store the right time but also stores, and tightly entangles into its very identity, that it is specifically in UTC and is not to be re-interpreted, moved to the local zone, or any other such shenanigans - at least, not unless you explicitly ask it to do so.
Date currentUtcTime = Date.from(Instant.now());
Note that Date is the old API and therefore necessarily broken. In this case, Date is a lying liar who lies - it doesn't represent a date, it represents an instant; it is badly named. (The second API is Calendar, also broken. For example, that is also a lying liar who lies: It doesn't represent a Calendar whatsoever. It represents some bizarre amalgamation of a zoned datetime and an instant and is fit to represent neither as a consequence). Any time you go to the Date API weirdness ensues, and something as simple as 'I just want the concept of the time, at some specific moment, in UTC' isn't possible in these APIs. You are now dependent on barely defined behaviour of all the various libraries up and down the chain - you're effectively stuck praying that they do the right thing, or delving into exotic settings to try to cajole these libraries into doing what you want.
TL;DR: Use java.time.
*) Note that ZonedDateTime is not absolute. For example, if you have the time January 20th, 2023, 8 in the morning, at Europe/Amsterdam, in the form of a ZonedDateTime object, then the amount of seconds that will pass between now and that moment sure seems like it does not change and will not change when e.g. amsterdam goes through an hour change due daylight savings. However, if the dutch government decrees that henceforth The Netherlands will no longer move the clocks at all and will stay in summer time forever (which is likely - EU directive is already in place, it's now just a matter of when), then at the moment the gavel lands, your appointment shifts by 1 hour exactly.
That hopefully provides crucial insight in the difference: Instant, representing events (hence why I like to call it 'solarflares time', to disentangle it from human time keeping concepts as much as possible), doesn't even understand the very concept of such a decision having an effect on things. ZonedDateTime on the other hand is inherently bound up in it - hence the Zone in ZonedDateTime.
If you want to store barber appointments and use Instant to do it, you WILL be an hour late or early sooner rather than later.

An Instant object and also a Date object by themselves
only contain a point in time, but no timezone information.
Furthermore, the toString() method of the Date class
implicitly chooses the timezone provided by the system environment,
which is not what you want.
Therefore you need to chose the timezone (in your case UTC) explicitly.
For example like this:
Instant instant = Instant.now();
OffsetDateTime offsetDateTime = instant.atOffset(ZoneOffset.UTC);
System.out.println("Current UTC time is " + offsetDateTime);
This will (independently from the operation system) print
Current UTC time is 2021-01-22T22:37:21.950354100Z
where the trailing Z denotes the zero timezone offset (i.e. UTC).

A simple method that could work!
My requirement was date time with milliseconds
2021-11-25 19:55:00.743
private String getUTCTimestamp() {
ZonedDateTime utc = ZonedDateTime.now(ZoneOffset.UTC);
return utc.format(DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss.SSS"));
}

Instant.now() is essentially the period of time since the epoch, (midnight 1 January 1970 in UTC), but you are using a Date to present that instant. Date is a reflection of the instant with millisecond precision, but as explained in the documentation at https://docs.oracle.com/javase/8/docs/api/java/util/Date.html, presenting a date should be done using a Calendar, as the presentation of a Date depends on the host. Essentially Date wraps the instant but is displayed according to other factors.
The simplest approach now if you want to output the instant is to use OffsetDateTime so that you can elect to present the instant in your desired timezone - UTC in your case. Use either OffsetDateTime.now() or OffsetDateTime.ofInstant() but if you are using the instant within your application logic then just stick with Instant.

Sometimes your program has to work with older java versions, so here is an example for 1.5:
java.text.SimpleDateFormat tfGMT = new java.text.SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
java.util.Calendar cUTC = java.util.Calendar.getInstance (java.util.TimeZone.getTimeZone ("GMT+0"));
tfGMT.setCalendar (cUTC);
java.util.Date d= new java.util.Date ();
String s= tfGMT.format (d);
System.out.printf ("now=%s [unix ts=%d.%03d]\n", s, d.getTime()/1000, d.getTime()%1000);
Mind you, the first three lines don't have to be repeat at every call, but keep in mind that SimpleDateFormat is not thread-safe. (Simple solution: create one for each thread.)
Example usage (it shows that setting TZ doesn't affect UTC-timestamp):
$ TZ=GMT+3 java5 now_utc; TZ=GMT-3 java5 now_utc
now=2021-01-24 12:56:14 [unix ts=1611492974.264]
now=2021-01-24 12:56:14 [unix ts=1611492974.726]

SimpleDateFormat parse method mystery

I am aware that SimpleDateFormat.parse rely on the Calendar API which depends on local JVM timezone (computer's). Assume JVM timezone is IST.
SimpleDateFormat srcDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
srcDateFormat.setTimeZone(TimeZone.getTimeZone("EST"));
Date objDt = srcDateFormat.parse("2018-10-16 11:28:25"); //Time : 21:58:25
From the output it seems it converts from EST to IST(JVM local timezone).
SimpleDateFormat srcDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
srcDateFormat.setTimeZone(TimeZone.getTimeZone("IST"));
Date objDt = srcDateFormat.parse("2018-10-16 11:28:25"); //Time : 11:28:25
It keeps time unmodified in this case. In this case I set timezone same as JVM local timezone.
Please help me to understand the behavior of the parse method. Nevertheless, I am curious to know the reason behind such behavior.
I know that java.util.Date and java.text.SimpleDateFormat legacy classes are obsolete now.
References:
Why SimpleDateFormat.format() and SimpleDateFormat.parse() are giving different time though setting only one TimeZone?
How do I convert date/time from one timezone to another?
SimpleDateFormat parses a string to wrong time
https://www.codeproject.com/Tips/1190426/When-Parsing-Formatting-Dates-in-Java-Make-Sure-Yo

First, you are correct that Date and SimpleDateFormat are legacy classes and now obsolete. So I recommend you don’t use them and use java.time, the modern Java date and time API, instead. Among many advantages it is much more explicit about conversions between time zones, which I would expect to help you understand what the code does.
Second, you are doing a number of things incorrectly or at least inadequately:
Don’t store date-times as strings. Always store them as date-time objects in Java. When you do this, you will never need to convert a date-time string from one zone to another. Instant (a class from java.time) is a point in time and as far as I can see the one you should use here.
Don’t rely in three letter time zone abbreviations. Very many of them are ambiguous, including both of IST and EST, and the latter isn’t a true time zone, so what you get at this time of year (when America/New_York zone uses EDT rather than EST), I don’t know.
And repeating myself, use the modern classes, not the obsolete ones.
Out of curiosity what happened?
An old-fashioned Date represents a point in time independently of time zone (internally it stores its value as a count of milliseconds since the epoch, but this is an implementation detail that we need not know or concern ourselves with).
In your first example your string is parsed into a point in time that corresponds to 16:28:25 UTC, 21:58:25 in India, 12:28:25 in New York or 11:28:25 in Jamaica. I mention Jamaica because it’s one of the few places that happens to use Eastern Standard Time (EST) all year. Most of the locations that use EST only do so in winter, not at this time of year. When you look at the Date in your debugger, the debugger calls toString on the Date to get a string to show you. toString in turn uses the JVM’s time zone for generating the string. In your case it’s Asia/Kolkata, which is why you get 21:58:25.
In the second case the same string is parsed into a point in time that corresponds to 05:58:25 UTC, 11:28:25 in India, 01:58:25 in New York or 00:58:25 in Jamaica. Your debugger again calls toString, which again uses your JVM’s time zone and converts back into 11:28:25 IST. When you parse and print in the same time zone, you get the same time of day back.
Links
EST – Eastern Standard Time / Eastern Time (Standard Time)
Oracle tutorial: Date Time explaining how to use java.time.
Time Zone Converter – Time Difference Calculator, online, practical for converting between Asia/Kolkata, UTC, Kingston (Jamaica), New York and other time zones.

Create company specific timezone for 'working day' in java

I work at a company where part of the work for a day is done in the early hours of the next day (i.e. shipping orders). Now for several processes (mainly reporting), we want to let the 'working day' end at 04:00 the next morning so we get more consistent reporting values per day.
We want this to always be at 04:00 the next morning and since we are affected by daylight saving times in our area (Europe - Netherlands) we effectively want a 4 hour shifted variant of our normal timezone 'Europe/Amsterdam' (in our case).
To make this as easy to use for all applications in our company I would like to create a small library that simply contains the code to provide my coworkers to get a modified instance of TimeZone that does this. That way all normal time/date manipulation methods can be used in conjunction with this special time zone.
I did a deep dive into the standard Java 8 code/Javadoc related to the TimeZone/ZoneInfo instances and at this moment I do not understand what the correct field is to change in the returned TimeZone/ZoneInfo instance.
At this point, my best guess is setting the RawOffset to 4 hours, but I'm not sure.
What is the correct way to achieve my goal?
Update:
I had a look at the suggested LocalTime and as I expected: It needs a timezone definition as being what it should use as "Local" when converting an existing timestamp (usually epoch milliseconds) into the "Local" timezone.
Looking at all these classes seems like I'll be using the LocalDate more often than the LocalTime.
Effectively the code I expect to have is something like this:
long epoch = 1525033875230L; // Obtained from some dataset
LocalDate localDate = LocalDateTime
.ofInstant(Instant.ofEpochMilli(epoch),
ZoneId.of("Europe/Amsterdam"))
.toLocalDate();
Where I expect that I need to change that Zone into the 'right one'.

If I have got that correctly, what you really need is a way to convert a milliseconds value since the epoch to a date in a way where days don’t change a 00:00 but not until 04:00.
static ZoneId zone = ZoneId.of("Europe/Amsterdam");
static LocalTime lastShiftEnds = LocalTime.of(4, 0);
public static LocalDate epochMilliToDate(long epoch) {
ZonedDateTime dateTime = Instant.ofEpochMilli(epoch)
.atZone(zone);
if (dateTime.toLocalTime().isAfter(lastShiftEnds)) { // normal date-time
return dateTime.toLocalDate();
} else { // belonging to previous day’s night shift
return dateTime.toLocalDate().minusDays(1);
}
}
Use for example like this:
long epoch = 1_525_050_875_230L;
System.out.println(Instant.ofEpochMilli(epoch));
LocalDate date = epochMilliToDate(epoch);
System.out.println(date);
Output is:
2018-04-30T01:14:35.230Z
2018-04-29
From printing the Instant you can see that the time is after midnight (really 03:14:35.230 in Amsterdam time zone). And the method has correctly deemed that this time belongs to April 29 rather than April 30.
Perhaps I am missing something? On the other hand, if that were me I’d go quite a long way to avoid inventing a time zone that doesn’t exist in real life. Such a time zone would be bound to confuse your coworkers.

Days with 25 hours on Java (Daylight saving days)

I have to prepare some app that will graph the use of resources over time, but there is one day on the year that has 25 hours (the day with 23 hours is not a big problem).
How can I represent that with a Date? What would be the best way of doing it?
I would like to use Date class, (as it works, is Comparable and so on) as a key, but I'm not sure if this would work... Any ideas?

The Date class itself simply represents an instant in time, from the UTC Unix epoch. It has no concept of time zones, calendars etc.
It's hard to know what exactly you're trying to represent, but in general Joda Time is a much better date/time API than the types in java.util.*.
My main advice on thinking about time-related issues is to be really, really clear about what concept each value is meant to be representing. If you're interested in a local date (a date within a particular calendar, with no reference to a particular time zone), then Joda Time's LocalDate class is probably what you're after. If you need to associate time zone information, then DateTime is probably your best bet - although that does represent an instant within a particular calendar and time zone, rather than a whole day.

It important not to confuse how time is represented and how it is displayed.
In its representation, you have only the number of milli-seconds since 1/1/1970. When you do calculations on this you are just comparing this long value.
When you display this time/date, depending on your timezone, you can have a period of 25 hours or 23 hours with the same day.