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BLOCKER - Change this code to not construct SQL queries directly from user-controlled data

Sonarqube is giving me this error:
[BLOCKER] Change this code to not construct SQL queries directly from user-controlled data
Here is my code:
String countSQL;
countSQL = (String.format("SELECT count(*) as total FROM ltid_owner.enty %s",additionalWhereClauses));
jdbcTemplateTMI.queryForObject(countSQL, Integer.class);
In the above code additionalWhereClauses could be something like this shown below which I am building on the fly when the user clicks on the grid to perform filtering on different columns:
additionalWhereClauses = where UPPER(enty_num) like '003%'
Can you please let me know how to resolve this issue?

Your code combines strings into SQL statements. If any of these strings contains user provided input, an attacker can sneak in code to trigger an SQL injection attack and possibly run arbitrary code on your computer (obligatory Bobby Tables reference).
Simple example:
String sql = "SELECT * FROM users WHERE name = '" + name + "' AND password = '" + password + "'";
If I enter ' OR 1=1 -- for the name (and "..." for the password, but that doesn't really matter anymore) the code becomes a valid SQL statement:
SELECT *
FROM users
WHERE name = '' OR 1=1 -- ' AND password = '...'
but the user name / password check is completely disabled.
To avoid this, use prepared statements. They build the SQL command in a way that SQL injection is impossible.
Maybe this never happens in your code as you don't accept user input, but Sonar doesn't know this (and human reviewers won't either). I'd always use prepared statements. Just because your code only passed column headers from a frontend, doesn't mean an attacker cannot manually call your web service endpoints and pass whatever they want, it your code runs as an HTTP endpoint.

How to replace a string in a string with integer type in java?

I have a requirement. The technology is quite old doesn't support spring at all . It is pure java application with jdbc connection.
Requirement is :
Suppose
select * from employee where empid = <<empid>> and designation = 'Doctor'
I am trying to replace <> with actual int value in java . How I can do it ?
String query = "select * from employee where empid = <<empid>> and designation = 'Doctor'";
if(query.contains("<<empid>>"))
/// Here I want to replace <<empid>> with actual int value in java
Any leads will be helpful

The code you didn't paste, that actually executes the SQL is either [A] a massive security leak that needs serious rewrites, or [B] is using PreparedStatement.
Here's the problem: SQL injection. Creating the SQL string by mixing a template or a bunch of string constants together with a bunch of user input is a security leak. For example, if you try to make SELECT * FROM users WHERE email = 'foo#bar.com' by e.g. String sql = "SELECT * FROM users WHERE email = '" + email + "'";, the problem is, what if the user puts in the web form, in the 'email' field: whatever#foo.com'; DROP TABLE users CASCADE; EXEC 'FORMAT C: /y /force'; --? Then the SQL becomes:
SELECT * FROM users WHERE email = 'whatever#foo.com'; DROP TABLE users CASCADE; EXEC 'FORMAT C: /y /force'; --';
That is legal SQL and you really, really, really don't want your DB engine to execute it.
Each DB engine has its own ideas on what's actually legal, and may do crazy things such as treating curly quotes as real quotes, etc. So, there is no feasible blacklist or whitelist technology you can think of that will properly cover all the bases: You need to ask your DB engine to do this for you, you can't fix this hole yourself.
Java supports this, via java.sql.PreparedStatement. You instead always pass a fully constant SQL string to the engine, and then fill in the blanks, so to speak:
PreparedStatement ps = con.prepareStatement("SELECT * FROM users WHERE email = ?");
ps.setString(1, "foo#whatever.com");
ps.query();
That's how you do it (and add try-with-resources just like you should already be doing here; statements and resultsets are resources you must always close). Even if you call .setString(1, "foo#whatever.com'; DROP TABLE users CASCADE; --"), then it'll simply look for a row in the database that has that mouthful in the email field. It will not delete the entire users table. Security hole eliminated (and this is the only feasible way to eliminate it).
So, check out that code. Is it using preparedstatement? In that case, well, one way or another that code needs to be calling:
ps.setInt(1, 999);
Where ps is the PreparedStatement object created with connection.prepareStatement(...) where ... is either an SQL constant or at least your input string where the <<empid>> was replaced with a question mark and never with any string input from an untrusted source. The 1 in ps.setInt(1, 999) is the position of the question mark (1 = the first question becomes 999), and the 999 is your actual number. It may look like:
if (input instanceof String) {
ps.setString(idx++, (String) input);
} else if (input instanceof Integer) {
ps.setInt(idx++, ((Integer) input).intValue());
} ...
etcetera. If you don't see that, find the setInt invoke and figure out how to get there. If you don't see any setInt, then what you want is not possible without making some updates to this code.
If you don't even see PreparedStatement anywhere in the code, oh dear! Take that server offline right now, research if a security leak has occurred, if this server stored european data you have 72 hours to notify all users if it has or you can't reasonably figure out e.g. by inspecting logs that it hasn't, or you're in breach of the GDPR. Then rewrite that part using PreparedStatement to solve the problem.

Handling dynamic queries with Spring

The problem I'm trying to solve here is, filtering the table using dynamic queries supplied by the user.
Entities needed to describe the problem:
Table: run_events
Columns: user_id, distance, time, speed, date, temperature, latitude, longitude
The problem statement is to get the run_events for a user, based on a filterQuery.
Query is of the format,
((date = '2018-06-01') AND ((distance < 20) OR (distance > 10))
And this query can combine multiple fields and multiple AND/OR operations.
One approach to solving this is using hibernate and concatenating the filterQuery with your query.
"select * from run_events where user_id=:userId and "+filterQuery;
This needs you to write the entire implementation and use sessions, i.e.
String q = select * from run_events where user_id=:userId and "+filterQuery;
Query query = getSession().createQuery(q);
query.setParameter("userId", userId);
List<Object[]> result = query.list();
List<RunEvent> runEvents = new ArrayList<>();
for(Object[] obj: result){
RunEvent datum = new RunEvent();
int index = -1;
datum.setId((long) obj[++index]);
datum.setDate((Timestamp) obj[++index]);
datum.setDistance((Long) obj[++index]);
datum.setTime((Long) obj[++index]);
datum.setSpeed((Double) obj[++index]);
datum.setLatitude((Double) obj[++index]);
datum.setLongitude((Double) obj[++index]);
datum.setTemperature((Double) obj[++index]);
runEvents.add(datum);
}
This just doesn't seem very elegant and I want to use the #Query annotation to do this i.e.
#Query(value = "select run_event from RunEvent where user_id = :userId and :query order by date asc")
List<RunEvent> getRunningData(#Param("userId") Long userId,
#Param("query") String query,
);
But this doesn't work because query as a parameter cannot be supplied that way in the query.
Is there a better, elegant approach to getting this done using JPA?
Using Specifications and Predicates seems very complicated for this sort of a query.

To answer the plain question: This is not possible with #Query.
It is also in at least 99% of the cases a bad design decision because constructing SQL queries by string concatenation using strings provided by a user (or any source not under tight control) opens you up for SQL injection attacks.
Instead you should encode the query in some kind of API (Criteria, Querydsl, Query By Example) and use that to create your query. There are plenty of questions and answers about this on SO so I won't repeat them here. See for example Dynamic spring data jpa repository query with arbitrary AND clauses
If you insist on using a SQL or JPQL snippet as input a custom implementation using String concatenation is the way to go.

This opens up attack for SQL injection. Maybe that’s why this feature is not possible.
It is generally a bad idea to construct query by appending random filters at the end and running them.
What if the queryString does something awkward like
Select * from Foo where ID=1234 or true;
thereby returning all the rows and bringing a heavy load on DB possibly ceasing your whole application?
Solution: You could use multiple Criteria for filtering it dynamically in JPA, but you’ll need to parse the queryString yourself and add the necessary criteria.

You can use kolobok and ignore fields with null values.
For example create one method like bellow
findByUserIdAndDistanceaLessThanAndDistancebGreaterThan....(String userid,...)
and call that method only with the filter parameters while other parameters are null

Dynamic bind select values in MySQL query jdbi

How can i write dynamic SQL query in Jbdi, like in my project customer will ask some details like first name,last name,mobile. so i will read those values into string and my idea was directly append that to SQL query dynamically like
select first name,last name,mobile from customer
and another user ask only first name then my query will change like
select first name from customer where customer Id=12345

I am doing something similar for dynamically generated search criteria strings in a Dropwizard application using JDBI.
#UseStringTemplate3StatementLocator
public interface ThingieDao {
#SqlQuery
#MapResultAsBean
Iterator<Thingie> search(#Define("criteria") String criteria);
}
The defined string "criteria" can then be used in the SQL template:
group ThingieDao;
search(criteria) ::= <<
SELECT * FROM table_name WHERE <criteria>
>>
You can use the same technique to insert any string in the SQL, the SELECT column names in your case.
The variable name in the interface does not matter, it is the #Define annotation string that matters.. Assuming Dropwizard doesn't add anything magic, and it usually doesn't, I guess that should work using plain JDBI as well.

How to Manipulate SQL specified in jrxml template

Problem: Report Templates are created by Admin Users who only decide what data to show where as the filter for the data is specified by the business user. In simpler SQL terms, query is specified by the Admin User, Business User specifies the WHERE clause.
Jasper allows user to specify parameters in SQL query like $P{city}. I have tried to retrieve the query dynamically using the method specfied in the link.
Possible Solution can be
Use WHERE clause parameters in JRXML and replace them while report creation - This will save me SQL parsing but I don't want to guide the admin user with this complexity. Parsing is not a huge problem.
Use my custom jdbc query executor and factory, only created to allow me extension point before jasper fire SQL query. I will be completely relying on vanilla Jasper JDBC data source but will only modify query before execution. JRAbstractQueryExecuter simplifies the query and replace the jasper related tokens before firing query - This will be very dirty and will force me to be implementation specific.
Do the same replacement as it is done in JRAbstractQueryExecuter in my application code base, parse the SQL query, modify it and set it again as specified in link
Can you please suggest a better way of doing this? I have a feeling that this can definitly be done in cleaner way.
Thanks for your help

You could create an input control to determine the desired WHERE clause and use a parameter to hold the contents of that WHERE clause. The default value expression would be something like:
$P{theParameter} == "value_1" ?
(" AND CONDITION_1 IN ('A', 'B', 'C') AND CONDITION_2 = 'Yes' "
) : " AND CONDITION_3 = 'Other' AND CONDITION_4 = 'No' "
Then in your WHERE clause you would reference it like:
WHERE
.... = .....
AND .... = ....
AND .... = ....
$P!{theParameter}
If your constraint columns are the same across your WHERE clauses, you could use $P! to bring in the parameter value literally, and reference it in your query:
WHERE
.... = .....
AND .... = ....
AND .... = ....
AND thisValue = $P!{theParameter}