The very simple answer here is don't
PHP is designed to, at every page request start up, execute a small series of scripts as a single operation, output the data associated with those scripts and then immediately die after generating the output. It literally does not have time to wait for your Java programs and libraries to do their thing, so don't try to put one in the other, which is why PHP scripts that rely on databases tend to have heavily optimised databases for immediate retrieval, instead of general databases that rely on joins and selects that take a few seconds to form the correct data response. Neither PHP or users browsing websites have time for that.
What you could do is wrap your java tools in Java Servlets and have them running on the same server/host that your PHP instance is running from, so that your scripts can access the Servlets as http://127.0.0.1:7254/... as it would any other restful API it needs to use while generating your script output, as long as you make damn sure that you're not going to make PHP wait: if it has to send data to your tools, that is a post-and-forget operation, PHP should not be getting any response back other than an immediate "data accepted" or "data rejected" before the data is then actually handled by your tools. If you need to post data and then get a result back, you're going to have to use two calls. One to post the data, and then a second call to request the result of that posting.
For instance:
- web page generation chain: WordPress CMS based on PHP -> your database
- web input for processing: WordPress CMS based on PHP -> Java Servlets for machine learning
- data processing chain: Java Servlets for machine learning -> your database
So you build pages only based on what's in your data base, you post data to your java Servlets only to get them to start doing something and you don't wait for a response, their result will end up in your database and you'll get it for pages once it's in, and your java programs do what they need to do independently of your WordPress setup.
And if you're going to do that, you should probably write that functionality as a WordPress plugin that can talk to your Java Servlets.
And now you have a second project you need to work on: turning your java programs into web servers. Not terribly complex, but definitely something you're going to lose some time on doing right (because you'll need to wrap with servlets, as well as make sure you can have those running without crashing on the same server as your wordpress instance, which is always fun)
