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Running postgres through java

Before I get to the problem, here is what I am trying to do. So I have an assignment where you are supposed to take some sort of variable based code, interpret it, then spit out java code that connects to a database based on the latter. So basically it is java code that reads a file, and outputs a java file based on what is in the file. The output java code has to be output into a different directory (THIS IS THE PROBLEM). Also he gave us files that help us login and help with authentication. Here is the problem when I am in the directory with the output java code, and I run it, it connects to the database no problem, but when I am in any other directory, the code runs fine, but it doesn't want to connect to the database. Here are the arguments I use to run the code.
java -cp /usr/share/java/postgresql-jdbc4-
9.1.jar:/home/undergrad/3/USERNAME/testDoc/bin/a1
-Djava.security.krb5.conf=krb5.conf
-Djava.security.auth.login.config=jaas.conf a1
Since this is an assignment I can't put all my code on here, but here is the code to add something to a database. Keep in mind that this is generated code, and that that is why it looks so ugly, but the assignment is due tonight, so I can't really change that.
The stacktrace says that
the GSS authentication failed, it ended in a PSQLException. So there was an error while connecting. Yea it said it couldn't find the authentication files.

Deleting a file that resides on an internal Linux server via my application

I've recently been working on an enhancement for an application at work that will allow users to delete presentations stored not on their local machine but on a Linux server present on the internal network. My problem is that I am not sure how to go about performing this delete. The location of the files are as follows:
http://ipaddress/dataconf/productusers/**ACCOUNT**/presentations/
I have access to the ACCOUNT name which is a parameter that will need to be passed in to navigate to the right directory. I will also have access to the presentation name which will be needed to specify the correct presentation to delete.
What I am having trouble with is where to begin.
I am using the Spring framework so my code is a mixture of Java, JSP, and JavaScript.
Essentially I have a .jsp page where I layout the presentations that are associated with each account. I.E when you click on an account it makes a call to a database and lists the presentations that are associated with that account. You can then select individual accounts and delete, or press one delete all button and delete them all.
I currently have it working so that when you delete a presentation in my application, it deletes the appropriate record from the database, but I also need to delete the physical presentation which is the basis for this question. Just as an FYI, these requests (get presentations from database, remove presentations from database) are all being handled through AJAX and JSON.
I am hoping to learn how to create a connection to the correct server, navigate to the proper directory as specified above, and issue the Linux command "sudo rm file-name" all in the same delete process that I described in the prior paragraph.
If you could point me in the right direction, any help would be much appreciated. Also, if you need any further clarification please feel free to let me know.
Thanks again,
Dave

This will not be easy. Or maybe it will. Please understand first that simply knowing where some files are published on an HTTP server is basically useless in terms of manipulating those files.
So I understand the following: You have your own web application on server A, a database somewhere, and some files located on another web server B. Internally on server B, the files will be in some weird directory e.g. /var/www/docs/whoknowswhat/somefolder/dataconf/productusers.
What you need to do is to somehow expose this folder from within server B over the network to your server A. Talk to your admin people. Maybe NFS is an option, or maybe Samba, or SSHFS. Make sure you have write permissions, and also make sure that noone else does.
Once you have mounted the location from B in your server A and it is available to you as some directory /mnt/serverB/productusers, then all you have to do is something like this, i.e. File f = ...; f.delete();

I did a little research and stumbled upon a neat solution to accomplish what I am trying to do. If you take a look at the following link:
http://www.journaldev.com/246/java-program-to-run-shell-commands-on-ssh-enabled-system
The above site describes a method in which you can open an ssh connection in Java and execute commands as if you were running them from the terminal. It has come in handy for my problem and I hope that if anyone else is experiencing the same problem that this will help them as well. Feel free to let me know what you think.

Java save method stops working when .jar is moved

I’m coding my first java Desktop application using eclipse and I’m having difficulty deploying it. My project uses JavaFX2 and the e(fx)clipse plugin, the latter is in charge of generating the build.xml file.
ABOUT THE APP
The app, amongst other things, provides an interface where the user can create categories and associate these with labels. All modifications are saved within a single file (the data is stored as a serialized object.) and are supposed to be loaded automatically when the app is reopened.
THE PROBLEM
When build as an executable jar using a .xml file (Ant), the project runs fine within the folder where it gets created. I can run my application, modify data, and save everything once I’m done. When I reopen the app everything gets loaded as it should.
However, if I copy the folder elsewhere, I can no longer save any data. Everything else seems to work; the app will even load the data that was saved when it was in its original directory. I assume that this means that the app can still see the data file, but can no longer write to it.
WHAT IVE TRIED
I’ve read that warping the .jar around an installer may fix the issue; however, one of the goals for the app was to make it as portable as possible. Meaning that it should be possible to move it around from one directory/computer to another, ideally in a manner that is cross-platform friendly, without the need of installing it.
I’ve tried various things to get it to work. I’ve shifted the whole project to Netbeans (to produce a different build), I’ve modified the save/load method file path to make sure the right document is targeted, I’ve tweaked the .xml file the best I could, and I even tried to build the project using the javafxpackager. No matter what I do, when the build works, I get the same results.
Right now, I’m thinking that there may still be something wrong with the .xml file but I’ve got a hard time understanding how to modify it. Perhaps the problem is somehow caused by the way the data gets serialized. I know that at one point when I moved things around within my project, both the save and load methods could no longer interact with the data.
What I find strange is that when the project is moved the load method still works. If the problem is caused by changing the file path, how come only the save method ceases to function?
APP FILES AND STRUCTURE
+src
-(Main.java)
+controller
-(misc.javas)
+modelData
-(Library.java) -->the object that is serialized
+modelLogic
-(misc.javas)
+view
-(misc.javas)
+files
-(library.data) -->the file where the serialized object is saved
+lib
-(empty.empty)
So, is their anything I can do to solve my problem?
Thanks in advance.

In the end, the problem was rather simple. When I was moving the app, I was always putting it on the desktop, which, in the case of my PC, sets by default all content as read-only (in relation to the app's privileges). Because of this, the app could not modify any files that were within folders on the desktop.
Therefore, all I had to do was to move the app to another directory, such as C:\randomFolder, and the problem was solved.
So, if anyone has a similar problem, moving the app elsewhere may be the solution. Alternatively, taking full ownership of the folder and its content can also work.
When possible, it is usually better to have the app ask its user for a specific location to save its data.

Using a Java program I made on a Web Server

I created a small application that, when run, creates or updates some tables in a database by extracting data from some PDF files. Everything works fine in this desktop application, but the next step for me would be to make it possible for an administrator on a website to upload a PDF file and my Java program would then run and update the tables accordingly.
The problem is I have no idea where to start with this (the site isn't done yet, but I'm running some tests and it is going to be coded in PHP). I'd like to know what kind of technologies I need to let the server run the program and update everything as it would in the offline version. Sometimes it takes a while to update everything, so ideally, the user uploading the PDF could continue browsing other pages while the server does its job. (I'll probably implement something that when the server is done processing the file, it says if the program ended successfully or not in a log file)
Can someone tell me what terms to search for on Google or give me some pointers? I haven't chosen where my website is going to be hosted either, so if someone could tell me what to look for to know if they support running applications like this, I'd really appreciate it as well!
This could also apply to other programming languages as I know a bit of Python and C++ as well, so in the future I might have some applications in those languages I'll want to use on the web.
If I'm not approaching this the right way, I'm open to other suggestions, but the best solution would be to keep my Java program intact as I know it works exactly like I want it to and I'd rather not have to start it all over again.

If your host is *NIX based you can use crontab (Automatic Task Scheduler) to run your program at set intervals. Make it check if a "new" PDF exists, and run the program if there is. There may be a way to use Windows Task Scheduler type programs to do it on Windows. This is probably the easiest way.
Alternately you can use You can use shell_exec() in your php to execute a command on your *NIX system directly to run your java program.

How to create installer once finished with Java Desktop Application with MySQL DB?

I have finished writing a Java Desktop application with a mySQL database. I want to make the application run outside netbeans and let it be installed on other computers. I know about building the project and creating the runnable jar file, however this requires me to export the database itself to the other computer I want the application to run on.
My question is two parts:
1)Is there a way I can create a setup file that also installs the database and the application together?
2)Also my database path is hard coded, does that mean I have to change the code every time I install my application for someone, what is the better way to do that?
Thanks

Yes. You can use some setup builder, like InnoSetup, for example. Personally, however, I like giving my customers a zip file, which they extract wherever they like. The executable jar should be able to handle everything by itself (I like it where there is no need to install the software, just unpack and run).
If it is hardcoded, then yes (but, what do you mean by hardcoded? path to file? ip address?). You should use properties or configuration files for paths and other external things your software depends on. The software should read from those files. Upon startup check for presence of such file(s) - if missing, the user should be shown a window in which the config can be entered.
As for deploying MySQL with your code - consider using a server for that, so that your users are not forced to install MySQL, instead they connect to it over the net. If you need the database only for storing data locally, why not using SQLite or a similar, file-based db engine?
The above answers are just suggestions and more-less reflect the way I am thinking. I would be happy to hear from someone with more experience. Nonetheless, I hope the answers help a little :)

I agree with Sorrow.
If I have to use MySQL, it is normally over the net since I don't want to allow my clients pass through the hazzles of installing MySQL themselves. If however you am stuck with using MySQL locally, investigate MySQL unattended installations + NSIS Installer.
If you can use any db you want, I just use javadb/derby. It comes bundled with most Java installations these days and if not all you need is to add a jar file to you application.
As per 'hardcoding' paths, I really don't understand what you mean. You really don't have 'paths' as it were, I am assuming what you mean is connection string. You don't have to hardcode your connection string, just put some parameters in a properties file and construct your connection string from them.

1) Is there a way I can create a setup file that also installs the database and the application together?
See my answer to Java based Standalone application.
2) Also my database path is hard coded, does that mean I have to change the code every time I install my application for someone, what is the better way to do that?
Have the DB installer pop a JFileChooser to ask the user where they want to install the DB. Store that path using the JNLP API PersistenceService. Here is my demo. of the PersistenceService.