TransmartApp on windows and Rserve on Ubuntu running on VM not working

[Santosh Maskar]

I have installed the transmartApp on Windows and Rserve on VM instance on the same machine. When I run the any analysis it does not find the study because the downloaded study directories are different.  I have mapped the network folder from ubuntu to windows but when R tries to change the working directory then it does not understand the windows folder. 

Just for testing I modified the R plugin to point to correct directory but then it does not find the r files which is available on the windows plugin directory. 

After looking into the transmart codebase, found that I will have to modify the couple of plugins to make it work. All the advance analysis code are in plugins.

Just wanted to get your opinion on what would be the best approach to get it working. I know that if R is running on ubuntu VM then why can't just deploy the transmart app on VM but that is the last option I can consider.

Just to summarize my setup

1. I have tomcat running on windows where I deployed the transmartApp.

2. Installed Ubuntu on VM inside the windows

3. R is running on VM

-Santosh

[Florian Guitton]

Dear Santosh,

I reckon what you are attempting to do should work so long as your folder mapping result in similar canonical path on both your Ubuntu and your Windows machines.

I understand Linux in general is not capable of understanding Windows-like path expression, however Windows is fully capable of understanding Linux ones.

Say you want to configure tranSMART so that R fetches the data in \tmp\transmart\jobs.

In that case you will have to configure in you external (Config.groovy) file the job path to "\tmp\transmart\jobs" and create the folder "C:/tmp/transmart/jobs"

Then you will have to map via your hypervisor "C:/tmp/transmart/jobs" (in Windows) on "\tmp\transmart\jobs" (in Ubuntu).

You will need to make sure the permissions are set properly on both operating system.

Be careful while permissions are very basic and simple on Linux they are much more comprehensive and intricate in Windows. You will have to work with the ACL as well as the Audit Enquiries.

All in all my opinion on this is rather mitigated.

You would be better of installing R on Windows, or firing tranSMART in your Ubuntu.

Is there a particular reason why you wouldn't want to do that ?

Particularly if one is virtualized inside the first. It makes no sense. If they had to be remote services or you were relying on an RCloud instead I'd understand.

Regards,

[Santosh Maskar]

Thanks Florian.

I did tried  transmart and R on windows but it is not working. While doing the survival analysis, R crashes (exits 0)  and following log was seen in transmart log file 

IllegalArgumentException occurred when processing request: GET /transmart/concepts/getCategories
Path cannot have empty parts (got '\Public Studies\'). Stacktrace follows:
java.lang.IllegalArgumentException: Path cannot have empty parts (got '\Public Studies\')
at org.transmartproject.db.concept.ConceptFullName.<init>(ConceptFullName.groovy:49)

Just wanted to check if anyone of you has tried transmart 1.2.4 on windows.

-Santosh