MOSS flags incorrect

[ahughes6]

The way MOSS is run in pymoss is broken and there is no clear fix from the code as given. There are comments that reference the flags set for the perl script and none of them exist within the mossnet perl script. In tmoss/code/pymoss/runner.py, it sets the MOSS flags as follows:

        # These options were hard-coded in the Perl script (some were vars but not user-settable).
        MAGIC_ARGS = ["-p", "24", "-t", "26", "-g", "10", "-w", "5"]

        args = ["-n", str(threshold), "-a", manifest, "-o", results]

Of these flags, only -n and -p are valid MOSS flags (and setting the port to 24 seems incorrect). It is unclear through reading the code as to the intent of the flags in MAGIC_ARGS. I am assuming the -a and -o have something to do with how the files are input and results are output, but that is also unclear. I don't see any variables within the MOSS script that can be hard-coded to the MAGIC_ARGS values, either.

If one removes MAGIC_ARGS and the -a and -o flags, then MOSS is run without any files as input. The value on execution of manifest is the string "manifest" and results contains the string "results". It would be very beneficial to see a copy of the version of MOSS used when using this tool to determine how to proceed or update this to work with the current MOSS. The software, as is, is inoperable.

[hychen20]

Having same issue running the script

[ahughes6]

As a follow-up from email correspondence with the author, there seems to be a (proprietary?) version of MOSS that runs as an executable. It was suggested to request this from the MOSS group, however I was personally never able to establish contact with them or determine where to start.

I hypothesized that this local executable is what allows all this batch processing of the jobs without bogging down the public MOSS server. I also hypothesized that due to the author working out of Stanford, this was what allowed access to such an executable. That said, if anyone does find contact info to acquire this for university usage please do share the process by which to obtain this.

[AndreasArne]

I managed to get in contact with the author of MOSS. He replied that he doesn't distribute the binary. So this project is unusable until the creator of MOSS change his mind or someone rewrites the code to work against the public MOSS web service.

For those interested, I found another project that does something similar and use the web service. https://github.com/danainschool/moss-taps
I got it to work after updating a dependency after following instructions in an issue.