Kill VirusTreeSimulator after x number of failures to coalesce

[niemasd]

VirusTreeSimulator infinite-loops if it keeps failing to coalesce the lineages. Add a way to kill VirusTreeSimulator (and throw an error) if it fails to coalesce after x attempts.

Configuration File

{
    "ContactNetwork":                "NetworkX",

    "ContactNetworkGenerator":       "Complete",
    "num_cn_nodes":                  10,

    "Driver":                        "Default",
    "out_dir":                       "out_NumBranchSample_Fixed",

    "EndCriteria":                   "Transmissions",
    "end_transmissions":             5,

    "Logging":                       "STDOUT",

    "NodeAvailability":              "Perfect",

    "NodeEvolution":                 "VirusTreeSimulator",
    "java_path":                     "java",
    "vts_growthRate":                2.851904,
    "vts_model":                     "constant",
    "vts_n0":                        100000,
    "vts_t50":                       -2,

    "NumBranchSample":               "Fixed",
    "num_viruses_per_cn_sample":     2,

    "NumTimeSample":                 "Once",

    "SeedSelection":                 "Random",
    "num_seeds":                     2,

    "SeedSequence":                  "Random",
    "seed_sequence_length":          10,

    "SequenceEvolution":             "NoMutation",

    "Sequencing":                    "Perfect",

    "SourceSample":                  "Random",

    "TimeSample":                    "End",

    "TransmissionNodeSample":        "RandomSingleInfection",

    "TransmissionTimeSample":        "Fixed",
    "fixed_transmission_time_delta": 1,

    "TreeNode":                      "Simple",

    "TreeUnit":                      "Same",
}

[niemasd]

Possible solution: https://stackoverflow.com/questions/22227569/check-a-condition-while-running-subprocess

[niemasd]

Potential Stack Overflow post to ask if I can't figure it out:

Stack Overflow post

I have a Python 3 script that calls an external tool that repeats itself until it succeeds, and depending on parameter choices to the tool, it may quickly (e.g. instantly) succeed, it may take a few times to succeed, or it may (seemingly) never succeed. When it fails, the tool prints in a manner like this:

Failed to coalesce lineages: 1
Failed to coalesce lineages: 2
Failed to coalesce lineages: 3
...

I am calling the tool like this:

subprocess.call(command, stdout=open("log.txt",'w'))

I want to kill the subprocess call (and throw an error message) after a certain number of failures occur, e.g. when the log file I'm redirecting to has the string Failed to coalesce lineages: 100 in it (meaning the tool failed 100 times). How can I do this cleanly?

[niemasd]

Potentially fixed in 1b4e9df

[niemasd]

Fix has been integrated into an official release (1.1.1): https://github.com/niemasd/FAVITES/releases/tag/1.1.1