Generated Provenance file appears to be missing values

Hello 👋

I'm a student over at UBC taking a graduate OS course with Prof. Margo Seltzer. I'm using rdt to collect provenance data in order to implement a new feature for a provenance debugger that another student worked on in the past.

Recently (or maybe I'm just noticing this now), I have noticed that some of the procedure nodes are not being accurately reported. For example, a conditional statement may be missing a brace or two, or otherwise have truncated information.

I've attached a minimum example that appears to reproduce the issue, as well as the provenance file that is generated from running the following on the command line:

cc @Alison-Li

Workflow

% R
% library(rdt)
% prov.run("test.R")

Test file: test.R

x <- 1

if (x == 1) {
    print("Is this going to get cut off?")
} else {
    print("This branch should not execute but should still be preserved...")
}

Generated prov.json

Note that the second branch of the conditional is not preserved in the provenance data at all.

{
"prefix": {
    "prov": "http://www.w3.org/ns/prov#",
    "rdt": "https://github.com/End-to-end-provenance/ExtendedProvJson/blob/master/JSON-format.md"
},

"agent" : {
    "rdt:a1": {
        "rdt:tool.name": "rdt",
        "rdt:tool.version": "3.3",
        "rdt:json.version": "2.3",
        "rdt:args.names": [
            "overwrite",
            "details",
            "annotate.inside.functions",
            "first.loop",
            "max.loops",
            "snapshot.size",
            "save.debug"
        ],
        "rdt:args.values": [
            "TRUE",
            "TRUE",
            "FALSE",
            "1",
            "0",
            "0",
            "FALSE"
        ],
        "rdt:args.types": [
            "logical",
            "logical",
            "logical",
            "integer",
            "integer",
            "numeric",
            "logical"
        ]
    }
},

"activity" : {
    "rdt:p1": {
        "rdt:name": "test.R",
        "rdt:type": "Start",
        "rdt:elapsedTime": "0.303",
        "rdt:scriptNum": 1,
        "rdt:startLine": "NA",
        "rdt:startCol": "NA",
        "rdt:endLine": "NA",
        "rdt:endCol": "NA"
    },
    "rdt:p2": {
        "rdt:name": "x <- 1",
        "rdt:type": "Operation",
        "rdt:elapsedTime": "0.106",
        "rdt:scriptNum": 1,
        "rdt:startLine": 1,
        "rdt:startCol": 1,
        "rdt:endLine": 1,
        "rdt:endCol": 6
    },
    "rdt:p3": {
        "rdt:name": "if (x == 1) {\n\tprint(\"Is this going to get cut off?\")\n} else",
        "rdt:type": "Operation",
        "rdt:elapsedTime": "0.206",
        "rdt:scriptNum": 1,
        "rdt:startLine": 3,
        "rdt:startCol": 1,
        "rdt:endLine": 7,
        "rdt:endCol": 1
    },
    "rdt:p4": {
        "rdt:name": "test.R",
        "rdt:type": "Finish",
        "rdt:elapsedTime": "0.01",
        "rdt:scriptNum": 1,
        "rdt:startLine": "NA",
        "rdt:startCol": "NA",
        "rdt:endLine": "NA",
        "rdt:endCol": "NA"
    }
},

"entity" : {
    "rdt:d1": {
        "rdt:name": "x",
        "rdt:value": "1",
        "rdt:valType": "{\"container\":\"vector\", \"dimension\":[1], \"type\":[\"numeric\"]}",
        "rdt:type": "Data",
        "rdt:scope": "R_GlobalEnv",
        "rdt:fromEnv": false,
        "rdt:hash": "",
        "rdt:timestamp": "",
        "rdt:location": ""
    },

    "rdt:environment": {
        "rdt:name": "environment",
        "rdt:architecture": "x86_64-apple-darwin17.0 (64-bit)",
        "rdt:operatingSystem": "macOS Big Sur 10.16",
        "rdt:language": "R",
        "rdt:langVersion": "R version 4.0.4 (2021-02-15)",
        "rdt:script": "/Users/jyoo/dev/cs508/test.R",
        "rdt:scriptTimeStamp": "2021-03-30T18.56.08PDT",
        "rdt:scriptHash": "6f286f2d8b2178ea769dfee626de6016",
        "rdt:totalElapsedTime": "0.625",
        "rdt:sourcedScripts": "",
        "rdt:sourcedScriptTimeStamps": "",
        "rdt:sourcedScriptHashes": "",
        "rdt:workingDirectory": "/Users/jyoo/dev/cs508",
        "rdt:provDirectory": "/private/var/folders/w1/72dtq_m95wjg8gk8dq_3pddh0000gn/T/RtmpZZZ0w3/prov_test",
        "rdt:provTimestamp": "2021-03-30T18.56.21PDT",
        "rdt:hashAlgorithm": "md5"
    },

    "rdt:l1": {
        "name": "base",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l2": {
        "name": "datasets",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l3": {
        "name": "graphics",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l4": {
        "name": "grDevices",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l5": {
        "name": "methods",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l6": {
        "name": "rdt",
        "version": "3.3",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l7": {
        "name": "stats",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    },
    "rdt:l8": {
        "name": "utils",
        "version": "4.0.4",
        "prov:type": {
            "$": "prov:Collection",
            "type": "xsd:QName"
        }
    }
},

"wasInformedBy" : {
    "rdt:pp1": {
        "prov:informant": "rdt:p1",
        "prov:informed": "rdt:p2"
    },
    "rdt:pp2": {
        "prov:informant": "rdt:p2",
        "prov:informed": "rdt:p3"
    },
    "rdt:pp3": {
        "prov:informant": "rdt:p3",
        "prov:informed": "rdt:p4"
    }
},

"wasGeneratedBy" : {
    "rdt:pd1": {
        "prov:activity": "rdt:p2",
        "prov:entity": "rdt:d1"
    }
},

"used" : {
    "rdt:dp1": {
        "prov:entity": "rdt:d1",
        "prov:activity": "rdt:p3"
    }
}
}

End-to-end-provenance / RDataTracker

Generated Provenance file appears to be missing values #659