submitIpfs

#!/usr/bin/env python

import logging, sys, optparse, types, subprocess, json
from collections import defaultdict
from os.path import join, basename, dirname, isfile

# === command line interface, options and help ===
parser = optparse.OptionParser("usage: %prog [options] JSONFile - write a directory of VCFs and JSON metadata to IPFS.")

parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
parser.add_option("-e", "--email", dest="email", action="store", help="email address of submitter")
parser.add_option("-n", "--name", dest="name", action="store", help="real name of submitter")
parser.add_option("-i", "--institution", dest="institution", action="store", help="institution of submitter")
#parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
#parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
(options, args) = parser.parse_args()

if options.debug:
    logging.basicConfig(level=logging.DEBUG)
else:
    logging.basicConfig(level=logging.INFO)

# ==== functions =====

def runCommand(cmd, ignoreErrors=False, verbose=False):
    """ run command in shell, exit if not successful """
    #if type(cmd)==types.ListType:
        #cmd = " ".join(cmd)
    msg = "Running shell command: %s" % cmd
    logging.debug(msg)
    if verbose:
        logging.info(msg)

    assert(type(cmd)==types.ListType)
    ret = subprocess.call(cmd)
    cmd = " ".join(cmd) # for debug output

    if ret!=0:
        if ignoreErrors:
            logging.info("Could not run command %s, retcode %s" % (cmd, str(ret)))
            return None
        else:
            raise Exception("Could not run command (Exitcode %d): %s" % (ret, cmd))
    return ret

def execOutput(cmd):
    " run command and return output "
    output = subprocess.check_output(cmd)
    return output

def ipfsAdd(path):
    " add file to ipfs and return hash "
    if not isfile(path):
        print "Error: %s does not exist" % path
        sys.exit(1)
    print "Adding %s to ipfs" % path
    cmd = ["ipfs", "add", "-q", path]
    ipfsHash = execOutput(cmd).strip()
    return ipfsHash

# ----------- main --------------
def main():
    if len(args)==0:
        parser.print_help()
        sys.exit(0)

    jsonFname = args[0]
    sampleMeta = json.load(open(jsonFname))

    if not options.name or not options.email or not options.institution:
        print "Please provide a value for the --email, --name and --institution options. -h for help."
        sys.exit(1)

    # go over meta data. Along the way, add files to ipfs and hashes to a new dict
    sampleMetaSub = {}
    for sampleId, sampleData in sampleMeta.iteritems():
        newSample = {}
        for key, val in sampleData.iteritems():
            if val=="":
                continue
            if key.endswith("_filename"):
                fname = join(dirname(jsonFname), sampleData[key])
                fileHash = ipfsAdd(fname)
                print "file hash: %s" % fileHash
                newSample[key.replace("_filename", "_ipfs_hash")] = fileHash
            newSample[key] = val

        sampleMetaSub[sampleId] = newSample

    submitMeta = {}
    submitMeta["submission_filename"] = basename(jsonFname)
    submitMeta["submitter_email"] = options.email
    submitMeta["submitter_institution"] = options.institution
    submitMeta["submitter_name"] = options.name
    submitMeta["sampleData"] = sampleMetaSub

    subJsonFname = jsonFname+".submitted"
    json.dump(submitMeta, open(subJsonFname, "w"), sort_keys=True, indent=4, separators=(',', ': '))
    print "Submission info JSON written to %s" % subJsonFname
    jsonHash = ipfsAdd(subJsonFname)

    subIdFname = jsonFname+".submissionId"
    open(subIdFname, "w").write(jsonHash)
    print "Submission ID written to %s" % subIdFname

    print "IPFS submission OK. Submission ID is %s" % jsonHash

main()