def run_idss(self,msg):
(filename,filepath,jobname,email)=msg.split("|")
with app.app_context():
log.debug("now going to do long IDSS job via celery")
message='processing...'
self.update_state(state='PROGRESS', meta={'status': message})
#set status to busy
set_status_to_busy(jobname)
seriation = IDSS()
arguments={'inputfile': filename, 'outputdirectory': filepath, 'debug':0 }
seriation.initialize(arguments)
log.debug("seriation initialized with args. Now running IDSS for %s and job %s", (filename, jobname))
(frequencyResults, continuityResults, exceptionList, statsMap) = seriation.seriate()
message='done. zipping results....'
self.update_state(state='PROGRESS',
meta={'status': message})
log.debug('Finished with IDSS processing for job %s', jobname)
zipFileURL = zipresults(jobname)
send_email(zipFileURL, email, jobname)
message='done. emailing results....'
self.update_state(state='PROGRESS', meta={'status': message})
set_status_to_free(jobname)
message='complete.'
self.update_state(state='PROGRESS', meta={'status': message})
def run_idss(self, msg):
(filename, filepath, jobname, email) = msg.split("|")
with app.app_context():
log.debug("now going to do long IDSS job via celery")
message = 'processing...'
self.update_state(state='PROGRESS', meta={'status': message})
#set status to busy
set_status_to_busy(jobname)
seriation = IDSS()
arguments = {
'inputfile': filename,
'outputdirectory': filepath,
'debug': 0
}
seriation.initialize(arguments)
log.debug(
"seriation initialized with args. Now running IDSS for %s and job %s",
(filename, jobname))
(frequencyResults, continuityResults, exceptionList,
statsMap) = seriation.seriate()
message = 'done. zipping results....'
self.update_state(state='PROGRESS', meta={'status': message})
log.debug('Finished with IDSS processing for job %s', jobname)
zipFileURL = zipresults(jobname)
send_email(zipFileURL, email, jobname)
message = 'done. emailing results....'
self.update_state(state='PROGRESS', meta={'status': message})
set_status_to_free(jobname)
message = 'complete.'
self.update_state(state='PROGRESS', meta={'status': message})
parser.add_argument('--excel', default=0,
help="Will create excel files with the assemblages in seriation order.")
parser.add_argument('--noheader',default=None,
help="If you do not use type names as the first line of the input file, use this option to read the data.")
parser.add_argument('--frequencyseriation', default=None, help="Generates graphical output for the results in a frequency seriation form.")
parser.add_argument('--verbose',default=True, help='Provides output for your information')
parser.add_argument('--occurrence', default=0, type=int, help="Treats data as just occurrence information and produces valid occurrence solutions.")
parser.add_argument('--occurrenceseriation', default=None, help="Generates graphical output for occurrence seriation.")
parser.add_argument('--spatialsignificance', default=None, help="Calculate the significance of the spatial aspect of the final solution. Default is None.")
parser.add_argument('--spatialbootstrapN',default=100, help='Set the number of resamples used for calculating the spatial significance. Default is 100.')
parser.add_argument('--minmaxbycount',default=None, help='Create a minmax solution from the aggregate set by weighting on the basis of # of times edges appear in solutions. Default is None.')
parser.add_argument('--delimiter', help="character delimiting the fields in inputfile", default='\t')
parser.add_argument('--preservepickle', help="Do not delete pickle directory, to allow for debugging", type=int, default=0)
parser.add_argument("--source_identifier", help="Identifier for the source of the input data, often used in large batches of simulation/seriation pairs to tie steps of an experiment together", type=str, default="none")
return parser.parse_args()
if __name__ == "__main__":
seriation = IDSS()
args = parse_arguments()
seriation.initialize(args,sys.argv)
(frequencyResults, continuityResults, exceptionList, statsMap, fileMap) = seriation.seriate()
parser.add_argument('--xyfile', default=None,
help="Enter the name of the XY file that contains the name of the assemblage and the X and Y coordinates for each.")
parser.add_argument('--inputfile',
help="<REQUIRED> Enter the name of the data file with the assemblage data to process.", required=True)
parser.add_argument('--outputdirectory', default='./',
help="If you want the output to go someplace other than the /output directory, specify that here.")
parser.add_argument('--delimiter', default='\t', help="delimiter for input file, defaults to tab character")
parser.add_argument('--noheader', default=0, help="Flag, value 1 if there is no header row with type names, 0 otherwise")
return parser.parse_args()
if __name__ == "__main__":
ser = IDSS()
args = parse_arguments()
ser.initialize(args,sys.argv)
filename = args.inputfile
ser.openFile(filename)
if args.xyfile is not None:
ser.openXYFile(args.xyfile)
base_file = os.path.basename(filename)
base_file = os.path.splitext(base_file)[0]
afile = args.outputdirectory + "/" + base_file + "-assemblages.pkl"
pickle.dump(ser.assemblages,open(afile,'wb'))
affile = args.outputdirectory + '/' + base_file + "-assemblage_freq.pkl"
help="The root of the graph figures (i.e., name of assemblage you want to treat as one end in the graphs.")
parser.add_argument('--continuityroot', default=None,
help="If you have a outgroup or root of the graph, set that here.")
parser.add_argument('--atlas', default=1,
help="If you want to have a figure that shows all of the results independently, set that here.")
parser.add_argument('--excel', default=1,
help="Will create excel files with the assemblages in seriation order.")
parser.add_argument('--noheader',default=None,
help="If you do not use type names as the first line of the input file, use this option to read the data.")
parser.add_argument('--frequencyseriation', default=None, help="Generates graphical output for the results in a frequency seriation form.")
parser.add_argument('--verbose',default=True, help='Provides output for your information')
parser.add_argument('--occurrence', default=None, help="Treats data as just occurrence information and produces valid occurrence solutions.")
parser.add_argument('--occurrenceseriation', default=None, help="Generates graphical output for occurrence seriation.")
parser.add_argument('--spatialsignificance', default=None, help="Calculate the significance of the spatial aspect of the final solution. Default is None.")
parser.add_argument('--spatialbootstrapN',default=100, help='Set the number of resamples used for calculating the spatial significance. Default is 100.')
parser.add_argument('--minmaxbycount',default=None, help='Create a minmax solution from the aggregate set by weighting on the basis of # of times edges appear in solutions. Default is None.')
return parser.parse_args()
if __name__ == "__main__":
seriation = IDSS()
args = parse_arguments()
seriation.initialize(args)
(frequencyResults, continuityResults, exceptionList, statsMap) = seriation.seriate()
