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()