def execute(self):
from os import mkdir, path, listdir
from flyingpigeon import segetalflora as sf
init_process_logger('log.txt')
self.output_log.setValue('log.txt')
logging.debug('starting segetalflora process execution')
self.status.set('starting calcualtion segetalflora', 5)
############################
# read argments to variables
############################
try:
resource = self.getInputValues(identifier='resource')
climate_type = self.climate_type.getValue()
culture_type = self.culture_type.getValue()
logging.info('urls for %s ncs found' % (len(resource)))
logging.info('culture type: %s ' % (culture_type))
except Exception as e:
logger.debug('failed to read in the arguments: %s ' % e)
try:
if type(climate_type) != list:
climate_type = list([climate_type])
if type(culture_type) != list:
culture_type = list([culture_type])
logger.info('arguments are lists')
except Exception as e:
logger.debug('failed to transform arguments to lists: %s ' % e)
#############################
# get yearly mean temperature
#############################
nc_tasmean = sf.get_yrmean(resource)
#######################################
# main call for segetalflora processing
#######################################
nc_sf = sf.get_segetalflora(resource=nc_tasmean,
culture_type=culture_type,
climate_type=climate_type)
####################
# tar file archiving
####################
try:
from flyingpigeon.utils import archive
self.status.set('files to tar archives', 99)
tar_sf = archive(nc_sf, format='tar', dir_output='.', mode='w')
tar_tasmean = archive(nc_tasmean,
format='tar',
dir_output='.',
mode='w')
logging.info('Archives prepared')
except Exception as e:
logger.debug('failed to archive files %s' % e)
# === set output parameter
self.out_segetalflora.setValue(tar_sf)
self.out_tasmean.setValue(tar_tasmean)
self.status.set("processing done", 100)
def execute(self):
from os import mkdir, path, listdir
# import tarfile
# from tempfile import mkstemp #, mkdtemp
# from datetime import datetime
from flyingpigeon import segetalflora as sf
logging.debug('starting segetalflora process execution')
self.status.set('starting calcualtion segetalflora', 5)
############################
# read argments to variables
############################
try:
resource = self.getInputValues(identifier='resource')
climate_type = self.climate_type.getValue()
culture_type = self.culture_type.getValue()
logging.info('urls for %s ncs found' % (len(resource)))
logging.info('culture type: %s ' % (culture_type))
except Exception as e:
logger.debug('failed to read in the arguments: %s ' % e)
try:
if type(climate_type) != list:
climate_type = list([climate_type])
if type(culture_type) != list:
culture_type = list([culture_type])
logger.info('arguments are lists')
except Exception as e:
logger.debug('failed to transform arguments to lists: %s ' % e)
#############################
# get yearly mean temperature
#############################
nc_tasmean = sf.get_yrmean(resource)
#######################################
# main call for segetalflora processing
#######################################
nc_sf = sf.get_segetalflora(resource=nc_tasmean,
culture_type=culture_type,
climate_type=climate_type)
#stepps = len(culture_type) * len(climate_type)
#for a, cult in enumerate(culture_type):
#for b, clim in enumerate(climate_type):
#start = (a + 1) * (b + 1)
#per = (start / stepps) * 95
#self.status.set('%s/%s processing for %s climate type: %s' %(start, stepps, culture_type, climate_type), per)
#try:
#sf_files = sf.get_segetalflora(resource=ncs, culture_type=cult, climate_type=clim) # dir_output=dir_tas,
#self.status.set("processing of %s segetalflora files done " % (len(sf_files)) , 95)
#except Exception as e:
#logging.exception('segetalflora calculation failed %s %s' % ( climate_type, culture_type))
#raise
## === fieldmeans
#from flyingpigeon import timeseries as ts
#self.status.set('processing fieldmeans' , 97)
#try:
#ncs = [path.join(dir_segetalflora,nc) for nc in listdir(dir_segetalflora)]
#ncs_fld = ts.fldmean(ncs, dir_output=dir_fieldmean)
#logging.debug('%s fieldmeans processed' % (len(ncs_fld)))
#except Exception as e:
#logging.exception('fieldmeans failed')
#raise
## === visualisation
#from flyingpigeon import visualisation as vs
#from os import rename
#self.status.set('processing visualisation' , 98)
## sort files for plotting
#try:
#ncs = listdir(dir_segetalflora)
#set_var = set()
#set_contry = set()
#for nc in ncs:
#set_var = set_var.union([nc.split('_')[0]])
#set_contry = set_contry.union([nc.split('_')[1]])
#logging.debug('%s files to plots sorted' % (len(ncs)))
#except Exception as e:
#logging.exception('files sorting failed')
#raise
## plot sorted files
#try:
#plots = []
#for v in set_var:
#for c in set_contry:
#ncs = [path.join(dir_segetalflora,nc) for nc in listdir(dir_segetalflora) if v in nc and c in nc ]
#p = vs.spaghetti(ncs,
#variable=v,
#title='Segetalflora %s in %s' % (v, c),
#dir_out=dir_plots)
#newname = path.dirname(p)+'/%s_%s_birdhouse_output.html' %(v,c)
#rename(p,newname)
#plots.append(newname)
#logging.debug('plot created and renamed for %s %s' % (v, c ))
#except Exception as e:
#logging.exception('ploting failed')
#raise
####################
# tar file archiving
####################
from flyingpigeon.utils import archive
try:
self.status.set('files to tar archives', 99)
tar_sf = archive(nc_sf, format='tar', dir_output='.', mode='w')
tar_tasmean = archive(nc_tasmean,
format='tar',
dir_output='.',
mode='w')
logging.info('Archives prepared')
except Exception as e:
logger.debug('failed to archive files %s' % e)
# === set output parameter
#self.out_fieldmeans.setValue( tarf_fieldmeans )
self.out_segetalflora.setValue(tar_sf)
self.out_tasmean.setValue(tar_tasmean)
#self.out_plots.setValue( tarf_plots )
self.status.set("processing done", 100)
def _handler(self, request, response):
init_process_logger('log.txt')
response.outputs['output_log'].file = 'log.txt'
process_start_time = time.time() # measure process execution time ...
response.update_status(
'execution started at: {}'.format(str(dt.now())), 5)
LOGGER.debug('starting segetalflora process execution')
response.update_status('starting calcualtion segetalflora', 5)
############################
# read argments to variables
############################
try:
resource = archiveextract(
resource=rename_complexinputs(request.inputs['resource']))
climate_type = request.inputs['climate_type'][0].data
culture_type = request.inputs['culture_type'][0].data
LOGGER.info('urls for {} ncs found'.format(len(resource)))
LOGGER.info('culture type: {}'.format(culture_type))
except Exception as ex:
msg = 'Failed to read in the arguments: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
if type(climate_type) != list:
climate_type = list([climate_type])
if type(culture_type) != list:
culture_type = list([culture_type])
LOGGER.info('arguments are lists')
except Exception as ex:
msg = 'Failed to transform arguments to lists: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
#############################
# get yearly mean temperature
#############################
nc_tasmean = sf.get_yrmean(resource)
#######################################
# main call for segetalflora processing
#######################################
nc_sf = sf.get_segetalflora(resource=nc_tasmean,
culture_type=culture_type,
climate_type=climate_type)
####################
# tar file archiving
####################
try:
response.update_status('preparing output', 99)
LOGGER.debug('length of sf: {}'.format(len(nc_sf)))
if len(nc_sf) == 1:
# TODO: fix pywps output formats OR use separate output params.
response.outputs['out_segetalflora'].file = nc_sf[0]
response.outputs['out_segetalflora'].format = FORMATS.NETCDF
else:
response.outputs['out_segetalflora'].file = archive(
nc_sf, format='tar', dir_output='.', mode='w')
response.outputs['out_segetalflora'].format = Format(
'application/x-tar')
if len(nc_tasmean) == 1:
response.outputs['out_tasmean'].file = nc_tasmean[0]
response.outputs['out_segetalflora'].format = FORMATS.NETCDF
else:
response.outputs['out_tasmean'].file = archive(nc_tasmean,
format='tar',
dir_output='.',
mode='w')
response.outputs['out_segetalflora'].format = Format(
'application/x-tar')
except Exception as ex:
msg = 'Failed to prepare output files: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
response.update_status('done', 100)
LOGGER.debug(
"total execution took {} seconds.".format(time.time() -
process_start_time))
return response