import logging
from pywps import ComplexInput, Format, LiteralInput, Process, FORMATS
# from pywps import Process, LiteralInput
from pywps.ext_autodoc import MetadataUrl
from pywps.inout.outputs import MetaFile, MetaLink4
from flyingpigeon.processes.wpsio import output, metalink
from flyingpigeon.subset import _CONTINENTS_
from flyingpigeon.subset import clipping
from flyingpigeon.utils import extract_archive
# from flyingpigeon.utils import rename_complexinputs
from os.path import abspath, basename
LOGGER = logging.getLogger("PYWPS")
[docs]class SubsetcontinentProcess(Process):
"""
TODO: opendap input support, additional metadata to display region names.
"""
def __init__(self):
inputs = [
LiteralInput('region', 'Region',
data_type='string',
abstract="Continent name.",
min_occurs=1,
max_occurs=len(_CONTINENTS_),
default='Africa',
allowed_values=_CONTINENTS_), # REGION_EUROPE #COUNTRIES
ComplexInput('resource', 'Resource',
abstract='NetCDF Files or archive (tar/zip) containing netCDF files.',
min_occurs=1,
max_occurs=1000,
supported_formats=[
Format('application/x-netcdf'),
Format('application/x-tar'),
Format('application/zip'),
]),
]
outputs = [output, metalink]
super(SubsetcontinentProcess, self).__init__(
self._handler,
identifier="subset_continents",
title="Subset Continents",
version="0.11",
abstract="Return the data whose grid cells intersect the selected continents for each input dataset.",
metadata=[
MetadataUrl('Doc',
'https://flyingpigeon.readthedocs.io/en/latest/processes_des.html#subset-processes',
anonymous=True),
],
inputs=inputs,
outputs=outputs,
status_supported=True,
store_supported=True,
)
def _handler(self, request, response):
# input files
LOGGER.debug("url={}, mime_type={}".format(request.inputs['resource'][0].url,
request.inputs['resource'][0].data_format.mime_type))
ncs = extract_archive(
resources=[inpt.file for inpt in request.inputs['resource']],
dir_output=self.workdir)
# mime_type=request.inputs['resource'][0].data_format.mime_type)
# mosaic option
# TODO: fix defaults in pywps 4.x
# regions used for subsetting
regions = [inp.data for inp in request.inputs['region']]
LOGGER.info('ncs: {}'.format(ncs))
LOGGER.info('regions: {}'.format(regions))
LOGGER.info('flyingpigeon dir_output : {}'.format(abspath(self.workdir)))
response.update_status("Arguments set for subset process", 0)
LOGGER.debug('starting: regions={}, num_files={}'.format(len(regions), len(ncs)))
try:
ml = MetaLink4('subset', workdir=self.workdir)
for nc in ncs:
out = clipping(
resource=nc,
polygons=regions,
mosaic=True,
spatial_wrapping='wrap',
# variable=variable,
dir_output=self.workdir,
# dimension_map=dimension_map,
)
LOGGER.info('result: {}'.format(out[0]))
prefix = basename(nc).replace('.nc', '')
mf = MetaFile(prefix, fmt=FORMATS.NETCDF)
mf.file = out[0]
ml.append(mf)
except Exception as ex:
msg = 'Clipping failed: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
response.outputs['output'].file = ml.files[0].file
response.outputs['metalink'].data = ml.xml
response.update_status("Completed", 100)
return response