def _handler(self, request, response):
# init_process_logger('log.txt')
# response.outputs['output_log'].file = 'log.txt'
ncs = extract_archive(
resources=[inpt.file for inpt in request.inputs['resource']],
dir_output=self.workdir)
LOGGER.info('ncs: {}'.format(ncs))
coords = []
for coord in request.inputs['coords']:
coords.append(coord.data)
LOGGER.info('coords {}'.format(coords))
filenames = []
nc_exp = sort_by_filename(ncs, historical_concatination=True)
for key in nc_exp.keys():
try:
LOGGER.info('start calculation for {}'.format(key))
ncs = nc_exp[key]
times = get_time(ncs)
concat_vals = times
header = 'date_time'
filename = join(self.workdir, '{}.csv'.format(key))
filenames.append(filename)
for p in coords:
try:
response.update_status('processing point: {}'.format(p), 20)
# define the point:
p = p.split(',')
point = Point(float(p[0]), float(p[1]))
# get the values
timeseries = call(resource=ncs, geom=point, select_nearest=True, dir_output=self.workdir)
vals = get_values(timeseries)
# concatenation of values
header = header + ',{}-{}'.format(p[0], p[1])
concat_vals = column_stack([concat_vals, vals])
except Exception as e:
LOGGER.debug('failed for point {} {}'.format(p, e))
response.update_status('*** all points processed for {0} ****'.format(key), 50)
# TODO: Ascertain whether this 'savetxt' is a valid command without string formatting argument: '%s'
savetxt(filename, concat_vals, fmt='%s', delimiter=',', header=header)
except Exception as ex:
LOGGER.debug('failed for {}: {}'.format(key, str(ex)))
# set the outputs
response.update_status('*** creating output tar archive ****', 90)
tarout_file = archive(filenames, dir_output=self.workdir)
response.outputs['tarout'].file = tarout_file
return response
def _handler(self, request, response):
tic = dt.now()
# init_process_logger('log.txt')
# response.outputs['output_log'].file = 'log.txt'
LOGGER.info('Start process')
response.update_status('Execution started at : {}'.format(tic), 1)
######################################
# Read inputs
######################################
try:
resource = extract_archive(
resources=[inpt.file for inpt in request.inputs['resource']],
dir_output=self.workdir)[0]
fmts = [e.data for e in request.inputs['fmt']]
title = request.inputs['title'][0].data
except Exception as ex:
msg = 'Failed to read input parameter {}'.format(ex)
LOGGER.error(msg)
raise Exception(msg)
response.update_status('Input parameters ingested', 2)
try:
fig = plot_spatial_analog(resource, title=title)
output = []
for fmt in fmts:
output.append(fig2plot(fig, fmt, dir_output=self.workdir))
except Exception as ex:
msg = "Failed to create figure: {}".format(ex)
LOGGER.error(msg)
raise Exception(msg)
finally:
plt.close()
if len(fmts) == 1:
output = output[0]
else:
output = archive(output, dir_output=self.workdir)
response.outputs['output_figure'].file = output
response.update_status("done", 100)
return response
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
if 'mosaic' in request.inputs:
mosaic = request.inputs['mosaic'][0].data
else:
mosaic = False
# 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('mosaic: {}'.format(mosaic))
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:
results = clipping(
resource=ncs,
polygons=regions,
mosaic=mosaic,
spatial_wrapping='wrap',
# variable=variable,
dir_output=self.workdir,
# dimension_map=dimension_map,
)
LOGGER.info('results %s' % results)
except Exception as ex:
msg = 'Clipping failed: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
if not results:
raise Exception('No results produced.')
# prepare tar file
try:
tarf = archive(results, dir_output=self.workdir)
LOGGER.info('Tar file prepared')
except Exception as ex:
msg = 'Tar file preparation failed: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
response.outputs['output'].file = tarf
i = next((i for i, x in enumerate(results) if x), None)
response.outputs['ncout'].file = results[i]
response.update_status("done", 100)
return response
def test_archive():
assert '.tar' in utils.archive([])
assert '.zip' in utils.archive([], format='zip')
with pytest.raises(Exception):
utils.archive([], format='zip2')
def test_extract_archive():
files = utils.extract_archive(
[utils.archive([]), utils.archive([], format='zip')])
assert len(files) == 0
def test_archive_zip():
result = utils.archive(local_path(TESTDATA['cmip5_tasmax_2006_nc']),
format='zip',
dir_output=tempfile.mkdtemp())
zipf = zipfile.ZipFile(result)
assert len(zipf.namelist()) == 1
def test_archive_tar():
result = utils.archive(local_path(TESTDATA['cmip5_tasmax_2006_nc']),
format='tar',
dir_output=tempfile.mkdtemp())
tar = tarfile.open(result)
assert len(tar.getnames()) == 1